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Skills to Develop
• Explain the characteristics of and differences between exponential and logistic growth patterns
• Give examples of exponential and logistic growth in natural populations
• Describe how natural selection and environmental adaptation led to the evolution of particular life history patterns
Although life histories describe the way many characteristics of a population (such as their age structure) change over time in a general way, population ecologists make use of a variety of methods to model population dynamics mathematically. These more precise models can then be used to accurately describe changes occurring in a population and better predict future changes. Certain models that have been accepted for decades are now being modified or even abandoned due to their lack of predictive ability, and scholars strive to create effective new models.
Exponential Growth
Charles Darwin, in his theory of natural selection, was greatly influenced by the English clergyman Thomas Malthus. Malthus published a book in 1798 stating that populations with unlimited natural resources grow very rapidly, and then population growth decreases as resources become depleted. This accelerating pattern of increasing population size is called exponential growth.
The best example of exponential growth is seen in bacteria. Bacteria are prokaryotes that reproduce by prokaryotic fission. This division takes about an hour for many bacterial species. If 1000 bacteria are placed in a large flask with an unlimited supply of nutrients (so the nutrients will not become depleted), after an hour, there is one round of division and each organism divides, resulting in 2000 organisms—an increase of 1000. In another hour, each of the 2000 organisms will double, producing 4000, an increase of 2000 organisms. After the third hour, there should be 8000 bacteria in the flask, an increase of 4000 organisms. The important concept of exponential growth is that the population growth rate—the number of organisms added in each reproductive generation—is accelerating; that is, it is increasing at a greater and greater rate. After 1 day and 24 of these cycles, the population would have increased from 1000 to more than 16 billion. When the population size, N, is plotted over time, a J-shaped growth curve is produced (Figure $1$).
The bacteria example is not representative of the real world where resources are limited. Furthermore, some bacteria will die during the experiment and thus not reproduce, lowering the growth rate. Therefore, when calculating the growth rate of a population, the death rate (D) (number organisms that die during a particular time interval) is subtracted from the birth rate (B) (number organisms that are born during that interval). This is shown in the following formula:
$\frac{\Delta N\;(\text{change in number})} {\Delta T\;(\text{change in time})} = B\;(\text{birth rate}) - D\;(\text{death rate}) \nonumber$
The birth rate is usually expressed on a per capita (for each individual) basis. Thus, B (birth rate) = bN (the per capita birth rate “b” multiplied by the number of individuals “N”) and D (death rate) =dN (the per capita death rate “d” multiplied by the number of individuals “N”). Additionally, ecologists are interested in the population at a particular point in time, an infinitely small time interval. For this reason, the terminology of differential calculus is used to obtain the “instantaneous” growth rate, replacing the change in number and time with an instant-specific measurement of number and time.
$\frac{d N} {d T} = bN - dN = (b - d)N \nonumber$
Notice that the “d” associated with the first term refers to the derivative (as the term is used in calculus) and is different from the death rate, also called “$d$.” The difference between birth and death rates is further simplified by substituting the term “r” (intrinsic rate of increase) for the relationship between birth and death rates:
$\frac{d N} {d T} = rN \nonumber$
The value “$r$” can be positive, meaning the population is increasing in size; or negative, meaning the population is decreasing in size; or zero, where the population’s size is unchanging, a condition known as zero population growth. A further refinement of the formula recognizes that different species have inherent differences in their intrinsic rate of increase (often thought of as the potential for reproduction), even under ideal conditions. Obviously, a bacterium can reproduce more rapidly and have a higher intrinsic rate of growth than a human. The maximal growth rate for a species is its biotic potential, or $r_{max}$, thus changing the equation to:
$\frac{d N} {d T} = r_\text{max}N \nonumber$
Logistic Growth
Exponential growth is possible only when infinite natural resources are available; this is not the case in the real world. Charles Darwin recognized this fact in his description of the “struggle for existence,” which states that individuals will compete (with members of their own or other species) for limited resources. The successful ones will survive to pass on their own characteristics and traits (which we know now are transferred by genes) to the next generation at a greater rate (natural selection). To model the reality of limited resources, population ecologists developed the logistic growth model.
Carrying Capacity and the Logistic Model
In the real world, with its limited resources, exponential growth cannot continue indefinitely. Exponential growth may occur in environments where there are few individuals and plentiful resources, but when the number of individuals gets large enough, resources will be depleted, slowing the growth rate. Eventually, the growth rate will plateau or level off (Figure $1$). This population size, which represents the maximum population size that a particular environment can support, is called the carrying capacity, or $K$.
The formula we use to calculate logistic growth adds the carrying capacity as a moderating force in the growth rate. The expression “$K – N$” is indicative of how many individuals may be added to a population at a given stage, and “$K – N$” divided by “$K$” is the fraction of the carrying capacity available for further growth. Thus, the exponential growth model is restricted by this factor to generate the logistic growth equation:
\begin{align} \dfrac{d N} {d T} &= r_\text{max} \frac{d N} {d T} \nonumber \[5pt] &= r_\text{max}N \frac{(K-N)} {K}\nonumber \end{align} \nonumber
Notice that when $N$ is very small, $(K-N)/K$ becomes close to $K/K$ or $1$, and the right side of the equation reduces to $r_{max}N$, which means the population is growing exponentially and is not influenced by carrying capacity. On the other hand, when $N$ is large, $(K-N)/K$ come close to zero, which means that population growth will be slowed greatly or even stopped. Thus, population growth is greatly slowed in large populations by the carrying capacity $K$. This model also allows for the population of a negative population growth, or a population decline. This occurs when the number of individuals in the population exceeds the carrying capacity (because the value of $(K-N)/K$ is negative).
A graph of this equation yields an S-shaped curve (Figure $1$), and it is a more realistic model of population growth than exponential growth. There are three different sections to an S-shaped curve. Initially, growth is exponential because there are few individuals and ample resources available. Then, as resources begin to become limited, the growth rate decreases. Finally, growth levels off at the carrying capacity of the environment, with little change in population size over time.
Role of Intraspecific Competition
The logistic model assumes that every individual within a population will have equal access to resources and, thus, an equal chance for survival. For plants, the amount of water, sunlight, nutrients, and the space to grow are the important resources, whereas in animals, important resources include food, water, shelter, nesting space, and mates.
In the real world, phenotypic variation among individuals within a population means that some individuals will be better adapted to their environment than others. The resulting competition between population members of the same species for resources is termed intraspecific competition (intra- = “within”; -specific = “species”). Intraspecific competition for resources may not affect populations that are well below their carrying capacity—resources are plentiful and all individuals can obtain what they need. However, as population size increases, this competition intensifies. In addition, the accumulation of waste products can reduce an environment’s carrying capacity.
Examples of Logistic Growth
Yeast, a microscopic fungus used to make bread and alcoholic beverages, exhibits the classical S-shaped curve when grown in a test tube (Figure $2$a). Its growth levels off as the population depletes the nutrients that are necessary for its growth. In the real world, however, there are variations to this idealized curve. Examples in wild populations include sheep and harbor seals (Figure $2$b). In both examples, the population size exceeds the carrying capacity for short periods of time and then falls below the carrying capacity afterwards. This fluctuation in population size continues to occur as the population oscillates around its carrying capacity. Still, even with this oscillation, the logistic model is confirmed.
Art Connection
If the major food source of the seals declines due to pollution or overfishing, which of the following would likely occur?
1. The carrying capacity of seals would decrease, as would the seal population.
2. The carrying capacity of seals would decrease, but the seal population would remain the same.
3. The number of seal deaths would increase but the number of births would also increase, so the population size would remain the same.
4. The carrying capacity of seals would remain the same, but the population of seals would decrease.
Summary
Populations with unlimited resources grow exponentially, with an accelerating growth rate. When resources become limiting, populations follow a logistic growth curve. The population of a species will level off at the carrying capacity of its environment.
Art Connections
Figure $2$b If the major food source of the seals declines due to pollution or overfishing, which of the following would likely occur?
1. The carrying capacity of seals would decrease, as would the seal population.
2. The carrying capacity of seals would decrease, but the seal population would remain the same.
3. The number of seal deaths would increase but the number of births would also increase, so the population size would remain the same.
4. The carrying capacity of seals would remain the same, but the population of seals would decrease.
Answer
A
Glossary
biotic potential (rmax)
maximal potential growth rate of a species
birth rate (B)
number of births within a population at a specific point in time
carrying capacity (K)
number of individuals of a species that can be supported by the limited resources of a habitat
death rate (D)
number of deaths within a population at a specific point in time
exponential growth
accelerating growth pattern seen in species under conditions where resources are not limiting
intraspecific competition
competition between members of the same species
J-shaped growth curve
shape of an exponential growth curve
logistic growth
leveling off of exponential growth due to limiting resources
population growth rate
number of organisms added in each reproductive generation
S-shaped growth curve
shape of a logistic growth curve
zero population growth
steady population size where birth rates and death rates are equal | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/8%3A_Ecology/45%3A_Population_and_Community_Ecology/45.3%3A_Environmental_Limits_to_Population_Growth.txt |
Skills to Develop
• Give examples of how the carrying capacity of a habitat may change
• Compare and contrast density-dependent growth regulation and density-independent growth regulation, giving examples
• Give examples of exponential and logistic growth in wild animal populations
• Describe how natural selection and environmental adaptation leads to the evolution of particular life-history patterns
The logistic model of population growth, while valid in many natural populations and a useful model, is a simplification of real-world population dynamics. Implicit in the model is that the carrying capacity of the environment does not change, which is not the case. The carrying capacity varies annually: for example, some summers are hot and dry whereas others are cold and wet. In many areas, the carrying capacity during the winter is much lower than it is during the summer. Also, natural events such as earthquakes, volcanoes, and fires can alter an environment and hence its carrying capacity. Additionally, populations do not usually exist in isolation. They engage in interspecific competition: that is, they share the environment with other species, competing with them for the same resources. These factors are also important to understanding how a specific population will grow.
Nature regulates population growth in a variety of ways. These are grouped into density-dependent factors, in which the density of the population at a given time affects growth rate and mortality, and density-independent factors, which influence mortality in a population regardless of population density. Note that in the former, the effect of the factor on the population depends on the density of the population at onset. Conservation biologists want to understand both types because this helps them manage populations and prevent extinction or overpopulation.
Density-dependent Regulation
Most density-dependent factors are biological in nature (biotic), and include predation, inter- and intraspecific competition, accumulation of waste, and diseases such as those caused by parasites. Usually, the denser a population is, the greater its mortality rate. For example, during intra- and interspecific competition, the reproductive rates of the individuals will usually be lower, reducing their population’s rate of growth. In addition, low prey density increases the mortality of its predator because it has more difficulty locating its food source.
An example of density-dependent regulation is shown in Figure \(1\) with results from a study focusing on the giant intestinal roundworm (Ascaris lumbricoides), a parasite of humans and other mammals.1 Denser populations of the parasite exhibited lower fecundity: they contained fewer eggs. One possible explanation for this is that females would be smaller in more dense populations (due to limited resources) and that smaller females would have fewer eggs. This hypothesis was tested and disproved in a 2009 study which showed that female weight had no influence.2 The actual cause of the density-dependence of fecundity in this organism is still unclear and awaiting further investigation.
Density-independent Regulation and Interaction with Density-dependent Factors
Many factors, typically physical or chemical in nature (abiotic), influence the mortality of a population regardless of its density, including weather, natural disasters, and pollution. An individual deer may be killed in a forest fire regardless of how many deer happen to be in that area. Its chances of survival are the same whether the population density is high or low. The same holds true for cold winter weather.
In real-life situations, population regulation is very complicated and density-dependent and independent factors can interact. A dense population that is reduced in a density-independent manner by some environmental factor(s) will be able to recover differently than a sparse population. For example, a population of deer affected by a harsh winter will recover faster if there are more deer remaining to reproduce.
Evolution Connection: Why Did the Woolly Mammoth Go Extinct?
It's easy to get lost in the discussion of dinosaurs and theories about why they went extinct 65 million years ago. Was it due to a meteor slamming into Earth near the coast of modern-day Mexico, or was it from some long-term weather cycle that is not yet understood? One hypothesis that will never be proposed is that humans had something to do with it. Mammals were small, insignificant creatures of the forest 65 million years ago, and no humans existed.
Woolly mammoths, however, began to go extinct about 10,000 years ago, when they shared the Earth with humans who were no different anatomically than humans today (Figure \(2\)). Mammoths survived in isolated island populations as recently as 1700 BC. We know a lot about these animals from carcasses found frozen in the ice of Siberia and other regions of the north. Scientists have sequenced at least 50 percent of its genome and believe mammoths are between 98 and 99 percent identical to modern elephants.
It is commonly thought that climate change and human hunting led to their extinction. A 2008 study estimated that climate change reduced the mammoth’s range from 3,000,000 square miles 42,000 years ago to 310,000 square miles 6,000 years ago.4 It is also well documented that humans hunted these animals. A 2012 study showed that no single factor was exclusively responsible for the extinction of these magnificent creatures.5 In addition to human hunting, climate change, and reduction of habitat, these scientists demonstrated another important factor in the mammoth’s extinction was the migration of humans across the Bering Strait to North America during the last ice age 20,000 years ago.
The maintenance of stable populations was and is very complex, with many interacting factors determining the outcome. It is important to remember that humans are also part of nature. Once we contributed to a species’ decline using primitive hunting technology only.
Life Histories of K-selected and r-selected Species
While reproductive strategies play a key role in life histories, they do not account for important factors like limited resources and competition. The regulation of population growth by these factors can be used to introduce a classical concept in population biology, that of K-selected versus r-selected species.
Early Theories about Life History: K-selected and r-selected Species
By the second half of the twentieth century, the concept of K- and r-selected species was used extensively and successfully to study populations. The concept relates not only reproductive strategies, but also to a species’ habitat and behavior, especially in the way that they obtain resources and care for their young. It includes length of life and survivorship factors as well. For this analysis, population biologists have grouped species into the two large categories—K-selected and r-selected—although they are really two ends of a continuum.
K-selected species are species selected by stable, predictable environments. Populations of K-selected species tend to exist close to their carrying capacity (hence the term K-selected) where intraspecific competition is high. These species have few, large offspring, a long gestation period, and often give long-term care to their offspring (Table \(1\)). While larger in size when born, the offspring are relatively helpless and immature at birth. By the time they reach adulthood, they must develop skills to compete for natural resources. In plants, scientists think of parental care more broadly: how long fruit takes to develop or how long it remains on the plant are determining factors in the time to the next reproductive event. Examples of K-selected species are primates including humans), elephants, and plants such as oak trees (Figure \(3\)a).
Oak trees grow very slowly and take, on average, 20 years to produce their first seeds, known as acorns. As many as 50,000 acorns can be produced by an individual tree, but the germination rate is low as many of these rot or are eaten by animals such as squirrels. In some years, oaks may produce an exceptionally large number of acorns, and these years may be on a two- or three-year cycle depending on the species of oak (r-selection).
As oak trees grow to a large size and for many years before they begin to produce acorns, they devote a large percentage of their energy budget to growth and maintenance. The tree’s height and size allow it to dominate other plants in the competition for sunlight, the oak’s primary energy resource. Furthermore, when it does reproduce, the oak produces large, energy-rich seeds that use their energy reserve to become quickly established (K-selection).
In contrast, r-selected species have a large number of small offspring (hence their r designation (Table \(1\)). This strategy is often employed in unpredictable or changing environments. Animals that are r-selected do not give long-term parental care and the offspring are relatively mature and self-sufficient at birth. Examples of r-selected species are marine invertebrates, such as jellyfish, and plants, such as the dandelion (Figure \(3\)b). Dandelions have small seeds that are wind dispersed long distances. Many seeds are produced simultaneously to ensure that at least some of them reach a hospitable environment. Seeds that land in inhospitable environments have little chance for survival since their seeds are low in energy content. Note that survival is not necessarily a function of energy stored in the seed itself.
Table \(1\): Characteristics of K-selected and r-selected species
Characteristics of K-selected species Characteristics of r-selected species
Mature late Mature early
Greater longevity Lower longevity
Increased parental care Decreased parental care
Increased competition Decreased competition
Fewer offspring More offspring
Larger offspring Smaller offspring
Modern Theories of Life History
The r- and K-selection theory, although accepted for decades and used for much groundbreaking research, has now been reconsidered, and many population biologists have abandoned or modified it. Over the years, several studies attempted to confirm the theory, but these attempts have largely failed. Many species were identified that did not follow the theory’s predictions. Furthermore, the theory ignored the age-specific mortality of the populations which scientists now know is very important. New demographic-based models of life history evolution have been developed which incorporate many ecological concepts included in r- and K-selection theory as well as population age structure and mortality factors.
Summary
Populations are regulated by a variety of density-dependent and density-independent factors. Species are divided into two categories based on a variety of features of their life history patterns: r-selected species, which have large numbers of offspring, and K-selected species, which have few offspring. The r- and K-selection theory has fallen out of use; however, many of its key features are still used in newer, demographically-based models of population dynamics.
Footnotes
1. 1 N.A. Croll et al., “The Population Biology and Control of Ascaris lumbricoides in a Rural Community in Iran.” Transactions of the Royal Society of Tropical Medicine and Hygiene 76, no. 2 (1982): 187-197, doi:10.1016/0035-9203(82)90272-3.
2. 2 Martin Walker et al., “Density-Dependent Effects on the Weight of Female Ascaris lumbricoides Infections of Humans and its Impact on Patterns of Egg Production.” Parasites & Vectors 2, no. 11 (February 2009), doi:10.1186/1756-3305-2-11.
3. 3 N.A. Croll et al., “The Population Biology and Control of Ascaris lumbricoides in a Rural Community in Iran.” Transactions of the Royal Society of Tropical Medicine and Hygiene 76, no. 2 (1982): 187-197, doi:10.1016/0035-9203(82)90272-3.
4. 4 David Nogués-Bravo et al., “Climate Change, Humans, and the Extinction of the Woolly Mammoth.” PLoS Biol 6 (April 2008): e79, doi:10.1371/journal.pbio.0060079.
5. 5 G.M. MacDonald et al., “Pattern of Extinction of the Woolly Mammoth in Beringia.” Nature Communications 3, no. 893 (June 2012), doi:10.1038/ncomms1881.
Glossary
demographic-based population model
modern model of population dynamics incorporating many features of the r- and K-selection theory
density-dependent regulation
regulation of population that is influenced by population density, such as crowding effects; usually involves biotic factors
density-independent regulation
regulation of populations by factors that operate independent of population density, such as forest fires and volcanic eruptions; usually involves abiotic factors
interspecific competition
competition between species for resources in a shared habitat or environment
K-selected species
species suited to stable environments that produce a few, relatively large offspring and provide parental care
r-selected species
species suited to changing environments that produce many offspring and provide little or no parental care | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/8%3A_Ecology/45%3A_Population_and_Community_Ecology/45.4%3A_Population_Dynamics_and_Regulation.txt |
Skills to Develop
• Discuss how human population growth can be exponential
• Explain how humans have expanded the carrying capacity of their habitat
• Relate population growth and age structure to the level of economic development in different countries
• Discuss the long-term implications of unchecked human population growth
Concepts of animal population dynamics can be applied to human population growth. Humans are not unique in their ability to alter their environment. For example, beaver dams alter the stream environment where they are built. Humans, however, have the ability to alter their environment to increase its carrying capacity sometimes to the detriment of other species (e.g., via artificial selection for crops that have a higher yield). Earth’s human population is growing rapidly, to the extent that some worry about the ability of the earth’s environment to sustain this population, as long-term exponential growth carries the potential risks of famine, disease, and large-scale death.
Although humans have increased the carrying capacity of their environment, the technologies used to achieve this transformation have caused unprecedented changes to Earth’s environment, altering ecosystems to the point where some may be in danger of collapse. The depletion of the ozone layer, erosion due to acid rain, and damage from global climate change are caused by human activities. The ultimate effect of these changes on our carrying capacity is unknown. As some point out, it is likely that the negative effects of increasing carrying capacity will outweigh the positive ones—the carrying capacity of the world for human beings might actually decrease.
The world’s human population is currently experiencing exponential growth even though human reproduction is far below its biotic potential (Figure \(1\)). To reach its biotic potential, all females would have to become pregnant every nine months or so during their reproductive years. Also, resources would have to be such that the environment would support such growth. Neither of these two conditions exists. In spite of this fact, human population is still growing exponentially.
A consequence of exponential human population growth is the time that it takes to add a particular number of humans to the Earth is becoming shorter. Figure \(2\) shows that 123 years were necessary to add 1 billion humans in 1930, but it only took 24 years to add two billion people between 1975 and 1999. As already discussed, at some point it would appear that our ability to increase our carrying capacity indefinitely on a finite world is uncertain. Without new technological advances, the human growth rate has been predicted to slow in the coming decades. However, the population will still be increasing and the threat of overpopulation remains.
Link to Learning
Click through this interactive view of how human populations have changed over time.
Overcoming Density-Dependent Regulation
Humans are unique in their ability to alter their environment with the conscious purpose of increasing its carrying capacity. This ability is a major factor responsible for human population growth and a way of overcoming density-dependent growth regulation. Much of this ability is related to human intelligence, society, and communication. Humans can construct shelter to protect them from the elements and have developed agriculture and domesticated animals to increase their food supplies. In addition, humans use language to communicate this technology to new generations, allowing them to improve upon previous accomplishments.
Other factors in human population growth are migration and public health. Humans originated in Africa, but have since migrated to nearly all inhabitable land on the Earth. Public health, sanitation, and the use of antibiotics and vaccines have decreased the ability of infectious disease to limit human population growth. In the past, diseases such as the bubonic plaque of the fourteenth century killed between 30 and 60 percent of Europe’s population and reduced the overall world population by as many as 100 million people. Today, the threat of infectious disease, while not gone, is certainly less severe. According to the World Health Organization, global death from infectious disease declined from 16.4 million in 1993 to 14.7 million in 1992. To compare to some of the epidemics of the past, the percentage of the world's population killed between 1993 and 2002 decreased from 0.30 percent of the world's population to 0.24 percent. Thus, it appears that the influence of infectious disease on human population growth is becoming less significant.
Age Structure, Population Growth, and Economic Development
The age structure of a population is an important factor in population dynamics. Age structure is the proportion of a population at different age ranges. Age structure allows better prediction of population growth, plus the ability to associate this growth with the level of economic development in the region. Countries with rapid growth have a pyramidal shape in their age structure diagrams, showing a preponderance of younger individuals, many of whom are of reproductive age or will be soon (Figure \(3\)). This pattern is most often observed in underdeveloped countries where individuals do not live to old age because of less-than-optimal living conditions. Age structures of areas with slow growth, including developed countries such as the United States, still have a pyramidal structure, but with many fewer young and reproductive-aged individuals and a greater proportion of older individuals. Other developed countries, such as Italy, have zero population growth. The age structure of these populations is more conical, with an even greater percentage of middle-aged and older individuals. The actual growth rates in different countries are shown in Figure \(4\), with the highest rates tending to be in the less economically developed countries of Africa and Asia.
Art Connection
Age structure diagrams for rapidly growing, slow growing and stable populations are shown in stages 1 through 3. What type of population change do you think stage 4 represents?
Long-Term Consequences of Exponential Human Population Growth
Many dire predictions have been made about the world’s population leading to a major crisis called the “population explosion.” In the 1968 book The Population Bomb, biologist Dr. Paul R. Ehrlich wrote, “The battle to feed all of humanity is over. In the 1970s hundreds of millions of people will starve to death in spite of any crash programs embarked upon now. At this late date nothing can prevent a substantial increase in the world death rate.”1 While many critics view this statement as an exaggeration, the laws of exponential population growth are still in effect, and unchecked human population growth cannot continue indefinitely.
Efforts to control population growth led to the one-child policy in China, which used to include more severe consequences, but now imposes fines on urban couples who have more than one child. Due to the fact that some couples wish to have a male heir, many Chinese couples continue to have more than one child. The policy itself, its social impacts, and the effectiveness of limiting overall population growth are controversial. In spite of population control policies, the human population continues to grow. At some point the food supply may run out because of the subsequent need to produce more and more food to feed our population. The United Nations estimates that future world population growth may vary from 6 billion (a decrease) to 16 billion people by the year 2100. There is no way to know whether human population growth will moderate to the point where the crisis described by Dr. Ehrlich will be averted.
Another result of population growth is the endangerment of the natural environment. Many countries have attempted to reduce the human impact on climate change by reducing their emission of the greenhouse gas carbon dioxide. However, these treaties have not been ratified by every country, and many underdeveloped countries trying to improve their economic condition may be less likely to agree with such provisions if it means slower economic development. Furthermore, the role of human activity in causing climate change has become a hotly debated socio-political issue in some developed countries, including the United States. Thus, we enter the future with considerable uncertainty about our ability to curb human population growth and protect our environment.
Link to Learning
Visit this website and select “Launch movie” for an animation discussing the global impacts of human population growth.
Summary
The world’s human population is growing at an exponential rate. Humans have increased the world’s carrying capacity through migration, agriculture, medical advances, and communication. The age structure of a population allows us to predict population growth. Unchecked human population growth could have dire long-term effects on our environment.
Art Connections
Figure \(3\): Age structure diagrams for rapidly growing, slow growing and stable populations are shown in stages 1 through 3. What type of population change do you think stage 4 represents?
Answer
Stage 4 represents a population that is decreasing.
Footnotes
1. 1 Paul R. Erlich, prologue to The Population Bomb, (1968; repr., New York: Ballantine, 1970).
Glossary
age structure
proportion of population members at specific age ranges
one-child policy
China’s policy to limit population growth by limiting urban couples to have only one child or face the penalty of a fine | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/8%3A_Ecology/45%3A_Population_and_Community_Ecology/45.5%3A_Human_Population_Growth.txt |
Skills to Develop
• Discuss the predator-prey cycle
• Give examples of defenses against predation and herbivory
• Describe the competitive exclusion principle
• Give examples of symbiotic relationships between species
• Describe community structure and succession
Populations rarely, if ever, live in isolation from populations of other species. In most cases, numerous species share a habitat. The interactions between these populations play a major role in regulating population growth and abundance. All populations occupying the same habitat form a community: populations inhabiting a specific area at the same time. The number of species occupying the same habitat and their relative abundance is known as species diversity. Areas with low diversity, such as the glaciers of Antarctica, still contain a wide variety of living things, whereas the diversity of tropical rainforests is so great that it cannot be counted. Ecology is studied at the community level to understand how species interact with each other and compete for the same resources.
Predation and Herbivory
Perhaps the classical example of species interaction is predation: the hunting of prey by its predator. Nature shows on television highlight the drama of one living organism killing another. Populations of predators and prey in a community are not constant over time: in most cases, they vary in cycles that appear to be related. The most often cited example of predator-prey dynamics is seen in the cycling of the lynx (predator) and the snowshoe hare (prey), using nearly 200 year-old trapping data from North American forests (Figure \(1\)). This cycle of predator and prey lasts approximately 10 years, with the predator population lagging 1–2 years behind that of the prey population. As the hare numbers increase, there is more food available for the lynx, allowing the lynx population to increase as well. When the lynx population grows to a threshold level, however, they kill so many hares that hare population begins to decline, followed by a decline in the lynx population because of scarcity of food. When the lynx population is low, the hare population size begins to increase due, at least in part, to low predation pressure, starting the cycle anew.
The idea that the population cycling of the two species is entirely controlled by predation models has come under question. More recent studies have pointed to undefined density-dependent factors as being important in the cycling, in addition to predation. One possibility is that the cycling is inherent in the hare population due to density-dependent effects such as lower fecundity (maternal stress) caused by crowding when the hare population gets too dense. The hare cycling would then induce the cycling of the lynx because it is the lynxes’ major food source. The more we study communities, the more complexities we find, allowing ecologists to derive more accurate and sophisticated models of population dynamics.
Herbivory describes the consumption of plants by insects and other animals, and it is another interspecific relationship that affects populations. Unlike animals, most plants cannot outrun predators or use mimicry to hide from hungry animals. Some plants have developed mechanisms to defend against herbivory. Other species have developed mutualistic relationships; for example, herbivory provides a mechanism of seed distribution that aids in plant reproduction.
Defense Mechanisms against Predation and Herbivory
The study of communities must consider evolutionary forces that act on the members of the various populations contained within it. Species are not static, but slowly changing and adapting to their environment by natural selection and other evolutionary forces. Species have evolved numerous mechanisms to escape predation and herbivory. These defenses may be mechanical, chemical, physical, or behavioral.
Mechanical defenses, such as the presence of thorns on plants or the hard shell on turtles, discourage animal predation and herbivory by causing physical pain to the predator or by physically preventing the predator from being able to eat the prey. Chemical defenses are produced by many animals as well as plants, such as the foxglove which is extremely toxic when eaten. Figure \(2\) shows some organisms’ defenses against predation and herbivory.
Many species use their body shape and coloration to avoid being detected by predators. The tropical walking stick is an insect with the coloration and body shape of a twig which makes it very hard to see when stationary against a background of real twigs (Figure \(3\)a). In another example, the chameleon can change its color to match its surroundings (Figure \(3\)b). Both of these are examples of camouflage, or avoiding detection by blending in with the background.
Some species use coloration as a way of warning predators that they are not good to eat. For example, the cinnabar moth caterpillar, the fire-bellied toad, and many species of beetle have bright colors that warn of a foul taste, the presence of toxic chemical, and/or the ability to sting or bite, respectively. Predators that ignore this coloration and eat the organisms will experience their unpleasant taste or presence of toxic chemicals and learn not to eat them in the future. This type of defensive mechanism is called aposematic coloration, or warning coloration (Figure \(4\)).
While some predators learn to avoid eating certain potential prey because of their coloration, other species have evolved mechanisms to mimic this coloration to avoid being eaten, even though they themselves may not be unpleasant to eat or contain toxic chemicals. In Batesian mimicry, a harmless species imitates the warning coloration of a harmful one. Assuming they share the same predators, this coloration then protects the harmless ones, even though they do not have the same level of physical or chemical defenses against predation as the organism they mimic. Many insect species mimic the coloration of wasps or bees, which are stinging, venomous insects, thereby discouraging predation (Figure \(5\)).
In Müllerian mimicry, multiple species share the same warning coloration, but all of them actually have defenses. Figure \(6\) shows a variety of foul-tasting butterflies with similar coloration. In Emsleyan/Mertensian mimicry, a deadly prey mimics a less dangerous one, such as the venomous coral snake mimicking the non-venomous milk snake. This type of mimicry is extremely rare and more difficult to understand than the previous two types. For this type of mimicry to work, it is essential that eating the milk snake has unpleasant but not fatal consequences. Then, these predators learn not to eat snakes with this coloration, protecting the coral snake as well. If the snake were fatal to the predator, there would be no opportunity for the predator to learn not to eat it, and the benefit for the less toxic species would disappear.
Link to Learning
Go to this website to view stunning examples of mimicry.
Competitive Exclusion Principle
Resources are often limited within a habitat and multiple species may compete to obtain them. All species have an ecological niche in the ecosystem, which describes how they acquire the resources they need and how they interact with other species in the community. The competitive exclusion principle states that two species cannot occupy the same niche in a habitat. In other words, different species cannot coexist in a community if they are competing for all the same resources. An example of this principle is shown in Figure \(7\), with two protozoan species, Paramecium aurelia and Paramecium caudatum. When grown individually in the laboratory, they both thrive. But when they are placed together in the same test tube (habitat), P. aurelia outcompetes P. caudatum for food, leading to the latter’s eventual extinction.
This exclusion may be avoided if a population evolves to make use of a different resource, a different area of the habitat, or feeds during a different time of day, called resource partitioning. The two organisms are then said to occupy different microniches. These organisms coexist by minimizing direct competition.
Symbiosis
Symbiotic relationships, or symbioses (plural), are close interactions between individuals of different species over an extended period of time which impact the abundance and distribution of the associating populations. Most scientists accept this definition, but some restrict the term to only those species that are mutualistic, where both individuals benefit from the interaction. In this discussion, the broader definition will be used.
Commensalism
A commensal relationship occurs when one species benefits from the close, prolonged interaction, while the other neither benefits nor is harmed. Birds nesting in trees provide an example of a commensal relationship (Figure \(8\)). The tree is not harmed by the presence of the nest among its branches. The nests are light and produce little strain on the structural integrity of the branch, and most of the leaves, which the tree uses to get energy by photosynthesis, are above the nest so they are unaffected. The bird, on the other hand, benefits greatly. If the bird had to nest in the open, its eggs and young would be vulnerable to predators. Another example of a commensal relationship is the clown fish and the sea anemone. The sea anemone is not harmed by the fish, and the fish benefits with protection from predators who would be stung upon nearing the sea anemone.
Mutualism
A second type of symbiotic relationship is called mutualism, where two species benefit from their interaction. Some scientists believe that these are the only true examples of symbiosis. For example, termites have a mutualistic relationship with protozoa that live in the insect’s gut (Figure \(9\)a). The termite benefits from the ability of bacterial symbionts within the protozoa to digest cellulose. The termite itself cannot do this, and without the protozoa, it would not be able to obtain energy from its food (cellulose from the wood it chews and eats). The protozoa and the bacterial symbionts benefit by having a protective environment and a constant supply of food from the wood chewing actions of the termite. Lichens have a mutualistic relationship between fungus and photosynthetic algae or bacteria (Figure \(9\)b). As these symbionts grow together, the glucose produced by the algae provides nourishment for both organisms, whereas the physical structure of the lichen protects the algae from the elements and makes certain nutrients in the atmosphere more available to the algae.
Parasitism
A parasite is an organism that lives in or on another living organism and derives nutrients from it. In this relationship, the parasite benefits, but the organism being fed upon, the host, is harmed. The host is usually weakened by the parasite as it siphons resources the host would normally use to maintain itself. The parasite, however, is unlikely to kill the host, especially not quickly, because this would allow no time for the organism to complete its reproductive cycle by spreading to another host.
The reproductive cycles of parasites are often very complex, sometimes requiring more than one host species. A tapeworm is a parasite that causes disease in humans when contaminated, undercooked meat such as pork, fish, or beef is consumed (Figure \(10\)). The tapeworm can live inside the intestine of the host for several years, benefiting from the food the host is bringing into its gut by eating, and may grow to be over 50 ft long by adding segments. The parasite moves from species to species in a cycle, making two hosts necessary to complete its life cycle. Another common parasite is Plasmodium falciparum, the protozoan cause of malaria, a significant disease in many parts of the world. Living in human liver and red blood cells, the organism reproduces asexually in the gut of blood-feeding mosquitoes to complete its life cycle. Thus malaria is spread from human to human by mosquitoes, one of many arthropod-borne infectious diseases.
Characteristics of Communities
Communities are complex entities that can be characterized by their structure (the types and numbers of species present) and dynamics (how communities change over time). Understanding community structure and dynamics enables community ecologists to manage ecosystems more effectively.
Foundation Species
Foundation species are considered the “base” or “bedrock” of a community, having the greatest influence on its overall structure. They are usually the primary producers: organisms that bring most of the energy into the community. Kelp, brown algae, is a foundation species, forming the basis of the kelp forests off the coast of California.
Foundation species may physically modify the environment to produce and maintain habitats that benefit the other organisms that use them. An example is the photosynthetic corals of the coral reef (Figure \(11\)). Corals themselves are not photosynthetic, but harbor symbionts within their body tissues (dinoflagellates called zooxanthellae) that perform photosynthesis; this is another example of a mutualism. The exoskeletons of living and dead coral make up most of the reef structure, which protects many other species from waves and ocean currents.
Biodiversity, Species Richness, and Relative Species Abundance
Biodiversity describes a community’s biological complexity: it is measured by the number of different species (species richness) in a particular area and their relative abundance (species evenness). The area in question could be a habitat, a biome, or the entire biosphere. Species richness is the term that is used to describe the number of species living in a habitat or biome. Species richness varies across the globe (Figure \(12\)). One factor in determining species richness is latitude, with the greatest species richness occurring in ecosystems near the equator, which often have warmer temperatures, large amounts of rainfall, and low seasonality. The lowest species richness occurs near the poles, which are much colder, drier, and thus less conducive to life in Geologic time (time since glaciations). The predictability of climate or productivity is also an important factor. Other factors influence species richness as well. For example, the study of island biogeography attempts to explain the relatively high species richness found in certain isolated island chains, including the Galápagos Islands that inspired the young Darwin. Relative species abundance is the number of individuals in a species relative to the total number of individuals in all species within a habitat, ecosystem, or biome. Foundation species often have the highest relative abundance of species.
Keystone Species
A keystone species is one whose presence is key to maintaining biodiversity within an ecosystem and to upholding an ecological community’s structure. The intertidal sea star, Pisaster ochraceus, of the northwestern United States is a keystone species (Figure \(13\)). Studies have shown that when this organism is removed from communities, populations of their natural prey (mussels) increase, completely altering the species composition and reducing biodiversity. Another keystone species is the banded tetra, a fish in tropical streams, which supplies nearly all of the phosphorus, a necessary inorganic nutrient, to the rest of the community. If these fish were to become extinct, the community would be greatly affected.
Everyday Connection: Invasive Species
Invasive species are non-native organisms that, when introduced to an area out of their native range, threaten the ecosystem balance of that habitat. Many such species exist in the United States, as shown in Figure \(14\). Whether enjoying a forest hike, taking a summer boat trip, or simply walking down an urban street, you have likely encountered an invasive species.
One of the many recent proliferations of an invasive species concerns the growth of Asian carp populations. Asian carp were introduced to the United States in the 1970s by fisheries and sewage treatment facilities that used the fish’s excellent filter feeding capabilities to clean their ponds of excess plankton. Some of the fish escaped, however, and by the 1980s they had colonized many waterways of the Mississippi River basin, including the Illinois and Missouri Rivers.
Voracious eaters and rapid reproducers, Asian carp may outcompete native species for food, potentially leading to their extinction. For example, black carp are voracious eaters of native mussels and snails, limiting this food source for native fish species. Silver carp eat plankton that native mussels and snails feed on, reducing this food source by a different alteration of the food web. In some areas of the Mississippi River, Asian carp species have become the most predominant, effectively outcompeting native fishes for habitat. In some parts of the Illinois River, Asian carp constitute 95 percent of the community's biomass. Although edible, the fish is bony and not a desired food in the United States. Moreover, their presence threatens the native fish and fisheries of the Great Lakes, which are important to local economies and recreational anglers. Asian carp have even injured humans. The fish, frightened by the sound of approaching motorboats, thrust themselves into the air, often landing in the boat or directly hitting the boaters.
The Great Lakes and their prized salmon and lake trout fisheries are also being threatened by these invasive fish. Asian carp have already colonized rivers and canals that lead into Lake Michigan. One infested waterway of particular importance is the Chicago Sanitary and Ship Channel, the major supply waterway linking the Great Lakes to the Mississippi River. To prevent the Asian carp from leaving the canal, a series of electric barriers have been successfully used to discourage their migration; however, the threat is significant enough that several states and Canada have sued to have the Chicago channel permanently cut off from Lake Michigan. Local and national politicians have weighed in on how to solve the problem, but no one knows whether the Asian carp will ultimately be considered a nuisance, like other invasive species such as the water hyacinth and zebra mussel, or whether it will be the destroyer of the largest freshwater fishery of the world.
The issues associated with Asian carp show how population and community ecology, fisheries management, and politics intersect on issues of vital importance to the human food supply and economy. Socio-political issues like this make extensive use of the sciences of population ecology (the study of members of a particular species occupying a particular area known as a habitat) and community ecology (the study of the interaction of all species within a habitat).
Community Dynamics
Community dynamics are the changes in community structure and composition over time. Sometimes these changes are induced by environmental disturbances such as volcanoes, earthquakes, storms, fires, and climate change. Communities with a stable structure are said to be at equilibrium. Following a disturbance, the community may or may not return to the equilibrium state.
Succession describes the sequential appearance and disappearance of species in a community over time. In primary succession, newly exposed or newly formed land is colonized by living things; in secondary succession, part of an ecosystem is disturbed and remnants of the previous community remain.
Primary Succession and Pioneer Species
Primary succession occurs when new land is formed or rock is exposed: for example, following the eruption of volcanoes, such as those on the Big Island of Hawaii. As lava flows into the ocean, new land is continually being formed. On the Big Island, approximately 32 acres of land is added each year. First, weathering and other natural forces break down the substrate enough for the establishment of certain hearty plants and lichens with few soil requirements, known as pioneer species (Figure \(15\)). These species help to further break down the mineral rich lava into soil where other, less hardy species will grow and eventually replace the pioneer species. In addition, as these early species grow and die, they add to an ever-growing layer of decomposing organic material and contribute to soil formation. Over time the area will reach an equilibrium state, with a set of organisms quite different from the pioneer species.
Secondary succession
A classic example of secondary succession occurs in oak and hickory forests cleared by wildfire (Figure \(16\)). Wildfires will burn most vegetation and kill those animals unable to flee the area. Their nutrients, however, are returned to the ground in the form of ash. Thus, even when areas are devoid of life due to severe fires, the area will soon be ready for new life to take hold.
Before the fire, the vegetation was dominated by tall trees with access to the major plant energy resource: sunlight. Their height gave them access to sunlight while also shading the ground and other low-lying species. After the fire, though, these trees are no longer dominant. Thus, the first plants to grow back are usually annual plants followed within a few years by quickly growing and spreading grasses and other pioneer species. Due to, at least in part, changes in the environment brought on by the growth of the grasses and other species, over many years, shrubs will emerge along with small pine, oak, and hickory trees. These organisms are called intermediate species. Eventually, over 150 years, the forest will reach its equilibrium point where species composition is no longer changing and resembles the community before the fire. This equilibrium state is referred to as the climax community, which will remain stable until the next disturbance.
Summary
Communities include all the different species living in a given area. The variety of these species is called species richness. Many organisms have developed defenses against predation and herbivory, including mechanical defenses, warning coloration, and mimicry, as a result of evolution and the interaction with other members of the community. Two species cannot exist in the same habitat competing directly for the same resources. Species may form symbiotic relationships such as commensalism or mutualism. Community structure is described by its foundation and keystone species. Communities respond to environmental disturbances by succession (the predictable appearance of different types of plant species) until a stable community structure is established.
Glossary
aposematic coloration
warning coloration used as a defensive mechanism against predation
Batesian mimicry
type of mimicry where a non-harmful species takes on the warning colorations of a harmful one
camouflage
avoid detection by blending in with the background.
climax community
final stage of succession, where a stable community is formed by a characteristic assortment of plant and animal species
commensalism
relationship between species wherein one species benefits from the close, prolonged interaction, while the other species neither benefits nor is harmed
competitive exclusion principle
no two species within a habitat can coexist when they compete for the same resources at the same place and time
Emsleyan/Mertensian mimicry
type of mimicry where a harmful species resembles a less harmful one
environmental disturbance
change in the environment caused by natural disasters or human activities
foundation species
species which often forms the major structural portion of the habitat
host
organism a parasite lives on
island biogeography
study of life on island chains and how their geography interacts with the diversity of species found there
keystone species
species whose presence is key to maintaining biodiversity in an ecosystem and to upholding an ecological community’s structure
Müllerian mimicry
type of mimicry where species share warning coloration and all are harmful to predators
mutualism
symbiotic relationship between two species where both species benefit
parasite
organism that uses resources from another species, the host
pioneer species
first species to appear in primary and secondary succession
primary succession
succession on land that previously has had no life
relative species abundance
absolute population size of a particular species relative to the population sizes of other species within the community
secondary succession
succession in response to environmental disturbances that move a community away from its equilibrium
species richness
number of different species in a community
symbiosis
close interaction between individuals of different species over an extended period of time that impacts the abundance and distribution of the associating populations | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/8%3A_Ecology/45%3A_Population_and_Community_Ecology/45.6%3A_Community_Ecology.txt |
Skills to Develop
• Compare innate and learned behavior
• Discuss how movement and migration behaviors are a result of natural selection
• Discuss the different ways members of a population communicate with each other
• Give examples of how species use energy for mating displays and other courtship behaviors
• Differentiate between various mating systems
• Describe different ways that species learn
Behavior is the change in activity of an organism in response to a stimulus. Behavioral biology is the study of the biological and evolutionary bases for such changes. The idea that behaviors evolved as a result of the pressures of natural selection is not new. Animal behavior has been studied for decades, by biologists in the science of ethology, by psychologists in the science of comparative psychology, and by scientists of many disciplines in the study of neurobiology. Although there is overlap between these disciplines, scientists in these behavioral fields take different approaches. Comparative psychology is an extension of work done in human and behavioral psychology. Ethology is an extension of genetics, evolution, anatomy, physiology, and other biological disciplines. Still, one cannot study behavioral biology without touching on both comparative psychology and ethology.
One goal of behavioral biology is to dissect out the innate behaviors, which have a strong genetic component and are largely independent of environmental influences, from the learned behaviors, which result from environmental conditioning. Innate behavior, or instinct, is important because there is no risk of an incorrect behavior being learned. They are “hard wired” into the system. On the other hand, learned behaviors, although riskier, are flexible, dynamic, and can be altered according to changes in the environment.
Innate Behaviors: Movement and Migration
Innate or instinctual behaviors rely on response to stimuli. The simplest example of this is a reflex action, an involuntary and rapid response to stimulus. To test the “knee-jerk” reflex, a doctor taps the patellar tendon below the kneecap with a rubber hammer. The stimulation of the nerves there leads to the reflex of extending the leg at the knee. This is similar to the reaction of someone who touches a hot stove and instinctually pulls his or her hand away. Even humans, with our great capacity to learn, still exhibit a variety of innate behaviors.
Kinesis and Taxis
Another activity or movement of innate behavior is kinesis, or the undirected movement in response to a stimulus. Orthokinesis is the increased or decreased speed of movement of an organism in response to a stimulus. Woodlice, for example, increase their speed of movement when exposed to high or low temperatures. This movement, although random, increases the probability that the insect spends less time in the unfavorable environment. Another example is klinokinesis, an increase in turning behaviors. It is exhibited by bacteria such as E. coli which, in association with orthokinesis, helps the organisms randomly find a more hospitable environment.
A similar, but more directed version of kinesis is taxis: the directed movement towards or away from a stimulus. This movement can be in response to light (phototaxis), chemical signals (chemotaxis), or gravity (geotaxis) and can be directed toward (positive) or away (negative) from the source of the stimulus. An example of a positive chemotaxis is exhibited by the unicellular protozoan Tetrahymena thermophila. This organism swims using its cilia, at times moving in a straight line, and at other times making turns. The attracting chemotactic agent alters the frequency of turning as the organism moves directly toward the source, following the increasing concentration gradient.
Fixed Action Patterns
A fixed action pattern is a series of movements elicited by a stimulus such that even when the stimulus is removed, the pattern goes on to completion. An example of such a behavior occurs in the three-spined stickleback, a small freshwater fish (Figure \(1\)). Males of this species develop a red belly during breeding season and show instinctual aggressiveness to other males during this time. In laboratory experiments, researchers exposed such fish to objects that in no way resemble a fish in their shape, but which were painted red on their lower halves. The male sticklebacks responded aggressively to the objects just as if they were real male sticklebacks.
Migration
Migration is the long-range seasonal movement of animals. It is an evolved, adapted response to variation in resource availability, and it is a common phenomenon found in all major groups of animals. Birds fly south for the winter to get to warmer climates with sufficient food, and salmon migrate to their spawning grounds. The popular 2005 documentary March of the Penguins followed the 62-mile migration of emperor penguins through Antarctica to bring food back to their breeding site and to their young. Wildebeests (Figure \(2\)) migrate over 1800 miles each year in search of new grasslands.
Although migration is thought of as innate behavior, only some migrating species always migrate (obligate migration). Animals that exhibit facultative migration can choose to migrate or not. Additionally, in some animals, only a portion of the population migrates, whereas the rest does not migrate (incomplete migration). For example, owls that live in the tundra may migrate in years when their food source, small rodents, is relatively scarce, but not migrate during the years when rodents are plentiful.
Foraging
Foraging is the act of searching for and exploiting food resources. Feeding behaviors that maximize energy gain and minimize energy expenditure are called optimal foraging behaviors, and these are favored by natural section. The painted stork, for example, uses its long beak to search the bottom of a freshwater marshland for crabs and other food (Figure \(3\)).
Innate Behaviors: Living in Groups
Not all animals live in groups, but even those that live relatively solitary lives, with the exception of those that can reproduce asexually, must mate. Mating usually involves one animal signaling another so as to communicate the desire to mate. There are several types of energy-intensive behaviors or displays associated with mating, called mating rituals. Other behaviors found in populations that live in groups are described in terms of which animal benefits from the behavior. In selfish behavior, only the animal in question benefits; in altruistic behavior, one animal’s actions benefit another animal; cooperative behavior describes when both animals benefit. All of these behaviors involve some sort of communication between population members.
Communication within a Species
Animals communicate with each other using stimuli known as signals. An example of this is seen in the three-spined stickleback, where the visual signal of a red region in the lower half of a fish signals males to become aggressive and signals females to mate. Other signals are chemical (pheromones), aural (sound), visual (courtship and aggressive displays), or tactile (touch). These types of communication may be instinctual or learned or a combination of both. These are not the same as the communication we associate with language, which has been observed only in humans and perhaps in some species of primates and cetaceans.
A pheromone is a secreted chemical signal used to obtain a response from another individual of the same species. The purpose of pheromones is to elicit a specific behavior from the receiving individual. Pheromones are especially common among social insects, but they are used by many species to attract the opposite sex, to sound alarms, to mark food trails, and to elicit other, more complex behaviors. Even humans are thought to respond to certain pheromones called axillary steroids. These chemicals influence human perception of other people, and in one study were responsible for a group of women synchronizing their menstrual cycles. The role of pheromones in human-to-human communication is still somewhat controversial and continues to be researched.
Songs are an example of an aural signal, one that needs to be heard by the recipient. Perhaps the best known of these are songs of birds, which identify the species and are used to attract mates. Other well-known songs are those of whales, which are of such low frequency that they can travel long distances underwater. Dolphins communicate with each other using a wide variety of vocalizations. Male crickets make chirping sounds using a specialized organ to attract a mate, repel other males, and to announce a successful mating.
Courtship displays are a series of ritualized visual behaviors (signals) designed to attract and convince a member of the opposite sex to mate. These displays are ubiquitous in the animal kingdom. Often these displays involve a series of steps, including an initial display by one member followed by a response from the other. If at any point, the display is performed incorrectly or a proper response is not given, the mating ritual is abandoned and the mating attempt will be unsuccessful. The mating display of the common stork is shown in Figure \(4\).
Aggressive displays are also common in the animal kingdom. An example is when a dog bares its teeth when it wants another dog to back down. Presumably, these displays communicate not only the willingness of the animal to fight, but also its fighting ability. Although these displays do signal aggression on the part of the sender, it is thought that these displays are actually a mechanism to reduce the amount of actual fighting that occurs between members of the same species: they allow individuals to assess the fighting ability of their opponent and thus decide whether it is “worth the fight.” The testing of certain hypotheses using game theory has led to the conclusion that some of these displays may overstate an animal’s actual fighting ability and are used to “bluff” the opponent. This type of interaction, even if “dishonest,” would be favored by natural selection if it is successful more times than not.
Distraction displays are seen in birds and some fish. They are designed to attract a predator away from the nest that contains their young. This is an example of an altruistic behavior: it benefits the young more than the individual performing the display, which is putting itself at risk by doing so.
Many animals, especially primates, communicate with other members in the group through touch. Activities such as grooming, touching the shoulder or root of the tail, embracing, lip contact, and greeting ceremonies have all been observed in the Indian langur, an Old World monkey. Similar behaviors are found in other primates, especially in the great apes.
Link to Learning
The killdeer bird distracts predators from its eggs by faking a broken wing display in this video taken in Boise, Idaho.
Altruistic Behaviors
Behaviors that lower the fitness of the individual but increase the fitness of another individual are termed altruistic. Examples of such behaviors are seen widely across the animal kingdom. Social insects such as worker bees have no ability to reproduce, yet they maintain the queen so she can populate the hive with her offspring. Meerkats keep a sentry standing guard to warn the rest of the colony about intruders, even though the sentry is putting itself at risk. Wolves and wild dogs bring meat to pack members not present during a hunt. Lemurs take care of infants unrelated to them. Although on the surface, these behaviors appear to be altruistic, it may not be so simple.
There has been much discussion over why altruistic behaviors exist. Do these behaviors lead to overall evolutionary advantages for their species? Do they help the altruistic individual pass on its own genes? And what about such activities between unrelated individuals? One explanation for altruistic-type behaviors is found in the genetics of natural selection. In the 1976 book, The Selfish Gene, scientist Richard Dawkins attempted to explain many seemingly altruistic behaviors from the viewpoint of the gene itself. Although a gene obviously cannot be selfish in the human sense, it may appear that way if the sacrifice of an individual benefits related individuals that share genes that are identical by descent (present in relatives because of common lineage). Mammal parents make this sacrifice to take care of their offspring. Emperor penguins migrate miles in harsh conditions to bring food back for their young. Selfish gene theory has been controversial over the years and is still discussed among scientists in related fields.
Even less-related individuals, those with less genetic identity than that shared by parent and offspring, benefit from seemingly altruistic behavior. The activities of social insects such as bees, wasps, ants, and termites are good examples. Sterile workers in these societies take care of the queen because they are closely related to it, and as the queen has offspring, she is passing on genes from the workers indirectly. Thus, it is of fitness benefit for the worker to maintain the queen without having any direct chance of passing on its genes due to its sterility. The lowering of individual fitness to enhance the reproductive fitness of a relative and thus one’s inclusive fitness evolves through kin selection. This phenomenon can explain many superficially altruistic behaviors seen in animals. However, these behaviors may not be truly defined as altruism in these cases because the actor is actually increasing its own fitness either directly (through its own offspring) or indirectly (through the inclusive fitness it gains through relatives that share genes with it).
Unrelated individuals may also act altruistically to each other, and this seems to defy the “selfish gene” explanation. An example of this observed in many monkey species where a monkey will present its back to an unrelated monkey to have that individual pick the parasites from its fur. After a certain amount of time, the roles are reversed and the first monkey now grooms the second monkey. Thus, there is reciprocity in the behavior. Both benefit from the interaction and their fitness is raised more than if neither cooperated nor if one cooperated and the other did not cooperate. This behavior is still not necessarily altruism, as the “giving” behavior of the actor is based on the expectation that it will be the “receiver” of the behavior in the future, termed reciprocal altruism. Reciprocal altruism requires that individuals repeatedly encounter each other, often the result of living in the same social group, and that cheaters (those that never “give back”) are punished.
Evolutionary game theory, a modification of classical game theory in mathematics, has shown that many of these so-called “altruistic behaviors” are not altruistic at all. The definition of “pure” altruism, based on human behavior, is an action that benefits another without any direct benefit to oneself. Most of the behaviors previously described do not seem to satisfy this definition, and game theorists are good at finding “selfish” components in them. Others have argued that the terms “selfish” and “altruistic” should be dropped completely when discussing animal behavior, as they describe human behavior and may not be directly applicable to instinctual animal activity. What is clear, though, is that heritable behaviors that improve the chances of passing on one’s genes or a portion of one’s genes are favored by natural selection and will be retained in future generations as long as those behaviors convey a fitness advantage. These instinctual behaviors may then be applied, in special circumstances, to other species, as long as it doesn’t lower the animal’s fitness.
Finding Sex Partners
Not all animals reproduce sexually, but many that do have the same challenge: they need to find a suitable mate and often have to compete with other individuals to obtain one. Significant energy is spent in the process of locating, attracting, and mating with the sex partner. Two types of selection occur during this process and can lead to traits that are important to reproduction called secondary sexual characteristics: intersexual selection, the choosing of a mate where individuals of one sex choose mates of the other sex, and intrasexual selection, the competition for mates between species members of the same sex. Intersexual selection is often complex because choosing a mate may be based on a variety of visual, aural, tactile, and chemical cues. An example of intersexual selection is when female peacocks choose to mate with the male with the brightest plumage. This type of selection often leads to traits in the chosen sex that do not enhance survival, but are those traits most attractive to the opposite sex (often at the expense of survival). Intrasexual selection involves mating displays and aggressive mating rituals such as rams butting heads—the winner of these battles is the one that is able to mate. Many of these rituals use up considerable energy but result in the selection of the healthiest, strongest, and/or most dominant individuals for mating. Three general mating systems, all involving innate as opposed to learned behaviors, are seen in animal populations: monogamous, polygynous, and polyandrous.
In monogamous systems, one male and one female are paired for at least one breeding season. In some animals, such as the gray wolf, these associations can last much longer, even a lifetime. Several explanations have been proposed for this type of mating system. The “mate-guarding hypothesis” states that males stay with the female to prevent other males from mating with her. This behavior is advantageous in such situations where mates are scarce and difficult to find. Another explanation is the “male-assistance hypothesis,” where males that remain with a female to help guard and rear their young will have more and healthier offspring. Monogamy is observed in many bird populations where, in addition to the parental care from the female, the male is also a major provider of parental care for the chicks. A third explanation for the evolutionary advantages of monogamy is the “female-enforcement hypothesis.” In this scenario, the female ensures that the male does not have other offspring that might compete with her own, so she actively interferes with the male’s signaling to attract other mates.
Polygynous mating refers to one male mating with multiple females. In these situations, the female must be responsible for most of the parental care as the single male is not capable of providing care to that many offspring. In resourced-based polygyny, males compete for territories with the best resources, and then mate with females that enter the territory, drawn to its resource richness. The female benefits by mating with a dominant, genetically fit male; however, it is at the cost of having no male help in caring for the offspring. An example is seen in the yellow-rumped honeyguide, a bird whose males defend beehives because the females feed on their wax. As the females approach, the male defending the nest will mate with them. Harem mating structures are a type of polygynous system where certain males dominate mating while controlling a territory with resources. Elephant seals, where the alpha male dominates the mating within the group are an example. A third type of polygyny is a lek system. Here there is a communal courting area where several males perform elaborate displays for females, and the females choose their mate from this group. This behavior is observed in several bird species including the sage grouse and the prairie chicken.
In polyandrous mating systems, one female mates with many males. These types of systems are much rarer than monogamous and polygynous mating systems. In pipefishes and seahorses, males receive the eggs from the female, fertilize them, protect them within a pouch, and give birth to the offspring (Figure \(5\)). Therefore, the female is able to provide eggs to several males without the burden of carrying the fertilized eggs.
Simple Learned Behaviors
The majority of the behaviors previously discussed were innate or at least have an innate component (variations on the innate behaviors may be learned). They are inherited and the behaviors do not change in response to signals from the environment. Conversely, learned behaviors, even though they may have instinctive components, allow an organism to adapt to changes in the environment and are modified by previous experiences. Simple learned behaviors include habituation and imprinting—both are important to the maturation process of young animals.
Habituation
Habituation is a simple form of learning in which an animal stops responding to a stimulus after a period of repeated exposure. This is a form of non-associative learning, as the stimulus is not associated with any punishment or reward. Prairie dogs typically sound an alarm call when threatened by a predator, but they become habituated to the sound of human footsteps when no harm is associated with this sound, therefore, they no longer respond to them with an alarm call. In this example, habituation is specific to the sound of human footsteps, as the animals still respond to the sounds of potential predators.
Imprinting
Imprinting is a type of learning that occurs at a particular age or a life stage that is rapid and independent of the species involved. Hatchling ducks recognize the first adult they see, their mother, and make a bond with her. A familiar sight is ducklings walking or swimming after their mothers (Figure \(6\)). This is another type of non-associative learning, but is very important in the maturation process of these animals as it encourages them to stay near their mother so they will be protected, greatly increasing their chances of survival. However, if newborn ducks see a human before they see their mother, they will imprint on the human and follow it in just the same manner as they would follow their real mother.
Link to Learning
The International Crane Foundation has helped raise the world’s population of whooping cranes from 21 individuals to about 600. Imprinting hatchlings has been a key to success: biologists wear full crane costumes so the birds never “see” humans. Watch this video to learn more.
Conditioned Behavior
Conditioned behaviors are types of associative learning, where a stimulus becomes associated with a consequence. During operant conditioning, the behavioral response is modified by its consequences, with regards to its form, strength, or frequency.
Classical Conditioning
In classical conditioning, a response called the conditioned response is associated with a stimulus that it had previously not been associated with, the conditioned stimulus. The response to the original, unconditioned stimulus is called the unconditioned response. The most cited example of classical conditioning is Ivan Pavlov’s experiments with dogs (Figure \(7\)). In Pavlov’s experiments, the unconditioned response was the salivation of dogs in response to the unconditioned stimulus of seeing or smelling their food. The conditioning stimulus that researchers associated with the unconditioned response was the ringing of a bell. During conditioning, every time the animal was given food, the bell was rung. This was repeated during several trials. After some time, the dog learned to associate the ringing of the bell with food and to respond by salivating. After the conditioning period was finished, the dog would respond by salivating when the bell was rung, even when the unconditioned stimulus, the food, was absent. Thus, the ringing of the bell became the conditioned stimulus and the salivation became the conditioned response. Although it is thought by some scientists that the unconditioned and conditioned responses are identical, even Pavlov discovered that the saliva in the conditioned dogs had characteristic differences when compared to the unconditioned dog.
It had been thought by some scientists that this type of conditioning required multiple exposures to the paired stimulus and response, but it is now known that this is not necessary in all cases, and that some conditioning can be learned in a single pairing experiment. Classical conditioning is a major tenet of behaviorism, a branch of psychological philosophy that proposes that all actions, thoughts, and emotions of living things are behaviors that can be treated by behavior modification and changes in the environment.
Operant Conditioning
In operant conditioning, the conditioned behavior is gradually modified by its consequences as the animal responds to the stimulus. A major proponent of such conditioning was psychologist B.F. Skinner, the inventor of the Skinner box. Skinner put rats in his boxes that contained a lever that would dispense food to the rat when depressed. While initially the rat would push the lever a few times by accident, it eventually associated pushing the lever with getting the food. This type of learning is an example of operant conditioning. Operant learning is the basis of most animal training. The conditioned behavior is continually modified by positive or negative reinforcement, often a reward such as food or some type of punishment, respectively. In this way, the animal is conditioned to associate a type of behavior with the punishment or reward, and, over time, can be induced to perform behaviors that they would not have done in the wild, such as the “tricks” dolphins perform at marine amusement park shows (Figure \(8\)).
Cognitive Learning
Classical and operant conditioning are inefficient ways for humans and other intelligent animals to learn. Some primates, including humans, are able to learn by imitating the behavior of others and by taking instructions. The development of complex language by humans has made cognitive learning, the manipulation of information using the mind, the most prominent method of human learning. In fact, that is how students are learning right now by reading this book. As students read, they can make mental images of objects or organisms and imagine changes to them, or behaviors by them, and anticipate the consequences. In addition to visual processing, cognitive learning is also enhanced by remembering past experiences, touching physical objects, hearing sounds, tasting food, and a variety of other sensory-based inputs. Cognitive learning is so powerful that it can be used to understand conditioning in detail. In the reverse scenario, conditioning cannot help someone learn about cognition.
Classic work on cognitive learning was done by Wolfgang Köhler with chimpanzees. He demonstrated that these animals were capable of abstract thought by showing that they could learn how to solve a puzzle. When a banana was hung in their cage too high for them to reach, and several boxes were placed randomly on the floor, some of the chimps were able to stack the boxes one on top of the other, climb on top of them, and get the banana. This implies that they could visualize the result of stacking the boxes even before they had performed the action. This type of learning is much more powerful and versatile than conditioning.
Cognitive learning is not limited to primates, although they are the most efficient in using it. Maze running experiments done with rats by H.C. Blodgett in the 1920s were the first to show cognitive skills in a simple mammal. The motivation for the animals to work their way through the maze was a piece of food at its end. In these studies, the animals in Group I were run in one trial per day and had food available to them each day on completion of the run (Figure \(9\)). Group II rats were not fed in the maze for the first six days and then subsequent runs were done with food for several days after. Group III rats had food available on the third day and every day thereafter. The results were that the control rats, Group I, learned quickly, and figured out how to run the maze in seven days. Group III did not learn much during the three days without food, but rapidly caught up to the control group when given the food reward. Group II learned very slowly for the six days with no reward to motivate them, and they did not begin to catch up to the control group until the day food was given, and then it took two days longer to learn the maze.
It may not be immediately obvious that this type of learning is different than conditioning. Although one might be tempted to believe that the rats simply learned how to find their way through a conditioned series of right and left turns, E.C. Tolman proved a decade later that the rats were making a representation of the maze in their minds, which he called a “cognitive map.” This was an early demonstration of the power of cognitive learning and how these abilities were not just limited to humans.
Sociobiology
Sociobiology is an interdisciplinary science originally popularized by social insect researcher E.O. Wilson in the 1970s. Wilson defined the science as “the extension of population biology and evolutionary theory to social organization.”1 The main thrust of sociobiology is that animal and human behavior, including aggressiveness and other social interactions, can be explained almost solely in terms of genetics and natural selection. This science is controversial; noted scientist such as the late Stephen Jay Gould criticized the approach for ignoring the environmental effects on behavior. This is another example of the “nature versus nurture” debate of the role of genetics versus the role of environment in determining an organism’s characteristics.
Sociobiology also links genes with behaviors and has been associated with “biological determinism,” the belief that all behaviors are hardwired into our genes. No one disputes that certain behaviors can be inherited and that natural selection plays a role retaining them. It is the application of such principles to human behavior that sparks this controversy, which remains active today.
Summary
Behaviors are responses to stimuli. They can either be instinctual/innate behaviors, which are not influenced by the environment, or learned behaviors, which are influenced by environmental changes. Instinctual behaviors include mating systems and methods of communication. Learned behaviors include imprinting and habituation, conditioning, and, most powerfully, cognitive learning. Although the connection between behavior, genetics, and evolution is well established, the explanation of human behavior as entirely genetic is controversial.
Footnotes
1. 1 Edward O. Wilson. On Human Nature (1978; repr., Cambridge: Harvard University Press, 2004), xx.
Glossary
aggressive display
visual display by a species member to discourage other members of the same species or different species
behavior
change in an organism’s activities in response to a stimulus
behavioral biology
study of the biology and evolution of behavior
classical conditioning
association of a specific stimulus and response through conditioning
cognitive learning
knowledge and skills acquired by the manipulation of information in the mind
conditioned behavior
behavior that becomes associated with a specific stimulus through conditioning
courtship display
visual display used to attract a mate
distraction display
visual display used to distract predators away from a nesting site
ethology
biological study of animal behavior
fixed action pattern
series of instinctual behaviors that, once initiated, always goes to completion regardless of changes in the environment
foraging
behaviors species use to find food
habituation
ability of a species to ignore repeated stimuli that have no consequence
imprinting
identification of parents by newborns as the first organism they see after birth
innate behavior
instinctual behavior that is not altered by changes in the environment
intersexual selection
selection of a desirable mate of the opposite sex
intrasexual selection
competition between members of the same sex for a mate
kin selection
sacrificing one’s own life so that one’s genes will be passed on to future generations by relatives
kinesis
undirected movement of an organism in response to a stimulus
learned behavior
behavior that responds to changes in the environment
migration
long-range seasonal movement of animal species
monogamy
mating system whereby one male and one female remain coupled for at least one mating season
operant conditioning
learned behaviors in response to positive and/or negative reinforcement
polyandry
mating system where one female mates with many males
polygyny
mating system where one male mates with many females
reflex action
action in response to direct physical stimulation of a nerve
signal
method of communication between animals including those obtained by the senses of smell, hearing, sight, or touch
taxis
directed movement in response to a stimulus | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/8%3A_Ecology/45%3A_Population_and_Community_Ecology/45.7%3A_Behavioral_Biology_-_Proximate_and_Ultimate_Causes_of_Behavior.txt |
45.1: Population Demography
Populations are dynamic entities. Populations consist all of the species living within a specific area, and populations fluctuate based on a number of factors: seasonal and yearly changes in the environment, natural disasters such as forest fires and volcanic eruptions, and competition for resources between and within species. The statistical study of population dynamics, demography, uses a series of mathematical tools to investigate how populations respond to changes in their environments.
Review Questions
Which of the following methods will tell an ecologist about both the size and density of a population?
1. mark and recapture
2. mark and release
3. quadrat
4. life table
Answer
C
Which of the following is best at showing the life expectancy of an individual within a population?
1. quadrat
2. mark and recapture
3. survivorship curve
4. life table
Answer
D
Humans have which type of survivorship curve?
1. Type I
2. Type II
3. Type III
4. Type IV
Answer
A
Free Response
Describe how a researcher would determine the size of a penguin population in Antarctica using the mark and release method.
Answer
The researcher would mark a certain number of penguins with a tag, release them back into the population, and, at a later time, recapture penguins to see what percentage of the recaptured penguins was tagged. This percentage would allow an estimation of the size of the penguin population.
45.2: Life Histories and Natural Selection
A species’ life history describes the series of events over its lifetime, such as how resources are allocated for growth, maintenance, and reproduction. Life history traits affect the life table of an organism. A species’ life history is genetically determined and shaped by the environment and natural selection.
Review Questions
Which of the following is associated with long-term parental care?
1. few offspring
2. many offspring
3. semelparity
4. fecundity
Answer
A
Which of the following is associated with multiple reproductive episodes during a species’ lifetime?
1. semiparity
2. iteroparity
3. semelparity
4. fecundity
Answer
B
Which of the following is associated with the reproductive potential of a species?
1. few offspring
2. many offspring
3. semelparity
4. fecundity
Answer
D
Free Response
Why is long-term parental care not associated with having many offspring during a reproductive episode?
Answer
Parental care is not feasible for organisms having many offspring because they do not have the energy available to take care of offspring. Most of their energy budget is used in the formation of seeds or offspring, so there is little left for parental care. Also, the sheer number of offspring would make individual parental care impossible.
45.3: Environmental Limits to Population Growth
Although life histories describe the way many characteristics of a population (such as their age structure) change over time in a general way, population ecologists make use of a variety of methods to model population dynamics mathematically. These more precise models can then be used to accurately describe changes occurring in a population and better predict future changes.
Review Questions
Species with limited resources usually exhibit a(n) ________ growth curve.
1. logistic
2. logical
3. experimental
4. exponential
Answer
A
The maximum rate of increased characteristic of a species is called its ________.
1. limit
2. carrying capacity
3. biotic potential
4. exponential growth pattern
Answer
C
The population size of a species capable of being supported by the environment is called its ________.
1. limit
2. carrying capacity
3. biotic potential
4. logistic growth pattern
Answer
B
Free Response
Describe the rate of population growth that would be expected at various parts of the S-shaped curve of logistic growth.
Answer
In the first part of the curve, when few individuals of the species are present and resources are plentiful, growth is exponential, similar to a J-shaped curve. Later, growth slows due to the species using up resources. Finally, the population levels off at the carrying capacity of the environment, and it is relatively stable over time.
45.4: Population Dynamics and Regulation
The logistic model of population growth, while valid in many natural populations and a useful model, is a simplification of real-world population dynamics. Implicit in the model is that the carrying capacity of the environment does not change, which is not the case. The carrying capacity varies annually: for example, some summers are hot and dry whereas others are cold and wet. In many areas, the carrying capacity during the winter is much lower than it is during the summer.
Review Questions
Species that have many offspring at one time are usually:
1. r-selected
2. K-selected
3. both r- and K-selected
4. not selected
Answer
A
A forest fire is an example of ________ regulation.
1. density-dependent
2. density-independent
3. r-selected
4. K-selected
Answer
B
Primates are examples of:
1. density-dependent species
2. density-independent species
3. r-selected species
4. K-selected species
Answer
D
Free Response
Give an example of how density-dependent and density-independent factors might interact.
Answer
If a natural disaster such as a fire happened in the winter, when populations are low, it would have a greater effect on the overall population and its recovery than if the same disaster occurred during the summer, when population levels are high.
45.5: Human Population Growth
Although humans have increased the carrying capacity of their environment, the technologies used to achieve this transformation have caused unprecedented changes to Earth’s environment, altering ecosystems to the point where some may be in danger of collapse. The depletion of the ozone layer, erosion due to acid rain, and damage from global climate change are caused by human activities. The ultimate effect of these changes on our carrying capacity is unknown.
Review Questions
A country with zero population growth is likely to be ________.
1. in Africa
2. in Asia
3. economically developed
4. economically underdeveloped
Answer
D
Which type of country has the greatest proportion of young individuals?
1. economically developed
2. economically underdeveloped
3. countries with zero population growth
4. countries in Europe
Answer
B
Which of the following is not a way that humans have increased the carrying capacity of the environment?
1. agriculture
2. using large amounts of natural resources
3. domestication of animals
4. use of language
Answer
B
Free Response
Describe the age structures in rapidly growing countries, slowly growing countries, and countries with zero population growth.
Answer
Rapidly growing countries have a large segment of the population at a reproductive age or younger. Slower growing populations have a lower percentage of these individuals, and countries with zero population growth have an even lower percentage. On the other hand, a high proportion of older individuals is seen mostly in countries with zero growth, and a low proportion is most common in rapidly growing countries.
45.6: Community Ecology
Populations rarely, if ever, live in isolation from populations of other species. In most cases, numerous species share a habitat. The interactions between these populations play a major role in regulating population growth and abundance. All populations occupying the same habitat form a community: populations inhabiting a specific area at the same time. The number of species occupying the same habitat and their relative abundance is known as species diversity.
Review Questions
The first species to live on new land, such as that formed from volcanic lava, are called ________.
1. climax community
2. keystone species
3. foundation species
4. pioneer species
Answer
D
Which type of mimicry involves multiple species with similar warning coloration that are all toxic to predators?
1. Batesian mimicry
2. Müllerian mimicry
3. Emsleyan/Mertensian mimicry
4. Mertensian mimicry
Answer
B
A symbiotic relationship where both of the coexisting species benefit from the interaction is called ________.
1. commensalism
2. parasitism
3. mutualism
4. communism
Answer
C
Free Response
Describe the competitive exclusion principle and its effects on competing species.
Answer
The competitive exclusion principle states that no two species competing for the same resources at the same time and place can coexist over time. Thus, one of the competing species will eventually dominate. On the other hand, if the species evolve such that they use resources from different parts of the habitat or at different times of day, the two species can exist together indefinitely.
45.7: Behavioral Biology: Proximate and Ultimate Causes of Behavior
One goal of behavioral biology is to dissect out the innate behaviors, which have a strong genetic component and are largely independent of environmental influences, from the learned behaviors, which result from environmental conditioning. Innate behavior, or instinct, is important because there is no risk of an incorrect behavior being learned. They are “hard wired” into the system. On the other hand, learned behaviors, although riskier, are flexible, dynamic, and can be altered.
Review Questions
The ability of rats to learn how to run a maze is an example of ________.
1. imprinting
2. classical conditioning
3. operant conditioning
4. cognitive learning
Answer
D
The training of animals usually involves ________.
1. imprinting
2. classical conditioning
3. operant conditioning
4. cognitive learning
Answer
C
The sacrifice of the life of an individual so that the genes of relatives may be passed on is called ________.
1. operant learning
2. kin selection
3. kinesis
4. imprinting
Answer
B
Free Response
Describe Pavlov’s dog experiments as an example of classical conditioning.
Answer
Dogs salivated in response to food. This was the unconditioned stimulus and response. Dogs exposed to food had a bell rung repeatedly at the same time, eventually learning to associate the bell with food. Over time, the dogs would salivate when the bell was rung, even in the absence of food. Thus, the bell became the conditioned stimulus, and the salivation in response to the bell became the conditioned response. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/8%3A_Ecology/45%3A_Population_and_Community_Ecology/45.E%3A_Population_and_Community_Ecology_%28Exercises%29.txt |
Ecosystem ecology is the integrated study of living (biotic) and non-living (abiotic) components of ecosystems and their interactions within an ecosystem framework. This science examines how ecosystems work and relates this to their components such as chemicals, bedrock, soil, plants, and animals.
• 46.0: Prelude to Ecosystems
In 1993, an interesting example of ecosystem dynamics occurred when a rare lung disease struck inhabitants of the southwestern United States. This disease had an alarming rate of fatalities, killing more than half of early patients, many of whom were Native Americans. These formerly healthy young adults died from complete respiratory failure.
• 46.1: Ecology of Ecosystems
An ecosystem is a community of living organisms and their interactions with their abiotic (non-living) environment. Ecosystems can be small, such as the tide pools found near the rocky shores of many oceans, or large, such as the Amazon Rainforest in Brazil.
• 46.2: Energy Flow through Ecosystems
All living things require energy in one form or another. Energy is required by most complex metabolic pathways (often in the form of adenosine triphosphate, ATP), especially those responsible for building large molecules from smaller compounds, and life itself is an energy-driven process. Living organisms would not be able to assemble macromolecules (proteins, lipids, nucleic acids, and complex carbohydrates) from their monomeric subunits without a constant energy input.
• 46.3: Biogeochemical Cycles
The matter that makes up living organisms is conserved and recycled. The six most common elements associated with organic molecules—carbon, nitrogen, hydrogen, oxygen, phosphorus, and sulfur—take a variety of chemical forms and may exist for long periods in the atmosphere, on land, in water, or beneath the Earth’s surface. Geologic processes, such as weathering, erosion, water drainage, and the subduction of the continental plates, all play a role in this recycling of materials.
• 46.E: Ecosystems (Exercises)
Thumbnail: A bumblebee pollinating a flower, one example of an ecosystem service. (CC BY-SA3.0; Roo72).
46: Ecosystems
In 1993, an interesting example of ecosystem dynamics occurred when a rare lung disease struck inhabitants of the southwestern United States. This disease had an alarming rate of fatalities, killing more than half of early patients, many of whom were Native Americans. These formerly healthy young adults died from complete respiratory failure. The disease was unknown, and the Centers for Disease Control (CDC), the United States government agency responsible for managing potential epidemics, was brought in to investigate. The scientists could have learned about the disease had they known to talk with the Navajo healers who lived in the area and who had observed the connection between rainfall and mice populations, thereby predicting the 1993 outbreak.
The cause of the disease, determined within a few weeks by the CDC investigators, was the hantavirus known as Sin Nombre, the virus with “no name.” With insights from traditional Navajo medicine, scientists were able to characterize the disease rapidly and institute effective health measures to prevent its spread. This example illustrates the importance of understanding the complexities of ecosystems and how they respond to changes in the environment.
46.1: Ecology of Ecosystems
Skills to Develop
• Describe the basic types of ecosystems on Earth
• Explain the methods that ecologists use to study ecosystem structure and dynamics
• Identify the different methods of ecosystem modeling
• Differentiate between food chains and food webs and recognize the importance of each
Life in an ecosystem is often about competition for limited resources, a characteristic of the theory of natural selection. Competition in communities (all living things within specific habitats) is observed both within species and among different species. The resources for which organisms compete include organic material from living or previously living organisms, sunlight, and mineral nutrients, which provide the energy for living processes and the matter to make up organisms’ physical structures. Other critical factors influencing community dynamics are the components of its physical and geographic environment: a habitat’s latitude, amount of rainfall, topography (elevation), and available species. These are all important environmental variables that determine which organisms can exist within a particular area.
An ecosystem is a community of living organisms and their interactions with their abiotic (non-living) environment. Ecosystems can be small, such as the tide pools found near the rocky shores of many oceans, or large, such as the Amazon Rainforest in Brazil (Figure \(1\)).
There are three broad categories of ecosystems based on their general environment: freshwater, ocean water, and terrestrial. Within these broad categories are individual ecosystem types based on the organisms present and the type of environmental habitat.
Ocean ecosystems are the most common, comprising 75 percent of the Earth's surface and consisting of three basic types: shallow ocean, deep ocean water, and deep ocean surfaces (the low depth areas of the deep oceans). The shallow ocean ecosystems include extremely biodiverse coral reef ecosystems, and the deep ocean surface is known for its large numbers of plankton and krill (small crustaceans) that support it. These two environments are especially important to aerobic respirators worldwide as the phytoplankton perform 40 percent of all photosynthesis on Earth. Although not as diverse as the other two, deep ocean ecosystems contain a wide variety of marine organisms. Such ecosystems exist even at the bottom of the ocean where light is unable to penetrate through the water.
Freshwater ecosystems are the rarest, occurring on only 1.8 percent of the Earth's surface. Lakes, rivers, streams, and springs comprise these systems; they are quite diverse, and they support a variety of fish, amphibians, reptiles, insects, phytoplankton, fungi, and bacteria.
Terrestrial ecosystems, also known for their diversity, are grouped into large categories called biomes, such as tropical rain forests, savannas, deserts, coniferous forests, deciduous forests, and tundra. Grouping these ecosystems into just a few biome categories obscures the great diversity of the individual ecosystems within them. For example, there is great variation in desert vegetation: the saguaro cacti and other plant life in the Sonoran Desert, in the United States, are relatively abundant compared to the desolate rocky desert of Boa Vista, an island off the coast of Western Africa (Figure \(2\)).
Ecosystems are complex with many interacting parts. They are routinely exposed to various disturbances, or changes in the environment that effect their compositions: yearly variations in rainfall and temperature and the slower processes of plant growth, which may take several years. Many of these disturbances are a result of natural processes. For example, when lightning causes a forest fire and destroys part of a forest ecosystem, the ground is eventually populated by grasses, then by bushes and shrubs, and later by mature trees, restoring the forest to its former state. The impact of environmental disturbances caused by human activities is as important as the changes wrought by natural processes. Human agricultural practices, air pollution, acid rain, global deforestation, overfishing, eutrophication, oil spills, and illegal dumping on land and into the ocean are all issues of concern to conservationists.
Equilibrium is the steady state of an ecosystem where all organisms are in balance with their environment and with each other. In ecology, two parameters are used to measure changes in ecosystems: resistance and resilience. The ability of an ecosystem to remain at equilibrium in spite of disturbances is called resistance. The speed at which an ecosystem recovers equilibrium after being disturbed, called its resilience. Ecosystem resistance and resilience are especially important when considering human impact. The nature of an ecosystem may change to such a degree that it can lose its resilience entirely. This process can lead to the complete destruction or irreversible altering of the ecosystem.
Food Chains and Food Webs
The term “food chain” is sometimes used metaphorically to describe human social situations. In this sense, food chains are thought of as a competition for survival, such as “who eats whom?” Someone eats and someone is eaten. Therefore, it is not surprising that in our competitive “dog-eat-dog” society, individuals who are considered successful are seen as being at the top of the food chain, consuming all others for their benefit, whereas the less successful are seen as being at the bottom.
The scientific understanding of a food chain is more precise than in its everyday usage. In ecology, a food chain is a linear sequence of organisms through which nutrients and energy pass: primary producers, primary consumers, and higher-level consumers are used to describe ecosystem structure and dynamics. There is a single path through the chain. Each organism in a food chain occupies what is called a trophic level. Depending on their role as producers or consumers, species or groups of species can be assigned to various trophic levels.
In many ecosystems, the bottom of the food chain consists of photosynthetic organisms (plants and/or phytoplankton), which are called primary producers. The organisms that consume the primary producers are herbivores: the primary consumers. Secondary consumers are usually carnivores that eat the primary consumers. Tertiary consumers are carnivores that eat other carnivores. Higher-level consumers feed on the next lower tropic levels, and so on, up to the organisms at the top of the food chain: the apex consumers. In the Lake Ontario food chain shown in Figure \(3\), the Chinook salmon is the apex consumer at the top of this food chain.
One major factor that limits the length of food chains is energy. Energy is lost as heat between each trophic level due to the second law of thermodynamics. Thus, after a limited number of trophic energy transfers, the amount of energy remaining in the food chain may not be great enough to support viable populations at yet a higher trophic level.
The loss of energy between trophic levels is illustrated by the pioneering studies of Howard T. Odum in the Silver Springs, Florida, ecosystem in the 1940s (Figure \(4\)). The primary producers generated 20,819 kcal/m2/yr (kilocalories per square meter per year), the primary consumers generated 3368 kcal/m2/yr, the secondary consumers generated 383 kcal/m2/yr, and the tertiary consumers only generated 21 kcal/m2/yr. Thus, there is little energy remaining for another level of consumers in this ecosystem.
There is a one problem when using food chains to accurately describe most ecosystems. Even when all organisms are grouped into appropriate trophic levels, some of these organisms can feed on species from more than one trophic level; likewise, some of these organisms can be eaten by species from multiple trophic levels. In other words, the linear model of ecosystems, the food chain, is not completely descriptive of ecosystem structure. A holistic model—which accounts for all the interactions between different species and their complex interconnected relationships with each other and with the environment—is a more accurate and descriptive model for ecosystems. A food web is a graphic representation of a holistic, non-linear web of primary producers, primary consumers, and higher-level consumers used to describe ecosystem structure and dynamics (Figure \(5\)).
A comparison of the two types of structural ecosystem models shows strength in both. Food chains are more flexible for analytical modeling, are easier to follow, and are easier to experiment with, whereas food web models more accurately represent ecosystem structure and dynamics, and data can be directly used as input for simulation modeling.
Link to Learning
Head to this online interactive simulator to investigate food web function. In the Interactive Labs box, under Food Web, click Step 1. Read the instructions first, and then click Step 2 for additional instructions. When you are ready to create a simulation, in the upper-right corner of the Interactive Labs box, click OPEN SIMULATOR.
Two general types of food webs are often shown interacting within a single ecosystem. A grazing food web (such as the Lake Ontario food web in Figure \(5\)) has plants or other photosynthetic organisms at its base, followed by herbivores and various carnivores. A detrital food web consists of a base of organisms that feed on decaying organic matter (dead organisms), called decomposers or detritivores. These organisms are usually bacteria or fungi that recycle organic material back into the biotic part of the ecosystem as they themselves are consumed by other organisms. As all ecosystems require a method to recycle material from dead organisms, most grazing food webs have an associated detrital food web. For example, in a meadow ecosystem, plants may support a grazing food web of different organisms, primary and other levels of consumers, while at the same time supporting a detrital food web of bacteria, fungi, and detrivorous invertebrates feeding off dead plants and animals.
Evolution Connection: Three-spined Stickleback
It is well established by the theory of natural selection that changes in the environment play a major role in the evolution of species within an ecosystem. However, little is known about how the evolution of species within an ecosystem can alter the ecosystem environment. In 2009, Dr. Luke Harmon, from the University of Idaho in Moscow, published a paper that for the first time showed that the evolution of organisms into subspecies can have direct effects on their ecosystem environment.1
The three-spines stickleback (Gasterosteus aculeatus) is a freshwater fish that evolved from a saltwater fish to live in freshwater lakes about 10,000 years ago, which is considered a recent development in evolutionary time (Figure \(6\)). Over the last 10,000 years, these freshwater fish then became isolated from each other in different lakes. Depending on which lake population was studied, findings showed that these sticklebacks then either remained as one species or evolved into two species. The divergence of species was made possible by their use of different areas of the pond for feeding called micro niches.
Dr. Harmon and his team created artificial pond microcosms in 250-gallon tanks and added muck from freshwater ponds as a source of zooplankton and other invertebrates to sustain the fish. In different experimental tanks they introduced one species of stickleback from either a single-species or double-species lake.
Over time, the team observed that some of the tanks bloomed with algae while others did not. This puzzled the scientists, and they decided to measure the water's dissolved organic carbon (DOC), which consists of mostly large molecules of decaying organic matter that give pond-water its slightly brownish color. It turned out that the water from the tanks with two-species fish contained larger particles of DOC (and hence darker water) than water with single-species fish. This increase in DOC blocked the sunlight and prevented algal blooming. Conversely, the water from the single-species tank contained smaller DOC particles, allowing more sunlight penetration to fuel the algal blooms.
This change in the environment, which is due to the different feeding habits of the stickleback species in each lake type, probably has a great impact on the survival of other species in these ecosystems, especially other photosynthetic organisms. Thus, the study shows that, at least in these ecosystems, the environment and the evolution of populations have reciprocal effects that may now be factored into simulation models.
Research into Ecosystem Dynamics: Ecosystem Experimentation and Modeling
The study of the changes in ecosystem structure caused by changes in the environment (disturbances) or by internal forces is called ecosystem dynamics. Ecosystems are characterized using a variety of research methodologies. Some ecologists study ecosystems using controlled experimental systems, while some study entire ecosystems in their natural state, and others use both approaches.
A holistic ecosystem model attempts to quantify the composition, interaction, and dynamics of entire ecosystems; it is the most representative of the ecosystem in its natural state. A food web is an example of a holistic ecosystem model. However, this type of study is limited by time and expense, as well as the fact that it is neither feasible nor ethical to do experiments on large natural ecosystems. To quantify all different species in an ecosystem and the dynamics in their habitat is difficult, especially when studying large habitats such as the Amazon Rainforest, which covers 1.4 billion acres (5.5 million km2) of the Earth’s surface.
For these reasons, scientists study ecosystems under more controlled conditions. Experimental systems usually involve either partitioning a part of a natural ecosystem that can be used for experiments, termed a mesocosm, or by re-creating an ecosystem entirely in an indoor or outdoor laboratory environment, which is referred to as a microcosm. A major limitation to these approaches is that removing individual organisms from their natural ecosystem or altering a natural ecosystem through partitioning may change the dynamics of the ecosystem. These changes are often due to differences in species numbers and diversity and also to environment alterations caused by partitioning (mesocosm) or re-creating (microcosm) the natural habitat. Thus, these types of experiments are not totally predictive of changes that would occur in the ecosystem from which they were gathered.
As both of these approaches have their limitations, some ecologists suggest that results from these experimental systems should be used only in conjunction with holistic ecosystem studies to obtain the most representative data about ecosystem structure, function, and dynamics.
Scientists use the data generated by these experimental studies to develop ecosystem models that demonstrate the structure and dynamics of ecosystems. Three basic types of ecosystem modeling are routinely used in research and ecosystem management: a conceptual model, an analytical model, and a simulation model. A conceptual model is an ecosystem model that consists of flow charts to show interactions of different compartments of the living and nonliving components of the ecosystem. A conceptual model describes ecosystem structure and dynamics and shows how environmental disturbances affect the ecosystem; however, its ability to predict the effects of these disturbances is limited. Analytical and simulation models, in contrast, are mathematical methods of describing ecosystems that are indeed capable of predicting the effects of potential environmental changes without direct experimentation, although with some limitations as to accuracy. An analytical model is an ecosystem model that is created using simple mathematical formulas to predict the effects of environmental disturbances on ecosystem structure and dynamics. A simulation model is an ecosystem model that is created using complex computer algorithms to holistically model ecosystems and to predict the effects of environmental disturbances on ecosystem structure and dynamics. Ideally, these models are accurate enough to determine which components of the ecosystem are particularly sensitive to disturbances, and they can serve as a guide to ecosystem managers (such as conservation ecologists or fisheries biologists) in the practical maintenance of ecosystem health.
Conceptual Models
Conceptual models are useful for describing ecosystem structure and dynamics and for demonstrating the relationships between different organisms in a community and their environment. Conceptual models are usually depicted graphically as flow charts. The organisms and their resources are grouped into specific compartments with arrows showing the relationship and transfer of energy or nutrients between them. Thus, these diagrams are sometimes called compartment models.
To model the cycling of mineral nutrients, organic and inorganic nutrients are subdivided into those that are bioavailable (ready to be incorporated into biological macromolecules) and those that are not. For example, in a terrestrial ecosystem near a deposit of coal, carbon will be available to the plants of this ecosystem as carbon dioxide gas in a short-term period, not from the carbon-rich coal itself. However, over a longer period, microorganisms capable of digesting coal will incorporate its carbon or release it as natural gas (methane, CH4), changing this unavailable organic source into an available one. This conversion is greatly accelerated by the combustion of fossil fuels by humans, which releases large amounts of carbon dioxide into the atmosphere. This is thought to be a major factor in the rise of the atmospheric carbon dioxide levels in the industrial age. The carbon dioxide released from burning fossil fuels is produced faster than photosynthetic organisms can use it. This process is intensified by the reduction of photosynthetic trees because of worldwide deforestation. Most scientists agree that high atmospheric carbon dioxide is a major cause of global climate change.
Conceptual models are also used to show the flow of energy through particular ecosystems. Figure \(7\) is based on Howard T. Odum’s classical study of the Silver Springs, Florida, holistic ecosystem in the mid-twentieth century.2 This study shows the energy content and transfer between various ecosystem compartments.
Exercise
Why do you think the value for gross productivity of the primary producers is the same as the value for total heat and respiration (20,810 kcal/m2/yr)?
Answer
According to the first law of thermodynamics, energy can neither be created nor destroyed. Eventually, all energy consumed by living systems is lost as heat or used for respiration, and the total energy output of the system must equal the energy that went into it.
Analytical and Simulation Models
The major limitation of conceptual models is their inability to predict the consequences of changes in ecosystem species and/or environment. Ecosystems are dynamic entities and subject to a variety of abiotic and biotic disturbances caused by natural forces and/or human activity. Ecosystems altered from their initial equilibrium state can often recover from such disturbances and return to a state of equilibrium. As most ecosystems are subject to periodic disturbances and are often in a state of change, they are usually either moving toward or away from their equilibrium state. There are many of these equilibrium states among the various components of an ecosystem, which affects the ecosystem overall. Furthermore, as humans have the ability to greatly and rapidly alter the species content and habitat of an ecosystem, the need for predictive models that enable understanding of how ecosystems respond to these changes becomes more crucial.
Analytical models often use simple, linear components of ecosystems, such as food chains, and are known to be complex mathematically; therefore, they require a significant amount of mathematical knowledge and expertise. Although analytical models have great potential, their simplification of complex ecosystems is thought to limit their accuracy. Simulation models that use computer programs are better able to deal with the complexities of ecosystem structure.
A recent development in simulation modeling uses supercomputers to create and run individual-based simulations, which accounts for the behavior of individual organisms and their effects on the ecosystem as a whole. These simulations are considered to be the most accurate and predictive of the complex responses of ecosystems to disturbances.
Link to Learning
Visit The Darwin Project to view a variety of ecosystem models.
Summary
Ecosystems exist on land, at sea, in the air, and underground. Different ways of modeling ecosystems are necessary to understand how environmental disturbances will affect ecosystem structure and dynamics. Conceptual models are useful to show the general relationships between organisms and the flow of materials or energy between them. Analytical models are used to describe linear food chains, and simulation models work best with holistic food webs.
Footnotes
1. 1 Nature (Vol. 458, April 1, 2009)
2. 2 Howard T. Odum, “Trophic Structure and Productivity of Silver Springs, Florida,” Ecological Monographs 27, no. 1 (1957): 47–112.
Glossary
analytical model
ecosystem model that is created with mathematical formulas to predict the effects of environmental disturbances on ecosystem structure and dynamics
apex consumer
organism at the top of the food chain
conceptual model
(also, compartment models) ecosystem model that consists of flow charts that show the interactions of different compartments of the living and non-living components of the ecosystem
detrital food web
type of food web in which the primary consumers consist of decomposers; these are often associated with grazing food webs within the same ecosystem
ecosystem
community of living organisms and their interactions with their abiotic environment
ecosystem dynamics
study of the changes in ecosystem structure caused by changes in the environment or internal forces
equilibrium
steady state of an ecosystem where all organisms are in balance with their environment and each other
food chain
linear representation of a chain of primary producers, primary consumers, and higher-level consumers used to describe ecosystem structure and dynamics
food web
graphic representation of a holistic, non-linear web of primary producers, primary consumers, and higher-level consumers used to describe ecosystem structure and dynamics
grazing food web
type of food web in which the primary producers are either plants on land or phytoplankton in the water; often associated with a detrital food web within the same ecosystem
holistic ecosystem model
study that attempts to quantify the composition, interactions, and dynamics of entire ecosystems; often limited by economic and logistical difficulties, depending on the ecosystem
mesocosm
portion of a natural ecosystem to be used for experiments
microcosm
re-creation of natural ecosystems entirely in a laboratory environment to be used for experiments
primary consumer
trophic level that obtains its energy from the primary producers of an ecosystem
primary producer
trophic level that obtains its energy from sunlight, inorganic chemicals, or dead and/or decaying organic material
resilience (ecological)
speed at which an ecosystem recovers equilibrium after being disturbed
resistance (ecological)
ability of an ecosystem to remain at equilibrium in spite of disturbances
secondary consumer
usually a carnivore that eat primary consumers
simulation model
ecosystem model that is created with computer programs to holistically model ecosystems and to predict the effects of environmental disturbances on ecosystem structure and dynamics
tertiary consumer
carnivore that eat other carnivores
trophic level
position of a species or group of species in a food chain or a food web | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/8%3A_Ecology/46%3A_Ecosystems/46.0%3A_Prelude_to_Ecosystems.txt |
Learning Objectives
• Describe how organisms acquire energy in a food web and in associated food chains
• Explain how the efficiency of energy transfers between trophic levels affects ecosystem structure and dynamics
• Discuss trophic levels and how ecological pyramids are used to model them
All living things require energy in one form or another. Energy is required by most complex metabolic pathways (often in the form of adenosine triphosphate, ATP), especially those responsible for building large molecules from smaller compounds, and life itself is an energy-driven process. Living organisms would not be able to assemble macromolecules (proteins, lipids, nucleic acids, and complex carbohydrates) from their monomeric subunits without a constant energy input.
It is important to understand how organisms acquire energy and how that energy is passed from one organism to another through food webs and their constituent food chains. Food webs illustrate how energy flows directionally through ecosystems, including how efficiently organisms acquire it, use it, and how much remains for use by other organisms of the food web.
How Organisms Acquire Energy in a Food Web
Energy is acquired by living things in three ways: photosynthesis, chemosynthesis, and the consumption and digestion of other living or previously living organisms by heterotrophs.
Photosynthetic and chemosynthetic organisms are both grouped into a category known as autotrophs: organisms capable of synthesizing their own food (more specifically, capable of using inorganic carbon as a carbon source). Photosynthetic autotrophs (photoautotrophs) use sunlight as an energy source, whereas chemosynthetic autotrophs (chemoautotrophs) use inorganic molecules as an energy source. Autotrophs are critical for all ecosystems. Without these organisms, energy would not be available to other living organisms and life itself would not be possible.
Photoautotrophs, such as plants, algae, and photosynthetic bacteria, serve as the energy source for a majority of the world’s ecosystems. These ecosystems are often described by grazing food webs. Photoautotrophs harness the solar energy of the sun by converting it to chemical energy in the form of ATP (and NADP). The energy stored in ATP is used to synthesize complex organic molecules, such as glucose.
Chemoautotrophs are primarily bacteria that are found in rare ecosystems where sunlight is not available, such as in those associated with dark caves or hydrothermal vents at the bottom of the ocean (Figure $1$). Many chemoautotrophs in hydrothermal vents use hydrogen sulfide (H2S), which is released from the vents as a source of chemical energy. This allows chemoautotrophs to synthesize complex organic molecules, such as glucose, for their own energy and in turn supplies energy to the rest of the ecosystem.
Productivity within Trophic Levels
Productivity within an ecosystem can be defined as the percentage of energy entering the ecosystem incorporated into biomass in a particular trophic level. Biomass is the total mass, in a unit area at the time of measurement, of living or previously living organisms within a trophic level. Ecosystems have characteristic amounts of biomass at each trophic level. For example, in the English Channel ecosystem the primary producers account for a biomass of 4 g/m2 (grams per meter squared), while the primary consumers exhibit a biomass of 21 g/m2.
The productivity of the primary producers is especially important in any ecosystem because these organisms bring energy to other living organisms by photoautotrophy or chemoautotrophy. The rate at which photosynthetic primary producers incorporate energy from the sun is called gross primary productivity. An example of gross primary productivity is shown in the compartment diagram of energy flow within the Silver Springs aquatic ecosystem as shown (Figure 46.1.7). In this ecosystem, the total energy accumulated by the primary producers (gross primary productivity) was shown to be 20,810 kcal/m2/yr.
Because all organisms need to use some of this energy for their own functions (like respiration and resulting metabolic heat loss) scientists often refer to the net primary productivity of an ecosystem. Net primary productivity is the energy that remains in the primary producers after accounting for the organisms’ respiration and heat loss. The net productivity is then available to the primary consumers at the next trophic level. In our Silver Spring example, 13,187 of the 20,810 kcal/m2/yr were used for respiration or were lost as heat, leaving 7,632 kcal/m2/yr of energy for use by the primary consumers.
Ecological Efficiency: The Transfer of Energy between Trophic Levels
As illustrated in Figure 46.1.7, large amounts of energy are lost from the ecosystem from one trophic level to the next level as energy flows from the primary producers through the various trophic levels of consumers and decomposers. The main reason for this loss is the second law of thermodynamics, which states that whenever energy is converted from one form to another, there is a tendency toward disorder (entropy) in the system. In biologic systems, this means a great deal of energy is lost as metabolic heat when the organisms from one trophic level consume the next level. In the Silver Springs ecosystem example (Figure 46.1.7), we see that the primary consumers produced 1103 kcal/m2/yr from the 7618 kcal/m2/yr of energy available to them from the primary producers. The measurement of energy transfer efficiency between two successive trophic levels is termed the trophic level transfer efficiency (TLTE) and is defined by the formula:
$\text{TLTE} = \frac{\text{production at present trophic level}}{\text{production at previous trophic level}} * 100 \nonumber$
In Silver Springs, the TLTE between the first two trophic levels was approximately 14.8 percent. The low efficiency of energy transfer between trophic levels is usually the major factor that limits the length of food chains observed in a food web. The fact is, after four to six energy transfers, there is not enough energy left to support another trophic level. In the Lake Ontario example shown in Figure 46.1.5, only three energy transfers occurred between the primary producer, (green algae), and the apex consumer (Chinook salmon).
Ecologists have many different methods of measuring energy transfers within ecosystems. Some transfers are easier or more difficult to measure depending on the complexity of the ecosystem and how much access scientists have to observe the ecosystem. In other words, some ecosystems are more difficult to study than others, and sometimes the quantification of energy transfers has to be estimated.
Another main parameter that is important in characterizing energy flow within an ecosystem is the net production efficiency. Net production efficiency (NPE) allows ecologists to quantify how efficiently organisms of a particular trophic level incorporate the energy they receive into biomass; it is calculated using the following formula:
$\text{NPE} = \frac{\text{net consumer productivity}}{\text{assimilation}} * 100 \nonumber$
Net consumer productivity is the energy content available to the organisms of the next trophic level. Assimilation is the biomass (energy content generated per unit area) of the present trophic level after accounting for the energy lost due to incomplete ingestion of food, energy used for respiration, and energy lost as waste. Incomplete ingestion refers to the fact that some consumers eat only a part of their food. For example, when a lion kills an antelope, it will eat everything except the hide and bones. The lion is missing the energy-rich bone marrow inside the bone, so the lion does not make use of all the calories its prey could provide.
Thus, NPE measures how efficiently each trophic level uses and incorporates the energy from its food into biomass to fuel the next trophic level. In general, cold-blooded animals (ectotherms), such as invertebrates, fish, amphibians, and reptiles, use less of the energy they obtain for respiration and heat than warm-blooded animals (endotherms), such as birds and mammals. The extra heat generated in endotherms, although an advantage in terms of the activity of these organisms in colder environments, is a major disadvantage in terms of NPE. Therefore, many endotherms have to eat more often than ectotherms to get the energy they need for survival. In general, NPE for ectotherms is an order of magnitude (10x) higher than for endotherms. For example, the NPE for a caterpillar eating leaves has been measured at 18 percent, whereas the NPE for a squirrel eating acorns may be as low as 1.6 percent.
The inefficiency of energy use by warm-blooded animals has broad implications for the world's food supply. It is widely accepted that the meat industry uses large amounts of crops to feed livestock, and because the NPE is low, much of the energy from animal feed is lost. For example, it costs about 1¢ to produce 1000 dietary calories (kcal) of corn or soybeans, but approximately $0.19 to produce a similar number of calories growing cattle for beef consumption. The same energy content of milk from cattle is also costly, at approximately$0.16 per 1000 kcal. Much of this difference is due to the low NPE of cattle. Thus, there has been a growing movement worldwide to promote the consumption of non-meat and non-dairy foods so that less energy is wasted feeding animals for the meat industry.
Modeling Ecosystems Energy Flow: Ecological Pyramids
The structure of ecosystems can be visualized with ecological pyramids, which were first described by the pioneering studies of Charles Elton in the 1920s. Ecological pyramids show the relative amounts of various parameters (such as number of organisms, energy, and biomass) across trophic levels.
Pyramids of numbers can be either upright or inverted, depending on the ecosystem. As shown in Figure $2$, typical grassland during the summer has a base of many plants and the numbers of organisms decrease at each trophic level. However, during the summer in a temperate forest, the base of the pyramid consists of few trees compared with the number of primary consumers, mostly insects. Because trees are large, they have great photosynthetic capability, and dominate other plants in this ecosystem to obtain sunlight. Even in smaller numbers, primary producers in forests are still capable of supporting other trophic levels.
Another way to visualize ecosystem structure is with pyramids of biomass. This pyramid measures the amount of energy converted into living tissue at the different trophic levels. Using the Silver Springs ecosystem example, this data exhibits an upright biomass pyramid (Figure $2$), whereas the pyramid from the English Channel example is inverted. The plants (primary producers) of the Silver Springs ecosystem make up a large percentage of the biomass found there. However, the phytoplankton in the English Channel example make up less biomass than the primary consumers, the zooplankton. As with inverted pyramids of numbers, this inverted pyramid is not due to a lack of productivity from the primary producers, but results from the high turnover rate of the phytoplankton. The phytoplankton are consumed rapidly by the primary consumers, thus, minimizing their biomass at any particular point in time. However, phytoplankton reproduce quickly, thus they are able to support the rest of the ecosystem.
Pyramid ecosystem modeling can also be used to show energy flow through the trophic levels. Notice that these numbers are the same as those used in the energy flow compartment diagram in Figure 46.1.7. Pyramids of energy are always upright, and an ecosystem without sufficient primary productivity cannot be supported. All types of ecological pyramids are useful for characterizing ecosystem structure. However, in the study of energy flow through the ecosystem, pyramids of energy are the most consistent and representative models of ecosystem structure (Figure $2$).
Exercise
Pyramids depicting the number of organisms or biomass may be inverted, upright, or even diamond-shaped. Energy pyramids, however, are always upright. Why?
Answer
Pyramids of organisms may be inverted or diamond-shaped because a large organism, such as a tree, can sustain many smaller organisms. Likewise, a low biomass of organisms can sustain a larger biomass at the next trophic level because the organisms reproduce rapidly and thus supply continuous nourishment. Energy pyramids, however, must always be upright because of the laws of thermodynamics. The first law of thermodynamics states that energy can neither be created nor destroyed; thus, each trophic level must acquire energy from the trophic level below. The second law of thermodynamics states that, during the transfer of energy, some energy is always lost as heat; thus, less energy is available at each higher trophic level.
Consequences of Food Webs: Biological Magnification
One of the most important environmental consequences of ecosystem dynamics is biomagnification. Biomagnification is the increasing concentration of persistent, toxic substances in organisms at each trophic level, from the primary producers to the apex consumers. Many substances have been shown to bioaccumulate, including classical studies with the pesticide dichlorodiphenyltrichloroethane (DDT), which was published in the 1960s bestseller, Silent Spring, by Rachel Carson. DDT was a commonly used pesticide before its dangers became known. In some aquatic ecosystems, organisms from each trophic level consumed many organisms of the lower level, which caused DDT to increase in birds (apex consumers) that ate fish. Thus, the birds accumulated sufficient amounts of DDT to cause fragility in their eggshells. This effect increased egg breakage during nesting and was shown to have adverse effects on these bird populations. The use of DDT was banned in the United States in the 1970s.
Other substances that biomagnify are polychlorinated biphenyls (PCBs), which were used in coolant liquids in the United States until their use was banned in 1979, and heavy metals, such as mercury, lead, and cadmium. These substances were best studied in aquatic ecosystems, where fish species at different trophic levels accumulate toxic substances brought through the ecosystem by the primary producers. As illustrated in a study performed by the National Oceanic and Atmospheric Administration (NOAA) in the Saginaw Bay of Lake Huron (Figure $3$), PCB concentrations increased from the ecosystem’s primary producers (phytoplankton) through the different trophic levels of fish species. The apex consumer (walleye) has more than four times the amount of PCBs compared to phytoplankton. Also, based on results from other studies, birds that eat these fish may have PCB levels at least one order of magnitude higher than those found in the lake fish.
Other concerns have been raised by the accumulation of heavy metals, such as mercury and cadmium, in certain types of seafood. The United States Environmental Protection Agency (EPA) recommends that pregnant women and young children should not consume any swordfish, shark, king mackerel, or tilefish because of their high mercury content. These individuals are advised to eat fish low in mercury: salmon, tilapia, shrimp, pollock, and catfish. Biomagnification is a good example of how ecosystem dynamics can affect our everyday lives, even influencing the food we eat.
Summary
Organisms in an ecosystem acquire energy in a variety of ways, which is transferred between trophic levels as the energy flows from the bottom to the top of the food web, with energy being lost at each transfer. The efficiency of these transfers is important for understanding the different behaviors and eating habits of warm-blooded versus cold-blooded animals. Modeling of ecosystem energy is best done with ecological pyramids of energy, although other ecological pyramids provide other vital information about ecosystem structure.
Glossary
assimilation
biomass consumed and assimilated from the previous trophic level after accounting for the energy lost due to incomplete ingestion of food, energy used for respiration, and energy lost as waste
biomagnification
increasing concentrations of persistent, toxic substances in organisms at each trophic level, from the primary producers to the apex consumers
biomass
total weight, at the time of measurement, of living or previously living organisms in a unit area within a trophic level
chemoautotroph
organism capable of synthesizing its own food using energy from inorganic molecules
ecological pyramid
(also, Eltonian pyramid) graphical representation of different trophic levels in an ecosystem based of organism numbers, biomass, or energy content
gross primary productivity
rate at which photosynthetic primary producers incorporate energy from the sun
net consumer productivity
energy content available to the organisms of the next trophic level
net primary productivity
energy that remains in the primary producers after accounting for the organisms’ respiration and heat loss
net production efficiency (NPE)
measure of the ability of a trophic level to convert the energy it receives from the previous trophic level into biomass
trophic level transfer efficiency (TLTE)
energy transfer efficiency between two successive trophic levels | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/8%3A_Ecology/46%3A_Ecosystems/46.2%3A_Energy_Flow_through_Ecosystems.txt |
Skills to Develop
• Discuss the biogeochemical cycles of water, carbon, nitrogen, phosphorus, and sulfur
• Explain how human activities have impacted these cycles and the potential consequences for Earth
Energy flows directionally through ecosystems, entering as sunlight (or inorganic molecules for chemoautotrophs) and leaving as heat during the many transfers between trophic levels. However, the matter that makes up living organisms is conserved and recycled. The six most common elements associated with organic molecules—carbon, nitrogen, hydrogen, oxygen, phosphorus, and sulfur—take a variety of chemical forms and may exist for long periods in the atmosphere, on land, in water, or beneath the Earth’s surface. Geologic processes, such as weathering, erosion, water drainage, and the subduction of the continental plates, all play a role in this recycling of materials. Because geology and chemistry have major roles in the study of this process, the recycling of inorganic matter between living organisms and their environment is called a biogeochemical cycle.
Water contains hydrogen and oxygen, which is essential to all living processes. The hydrosphere is the area of the Earth where water movement and storage occurs: as liquid water on the surface and beneath the surface or frozen (rivers, lakes, oceans, groundwater, polar ice caps, and glaciers), and as water vapor in the atmosphere. Carbon is found in all organic macromolecules and is an important constituent of fossil fuels. Nitrogen is a major component of our nucleic acids and proteins and is critical to human agriculture. Phosphorus, a major component of nucleic acid (along with nitrogen), is one of the main ingredients in artificial fertilizers used in agriculture and their associated environmental impacts on our surface water. Sulfur, critical to the 3–D folding of proteins (as in disulfide binding), is released into the atmosphere by the burning of fossil fuels, such as coal.
The cycling of these elements is interconnected. For example, the movement of water is critical for the leaching of nitrogen and phosphate into rivers, lakes, and oceans. Furthermore, the ocean itself is a major reservoir for carbon. Thus, mineral nutrients are cycled, either rapidly or slowly, through the entire biosphere, from one living organism to another, and between the biotic and abiotic world.
The Water (Hydrologic) Cycle
Water is the basis of all living processes. The human body is more than 1/2 water and human cells are more than 70 percent water. Thus, most land animals need a supply of fresh water to survive. However, when examining the stores of water on Earth, 97.5 percent of it is non-potable salt water (Figure $1$). Of the remaining water, 99 percent is locked underground as water or as ice. Thus, less than 1 percent of fresh water is easily accessible from lakes and rivers. Many living things, such as plants, animals, and fungi, are dependent on the small amount of fresh surface water supply, a lack of which can have massive effects on ecosystem dynamics. Humans, of course, have developed technologies to increase water availability, such as digging wells to harvest groundwater, storing rainwater, and using desalination to obtain drinkable water from the ocean. Although this pursuit of drinkable water has been ongoing throughout human history, the supply of fresh water is still a major issue in modern times.
Water cycling is extremely important to ecosystem dynamics. Water has a major influence on climate and, thus, on the environments of ecosystems, some located on distant parts of the Earth. Most of the water on Earth is stored for long periods in the oceans, underground, and as ice. Figure $2$ illustrates the average time that an individual water molecule may spend in the Earth’s major water reservoirs. Residence time is a measure of the average time an individual water molecule stays in a particular reservoir. A large amount of the Earth’s water is locked in place in these reservoirs as ice, beneath the ground, and in the ocean, and, thus, is unavailable for short-term cycling (only surface water can evaporate).
There are various processes that occur during the cycling of water, shown in Figure $3$. These processes include the following:
• evaporation/sublimation
• condensation/precipitation
• subsurface water flow
• surface runoff/snowmelt
• streamflow
The water cycle is driven by the sun’s energy as it warms the oceans and other surface waters. This leads to the evaporation (water to water vapor) of liquid surface water and the sublimation (ice to water vapor) of frozen water, which deposits large amounts of water vapor into the atmosphere. Over time, this water vapor condenses into clouds as liquid or frozen droplets and is eventually followed by precipitation (rain or snow), which returns water to the Earth’s surface. Rain eventually permeates into the ground, where it may evaporate again if it is near the surface, flow beneath the surface, or be stored for long periods. More easily observed is surface runoff: the flow of fresh water either from rain or melting ice. Runoff can then make its way through streams and lakes to the oceans or flow directly to the oceans themselves.
Link to Learning
Head to this website to learn more about the world’s fresh water supply.
Rain and surface runoff are major ways in which minerals, including carbon, nitrogen, phosphorus, and sulfur, are cycled from land to water. The environmental effects of runoff will be discussed later as these cycles are described.
The Carbon Cycle
Carbon is the second most abundant element in living organisms. Carbon is present in all organic molecules, and its role in the structure of macromolecules is of primary importance to living organisms. Carbon compounds contain especially high energy, particularly those derived from fossilized organisms, mainly plants, which humans use as fuel. Since the 1800s, the number of countries using massive amounts of fossil fuels has increased. Since the beginning of the Industrial Revolution, global demand for the Earth’s limited fossil fuel supplies has risen; therefore, the amount of carbon dioxide in our atmosphere has increased. This increase in carbon dioxide has been associated with climate change and other disturbances of the Earth’s ecosystems and is a major environmental concern worldwide. Thus, the “carbon footprint” is based on how much carbon dioxide is produced and how much fossil fuel countries consume.
The carbon cycle is most easily studied as two interconnected sub-cycles: one dealing with rapid carbon exchange among living organisms and the other dealing with the long-term cycling of carbon through geologic processes. The entire carbon cycle is shown in Figure $4$.
Link to Learning
Click this link to read information about the United States Carbon Cycle Science Program.
The Biological Carbon Cycle
Living organisms are connected in many ways, even between ecosystems. A good example of this connection is the exchange of carbon between autotrophs and heterotrophs within and between ecosystems by way of atmospheric carbon dioxide. Carbon dioxide is the basic building block that most autotrophs use to build multi-carbon, high energy compounds, such as glucose. The energy harnessed from the sun is used by these organisms to form the covalent bonds that link carbon atoms together. These chemical bonds thereby store this energy for later use in the process of respiration. Most terrestrial autotrophs obtain their carbon dioxide directly from the atmosphere, while marine autotrophs acquire it in the dissolved form (carbonic acid, H2CO3). However carbon dioxide is acquired, a by-product of the process is oxygen. The photosynthetic organisms are responsible for depositing approximately 21 percent oxygen content of the atmosphere that we observe today.
Heterotrophs and autotrophs are partners in biological carbon exchange (especially the primary consumers, largely herbivores). Heterotrophs acquire the high-energy carbon compounds from the autotrophs by consuming them, and breaking them down by respiration to obtain cellular energy, such as ATP. The most efficient type of respiration, aerobic respiration, requires oxygen obtained from the atmosphere or dissolved in water. Thus, there is a constant exchange of oxygen and carbon dioxide between the autotrophs (which need the carbon) and the heterotrophs (which need the oxygen). Gas exchange through the atmosphere and water is one way that the carbon cycle connects all living organisms on Earth.
The Biogeochemical Carbon Cycle
The movement of carbon through the land, water, and air is complex, and in many cases, it occurs much more slowly geologically than as seen between living organisms. Carbon is stored for long periods in what are known as carbon reservoirs, which include the atmosphere, bodies of liquid water (mostly oceans), ocean sediment, soil, land sediments (including fossil fuels), and the Earth’s interior.
As stated, the atmosphere is a major reservoir of carbon in the form of carbon dioxide and is essential to the process of photosynthesis. The level of carbon dioxide in the atmosphere is greatly influenced by the reservoir of carbon in the oceans. The exchange of carbon between the atmosphere and water reservoirs influences how much carbon is found in each location, and each one affects the other reciprocally. Carbon dioxide (CO2) from the atmosphere dissolves in water and combines with water molecules to form carbonic acid, and then it ionizes to carbonate and bicarbonate ions (Figure $5$)
The equilibrium coefficients are such that more than 90 percent of the carbon in the ocean is found as bicarbonate ions. Some of these ions combine with seawater calcium to form calcium carbonate (CaCO3), a major component of marine organism shells. These organisms eventually form sediments on the ocean floor. Over geologic time, the calcium carbonate forms limestone, which comprises the largest carbon reservoir on Earth.
On land, carbon is stored in soil as a result of the decomposition of living organisms (by decomposers) or from weathering of terrestrial rock and minerals. This carbon can be leached into the water reservoirs by surface runoff. Deeper underground, on land and at sea, are fossil fuels: the anaerobically decomposed remains of plants that take millions of years to form. Fossil fuels are considered a non-renewable resource because their use far exceeds their rate of formation. A non-renewable resource, such as fossil fuel, is either regenerated very slowly or not at all. Another way for carbon to enter the atmosphere is from land (including land beneath the surface of the ocean) by the eruption of volcanoes and other geothermal systems. Carbon sediments from the ocean floor are taken deep within the Earth by the process of subduction: the movement of one tectonic plate beneath another. Carbon is released as carbon dioxide when a volcano erupts or from volcanic hydrothermal vents.
Carbon dioxide is also added to the atmosphere by the animal husbandry practices of humans. The large numbers of land animals raised to feed the Earth’s growing population results in increased carbon dioxide levels in the atmosphere due to farming practices and the respiration and methane production. This is another example of how human activity indirectly affects biogeochemical cycles in a significant way. Although much of the debate about the future effects of increasing atmospheric carbon on climate change focuses on fossils fuels, scientists take natural processes, such as volcanoes and respiration, into account as they model and predict the future impact of this increase.
The Nitrogen Cycle
Getting nitrogen into the living world is difficult. Plants and phytoplankton are not equipped to incorporate nitrogen from the atmosphere (which exists as tightly bonded, triple covalent N2) even though this molecule comprises approximately 78 percent of the atmosphere. Nitrogen enters the living world via free-living and symbiotic bacteria, which incorporate nitrogen into their macromolecules through nitrogen fixation (conversion of N2). Cyanobacteria live in most aquatic ecosystems where sunlight is present; they play a key role in nitrogen fixation. Cyanobacteria are able to use inorganic sources of nitrogen to “fix” nitrogen. Rhizobium bacteria live symbiotically in the root nodules of legumes (such as peas, beans, and peanuts) and provide them with the organic nitrogen they need. Free-living bacteria, such as Azotobacter, are also important nitrogen fixers.
Organic nitrogen is especially important to the study of ecosystem dynamics since many ecosystem processes, such as primary production and decomposition, are limited by the available supply of nitrogen. As shown in Figure $6$, the nitrogen that enters living systems by nitrogen fixation is successively converted from organic nitrogen back into nitrogen gas by bacteria. This process occurs in three steps in terrestrial systems: ammonification, nitrification, and denitrification. First, the ammonification process converts nitrogenous waste from living animals or from the remains of dead animals into ammonium (NH4+) by certain bacteria and fungi. Second, the ammonium is converted to nitrites (NO2) by nitrifying bacteria, such as Nitrosomonas, through nitrification. Subsequently, nitrites are converted to nitrates (NO3) by similar organisms. Third, the process of denitrification occurs, whereby bacteria, such as Pseudomonas and Clostridium, convert the nitrates into nitrogen gas, allowing it to re-enter the atmosphere.
Exercise
Which of the following statements about the nitrogen cycle is false?
1. Ammonification converts organic nitrogenous matter from living organisms into ammonium (NH4+).
2. Denitrification by bacteria converts nitrates (NO3) to nitrogen gas (N2).
3. Nitrification by bacteria converts nitrates (NO3) to nitrites (NO2).
4. Nitrogen fixing bacteria convert nitrogen gas (N2) into organic compounds.
Answer
C: Nitrification by bacteria converts nitrates (NO3) to nitrites (NO2).
Human activity can release nitrogen into the environment by two primary means: the combustion of fossil fuels, which releases different nitrogen oxides, and by the use of artificial fertilizers in agriculture, which are then washed into lakes, streams, and rivers by surface runoff. Atmospheric nitrogen is associated with several effects on Earth’s ecosystems including the production of acid rain (as nitric acid, HNO3) and greenhouse gas (as nitrous oxide, N2O) potentially causing climate change. A major effect from fertilizer runoff is saltwater and freshwater eutrophication, a process whereby nutrient runoff causes the excess growth of microorganisms, depleting dissolved oxygen levels and killing ecosystem fauna.
A similar process occurs in the marine nitrogen cycle, where the ammonification, nitrification, and denitrification processes are performed by marine bacteria. Some of this nitrogen falls to the ocean floor as sediment, which can then be moved to land in geologic time by uplift of the Earth’s surface and thereby incorporated into terrestrial rock. Although the movement of nitrogen from rock directly into living systems has been traditionally seen as insignificant compared with nitrogen fixed from the atmosphere, a recent study showed that this process may indeed be significant and should be included in any study of the global nitrogen cycle.1
The Phosphorus Cycle
Phosphorus is an essential nutrient for living processes; it is a major component of nucleic acid and phospholipids, and, as calcium phosphate, makes up the supportive components of our bones. Phosphorus is often the limiting nutrient (necessary for growth) in aquatic ecosystems (Figure $7$).
Phosphorus occurs in nature as the phosphate ion (PO43−). In addition to phosphate runoff as a result of human activity, natural surface runoff occurs when it is leached from phosphate-containing rock by weathering, thus sending phosphates into rivers, lakes, and the ocean. This rock has its origins in the ocean. Phosphate-containing ocean sediments form primarily from the bodies of ocean organisms and from their excretions. However, in remote regions, volcanic ash, aerosols, and mineral dust may also be significant phosphate sources. This sediment then is moved to land over geologic time by the uplifting of areas of the Earth’s surface.
Phosphorus is also reciprocally exchanged between phosphate dissolved in the ocean and marine ecosystems. The movement of phosphate from the ocean to the land and through the soil is extremely slow, with the average phosphate ion having an oceanic residence time between 20,000 and 100,000 years.
Excess phosphorus and nitrogen that enters these ecosystems from fertilizer runoff and from sewage causes excessive growth of microorganisms and depletes the dissolved oxygen, which leads to the death of many ecosystem fauna, such as shellfish and finfish. This process is responsible for dead zones in lakes and at the mouths of many major rivers (Figure $8$).
A dead zone is an area within a freshwater or marine ecosystem where large areas are depleted of their normal flora and fauna; these zones can be caused by eutrophication, oil spills, dumping of toxic chemicals, and other human activities. The number of dead zones has been increasing for several years, and more than 400 of these zones were present as of 2008. One of the worst dead zones is off the coast of the United States in the Gulf of Mexico, where fertilizer runoff from the Mississippi River basin has created a dead zone of over 8463 square miles. Phosphate and nitrate runoff from fertilizers also negatively affect several lake and bay ecosystems including the Chesapeake Bay in the eastern United States.
Everyday Connection: Chesapeake Bay
The Chesapeake Bay has long been valued as one of the most scenic areas on Earth; it is now in distress and is recognized as a declining ecosystem. In the 1970s, the Chesapeake Bay was one of the first ecosystems to have identified dead zones, which continue to kill many fish and bottom-dwelling species, such as clams, oysters, and worms. Several species have declined in the Chesapeake Bay due to surface water runoff containing excess nutrients from artificial fertilizer used on land. The source of the fertilizers (with high nitrogen and phosphate content) is not limited to agricultural practices. There are many nearby urban areas and more than 150 rivers and streams empty into the bay that are carrying fertilizer runoff from lawns and gardens. Thus, the decline of the Chesapeake Bay is a complex issue and requires the cooperation of industry, agriculture, and everyday homeowners.
Of particular interest to conservationists is the oyster population; it is estimated that more than 200,000 acres of oyster reefs existed in the bay in the 1700s, but that number has now declined to only 36,000 acres. Oyster harvesting was once a major industry for Chesapeake Bay, but it declined 88 percent between 1982 and 2007. This decline was due not only to fertilizer runoff and dead zones but also to overharvesting. Oysters require a certain minimum population density because they must be in close proximity to reproduce. Human activity has altered the oyster population and locations, greatly disrupting the ecosystem.
The restoration of the oyster population in the Chesapeake Bay has been ongoing for several years with mixed success. Not only do many people find oysters good to eat, but they also clean up the bay. Oysters are filter feeders, and as they eat, they clean the water around them. In the 1700s, it was estimated that it took only a few days for the oyster population to filter the entire volume of the bay. Today, with changed water conditions, it is estimated that the present population would take nearly a year to do the same job.
Restoration efforts have been ongoing for several years by non-profit organizations, such as the Chesapeake Bay Foundation. The restoration goal is to find a way to increase population density so the oysters can reproduce more efficiently. Many disease-resistant varieties (developed at the Virginia Institute of Marine Science for the College of William and Mary) are now available and have been used in the construction of experimental oyster reefs. Efforts to clean and restore the bay by Virginia and Delaware have been hampered because much of the pollution entering the bay comes from other states, which stresses the need for inter-state cooperation to gain successful restoration.
The new, hearty oyster strains have also spawned a new and economically viable industry—oyster aquaculture—which not only supplies oysters for food and profit, but also has the added benefit of cleaning the bay.
The Sulfur Cycle
Sulfur is an essential element for the macromolecules of living things. As a part of the amino acid cysteine, it is involved in the formation of disulfide bonds within proteins, which help to determine their 3-D folding patterns, and hence their functions. As shown in Figure $10$, sulfur cycles between the oceans, land, and atmosphere. Atmospheric sulfur is found in the form of sulfur dioxide (SO2) and enters the atmosphere in three ways: from the decomposition of organic molecules, from volcanic activity and geothermal vents, and from the burning of fossil fuels by humans.
On land, sulfur is deposited in four major ways: precipitation, direct fallout from the atmosphere, rock weathering, and geothermal vents (Figure $11$). Atmospheric sulfur is found in the form of sulfur dioxide (SO2), and as rain falls through the atmosphere, sulfur is dissolved in the form of weak sulfuric acid (H2SO4). Sulfur can also fall directly from the atmosphere in a process called fallout. Also, the weathering of sulfur-containing rocks releases sulfur into the soil. These rocks originate from ocean sediments that are moved to land by the geologic uplifting of ocean sediments. Terrestrial ecosystems can then make use of these soil sulfates ($\text{SO}_4^{2-}$), and upon the death and decomposition of these organisms, release the sulfur back into the atmosphere as hydrogen sulfide (H2S) gas.
Sulfur enters the ocean via runoff from land, from atmospheric fallout, and from underwater geothermal vents. Some ecosystems rely on chemoautotrophs using sulfur as a biological energy source. This sulfur then supports marine ecosystems in the form of sulfates.
Human activities have played a major role in altering the balance of the global sulfur cycle. The burning of large quantities of fossil fuels, especially from coal, releases larger amounts of hydrogen sulfide gas into the atmosphere. As rain falls through this gas, it creates the phenomenon known as acid rain. Acid rain is corrosive rain caused by rainwater falling to the ground through sulfur dioxide gas, turning it into weak sulfuric acid, which causes damage to aquatic ecosystems. Acid rain damages the natural environment by lowering the pH of lakes, which kills many of the resident fauna; it also affects the man-made environment through the chemical degradation of buildings. For example, many marble monuments, such as the Lincoln Memorial in Washington, DC, have suffered significant damage from acid rain over the years. These examples show the wide-ranging effects of human activities on our environment and the challenges that remain for our future.
Link to Learning
Click this link to learn more about global climate change.
Summary
Mineral nutrients are cycled through ecosystems and their environment. Of particular importance are water, carbon, nitrogen, phosphorus, and sulfur. All of these cycles have major impacts on ecosystem structure and function. As human activities have caused major disturbances to these cycles, their study and modeling is especially important. A variety of human activities, such as pollution, oil spills, and other events have damaged ecosystems, potentially causing global climate change. The health of Earth depends on understanding these cycles and how to protect the environment from irreversible damage.
Footnotes
1. 1 Scott L. Morford, Benjamin Z. Houlton, and Randy A. Dahlgren, “Increased Forest Ecosystem Carbon and Nitrogen Storage from Nitrogen Rich Bedrock,” Nature 477, no. 7362 (2011): 78–81.
Glossary
acid rain
corrosive rain caused by rainwater falling to the ground through sulfur dioxide gas, turning it into weak sulfuric acid; can damage structures and ecosystems
biogeochemical cycle
cycling of mineral nutrients through ecosystems and through the non-living world
dead zone
area within an ecosystem in lakes and near the mouths of rivers where large areas of ecosystems are depleted of their normal flora and fauna; these zones can be caused by eutrophication, oil spills, dumping of toxic chemicals, and other human activities
eutrophication
process whereby nutrient runoff causes the excess growth of microorganisms, depleting dissolved oxygen levels and killing ecosystem fauna
fallout
direct deposit of solid minerals on land or in the ocean from the atmosphere
hydrosphere
area of the Earth where water movement and storage occurs
non-renewable resource
resource, such as fossil fuel, that is either regenerated very slowly or not at all
residence time
measure of the average time an individual water molecule stays in a particular reservoir
subduction
movement of one tectonic plate beneath another | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/8%3A_Ecology/46%3A_Ecosystems/46.3%3A_Biogeochemical_Cycles.txt |
46.1: Ecology of Ecosystems
Review Questions
The ability of an ecosystem to return to its equilibrium state after an environmental disturbance is called ________.
1. resistance
2. restoration
3. reformation
4. resilience
Answer
D
A re-created ecosystem in a laboratory environment is known as a ________.
1. mesocosm
2. simulation
3. microcosm
4. reproduction
Answer
C
Decomposers are associated with which class of food web?
1. grazing
2. detrital
3. inverted
4. aquatic
Answer
B
The primary producers in an ocean grazing food web are usually ________.
1. plants
2. animals
3. fungi
4. phytoplankton
Answer
D
What term describes the use of mathematical equations in the modeling of linear aspects of ecosystems?
1. analytical modeling
2. simulation modeling
3. conceptual modeling
4. individual-based modeling
Answer
A
The position of an organism along a food chain is known as its ________.
1. locus
2. location
3. trophic level
4. microcosm
Answer
C
Free Response
Compare and contrast food chains and food webs. What are the strengths of each concept in describing ecosystems?
Answer
Food webs show interacting groups of different species and their many interconnections with each other and the environment. Food chains are linear aspects of food webs that describe the succession of organisms consuming one another at defined trophic levels. Food webs are a more accurate representation of the structure and dynamics of an ecosystem. Food chains are easier to model and use for experimental studies.
Describe freshwater, ocean, and terrestrial ecosystems.
Answer
Freshwater ecosystems are the rarest, but have great diversity of freshwater fish and other aquatic life. Ocean ecosystems are the most common and are responsible for much of the photosynthesis that occurs on Earth. Terrestrial ecosystems are very diverse; they are grouped based on their species and environment (biome), which includes forests, deserts, and tundras.
Compare grazing and detrital food webs. Why would they both be present in the same ecosystem?
Answer
Grazing food webs have a primary producer at their base, which is either a plant for terrestrial ecosystems or a phytoplankton for aquatic ecosystems. The producers pass their energy to the various trophic levels of consumers. At the base of detrital food webs are the decomposers, which pass this energy to a variety of other consumers. Detrital food webs are important for the health of many grazing food webs because they eliminate dead and decaying organic material, thus, clearing space for new organisms and removing potential causes of disease. By breaking down dead organic matter, decomposers also make mineral nutrients available to primary producers; this process is a vital link in nutrient cycling.
46.2: Energy Flow through Ecosystems
Review Questions
The weight of living organisms in an ecosystem at a particular point in time is called:
1. energy
2. production
3. entropy
4. biomass
Answer
D
Which term describes the process whereby toxic substances increase along trophic levels of an ecosystem?
1. biomassification
2. biomagnification
3. bioentropy
4. heterotrophy
Answer
B
Organisms that can make their own food using inorganic molecules are called:
1. autotrophs
2. heterotrophs
3. photoautotrophs
4. chemoautotrophs
Answer
D
In the English Channel ecosystem, the number of primary producers is smaller than the number of primary consumers because________.
1. the apex consumers have a low turnover rate
2. the primary producers have a low turnover rate
3. the primary producers have a high turnover rate
4. the primary consumers have a high turnover rate
Answer
C
What law of chemistry determines how much energy can be transferred when it is converted from one form to another?
1. the first law of thermodynamics
2. the second law of thermodynamics
3. the conservation of matter
4. the conservation of energy
Answer
B
Free Response
Compare the three types of ecological pyramids and how well they describe ecosystem structure. Identify which ones can be inverted and give an example of an inverted pyramid for each.
Answer
Pyramids of numbers display the number of individual organisms on each trophic level. These pyramids can be either upright or inverted, depending on the number of the organisms. Pyramids of biomass display the weight of organisms at each level. Inverted pyramids of biomass can occur when the primary producer has a high turnover rate. Pyramids of energy are usually upright and are the best representation of energy flow and ecosystem structure.
How does the amount of food a warm blooded-animal (endotherm) eats relate to its net production efficiency (NPE)?
Answer
NPE measures the rate at which one trophic level can use and make biomass from what it attained in the previous level, taking into account respiration, defecation, and heat loss. Endotherms have high metabolism and generate a lot of body heat. Although this gives them advantages in their activity level in colder temperatures, these organisms are 10 times less efficient at harnessing the energy from the food they eat compared with cold-blooded animals, and thus have to eat more and more often.
46.3: Biogeochemical Cycles
Review Questions
The movement of mineral nutrients through organisms and their environment is called a ________ cycle.
1. biological
2. bioaccumulation
3. biogeochemical
4. biochemical
Answer
C
Carbon is present in the atmosphere as ________.
1. carbon dioxide
2. carbonate ion
3. carbon dust
4. carbon monoxide
Answer
A
The majority of water found on Earth is:
1. ice
2. water vapor
3. fresh water
4. salt water
Answer
D
The average time a molecule spends in its reservoir is known as ________.
1. residence time
2. restriction time
3. resilience time
4. storage time
Answer
A
The process whereby oxygen is depleted by the growth of microorganisms due to excess nutrients in aquatic systems is called ________.
1. dead zoning
2. eutrophication
3. retrofication
4. depletion
Answer
B
The process whereby nitrogen is brought into organic molecules is called ________.
1. nitrification
2. denitrification
3. nitrogen fixation
4. nitrogen cycling
Answer
C
Free Response
Describe nitrogen fixation and why it is important to agriculture.
Answer
Nitrogen fixation is the process of bringing nitrogen gas from the atmosphere and incorporating it into organic molecules. Most plants do not have this capability and must rely on free-living or symbiotic bacteria to do this. As nitrogen is often the limiting nutrient in the growth of crops, farmers make use of artificial fertilizers to provide a nitrogen source to the plants as they grow.
What are the factors that cause dead zones? Describe eutrophication, in particular, as a cause.
Answer
Many factors can kill life in a lake or ocean, such as eutrophication by nutrient-rich surface runoff, oil spills, toxic waste spills, changes in climate, and the dumping of garbage into the ocean. Eutrophication is a result of nutrient-rich runoff from land using artificial fertilizers high in nitrogen and phosphorus. These nutrients cause the rapid and excessive growth of microorganisms, which deplete local dissolved oxygen and kill many fish and other aquatic organisms.
Why are drinking water supplies still a major concern for many countries?
Answer
Most of the water on Earth is salt water, which humans cannot drink unless the salt is removed. Some fresh water is locked in glaciers and polar ice caps, or is present in the atmosphere. The Earth’s water supplies are threatened by pollution and exhaustion. The effort to supply fresh drinking water to the planet’s ever-expanding human population is seen as a major challenge in this century. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/8%3A_Ecology/46%3A_Ecosystems/46.E%3A_Ecosystems_%28Exercises%29.txt |
Conservation biology is the management of nature and of Earth's biodiversity with the aim of protecting species, their habitats, and ecosystems from excessive rates of extinction and the erosion of biotic interactions. It is an interdisciplinary subject drawing on natural and social sciences, and the practice of natural resource management.
• 47.0: Prelude to Conservation Biology and Biodiversity
Biologists were studying species of a family of fish called cichlids. They found that as they sampled for fish in different locations of the lake, they never stopped finding new species, and they identified nearly 500 evolved types of cichlids. But while studying these variations, they quickly discovered that the invasive Nile Perch was destroying the lake’s cichlid population, bringing hundreds of cichlid species to extinction with devastating rapidity.
• 47.1: The Biodiversity Crisis
Scientists generally accept that the term biodiversity describes the number and kinds of species in a location or on the planet. Species can be difficult to define, but most biologists still feel comfortable with the concept and are able to identify and count eukaryotic species in most contexts. Biologists have also identified alternate measures of biodiversity, some of which are important for planning how to preserve biodiversity.
• 47.2: The Importance of Biodiversity to Human Life
Agriculture began after early hunter-gatherer societies first settled in one place and heavily modified their immediate environment. This cultural transition has made it difficult for humans to recognize their dependence on undomesticated living things on the planet. Biologists recognize the human species is embedded in ecosystems and is dependent on them, just as every other species on the planet is dependent.
• 47.3: Threats to Biodiversity
The core threat to biodiversity on the planet, and therefore a threat to human welfare, is the combination of human population growth and resource exploitation. The human population requires resources to survive and grow, and those resources are being removed unsustainably from the environment. The three greatest proximate threats to biodiversity are habitat loss, overharvesting, and introduction of exotic species.
• 47.4: Preserving Biodiversity
Preserving biodiversity is an extraordinary challenge that must be met by greater understanding of biodiversity itself, changes in human behavior and beliefs, and various preservation strategies.
• 47.E: Conservation Biology and Biodiversity (Exercises)
47: Conservation Biology and Biodiversity
In the 1980s, biologists working in Lake Victoria in Africa discovered one of the most extraordinary products of evolution on the planet. Located in the Great Rift Valley, Lake Victoria is a large lake about 68,900 km2 in area (larger than Lake Huron, the second largest of North America’s Great Lakes). Biologists were studying species of a family of fish called cichlids. They found that as they sampled for fish in different locations of the lake, they never stopped finding new species, and they identified nearly 500 evolved types of cichlids. But while studying these variations, they quickly discovered that the invasive Nile Perch was destroying the lake’s cichlid population, bringing hundreds of cichlid species to extinction with devastating rapidity.
47.1: The Biodiversity Crisis
Skills to Develop
• Define biodiversity
• Describe biodiversity as the equilibrium of naturally fluctuating rates of extinction and speciation
• Identify historical causes of high extinction rates in Earth’s history
Traditionally, ecologists have measured biodiversity, a general term for the variety present in the biosphere, by taking into account both the number of species and their commonness. Biodiversity can be estimated at a number of levels of organization of living things. These estimation indexes, which came from information theory, are most useful as a first step in quantifying biodiversity between and within ecosystems; they are less useful when the main concern among conservation biologists is simply the loss of biodiversity. However, biologists recognize that measures of biodiversity, in terms of species diversity, may help focus efforts to preserve the biologically or technologically important elements of biodiversity.
The Lake Victoria cichlids provide an example through which we can begin to understand biodiversity. The biologists studying cichlids in the 1980s discovered hundreds of cichlid species representing a variety of specializations to particular habitat types and specific feeding strategies: eating plankton floating in the water, scraping and then eating algae from rocks, eating insect larvae from the bottom, and eating the eggs of other species of cichlid. The cichlids of Lake Victoria are the product of an adaptive radiation. An adaptive radiation is a rapid (less than three million years in the case of the Lake Victoria cichlids) branching through speciation of a phylogenetic tree into many closely related species; typically, the species “radiate” into different habitats and niches. The Galápagos finches are an example of a modest adaptive radiation with 15 species. The cichlids of Lake Victoria are an example of a spectacular adaptive radiation that includes about 500 species.
At the time biologists were making this discovery, some species began to quickly disappear. A culprit in these declines was a species of large fish that was introduced to Lake Victoria by fisheries to feed the people living around the lake. The Nile perch was introduced in 1963, but lay low until the 1980s when its populations began to surge. The Nile perch population grew by consuming cichlids, driving species after species to the point of extinction (the disappearance of a species). In fact, there were several factors that played a role in the extinction of perhaps 200 cichlid species in Lake Victoria: the Nile perch, declining lake water quality due to agriculture and land clearing on the shores of Lake Victoria, and increased fishing pressure. Scientists had not even catalogued all of the species present—so many were lost that were never named. The diversity is now a shadow of what it once was.
The cichlids of Lake Victoria are a thumbnail sketch of contemporary rapid species loss that occurs all over Earth and is caused by human activity. Extinction is a natural process of macroevolution that occurs at the rate of about one out of 1 million species becoming extinct per year. The fossil record reveals that there have been five periods of mass extinction in history with much higher rates of species loss, and the rate of species loss today is comparable to those periods of mass extinction. However, there is a major difference between the previous mass extinctions and the current extinction we are experiencing: human activity. Specifically, three human activities have a major impact: destruction of habitat, introduction of exotic species, and over-harvesting. Predictions of species loss within the next century, a tiny amount of time on geological timescales, range from 10 percent to 50 percent. Extinctions on this scale have only happened five other times in the history of the planet, and they have been caused by cataclysmic events that changed the course of the history of life in each instance. Earth is now in one of those times.
Types of Biodiversity
Scientists generally accept that the term biodiversity describes the number and kinds of species in a location or on the planet. Species can be difficult to define, but most biologists still feel comfortable with the concept and are able to identify and count eukaryotic species in most contexts. Biologists have also identified alternate measures of biodiversity, some of which are important for planning how to preserve biodiversity.
Genetic diversity is one of those alternate concepts. Genetic diversity or variation is the raw material for adaptation in a species. A species’ future potential for adaptation depends on the genetic diversity held in the genomes of the individuals in populations that make up the species. The same is true for higher taxonomic categories. A genus with very different types of species will have more genetic diversity than a genus with species that look alike and have similar ecologies. If there were a choice between one of these genera of species being preserved, the one with the greatest potential for subsequent evolution is the most genetically diverse one. It would be ideal not to have to make such choices, but increasingly this may be the norm.
Many genes code for proteins, which in turn carry out the metabolic processes that keep organisms alive and reproducing. Genetic diversity can be measured as chemical diversity in that different species produce a variety of chemicals in their cells, both the proteins as well as the products and byproducts of metabolism. This chemical diversity has potential benefit for humans as a source of pharmaceuticals, so it provides one way to measure diversity that is important to human health and welfare.
Humans have generated diversity in domestic animals, plants, and fungi. This diversity is also suffering losses because of migration, market forces, and increasing globalism in agriculture, especially in heavily populated regions such as China, India, and Japan. The human population directly depends on this diversity as a stable food source, and its decline is troubling biologists and agricultural scientists.
It is also useful to define ecosystem diversity, meaning the number of different ecosystems on the planet or in a given geographic area (Figure \(1\)). Whole ecosystems can disappear even if some of the species might survive by adapting to other ecosystems. The loss of an ecosystem means the loss of interactions between species, the loss of unique features of coadaptation, and the loss of biological productivity that an ecosystem is able to create. An example of a largely extinct ecosystem in North America is the prairie ecosystem. Prairies once spanned central North America from the boreal forest in northern Canada down into Mexico. They are now all but gone, replaced by crop fields, pasture lands, and suburban sprawl. Many of the species survive, but the hugely productive ecosystem that was responsible for creating the most productive agricultural soils is now gone. As a consequence, soils are disappearing or must be maintained at greater expense.
Current Species Diversity
Despite considerable effort, knowledge of the species that inhabit the planet is limited. A recent estimate suggests that the eukaryote species for which science has names, about 1.5 million species, account for less than 20 percent of the total number of eukaryote species present on the planet (8.7 million species, by one estimate). Estimates of numbers of prokaryotic species are largely guesses, but biologists agree that science has only begun to catalog their diversity. Even with what is known, there is no central repository of names or samples of the described species; therefore, there is no way to be sure that the 1.5 million descriptions is an accurate number. It is a best guess based on the opinions of experts in different taxonomic groups. Given that Earth is losing species at an accelerating pace, science is very much in the place it was with the Lake Victoria cichlids: knowing little about what is being lost. Table \(1\) presents recent estimates of biodiversity in different groups.
Table \(1\): Estimates of the described and predicted species by Taxonomic group
Mora et al. 20111 Chapman 20092 Groombridge & Jenkins 20023
Described Predicted Described Predicted Described Predicted
Animalia 1,124,516 9,920,000 1,424,153 6,836,330 1,225,500 10,820,000
Chromista 17,892 34,900 25,044 200,500
Fungi 44,368 616,320 98,998 1,500,000 72,000 1,500,000
Plantae 224,244 314,600 310,129 390,800 270,000 320,000
Protozoa 16,236 72,800 28,871 1,000,000 80,000 600,000
Prokaryotes 10,307 1,000,000 10,175
Total 1,438,769 10,960,000 1,897,502 10,897,630 1,657,675 13,240,000
There are various initiatives to catalog described species in accessible ways, and the internet is facilitating that effort. Nevertheless, it has been pointed out that at the current rate of species description, which according to the State of Observed Species Report is 17,000 to 20,000 new species per year, it will take close to 500 years to finish describing life on this planet.4 Over time, the task becomes both increasingly impossible and increasingly easier as extinction removes species from the planet.
Naming and counting species may seem an unimportant pursuit given the other needs of humanity, but it is not simply an accounting. Describing species is a complex process by which biologists determine an organism’s unique characteristics and whether or not that organism belongs to any other described species. It allows biologists to find and recognize the species after the initial discovery, and allows them to follow up on questions about its biology. In addition, the unique characteristics of each species make it potentially valuable to humans or other species on which humans depend. Understanding these characteristics is the value of finding and naming species.
Patterns of Biodiversity
Biodiversity is not evenly distributed on Earth. Lake Victoria contained almost 500 species of cichlids alone, ignoring the other fish families present in the lake. All of these species were found only in Lake Victoria; therefore, the 500 species of cichlids were endemic. Endemic species are found in only one location. Endemics with highly restricted distributions are particularly vulnerable to extinction. Higher taxonomic levels, such as genera and families, can also be endemic. Lake Huron contains about 79 species of fish, all of which are found in many other lakes in North America. What accounts for the difference in fish diversity in these two lakes? Lake Victoria is a tropical lake, while Lake Huron is a temperate lake. Lake Huron in its present form is only about 7,000 years old, while Lake Victoria in its present form is about 15,000 years old. Biogeographers have suggested these two factors, latitude and age, are two of several hypotheses to explain biodiversity patterns on the planet.
Career Connection: Biogeographer
Biogeography is the study of the distribution of the world’s species—both in the past and in the present. The work of biogeographers is critical to understanding our physical environment, how the environment affects species, and how environmental changes impact the distribution of a species; it has also been critical to developing evolutionary theory. Biogeographers need to understand both biology and ecology. They also need to be well-versed in evolutionary studies, soil science, and climatology.
There are three main fields of study under the heading of biogeography: ecological biogeography, historical biogeography (called paleobiogeography), and conservation biogeography. Ecological biogeography studies the current factors affecting the distribution of plants and animals. Historical biogeography, as the name implies, studies the past distribution of species. Conservation biogeography, on the other hand, is focused on the protection and restoration of species based upon known historical and current ecological information. Each of these fields considers both zoogeography and phytogeography—the past and present distribution of animals and plants.
One of the oldest observed patterns in ecology is that species biodiversity in almost every taxonomic group increases as latitude declines. In other words, biodiversity increases closer to the equator (Figure \(2\)).
It is not yet clear why biodiversity increases closer to the equator, but hypotheses include the greater age of the ecosystems in the tropics versus temperate regions that were largely devoid of life or drastically impoverished during the last glaciation. The idea is that greater age provides more time for speciation. Another possible explanation is the increased energy the tropics receive from the sun versus the decreased energy that temperate and polar regions receive. It is not entirely clear how greater energy input could translate into more species. The complexity of tropical ecosystems may promote speciation by increasing the heterogeneity, or number of ecological niches, in the tropics relative to higher latitudes. The greater heterogeneity provides more opportunities for coevolution, specialization, and perhaps greater selection pressures leading to population differentiation. However, this hypothesis suffers from some circularity—ecosystems with more species encourage speciation, but how did they get more species to begin with? The tropics have been perceived as being more stable than temperate regions, which have a pronounced climate and day-length seasonality. The tropics have their own forms of seasonality, such as rainfall, but they are generally assumed to be more stable environments and this stability might promote speciation.
Regardless of the mechanisms, it is certainly true that all levels of biodiversity are greatest in the tropics. Additionally, the rate of endemism is highest, and there are more biodiversity hotspots. However, this richness of diversity also means that knowledge of species is lowest, and there is a high potential for biodiversity loss.
Conservation of Biodiversity
In 1988, British environmentalist Norman Myers developed a conservation concept to identify areas rich in species and at significant risk for species loss: biodiversity hotspots. Biodiversity hotspots are geographical areas that contain high numbers of endemic species. The purpose of the concept was to identify important locations on the planet for conservation efforts, a kind of conservation triage. By protecting hotspots, governments are able to protect a larger number of species. The original criteria for a hotspot included the presence of 1500 or more endemic plant species and 70 percent of the area disturbed by human activity. There are now 34 biodiversity hotspots (Figure \(3\)) containing large numbers of endemic species, which include half of Earth’s endemic plants.
Biodiversity Change through Geological Time
The number of species on the planet, or in any geographical area, is the result of an equilibrium of two evolutionary processes that are ongoing: speciation and extinction. Both are natural “birth” and “death” processes of macroevolution. When speciation rates begin to outstrip extinction rates, the number of species will increase; likewise, the number of species will decrease when extinction rates begin to overtake speciation rates. Throughout Earth’s history, these two processes have fluctuated—sometimes leading to dramatic changes in the number of species on Earth as reflected in the fossil record (Figure \(4\)).
Paleontologists have identified five strata in the fossil record that appear to show sudden and dramatic (greater than half of all extant species disappearing from the fossil record) losses in biodiversity. These are called mass extinctions. There are many lesser, yet still dramatic, extinction events, but the five mass extinctions have attracted the most research. An argument can be made that the five mass extinctions are only the five most extreme events in a continuous series of large extinction events throughout the Phanerozoic (since 542 million years ago). In most cases, the hypothesized causes are still controversial; however, the most recent event seems clear.
The Five Mass Extinctions
The fossil record of the mass extinctions was the basis for defining periods of geological history, so they typically occur at the transition point between geological periods. The transition in fossils from one period to another reflects the dramatic loss of species and the gradual origin of new species. These transitions can be seen in the rock strata. Table \(2\) provides data on the five mass extinctions.
This table shows the names and dates for the five mass extinctions in Earth’s history.
Table \(2\): Mass extinctions
Geological Period Mass Extinction Name Time (millions of years ago)
Ordovician–Silurian end-Ordovician O–S 450–440
Late Devonian end-Devonian 375–360
Permian–Triassic end-Permian 251
Triassic–Jurassic end-Triassic 205
Cretaceous–Paleogene end-Cretaceous K–Pg (K–T) 65.5
The Ordovician-Silurian extinction event is the first recorded mass extinction and the second largest. During this period, about 85 percent of marine species (few species lived outside the oceans) became extinct. The main hypothesis for its cause is a period of glaciation and then warming. The extinction event actually consists of two extinction events separated by about 1 million years. The first event was caused by cooling, and the second event was due to the subsequent warming. The climate changes affected temperatures and sea levels. Some researchers have suggested that a gamma-ray burst, caused by a nearby supernova, is a possible cause of the Ordovician-Silurian extinction. The gamma-ray burst would have stripped away the Earth’s ozone layer causing intense ultraviolet radiation from the sun and may account for climate changes observed at the time. The hypothesis is speculative, but extraterrestrial influences on Earth’s history are an active line of research. Recovery of biodiversity after the mass extinction took from 5 to 20 million years, depending on the location.
The late Devonian extinction may have occurred over a relatively long period of time. It appears to have affected marine species and not the plants or animals inhabiting terrestrial habitats. The causes of this extinction are poorly understood.
The end-Permian extinction was the largest in the history of life. Indeed, an argument could be made that Earth nearly became devoid of life during this extinction event. The planet looked very different before and after this event. Estimates are that 96 percent of all marine species and 70 percent of all terrestrial species were lost. It was at this time, for example, that the trilobites, a group that survived the Ordovician–Silurian extinction, became extinct. The causes for this mass extinction are not clear, but the leading suspect is extended and widespread volcanic activity that led to a runaway global-warming event. The oceans became largely anoxic, suffocating marine life. Terrestrial tetrapod diversity took 30 million years to recover after the end-Permian extinction. The Permian extinction dramatically altered Earth’s biodiversity makeup and the course of evolution.
The causes of the Triassic–Jurassic extinction event are not clear and hypotheses of climate change, asteroid impact, and volcanic eruptions have been argued. The extinction event occurred just before the breakup of the supercontinent Pangaea, although recent scholarship suggests that the extinctions may have occurred more gradually throughout the Triassic.
The causes of the end-Cretaceous extinction event are the ones that are best understood. It was during this extinction event about 65 million years ago that the dinosaurs, the dominant vertebrate group for millions of years, disappeared from the planet (with the exception of a theropod clade that gave rise to birds). Indeed, every land animal that weighed more then 25 kg became extinct. The cause of this extinction is now understood to be the result of a cataclysmic impact of a large meteorite, or asteroid, off the coast of what is now the Yucatán Peninsula. This hypothesis, proposed first in 1980, was a radical explanation based on a sharp spike in the levels of iridium (which rains down from space in meteors at a fairly constant rate but is otherwise absent on Earth’s surface) at the rock stratum that marks the boundary between the Cretaceous and Paleogene periods (Figure \(5\)). This boundary marked the disappearance of the dinosaurs in fossils as well as many other taxa. The researchers who discovered the iridium spike interpreted it as a rapid influx of iridium from space to the atmosphere (in the form of a large asteroid) rather than a slowing in the deposition of sediments during that period. It was a radical explanation, but the report of an appropriately aged and sized impact crater in 1991 made the hypothesis more believable. Now an abundance of geological evidence supports the theory. Recovery times for biodiversity after the end-Cretaceous extinction are shorter, in geological time, than for the end-Permian extinction, on the order of 10 million years.
Art Connection
Scientists measured the relative abundance of fern spores above and below the K–Pg boundary in this rock sample. Which of the following statements most likely represents their findings?
1. An abundance of fern spores from several species was found below the K–Pg boundary, but none was found above.
2. An abundance of fern spores from several species was found above the K–Pg boundary, but none was found below.
3. An abundance of fern spores was found both above and below the K–Pg boundary, but only one species was found below the boundary, and many species were found above the boundary.
4. Many species of fern spores were found both above and below the boundary, but the total number of spores was greater below the boundary.
Link to Learning
Explore this interactive website about mass extinctions.
The Pleistocene Extinction
The Pleistocene Extinction is one of the lesser extinctions, and a recent one. It is well known that the North American, and to some degree Eurasian, megafauna, or large animals, disappeared toward the end of the last glaciation period. The extinction appears to have happened in a relatively restricted time period of 10,000–12,000 years ago. In North America, the losses were quite dramatic and included the woolly mammoths (last dated about 4,000 years ago in an isolated population), mastodon, giant beavers, giant ground sloths, saber-toothed cats, and the North American camel, just to name a few. The possibility that the rapid extinction of these large animals was caused by over-hunting was first suggested in the 1900s. Research into this hypothesis continues today. It seems likely that over-hunting caused many pre-written history extinctions in many regions of the world.
In general, the timing of the Pleistocene extinctions correlated with the arrival of humans and not with climate-change events, which is the main competing hypothesis for these extinctions. The extinctions began in Australia about 40,000 to 50,000 years ago, just after the arrival of humans in the area: a marsupial lion, a giant one-ton wombat, and several giant kangaroo species disappeared. In North America, the extinctions of almost all of the large mammals occurred 10,000–12,000 years ago. All that are left are the smaller mammals such as bears, elk, moose, and cougars. Finally, on many remote oceanic islands, the extinctions of many species occurred coincident with human arrivals. Not all of the islands had large animals, but when there were large animals, they were lost. Madagascar was colonized about 2,000 years ago and the large mammals that lived there became extinct. Eurasia and Africa do not show this pattern, but they also did not experience a recent arrival of humans. Humans arrived in Eurasia hundreds of thousands of years ago after the origin of the species in Africa. This topic remains an area of active research and hypothesizing. It seems clear that even if climate played a role, in most cases human hunting precipitated the extinctions.
Present-Time Extinctions
The sixth, or Holocene, mass extinction appears to have begun earlier than previously believed and has mostly to do with the activities of Homo sapiens. Since the beginning of the Holocene period, there are numerous recent extinctions of individual species that are recorded in human writings. Most of these are coincident with the expansion of the European colonies since the 1500s.
One of the earlier and popularly known examples is the dodo bird. The dodo bird lived in the forests of Mauritius, an island in the Indian Ocean. The dodo bird became extinct around 1662. It was hunted for its meat by sailors and was easy prey because the dodo, which did not evolve with humans, would approach people without fear. Introduced pigs, rats, and dogs brought to the island by European ships also killed dodo young and eggs.
Steller's sea cow became extinct in 1768; it was related to the manatee and probably once lived along the northwest coast of North America. Steller's sea cow was first discovered by Europeans in 1741 and was hunted for meat and oil. The last sea cow was killed in 1768. That amounts to 27 years between the sea cow’s first contact with Europeans and extinction of the species.
In 1914, the last living passenger pigeon died in a zoo in Cincinnati, Ohio. This species had once darkened the skies of North America during its migrations, but it was hunted and suffered from habitat loss through the clearing of forests for farmland. In 1918, the last living Carolina parakeet died in captivity. This species was once common in the eastern United States, but it suffered from habitat loss. The species was also hunted because it ate orchard fruit when its native foods were destroyed to make way for farmland. The Japanese sea lion, which inhabited a broad area around Japan and the coast of Korea, became extinct in the 1950s due to fishermen. The Caribbean monk seal was distributed throughout the Caribbean Sea but was driven to extinction via hunting by 1952.
These are only a few of the recorded extinctions in the past 500 years. The International Union for Conservation of Nature (IUCN) keeps a list of extinct and endangered species called the Red List. The list is not complete, but it describes 380 extinct species of vertebrates after 1500 AD, 86 of which were driven extinct by overhunting or overfishing.
Estimates of Present-Time Extinction Rates
Estimates of extinction rates are hampered by the fact that most extinctions are probably happening without observation. The extinction of a bird or mammal is likely to be noticed by humans, especially if it has been hunted or used in some other way. But there are many organisms that are of less interest to humans (not necessarily of less value) and many that are undescribed.
The background extinction rate is estimated to be about one per million species per year (E/MSY). For example, assuming there are about ten million species in existence, the expectation is that ten species would become extinct each year (each year represents ten million species per year).
One contemporary extinction rate estimate uses the extinctions in the written record since the year 1500. For birds alone this method yields an estimate of 26 E/MSY. However, this value may be underestimated for three reasons. First, many species would not have been described until much later in the time period, so their loss would have gone unnoticed. Second, the number of recently extinct species is increasing because extinct species now are being described from skeletal remains. And third, some species are probably already extinct even though conservationists are reluctant to name them as such. Taking these factors into account raises the estimated extinction rate closer to 100 E/MSY. The predicted rate by the end of the century is 1500 E/MSY.
A second approach to estimating present-time extinction rates is to correlate species loss with habitat loss by measuring forest-area loss and understanding species-area relationships. The species-area relationship is the rate at which new species are seen when the area surveyed is increased. Studies have shown that the number of species present increases as the size of the island increases. This phenomenon has also been shown to hold true in other habitats as well. Turning this relationship around, if the habitat area is reduced, the number of species living there will also decline. Estimates of extinction rates based on habitat loss and species-area relationships have suggested that with about 90 percent habitat loss an expected 50 percent of species would become extinct. Species-area estimates have led to species extinction rate calculations of about 1000 E/MSY and higher. In general, actual observations do not show this amount of loss and suggestions have been made that there is a delay in extinction. Recent work has also called into question the applicability of the species-area relationship when estimating the loss of species. This work argues that the species-area relationship leads to an overestimate of extinction rates. A better relationship to use may be the endemics-area relationship. Using this method would bring estimates down to around 500 E/MSY in the coming century. Note that this value is still 500 times the background rate.
Link to Learning
Check out this interactive exploration of endangered and extinct species, their ecosystems, and the causes of the endangerment or extinction.
Summary
Biodiversity exists at multiple levels of organization and is measured in different ways depending on the goals of those taking the measurements. These measurements include numbers of species, genetic diversity, chemical diversity, and ecosystem diversity. The number of described species is estimated to be 1.5 million with about 17,000 new species being described each year. Estimates for the total number of species on Earth vary but are on the order of 10 million. Biodiversity is negatively correlated with latitude for most taxa, meaning that biodiversity is higher in the tropics. The mechanism for this pattern is not known with certainty, but several plausible hypotheses have been advanced.
Five mass extinctions with losses of more than 50 percent of extant species are observable in the fossil record. Biodiversity recovery times after mass extinctions vary, but have been up to 30 million years. Recent extinctions are recorded in written history and are the basis for one method of estimating contemporary extinction rates. The other method uses measures of habitat loss and species-area relationships. Estimates of contemporary extinction rates vary, but some rates are as high as 500 times the background rate, as determined from the fossil record, and are predicted to rise.
Art Connections
Figure \(5\): Scientists measured the relative abundance of fern spores above and below the K-Pg boundary in this rock sample. Which of the following statements most likely represents their findings?
1. An abundance of fern spores from several species was found below the K-Pg boundary, but none was found above.
2. An abundance of fern spores from several species was found above the K-Pg boundary, but none was found below.
3. An abundance of fern spores was found both above and below the K-Pg boundary, but only one species was found below the boundary , and many species were found above the boundary.
4. Many species of fern spores were found both above and below the boundary, but the total number of spores was greater below the boundary.
Answer
A. An abundance of fern spores from several species was found below the K-Pg boundary, but none was found above.
Footnotes
1. 1 Mora Camilo et al., “How Many Species Are There on Earth and in the Ocean?” PLoS Biology (2011), doi:10.1371/journal.pbio.1001127.
2. 2 Arthur D. Chapman, Numbers of Living Species in Australia and the World, 2nd ed. (Canberra, AU: Australian Biological Resources Study, 2009). www.environment.gov.au/biodiv...d-complete.pdf.
3. 3 Brian Groombridge and Martin D. Jenkins. World Atlas of Biodiversity: Earth’s Living Resources in the 21st Century. Berkeley: University of California Press, 2002.
4. 4 International Institute for Species Exploration (IISE), 2011 State of Observed Species (SOS). Tempe, AZ: IISE, 2011. Accessed May, 20, 2012. species.asu.edu/SOS.
Glossary
adaptive radiation
rapid branching through speciation of a phylogenetic tree into many closely related species
biodiversity
variety of a biological system, typically conceived as the number of species, but also applying to genes, biochemistry, and ecosystems
biodiversity hotspot
concept originated by Norman Myers to describe a geographical region with a large number of endemic species and a large percentage of degraded habitat
chemical diversity
variety of metabolic compounds in an ecosystem
ecosystem diversity
variety of ecosystems
endemic species
species native to one place
extinction
disappearance of a species from Earth; local extinction is the disappearance of a species from a region
extinction rate
number of species becoming extinct over time, sometimes defined as extinctions per million species–years to make numbers manageable (E/MSY)
genetic diversity
variety of genes in a species or other taxonomic group or ecosystem, the term can refer to allelic diversity or genome-wide diversity
heterogeneity
number of ecological niches
megafauna
large animals
species-area relationship
relationship between area surveyed and number of species encountered; typically measured by incrementally increasing the area of a survey and determining the cumulative numbers of species | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/8%3A_Ecology/47%3A_Conservation_Biology_and_Biodiversity/47.0%3A_Prelude_to_Conservation_Biology_and_Biodiversity.txt |
Skills to Develop
• Identify chemical diversity benefits to humans
• Identify biodiversity components that support human agriculture
• Describe ecosystem services
It may not be clear why biologists are concerned about biodiversity loss. When biodiversity loss is thought of as the extinction of the passenger pigeon, the dodo bird, and even the woolly mammoth, the loss may appear to be an emotional one. But is the loss practically important for the welfare of the human species? From the perspective of evolution and ecology, the loss of a particular individual species is unimportant (however, the loss of a keystone species can lead to ecological disaster). Extinction is a normal part of macroevolution. But the accelerated extinction rate means the loss of tens of thousands of species within our lifetimes, and it is likely to have dramatic effects on human welfare through the collapse of ecosystems and in added costs to maintain food production, clean air and water, and human health.
Agriculture began after early hunter-gatherer societies first settled in one place and heavily modified their immediate environment. This cultural transition has made it difficult for humans to recognize their dependence on undomesticated living things on the planet. Biologists recognize the human species is embedded in ecosystems and is dependent on them, just as every other species on the planet is dependent. Technology smoothes out the extremes of existence, but ultimately the human species cannot exist without its ecosystem.
Human Health
Contemporary societies that live close to the land often have a broad knowledge of the medicinal uses of plants growing in their area. Most plants produce secondary plant compounds, which are toxins used to protect the plant from insects and other animals that eat them, but some of which also work as medication. For centuries in Europe, older knowledge about the medical uses of plants was compiled in herbals—books that identified plants and their uses. Humans are not the only species to use plants for medicinal reasons: the great apes, orangutans, chimpanzees, bonobos, and gorillas have all been observed self-medicating with plants.
Modern pharmaceutical science also recognizes the importance of these plant compounds. Examples of significant medicines derived from plant compounds include aspirin, codeine, digoxin, atropine, and vincristine (Figure \(1\)). Many medicines were once derived from plant extracts but are now synthesized. It is estimated that, at one time, 25 percent of modern drugs contained at least one plant extract. That number has probably decreased to about 10 percent as natural plant ingredients are replaced by synthetic versions. Antibiotics, which are responsible for extraordinary improvements in health and lifespans in developed countries, are compounds largely derived from fungi and bacteria.
In recent years, animal venoms and poisons have excited intense research for their medicinal potential. By 2007, the FDA had approved five drugs based on animal toxins to treat diseases such as hypertension, chronic pain, and diabetes. Another five drugs are undergoing clinical trials, and at least six drugs are being used in other countries. Other toxins under investigation come from mammals, snakes, lizards, various amphibians, fish, snails, octopuses, and scorpions.
Aside from representing billions of dollars in profits, these medicines improve people’s lives. Pharmaceutical companies are actively looking for new compounds synthesized by living organisms that can function as medicine. It is estimated that 1/3 of pharmaceutical research and development is spent on natural compounds and that about 35 percent of new drugs brought to market between 1981 and 2002 were from natural compounds. The opportunities for new medications will be reduced in direct proportion to the disappearance of species.
Agricultural Diversity
Since the beginning of human agriculture more than 10,000 years ago, human groups have been breeding and selecting crop varieties. This crop diversity matched the cultural diversity of highly subdivided populations of humans. For example, potatoes were domesticated beginning around 7,000 years ago in the central Andes of Peru and Bolivia. The potatoes grown in that region belong to seven species and the number of varieties likely is in the thousands. Each variety has been bred to thrive at particular elevations and soil and climate conditions. The diversity is driven by the diverse demands of the topography, the limited movement of people, and the demands created by crop rotation for different varieties that will do well in different fields.
Potatoes are only one example of human-generated diversity. Every plant, animal, and fungus that has been cultivated by humans has been bred from original wild ancestor species into diverse varieties arising from the demands for food value, adaptation to growing conditions, and resistance to pests. The potato demonstrates a well-known example of the risks of low crop diversity: the tragic Irish potato famine when the single variety grown in Ireland became susceptible to a potato blight, wiping out the crop. The loss of the crop led to famine, death, and mass emigration. Resistance to disease is a chief benefit to maintaining crop biodiversity, and lack of diversity in contemporary crop species carries similar risks. Seed companies, which are the source of most crop varieties in developed countries, must continually breed new varieties to keep up with evolving pest organisms. These same seed companies, however, have participated in the decline of the number of varieties available as they focus on selling fewer varieties in more areas of the world.
The ability to create new crop varieties relies on the diversity of varieties available and the accessibility of wild forms related to the crop plant. These wild forms are often the source of new gene variants that can be bred with existing varieties to create varieties with new attributes. Loss of wild species related to a crop will mean the loss of potential in crop improvement. Maintaining the genetic diversity of wild species related to domesticated species ensures our continued food supply.
Since the 1920s, government agriculture departments have maintained seed banks of crop varieties as a way to maintain crop diversity. This system has flaws because, over time, seed banks are lost through accidents, and there is no way to replace them. In 2008, the Svalbard Global Seed Vault (Figure \(2\)) began storing seeds from around the world as a backup system to the regional seed banks. If a regional seed bank stores varieties in Svalbard, losses can be replaced from Svalbard. The seed vault is located deep into the rock of an arctic island. Conditions within the vault are maintained at ideal temperature and humidity for seed survival, but the deep underground location of the vault in the arctic means that failure of the vault’s systems will not compromise the climatic conditions inside the vault.
Art Connection
The Svalbard Global Seed Vault is located on Spitsbergen island in Norway, which has an arctic climate. Why might an arctic climate be good for seed storage?
Crop success is largely dependent on the quality of the soil. Although some agricultural soils are rendered sterile using controversial cultivation and chemical treatments, most contain a huge diversity of organisms that maintain nutrient cycles—breaking down organic matter into nutrient compounds that crops need for growth. These organisms also maintain soil texture that affects water and oxygen dynamics in the soil that are necessary for plant growth. If farmers had to maintain arable soil using alternate means, the cost of food would be much higher than it is now. These kinds of processes are called ecosystem services. They occur within ecosystems, such as soil ecosystems, as a result of the diverse metabolic activities of the organisms living there, but they provide benefits to human food production, drinking water availability, and breathable air.
Other key ecosystem services related to food production are plant pollination and crop pest control. Over 150 crops in the United States require pollination to produce. One estimate of the benefit of honeybee pollination within the United States is \$1.6 billion per year; other pollinators contribute up to \$6.7 billion more.
Many honeybee populations are managed by apiarists who rent out their hives’ services to farmers. Honeybee populations in North America have been suffering large losses caused by a syndrome known as colony collapse disorder, whose cause is unclear. Other pollinators include a diverse array of other bee species and various insects and birds. Loss of these species would make growing crops requiring pollination impossible, increasing dependence on other crops.
Finally, humans compete for their food with crop pests, most of which are insects. Pesticides control these competitors; however, pesticides are costly and lose their effectiveness over time as pest populations adapt. They also lead to collateral damage by killing non-pest species and risking the health of consumers and agricultural workers. Ecologists believe that the bulk of the work in removing pests is actually done by predators and parasites of those pests, but the impact has not been well studied. A review found that in 74 percent of studies that looked for an effect of landscape complexity on natural enemies of pests, the greater the complexity, the greater the effect of pest-suppressing organisms. An experimental study found that introducing multiple enemies of pea aphids (an important alfalfa pest) increased the yield of alfalfa significantly. This study shows the importance of landscape diversity via the question of whether a diversity of pests is more effective at control than one single pest; the results showed this to be the case. Loss of diversity in pest enemies will inevitably make it more difficult and costly to grow food.
Wild Food Sources
In addition to growing crops and raising animals for food, humans obtain food resources from wild populations, primarily fish populations. For approximately 1 billion people, aquatic resources provide the main source of animal protein. But since 1990, global fish production has declined. Despite considerable effort, few fisheries on the planet are managed for sustainability.
Fishery extinctions rarely lead to complete extinction of the harvested species, but rather to a radical restructuring of the marine ecosystem in which a dominant species is so over-harvested that it becomes a minor player, ecologically. In addition to humans losing the food source, these alterations affect many other species in ways that are difficult or impossible to predict. The collapse of fisheries has dramatic and long-lasting effects on local populations that work in the fishery. In addition, the loss of an inexpensive protein source to populations that cannot afford to replace it will increase the cost of living and limit societies in other ways. In general, the fish taken from fisheries have shifted to smaller species as larger species are fished to extinction. The ultimate outcome could clearly be the loss of aquatic systems as food sources.
Psychological and Moral Value
Finally, it has been argued that humans benefit psychologically from living in a biodiverse world. A chief proponent of this idea is entomologist E. O. Wilson. He argues that human evolutionary history has adapted us to live in a natural environment and that built environments generate stressors that affect human health and well-being. There is considerable research into the psychological regenerative benefits of natural landscapes that suggests the hypothesis may hold some truth. In addition, there is a moral argument that humans have a responsibility to inflict as little harm as possible on other species.
Summary
Humans use many compounds that were first discovered or derived from living organisms as medicines: secondary plant compounds, animal toxins, and antibiotics produced by bacteria and fungi. More medicines are expected to be discovered in nature. Loss of biodiversity will impact the number of pharmaceuticals available to humans.
Crop diversity is a requirement for food security, and it is being lost. The loss of wild relatives to crops also threatens breeders’ abilities to create new varieties. Ecosystems provide ecosystem services that support human agriculture: pollination, nutrient cycling, pest control, and soil development and maintenance. Loss of biodiversity threatens these ecosystem services and risks making food production more expensive or impossible. Wild food sources are mainly aquatic, but few are being managed for sustainability. Fisheries’ ability to provide protein to human populations is threatened when extinction occurs.
Biodiversity may provide important psychological benefits to humans. Additionally, there are moral arguments for the maintenance of biodiversity.
Art Connections
Figure \(2\): The Svalbard Global Seed Vault is located on Spitsbergen island in Norway, which has an arctic climate. Why might an arctic climate be good for seed storage?
Answer
The ground is permanently frozen so the seeds will keep even if the electricity fails.
Glossary
secondary plant compound
compound produced as byproducts of plant metabolic processes that is usually toxic, but is sequestered by the plant to defend against herbivores | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/8%3A_Ecology/47%3A_Conservation_Biology_and_Biodiversity/47.2%3A_The_Importance_of_Biodiversity_to_Human_Life.txt |
Skills to Develop
• Identify significant threats to biodiversity
• Explain the effects of habitat loss, exotic species, and hunting on biodiversity
• Identify the early and predicted effects of climate change on biodiversity
The core threat to biodiversity on the planet, and therefore a threat to human welfare, is the combination of human population growth and resource exploitation. The human population requires resources to survive and grow, and those resources are being removed unsustainably from the environment. The three greatest proximate threats to biodiversity are habitat loss, overharvesting, and introduction of exotic species. The first two of these are a direct result of human population growth and resource use. The third results from increased mobility and trade. A fourth major cause of extinction, anthropogenic climate change, has not yet had a large impact, but it is predicted to become significant during this century. Global climate change is also a consequence of human population needs for energy and the use of fossil fuels to meet those needs (Figure \(1\)). Environmental issues, such as toxic pollution, have specific targeted effects on species, but they are not generally seen as threats at the magnitude of the others.
Habitat Loss
Humans rely on technology to modify their environment and replace certain functions that were once performed by the natural ecosystem. Other species cannot do this. Elimination of their ecosystem—whether it is a forest, a desert, a grassland, a freshwater estuarine, or a marine environment—will kill the individuals in the species. Remove the entire habitat within the range of a species and, unless they are one of the few species that do well in human-built environments, the species will become extinct. Human destruction of habitats accelerated in the latter half of the twentieth century. Consider the exceptional biodiversity of Sumatra: it is home to one species of orangutan, a species of critically endangered elephant, and the Sumatran tiger, but half of Sumatra’s forest is now gone. The neighboring island of Borneo, home to the other species of orangutan, has lost a similar area of forest. Forest loss continues in protected areas of Borneo. The orangutan in Borneo is listed as endangered by the International Union for Conservation of Nature (IUCN), but it is simply the most visible of thousands of species that will not survive the disappearance of the forests of Borneo. The forests are removed for timber and to plant palm oil plantations (Figure \(2\)). Palm oil is used in many products including food products, cosmetics, and biodiesel in Europe. A five-year estimate of global forest cover loss for the years 2000–2005 was 3.1 percent. In the humid tropics where forest loss is primarily from timber extraction, 272,000 km2 was lost out of a global total of 11,564,000 km2 (or 2.4 percent). In the tropics, these losses certainly also represent the extinction of species because of high levels of endemism.
Everyday Connection: Preventing Habitat Destruction with Wise Wood Choices
Most consumers do not imagine that the home improvement products they buy might be contributing to habitat loss and species extinctions. Yet the market for illegally harvested tropical timber is huge, and the wood products often find themselves in building supply stores in the United States. One estimate is that 10 percent of the imported timber stream in the United States, which is the world’s largest consumer of wood products, is potentially illegally logged. In 2006, this amounted to \$3.6 billion in wood products. Most of the illegal products are imported from countries that act as intermediaries and are not the originators of the wood.
How is it possible to determine if a wood product, such as flooring, was harvested sustainably or even legally? The Forest Stewardship Council (FSC) certifies sustainably harvested forest products, therefore, looking for their certification on flooring and other hardwood products is one way to ensure that the wood has not been taken illegally from a tropical forest. Certification applies to specific products, not to a producer; some producers’ products may not have certification while other products are certified. While there are other industry-backed certifications other than the FSC, these are unreliable due to lack of independence from the industry. Another approach is to buy domestic wood species. While it would be great if there was a list of legal versus illegal wood products, it is not that simple. Logging and forest management laws vary from country to country; what is illegal in one country may be legal in another. Where and how a product is harvested and whether the forest from which it comes is being maintained sustainably all factor into whether a wood product will be certified by the FSC. It is always a good idea to ask questions about where a wood product came from and how the supplier knows that it was harvested legally.
Habitat destruction can affect ecosystems other than forests. Rivers and streams are important ecosystems and are frequently modified through land development and from damming or water removal. Damming of rivers affects the water flow and access to all parts of a river. Differing flow regimes can reduce or eliminate populations that are adapted to these changes in flow patterns. For example, an estimated 91percent of river lengths in the United States have been developed: they have modifications like dams, to create energy or store water; levees, to prevent flooding; or dredging or rerouting, to create land that is more suitable for human development. Many fish species in the United States, especially rare species or species with restricted distributions, have seen declines caused by river damming and habitat loss. Research has confirmed that species of amphibians that must carry out parts of their life cycles in both aquatic and terrestrial habitats have a greater chance of suffering population declines and extinction because of the increased likelihood that one of their habitats or access between them will be lost.
Overharvesting
Overharvesting is a serious threat to many species, but particularly to aquatic species. There are many examples of regulated commercial fisheries monitored by fisheries scientists that have nevertheless collapsed. The western Atlantic cod fishery is the most spectacular recent collapse. While it was a hugely productive fishery for 400 years, the introduction of modern factory trawlers in the 1980s and the pressure on the fishery led to it becoming unsustainable. The causes of fishery collapse are both economic and political in nature. Most fisheries are managed as a common (shared) resource even when the fishing territory lies within a country’s territorial waters. Common resources are subject to an economic pressure known as the tragedy of the commons in which essentially no fisher has a motivation to exercise restraint in harvesting a fishery when it is not owned by that fisher. The natural outcome of harvests of resources held in common is their overexploitation. While large fisheries are regulated to attempt to avoid this pressure, it still exists in the background. This overexploitation is exacerbated when access to the fishery is open and unregulated and when technology gives fishers the ability to overfish. In a few fisheries, the biological growth of the resource is less than the potential growth of the profits made from fishing if that time and money were invested elsewhere. In these cases—whales are an example—economic forces will always drive toward fishing the population to extinction.
Link to Learning
Explore a U.S. Fish & Wildlife Service interactive map of critical habitat for endangered and threatened species in the United States. To begin, select “Visit the online mapper.”
For the most part, fishery extinction is not equivalent to biological extinction—the last fish of a species is rarely fished out of the ocean. At the same time, fishery extinction is still harmful to fish species and their ecosystems. There are some instances in which true extinction is a possibility. Whales have slow-growing populations and are at risk of complete extinction through hunting. There are some species of sharks with restricted distributions that are at risk of extinction. The groupers are another population of generally slow-growing fishes that, in the Caribbean, includes a number of species that are at risk of extinction from overfishing.
Coral reefs are extremely diverse marine ecosystems that face peril from several processes. Reefs are home to 1/3 of the world’s marine fish species—about 4,000 species—despite making up only 1 percent of marine habitat. Most home marine aquaria are stocked with wild-caught organisms, not cultured organisms. Although no species is known to have been driven extinct by the pet trade in marine species, there are studies showing that populations of some species have declined in response to harvesting, indicating that the harvest is not sustainable at those levels. There are concerns about the effect of the pet trade on some terrestrial species such as turtles, amphibians, birds, plants, and even the orangutan.
Bush meat is the generic term used for wild animals killed for food. Hunting is practiced throughout the world, but hunting practices, particularly in equatorial Africa and parts of Asia, are believed to threaten several species with extinction. Traditionally, bush meat in Africa was hunted to feed families directly; however, recent commercialization of the practice now has bush meat available in grocery stores, which has increased harvest rates to the level of unsustainability. Additionally, human population growth has increased the need for protein foods that are not being met from agriculture. Species threatened by the bush meat trade are mostly mammals including many primates living in the Congo basin.
Exotic Species
Exotic species are species that have been intentionally or unintentionally introduced by humans into an ecosystem in which they did not evolve. Such introductions likely occur frequently as natural phenomena. For example, Kudzu (Pueraria lobata), which is native to Japan, was introduced in the United States in 1876. It was later planted for soil conservation. Problematically, it grows too well in the southeastern United States—up to a foot a day. It is now a pest species and covers over 7 million acres in the southeastern United States. If an introduced species is able to survive in its new habitat, that introduction is now reflected in the observed range of the species. Human transportation of people and goods, including the intentional transport of organisms for trade, has dramatically increased the introduction of species into new ecosystems, sometimes at distances that are well beyond the capacity of the species to ever travel itself and outside the range of the species’ natural predators.
Most exotic species introductions probably fail because of the low number of individuals introduced or poor adaptation to the ecosystem they enter. Some species, however, possess preadaptations that can make them especially successful in a new ecosystem. These exotic species often undergo dramatic population increases in their new habitat and reset the ecological conditions in the new environment, threatening the species that exist there. For this reason, exotic species are also called invasive species. Exotic species can threaten other species through competition for resources, predation, or disease.
Link to Learning
Explore an interactive global database of exotic or invasive species.
Lakes and islands are particularly vulnerable to extinction threats from introduced species. In Lake Victoria, as mentioned earlier, the intentional introduction of the Nile perch was largely responsible for the extinction of about 200 species of cichlids. The accidental introduction of the brown tree snake via aircraft (Figure \(3\)) from the Solomon Islands to Guam in 1950 has led to the extinction of three species of birds and three to five species of reptiles endemic to the island. Several other species are still threatened. The brown tree snake is adept at exploiting human transportation as a means to migrate; one was even found on an aircraft arriving in Corpus Christi, Texas. Constant vigilance on the part of airport, military, and commercial aircraft personnel is required to prevent the snake from moving from Guam to other islands in the Pacific, especially Hawaii. Islands do not make up a large area of land on the globe, but they do contain a disproportionate number of endemic species because of their isolation from mainland ancestors.
It now appears that the global decline in amphibian species recognized in the 1990s is, in some part, caused by the fungus Batrachochytrium dendrobatidis, which causes the disease chytridiomycosis (Figure \(4\)). There is evidence that the fungus is native to Africa and may have been spread throughout the world by transport of a commonly used laboratory and pet species: the African clawed toad (Xenopus laevis). It may well be that biologists themselves are responsible for spreading this disease worldwide. The North American bullfrog, Rana catesbeiana, which has also been widely introduced as a food animal but which easily escapes captivity, survives most infections of Batrachochytrium dendrobatidis and can act as a reservoir for the disease.
Early evidence suggests that another fungal pathogen, Geomyces destructans, introduced from Europe is responsible for white-nose syndrome, which infects cave-hibernating bats in eastern North America and has spread from a point of origin in western New York State (Figure \(5\)). The disease has decimated bat populations and threatens extinction of species already listed as endangered: the Indiana bat, Myotis sodalis, and potentially the Virginia big-eared bat, Corynorhinus townsendii virginianus. How the fungus was introduced is unclear, but one logical presumption would be that recreational cavers unintentionally brought the fungus on clothes or equipment from Europe.
Climate Change
Climate change, and specifically the anthropogenic (meaning, caused by humans) warming trend presently underway, is recognized as a major extinction threat, particularly when combined with other threats such as habitat loss. Scientists disagree about the likely magnitude of the effects, with extinction rate estimates ranging from 15 percent to 40 percent of species committed to extinction by 2050. Scientists do agree, however, that climate change will alter regional climates, including rainfall and snowfall patterns, making habitats less hospitable to the species living in them. The warming trend will shift colder climates toward the north and south poles, forcing species to move with their adapted climate norms while facing habitat gaps along the way. The shifting ranges will impose new competitive regimes on species as they find themselves in contact with other species not present in their historic range. One such unexpected species contact is between polar bears and grizzly bears. Previously, these two species had separate ranges. Now, their ranges are overlapping and there are documented cases of these two species mating and producing viable offspring. Changing climates also throw off species’ delicate timing adaptations to seasonal food resources and breeding times. Many contemporary mismatches to shifts in resource availability and timing have already been documented.
Range shifts are already being observed: for example, some European bird species ranges have moved 91 km northward. The same study suggested that the optimal shift based on warming trends was double that distance, suggesting that the populations are not moving quickly enough. Range shifts have also been observed in plants, butterflies, other insects, freshwater fishes, reptiles, and mammals.
Climate gradients will also move up mountains, eventually crowding species higher in altitude and eliminating the habitat for those species adapted to the highest elevations. Some climates will completely disappear. The rate of warming appears to be accelerated in the arctic, which is recognized as a serious threat to polar bear populations that require sea ice to hunt seals during the winter months: seals are the only source of protein available to polar bears. A trend to decreasing sea ice coverage has occurred since observations began in the mid-twentieth century. The rate of decline observed in recent years is far greater than previously predicted by climate models.
Finally, global warming will raise ocean levels due to melt water from glaciers and the greater volume of warmer water. Shorelines will be inundated, reducing island size, which will have an effect on some species, and a number of islands will disappear entirely. Additionally, the gradual melting and subsequent refreezing of the poles, glaciers, and higher elevation mountains—a cycle that has provided freshwater to environments for centuries—will also be jeopardized. This could result in an overabundance of salt water and a shortage of fresh water.
Summary
The core threats to biodiversity are human population growth and unsustainable resource use. To date, the most significant causes of extinctions are habitat loss, introduction of exotic species, and overharvesting. Climate change is predicted to be a significant cause of extinctions in the coming century. Habitat loss occurs through deforestation, damming of rivers, and other activities. Overharvesting is a threat particularly to aquatic species, while the taking of bush meat in the humid tropics threatens many species in Asia, Africa, and the Americas. Exotic species have been the cause of a number of extinctions and are especially damaging to islands and lakes. Exotic species’ introductions are increasing because of the increased mobility of human populations and growing global trade and transportation. Climate change is forcing range changes that may lead to extinction. It is also affecting adaptations to the timing of resource availability that negatively affects species in seasonal environments. The impacts of climate change are greatest in the arctic. Global warming will also raise sea levels, eliminating some islands and reducing the area of all others.
Art Connections
Converting a prairie to a farm field is an example of ________.
1. overharvesting
2. habitat loss
3. exotic species
4. climate change
Answer
B
Glossary
bush meat
wild-caught animal used as food (typically mammals, birds, and reptiles); usually referring to hunting in the tropics of sub-Saharan Africa, Asia, and the Americas
chytridiomycosis
disease of amphibians caused by the fungus Batrachochytrium dendrobatidis; thought to be a major cause of the global amphibian decline
exotic species
(also, invasive species) species that has been introduced to an ecosystem in which it did not evolve
tragedy of the commons
economic principle that resources held in common will inevitably be overexploited
white-nose syndrome
disease of cave-hibernating bats in the eastern United States and Canada associated with the fungus Geomyces destructans | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/8%3A_Ecology/47%3A_Conservation_Biology_and_Biodiversity/47.3%3A_Threats_to_Biodiversity.txt |
Skills to Develop
• Identify new technologies for describing biodiversity
• Explain the legislative framework for conservation
• Describe principles and challenges of conservation preserve design
• Identify examples of the effects of habitat restoration
• Discuss the role of zoos in biodiversity conservation
Preserving biodiversity is an extraordinary challenge that must be met by greater understanding of biodiversity itself, changes in human behavior and beliefs, and various preservation strategies.
Measuring Biodiversity
The technology of molecular genetics and data processing and storage are maturing to the point where cataloguing the planet’s species in an accessible way is close to feasible. DNA barcoding is one molecular genetic method, which takes advantage of rapid evolution in a mitochondrial gene present in eukaryotes, excepting the plants, to identify species using the sequence of portions of the gene. Plants may be barcoded using a combination of chloroplast genes. Rapid mass sequencing machines make the molecular genetics portion of the work relatively inexpensive and quick. Computer resources store and make available the large volumes of data. Projects are currently underway to use DNA barcoding to catalog museum specimens, which have already been named and studied, as well as testing the method on less studied groups. As of mid 2012, close to 150,000 named species had been barcoded. Early studies suggest there are significant numbers of undescribed species that looked too much like sibling species to previously be recognized as different. These now can be identified with DNA barcoding.
Numerous computer databases now provide information about named species and a framework for adding new species. However, as already noted, at the present rate of description of new species, it will take close to 500 years before the complete catalog of life is known. Many, perhaps most, species on the planet do not have that much time.
There is also the problem of understanding which species known to science are threatened and to what degree they are threatened. This task is carried out by the non-profit IUCN which, as previously mentioned, maintains the Red List—an online listing of endangered species categorized by taxonomy, type of threat, and other criteria (Figure \(1\)). The Red List is supported by scientific research. In 2011, the list contained 61,000 species, all with supporting documentation.
Art Connection
Which of the following statements is not supported by this graph?
1. There are more vulnerable fishes than critically endangered and endangered fishes combined.
2. There are more critically endangered amphibians than vulnerable, endangered and critically endangered reptiles combined.
3. Within each group, there are more critically endangered species than vulnerable species.
4. A greater percentage of bird species are critically endangered than mollusk species.
Changing Human Behavior
Legislation throughout the world has been enacted to protect species. The legislation includes international treaties as well as national and state laws. The Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) treaty came into force in 1975. The treaty, and the national legislation that supports it, provides a legal framework for preventing approximately 33,000 listed species from being transported across nations’ borders, thus protecting them from being caught or killed when international trade is involved. The treaty is limited in its reach because it only deals with international movement of organisms or their parts. It is also limited by various countries’ ability or willingness to enforce the treaty and supporting legislation. The illegal trade in organisms and their parts is probably a market in the hundreds of millions of dollars. Illegal wildlife trade is monitored by another non-profit: Trade Records Analysis of Flora and Fauna in Commerce (TRAFFIC).
Within many countries there are laws that protect endangered species and regulate hunting and fishing. In the United States, the Endangered Species Act (ESA) was enacted in 1973. Species at risk are listed by the Act; the U.S. Fish & Wildlife Service is required by law to develop management plans that protect the listed species and bring them back to sustainable numbers. The Act, and others like it in other countries, is a useful tool, but it suffers because it is often difficult to get a species listed, or to get an effective management plan in place once it is listed. Additionally, species may be controversially taken off the list without necessarily having had a change in their situation. More fundamentally, the approach to protecting individual species rather than entire ecosystems is both inefficient and focuses efforts on a few highly visible and often charismatic species, perhaps at the expense of other species that go unprotected. At the same time, the Act has a critical habitat provision outlined in the recovery mechanism that may benefit species other than the one targeted for management.
The Migratory Bird Treaty Act (MBTA) is an agreement between the United States and Canada that was signed into law in 1918 in response to declines in North American bird species caused by hunting. The Act now lists over 800 protected species. It makes it illegal to disturb or kill the protected species or distribute their parts (much of the hunting of birds in the past was for their feathers).
The international response to global warming has been mixed. The Kyoto Protocol, an international agreement that came out of the United Nations Framework Convention on Climate Change that committed countries to reducing greenhouse gas emissions by 2012, was ratified by some countries, but spurned by others. Two important countries in terms of their potential impact that did not ratify the Kyoto Protocol were the United States and China. The United States rejected it as a result of a powerful fossil fuel industry and China because of a concern it would stifle the nation’s growth. Some goals for reduction in greenhouse gasses were met and exceeded by individual countries, but worldwide, the effort to limit greenhouse gas production is not succeeding. The intended replacement for the Kyoto Protocol has not materialized because governments cannot agree on timelines and benchmarks. Meanwhile, climate scientists predict the resulting costs to human societies and biodiversity will be high.
As already mentioned, the private non-profit sector plays a large role in the conservation effort both in North America and around the world. The approaches range from species-specific organizations to the broadly focused IUCN and TRAFFIC. The Nature Conservancy takes a novel approach. It purchases land and protects it in an attempt to set up preserves for ecosystems. Ultimately, human behavior will change when human values change. At present, the growing urbanization of the human population is a force that poses challenges to the valuing of biodiversity.
Conservation in Preserves
Establishment of wildlife and ecosystem preserves is one of the key tools in conservation efforts. A preserve is an area of land set aside with varying degrees of protection for the organisms that exist within the boundaries of the preserve. Preserves can be effective in the short term for protecting both species and ecosystems, but they face challenges that scientists are still exploring to strengthen their viability as long-term solutions.
How Much Area to Preserve?
Due to the way protected lands are allocated (they tend to contain less economically valuable resources rather than being set aside specifically for the species or ecosystems at risk) and the way biodiversity is distributed, determining a target percentage of land or marine habitat that should be protected to maintain biodiversity levels is challenging. The IUCN World Parks Congress estimated that 11.5 percent of Earth’s land surface was covered by preserves of various kinds in 2003. This area is greater than previous goals; however, it only represents 9 out of 14 recognized major biomes. Research has shown that 12 percent of all species live only outside preserves; these percentages are much higher when only threatened species and high quality preserves are considered. For example, high quality preserves include only about 50 percent of threatened amphibian species. The conclusion must be that either the percentage of area protected must increase, or the percentage of high quality preserves must increase, or preserves must be targeted with greater attention to biodiversity protection. Researchers argue that more attention to the latter solution is required.
Preserve Design
There has been extensive research into optimal preserve designs for maintaining biodiversity. The fundamental principle behind much of the research has been the seminal theoretical work of Robert H. MacArthur and Edward O. Wilson published in 1967 on island biogeography.1 This work sought to understand the factors affecting biodiversity on islands. The fundamental conclusion was that biodiversity on an island was a function of the origin of species through migration, speciation, and extinction on that island. Islands farther from a mainland are harder to get to, so migration is lower and the equilibrium number of species is lower. Within island populations, evidence suggests that the number of species gradually increases to a level similar to the numbers on the mainland from which the species is suspected to have migrated. In addition, smaller islands are harder to find, so their immigration rates for new species are lower. Smaller islands are also less geographically diverse so there are fewer niches to promote speciation. And finally, smaller islands support smaller populations, so the probability of extinction is higher.
As islands get larger, the number of species accelerates, although the effect of island area on species numbers is not a direct correlation. Conservation preserves can be seen as “islands” of habitat within “an ocean” of non-habitat. For a species to persist in a preserve, the preserve must be large enough. The critical size depends, in part, on the home range that is characteristic of the species. A preserve for wolves, which range hundreds of kilometers, must be much larger than a preserve for butterflies, which might range within ten kilometers during its lifetime. But larger preserves have more core area of optimal habitat for individual species, they have more niches to support more species, and they attract more species because they can be found and reached more easily.
Preserves perform better when there are buffer zones around them of suboptimal habitat. The buffer allows organisms to exit the boundaries of the preserve without immediate negative consequences from predation or lack of resources. One large preserve is better than the same area of several smaller preserves because there is more core habitat unaffected by edges. For this same reason, preserves in the shape of a square or circle will be better than a preserve with many thin “arms.” If preserves must be smaller, then providing wildlife corridors between them so that individuals and their genes can move between the preserves, for example along rivers and streams, will make the smaller preserves behave more like a large one. All of these factors are taken into consideration when planning the nature of a preserve before the land is set aside.
In addition to the physical, biological, and ecological specifications of a preserve, there are a variety of policy, legislative, and enforcement specifications related to uses of the preserve for functions other than protection of species. These can include anything from timber extraction, mineral extraction, regulated hunting, human habitation, and nondestructive human recreation. Many of these policy decisions are made based on political pressures rather than conservation considerations. In some cases, wildlife protection policies have been so strict that subsistence-living indigenous populations have been forced from ancestral lands that fell within a preserve. In other cases, even if a preserve is designed to protect wildlife, if the protections are not or cannot be enforced, the preserve status will have little meaning in the face of illegal poaching and timber extraction. This is a widespread problem with preserves in areas of the tropics.
Limitations on Preserves
Some of the limitations on preserves as conservation tools are evident from the discussion of preserve design. Political and economic pressures typically make preserves smaller, never larger, so setting aside areas that are large enough is difficult. If the area set aside is sufficiently large, there may not be sufficient area to create a buffer around the preserve. In this case, an area on the outer edges of the preserve inevitably becomes a riskier suboptimal habitat for the species in the preserve. Enforcement of protections is also a significant issue in countries without the resources or political will to prevent poaching and illegal resource extraction.
Climate change will create inevitable problems with the location of preserves. The species within them will migrate to higher latitudes as the habitat of the preserve becomes less favorable. Scientists are planning for the effects of global warming on future preserves and striving to predict the need for new preserves to accommodate anticipated changes to habitats; however, the end effectiveness is tenuous since these efforts are prediction based.
Finally, an argument can be made that conservation preserves reinforce the cultural perception that humans are separate from nature, can exist outside of it, and can only operate in ways that do damage to biodiversity. Creating preserves reduces the pressure on human activities outside the preserves to be sustainable and non-damaging to biodiversity. Ultimately, the political, economic, and human demographic pressures will degrade and reduce the size of conservation preserves if the activities outside them are not altered to be less damaging to biodiversity.
Link to Learning
An interactive global data system of protected areas can be found at website. Review data about individual protected areas by location or study statistics on protected areas by country or region.
Habitat Restoration
Habitat restoration holds considerable promise as a mechanism for restoring and maintaining biodiversity. Of course once a species has become extinct, its restoration is impossible. However, restoration can improve the biodiversity of degraded ecosystems. Reintroducing wolves, a top predator, to Yellowstone National Park in 1995 led to dramatic changes in the ecosystem that increased biodiversity. The wolves (Figure \(2\)) function to suppress elk and coyote populations and provide more abundant resources to the guild of carrion eaters. Reducing elk populations has allowed revegetation of riparian areas, which has increased the diversity of species in that habitat. Decreasing the coyote population has increased the populations of species that were previously suppressed by this predator. The number of species of carrion eaters has increased because of the predatory activities of the wolves. In this habitat, the wolf is a keystone species, meaning a species that is instrumental in maintaining diversity in an ecosystem. Removing a keystone species from an ecological community may cause a collapse in diversity. The results from the Yellowstone experiment suggest that restoring a keystone species can have the effect of restoring biodiversity in the community. Ecologists have argued for the identification of keystone species where possible and for focusing protection efforts on those species; likewise, it also makes sense to attempt to return them to their ecosystem if they have been removed.
Other large-scale restoration experiments underway involve dam removal. In the United States, since the mid-1980s, many aging dams are being considered for removal rather than replacement because of shifting beliefs about the ecological value of free-flowing rivers and because many dams no longer provide the benefit and functions that they did when they were first built. The measured benefits of dam removal include restoration of naturally fluctuating water levels (the purpose of dams is frequently to reduce variation in river flows), which leads to increased fish diversity and improved water quality. In the Pacific Northwest, dam removal projects are expected to increase populations of salmon, which is considered a keystone species because it transports key nutrients to inland ecosystems during its annual spawning migrations. In other regions such as the Atlantic coast, dam removal has allowed the return of spawning anadromous fish species (species that are born in fresh water, live most of their lives in salt water, and return to fresh water to spawn). Some of the largest dam removal projects have yet to occur or have happened too recently for the consequences to be measured. The large-scale ecological experiments that these removal projects constitute will provide valuable data for other dam projects slated either for removal or construction.
The Role of Captive Breeding
Zoos have sought to play a role in conservation efforts both through captive breeding programs and education. The transformation of the missions of zoos from collection and exhibition facilities to organizations that are dedicated to conservation is ongoing. In general, it has been recognized that, except in some specific targeted cases, captive breeding programs for endangered species are inefficient and often prone to failure when the species are reintroduced to the wild. Zoo facilities are far too limited to contemplate captive breeding programs for the numbers of species that are now at risk. Education is another potential positive impact of zoos on conservation efforts, particularly given the global trend to urbanization and the consequent reduction in contacts between people and wildlife. A number of studies have been performed to look at the effectiveness of zoos on people’s attitudes and actions regarding conservation; at present, the results tend to be mixed.
Summary
New technological methods such as DNA barcoding and information processing and accessibility are facilitating the cataloging of the planet’s biodiversity. There is also a legislative framework for biodiversity protection. International treaties such as CITES regulate the transportation of endangered species across international borders. Legislation within individual countries protecting species and agreements on global warming have had limited success; there is at present no international agreement on targets for greenhouse gas emissions. In the United States, the Endangered Species Act protects listed species but is hampered by procedural difficulties and a focus on individual species. The Migratory Bird Act is an agreement between Canada and the United States to protect migratory birds. The non-profit sector is also very active in conservation efforts in a variety of ways.
Conservation preserves are a major tool in biodiversity protection. Presently, 11 percent of Earth’s land surface is protected in some way. The science of island biogeography has informed the optimal design of preserves; however, preserves have limitations imposed by political and economic forces. In addition, climate change will limit the effectiveness of preserves in the future. A downside of preserves is that they may lessen the pressure on human societies to function more sustainably outside the preserves.
Habitat restoration has the potential to restore ecosystems to previous biodiversity levels before species become extinct. Examples of restoration include reintroduction of keystone species and removal of dams on rivers. Zoos have attempted to take a more active role in conservation and can have a limited role in captive breeding programs. Zoos also may have a useful role in education.
Art Connections
Figure \(1\): Which of the following statements is not supported by this graph?
1. There are more vulnerable fishes than critically endangered and endangered fishes combined.
2. There are more critically endangered amphibians than vulnerable, endangered and critically endangered reptiles combined.
3. Within each group, there are more critically endangered species than vulnerable species.
4. A greater percentage of bird species are critically endangered than mollusk species.
Answer
C
Footnotes
1. 1 Robert H. MacArthur and Edward O. Wilson, E. O., The Theory of Island Biogeography (Princeton, N.J.: Princeton University Press, 1967).
Glossary
DNA barcoding
molecular genetic method for identifying a unique genetic sequence to associate with a species | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/8%3A_Ecology/47%3A_Conservation_Biology_and_Biodiversity/47.4%3A_Preserving_Biodiversity.txt |
47.1: The Biodiversity Crisis
Review Questions
With an extinction rate of 100 E/MSY and an estimated 10 million species, how many extinctions are expected to occur in a century?
1. 100
2. 10, 000
3. 100, 000
4. 1, 000, 000
Answer
C
An adaptive radiation is________.
1. a burst of speciation
2. a healthy level of UV radiation
3. a hypothesized cause of a mass extinction
4. evidence of an asteroid impact
Answer
A
The number of currently described species on the planet is about ________.
1. 17,000
2. 150,000
3. 1.5 million
4. 10 million
Answer
C
A mass extinction is defined as ________.
1. a loss of 95 percent of species
2. an asteroid impact
3. a boundary between geological periods
4. a loss of 50 percent of species
Answer
D
Free Response
Describe the evidence for the cause of the Cretaceous–Paleogene (K–Pg) mass extinction.
Answer
The hypothesized cause of the K–Pg extinction event is an asteroid impact. The first piece of evidence of the impact is a spike in iridium (an element that is rare on Earth, but common in meteors) in the geological layers that mark the K–Pg transition. The second piece of evidence is an impact crater off the Yucatán Peninsula that is the right size and age to have caused the extinction event.
Describe the two methods used to calculate contemporary extinction rates.
Answer
Extinction rates are calculated based on the recorded extinction of species in the past 500 years. Adjustments are made for unobserved extinctions and undiscovered species. The second method is a calculation based on the amount of habitat destruction and species-area curves.
47.2: The Importance of Biodiversity to Human Life
Review Questions
A secondary plant compound might be used for which of the following?
1. a new crop variety
2. a new drug
3. a soil nutrient
4. a pest of a crop pest
Answer
B
Pollination is an example of ________.
1. a possible source of new drugs
2. chemical diversity
3. an ecosystem service
4. crop pest control
Answer
C
What is an ecosystem service that performs the same function as a pesticide?
1. pollination
2. secondary plant compounds
3. crop diversity
4. predators of pests
Answer
D
Free Response
Explain how biodiversity loss can impact crop diversity.
Answer
Crop plants are derived from wild plants, and genes from wild relatives are frequently brought into crop varieties by plant breeders to add valued characteristics to the crops. If the wild species are lost, then this genetic variation would no longer be available.
Describe two types of compounds from living things that are used as medications.
Answer
Secondary plant compounds are toxins produced by plants to kill predators trying to eat them; some of these compounds can be used as drugs. Animal toxins such as snake venom can also be used as drugs. (Alternate answer: antibiotics are compounds produced by bacteria and fungi which can be used to kill bacteria.)
47.3: Threats to Biodiversity
Review Questions
Which two extinction risks may be a direct result of the pet trade?
1. climate change and exotic species introduction
2. habitat loss and overharvesting
3. overharvesting and exotic species introduction
4. habitat loss and climate change
Answer
C
Exotic species are especially threatening to what kind of ecosystem?
1. deserts
2. marine ecosystems
3. islands
4. tropical forests
Answer
C
Free Response
Describe the mechanisms by which human population growth and resource use causes increased extinction rates.
Answer
Human population growth leads to unsustainable resource use, which causes habitat destruction to build new human settlements, create agricultural fields, and so on. Larger human populations have also led to unsustainable fishing and hunting of wild animal populations. Excessive use of fossil fuels also leads to global warming.
Explain what extinction threats a frog living on a mountainside in Costa Rica might face.
Answer
The frog is at risk from global warming shifting its preferred habitat up the mountain. In addition, it will be at risk from exotic species, either as a new predator or through the impact of transmitted diseases such as chytridiomycosis. It is also possible that habitat destruction will threaten the species.
47.4: Preserving Biodiversity
Review Questions
Certain parrot species cannot be brought to the United States to be sold as pets. What is the name of the legislation that makes this illegal?
1. Red List
2. Migratory Bird Act
3. CITES
4. Endangered Species Act (ESA)
Answer
C
What was the name of the first international agreement on climate change?
1. Red List
2. Montreal Protocol
3. International Union for the Conservation of Nature (IUCN)
4. Kyoto Protocol
Answer
D
About what percentage of land on the planet is set aside as a preserve of some type?
1. 1 percent
2. 6 percent
3. 11 percent
4. 15 percent
Answer
C
Free Response
Describe two considerations in conservation preserve design.
Answer
Larger preserves will contain more species. Preserves should have a buffer around them to protect species from edge effects. Preserves that are round or square are better than preserves with many thin arms.
Describe what happens to an ecosystem when a keystone species is removed.
Answer
When a keystone species is removed many species will disappear from the ecosystem. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/8%3A_Ecology/47%3A_Conservation_Biology_and_Biodiversity/47.E%3A_Conservation_Biology_and_Biodiversity_%28Exercises%29.txt |
Our opening unit introduces students to the sciences, including the scientific method and the fundamental concepts of chemistry and physics that provide a framework within which learners comprehend biological processes.
• 1.1: The Study of Life
• 1.2: The Chemical Foundation of Life
Elements in various combinations comprise all matter, including living things. Some of the most abundant elements in living organisms include carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. These form the nucleic acids, proteins, carbohydrates, and lipids that are the fundamental components of living matter. Biologists must understand these important building blocks and the unique structures of the atoms that make up molecules, allowing for the formation of life.
• 1.3: Biological Macromolecules
Food provides the body with the nutrients it needs to survive. Many of these critical nutrients are biological macromolecules, or large molecules, necessary for life. These macromolecules (polymers) are built from different combinations of smaller organic molecules (monomers). What specific types of biological macromolecules do living things require? How are these molecules formed? What functions do they serve? In this chapter, these questions will be explored.
Thumbnail: A cluster of Escherichia coli bacteria magnified 10,000 times. (Public Domain; Eric Erbe, digital colorization by Christopher Pooley, both of USDA, ARS, EMU).
Contributors
Connie Rye (East Mississippi Community College), Robert Wise (University of Wisconsin, Oshkosh), Vladimir Jurukovski (Suffolk County Community College), Jean DeSaix (University of North Carolina at Chapel Hill), Jung Choi (Georgia Institute of Technology), Yael Avissar (Rhode Island College) among other contributing authors. Original content by OpenStax (CC BY 4.0; Download for free at http://cnx.org/contents/[email protected]).
01: Unit I- The Chemistry of Life
• 1.1.1: Introduction
The first forms of life on Earth are thought to have been microorganisms that existed for billions of years in the ocean before plants and animals appeared. The mammals, birds, and flowers so familiar to us are all relatively recent, originating 130 to 200 million years ago. Humans have inhabited this planet for only the last 2.5 million years, and only in the last 200,000 years have humans started looking like we do today.
• 1.1.2: The Science of Biology
In simple terms, biology is the study of living organisms and their interactions with one another and their environments. This is a very broad definition because the scope of biology is vast. Biologists may study anything from the microscopic or submicroscopic view of a cell to ecosystems and the whole living planet.
• 1.1.3: Themes and Concepts of Biology
From its earliest beginnings, biology has wrestled with three questions: What are the shared properties that make something “alive”? And once we know something is alive, how do we find meaningful levels of organization in its structure? And, finally, when faced with the remarkable diversity of life, how do we organize the different kinds of organisms so that we can better understand them? As new organisms are discovered every day, biologists continue to seek answers to these and other questions.
• 1.1.4: Key Terms
• 1.1.5: Chapter Summary
• 1.1.6: Visual Connection Questions
• 1.1.7: Review Questions
• 1.1.8: Critical Thinking Questions
Thumbnail: A cluster of Escherichia coli bacteria magnified 10,000 times. (Public Domain; Eric Erbe, digital colorization by Christopher Pooley, both of USDA, ARS, EMU).
1.01: The Study of Life
Viewed from space, Earth offers no clues about the diversity of life forms that reside there. Scientists believe that the first forms of life on Earth were microorganisms that existed for billions of years in the ocean before plants and animals appeared. The mammals, birds, and flowers so familiar to us are all relatively recent, originating 130 to 250 million years ago. The earliest representatives of the genus Homo, to which we belong, have inhabited this planet for only the last 2.5 million years, and only in the last 300,000 years have humans started looking like we do today.
Figure 1.1 This NASA image is a composite of several satellite-based views of Earth. To make the whole-Earth image, NASA scientists combine observations of different parts of the planet. (credit: NASA/GSFC/NOAA/USGS) | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/01%3A_Unit_I-_The_Chemistry_of_Life/1.01%3A_The_Study_of_Life/1.1.01%3A_Introduction.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Identify the shared characteristics of the natural sciences
• Summarize the steps of the scientific method
• Compare inductive reasoning with deductive reasoning
• Describe the goals of basic science and applied science
Figure 1.2 Formerly called blue-green algae, these (a) cyanobacteria, magnified 300x under a light microscope, are some of Earth’s oldest life forms. These (b) stromatolites along the shores of Lake Thetis in Western Australia are ancient structures formed by layering cyanobacteria in shallow waters. (credit a: modification of work by NASA; credit b: modification of work by Ruth Ellison; scale-bar data from Matt Russell)
What is biology? In simple terms, biology is the study of life. This is a very broad definition because the scope of biology is vast. Biologists may study anything from the microscopic or submicroscopic view of a cell to ecosystems and the whole living planet (Figure 1.2). Listening to the daily news, you will quickly realize how many aspects of biology we discuss every day. For example, recent news topics include Escherichia coli (Figure 1.3) outbreaks in spinach and Salmonella contamination in peanut butter. Other subjects include efforts toward finding a cure for AIDS, Alzheimer’s disease, and cancer. On a global scale, many researchers are committed to finding ways to protect the planet, solve environmental issues, and reduce the effects of climate change. All of these diverse endeavors are related to different facets of the discipline of biology.
Figure 1.3 Escherichia coli (E. coli) bacteria, in this scanning electron micrograph, are normal residents of our digestive tracts that aid in absorbing vitamin K and other nutrients. However, virulent strains are sometimes responsible for disease outbreaks. (credit: Eric Erbe, digital colorization by Christopher Pooley, both of USDA, ARS, EMU)
The Process of Science
Biology is a science, but what exactly is science? What does the study of biology share with other scientific disciplines? We can define science (from the Latin scientia, meaning “knowledge”) as knowledge that covers general truths or the operation of general laws, especially when acquired and tested by the scientific method. It becomes clear from this definition that applying scientific method plays a major role in science. The scientific method is a method of research with defined steps that include experiments and careful observation.
We will examine scientific method steps in detail later, but one of the most important aspects of this method is the testing of hypotheses by means of repeatable experiments. A hypothesis is a suggested explanation for an event, which one can test. Although using the scientific method is inherent to science, it is inadequate in determining what science is. This is because it is relatively easy to apply the scientific method to disciplines such as physics and chemistry, but when it comes to disciplines like archaeology, psychology, and geology, the scientific method becomes less applicable as repeating experiments becomes more difficult.
These areas of study are still sciences, however. Consider archaeology—even though one cannot perform repeatable experiments, hypotheses may still be supported. For instance, archaeologists can hypothesize that an ancient culture existed based on finding a piece of pottery. They could make further hypotheses about various characteristics of this culture, which could be correct or false through continued support or contradictions from other findings. A hypothesis may become a verified theory. A theory is a tested and confirmed explanation for observations or phenomena. Therefore, we may be better off to define science as fields of study that attempt to comprehend the nature of the universe.
Natural Sciences
What would you expect to see in a museum of natural sciences? Frogs? Plants? Dinosaur skeletons? Exhibits about how the brain functions? A planetarium? Gems and minerals? Maybe all of the above? Science includes such diverse fields as astronomy, biology, computer sciences, geology, logic, physics, chemistry, and mathematics (Figure 1.4). However, scientists consider those fields of science related to the physical world and its phenomena and processes natural sciences. Thus, a museum of natural sciences might contain any of the items listed above.
Figure 1.4 The diversity of scientific fields includes astronomy, biology, computer science, geology, logic, physics, chemistry, mathematics, and many other fields. (credit: “Image Editor”/Flickr)
There is no complete agreement when it comes to defining what the natural sciences include, however. For some experts, the natural sciences are astronomy, biology, chemistry, earth science, and physics. Other scholars choose to divide natural sciences into life sciences, which study living things and include biology, and physical sciences, which study nonliving matter and include astronomy, geology, physics, and chemistry. Some disciplines such as biophysics and biochemistry build on both life and physical sciences and are interdisciplinary. Some refer to natural sciences as “hard science” because they rely on the use of quantitative data. Social sciences that study society and human behavior are more likely to use qualitative assessments to drive investigations and findings.
Not surprisingly, the natural science of biology has many branches or subdisciplines. Cell biologists study cell structure and function, while biologists who study anatomy investigate the structure of an entire organism. Those biologists studying physiology, however, focus on the internal functioning of an organism. Some areas of biology focus on only particular types of living things. For example, botanists explore plants, while zoologists specialize in animals.
Scientific Reasoning
One thing is common to all forms of science: an ultimate goal “to know.” Curiosity and inquiry are the driving forces for the development of science. Scientists seek to understand the world and the way it operates. To do this, they use two methods of logical thinking: inductive reasoning and deductive reasoning.
Inductive reasoning is a form of logical thinking that uses related observations to arrive at a general conclusion. This type of reasoning is common in descriptive science. A life scientist such as a biologist makes observations and records them. These data can be qualitative or quantitative, and one can supplement the raw data with drawings, pictures, photos, or videos. From many observations, the scientist can infer conclusions (inductions) based on evidence. Inductive reasoning involves formulating generalizations inferred from careful observation and analyzing a large amount of data. Brain studies provide an example. In this type of research, scientists observe many live brains while people are engaged in a specific activity, such as viewing images of food. The scientist then predicts the part of the brain that “lights up” during this activity to be the part controlling the response to the selected stimulus, in this case, images of food. Excess absorption of radioactive sugar derivatives by active areas of the brain causes the various areas to "light up". Scientists use a scanner to observe the resultant increase in radioactivity. Then, researchers can stimulate that part of the brain to see if similar responses result.
Deductive reasoning or deduction is the type of logic used in hypothesis-based science. In deductive reasoning, the pattern of thinking moves in the opposite direction as compared to inductive reasoning. Deductive reasoning is a form of logical thinking that uses a general principle or law to predict specific results. From those general principles, a scientist can deduce and predict the specific results that would be valid as long as the general principles are valid. Studies in climate change can illustrate this type of reasoning. For example, scientists may predict that if the climate becomes warmer in a particular region, then the distribution of plants and animals should change.
Both types of logical thinking are related to the two main pathways of scientific study: descriptive science and hypothesis-based science. Descriptive (or discovery) science, which is usually inductive, aims to observe, explore, and discover, while hypothesis-based science, which is usually deductive, begins with a specific question or problem and a potential answer or solution that one can test. The boundary between these two forms of study is often blurred, and most scientific endeavors combine both approaches. The fuzzy boundary becomes apparent when thinking about how easily observation can lead to specific questions. For example, a gentleman in the 1940s observed that the burr seeds that stuck to his clothes and his dog’s fur had a tiny hook structure. On closer inspection, he discovered that the burrs’ gripping device was more reliable than a zipper. He eventually experimented to find the best material that acted similarly, and produced the hook-and-loop fastener popularly known today as Velcro. Descriptive science and hypothesis-based science are in continuous dialogue.
The Scientific Method
Biologists study the living world by posing questions about it and seeking science-based responses. Known as scientific method, this approach is common to other sciences as well. The scientific method was used even in ancient times, but England’s Sir Francis Bacon (1561–1626) first documented it (Figure 1.5). He set up inductive methods for scientific inquiry. The scientific method is not used only by biologists; researchers from almost all fields of study can apply it as a logical, rational problem-solving method.
Figure 1.5 Historians credit Sir Francis Bacon (1561–1626) as the first to define the scientific method. (credit: Paul van Somer)
The scientific process typically starts with an observation (often a problem to solve) that leads to a question. Let’s think about a simple problem that starts with an observation and apply the scientific method to solve the problem. One Monday morning, a student arrives at class and quickly discovers that the classroom is too warm. That is an observation that also describes a problem: the classroom is too warm. The student then asks a question: “Why is the classroom so warm?”
Proposing a Hypothesis
Recall that a hypothesis is a suggested explanation that one can test. To solve a problem, one can propose several hypotheses. For example, one hypothesis might be, “The classroom is warm because no one turned on the air conditioning.” However, there could be other responses to the question, and therefore one may propose other hypotheses. A second hypothesis might be, “The classroom is warm because there is a power failure, and so the air conditioning doesn’t work.”
Once one has selected a hypothesis, the student can make a prediction. A prediction is similar to a hypothesis but it typically has the format “If . . . then . . . .” For example, the prediction for the first hypothesis might be, “If the student turns on the air conditioning, then the classroom will no longer be too warm.”
Testing a Hypothesis
A valid hypothesis must be testable. It should also be falsifiable, meaning that experimental results can disprove it. Importantly, science does not claim to “prove” anything because scientific understandings are always subject to modification with further information. This step—openness to disproving ideas—is what distinguishes sciences from non-sciences. The presence of the supernatural, for instance, is neither testable nor falsifiable. To test a hypothesis, a researcher will conduct one or more experiments designed to eliminate one or more of the hypotheses. Each experiment will have one or more variables and one or more controls. A variable is any part of the experiment that can vary or change during the experiment. The control group contains every feature of the experimental group except it is not given the manipulation that the researcher hypothesizes. Therefore, if the experimental group's results differ from the control group, the difference must be due to the hypothesized manipulation, rather than some outside factor. Look for the variables and controls in the examples that follow. To test the first hypothesis, the student would find out if the air conditioning is on. If the air conditioning is turned on but does not work, there should be another reason, and the student should reject this hypothesis. To test the second hypothesis, the student could check if the lights in the classroom are functional. If so, there is no power failure and the student should reject this hypothesis. The students should test each hypothesis by carrying out appropriate experiments. Be aware that rejecting one hypothesis does not determine whether or not one can accept the other hypotheses. It simply eliminates one hypothesis that is not valid (Figure 1.6). Using the scientific method, the student rejects the hypotheses that are inconsistent with experimental data.
While this “warm classroom” example is based on observational results, other hypotheses and experiments might have clearer controls. For instance, a student might attend class on Monday and realize she had difficulty concentrating on the lecture. One observation to explain this occurrence might be, “When I eat breakfast before class, I am better able to pay attention.” The student could then design an experiment with a control to test this hypothesis.
In hypothesis-based science, researchers predict specific results from a general premise. We call this type of reasoning deductive reasoning: deduction proceeds from the general to the particular. However, the reverse of the process is also possible: sometimes, scientists reach a general conclusion from a number of specific observations. We call this type of reasoning inductive reasoning, and it proceeds from the particular to the general. Researchers often use inductive and deductive reasoning in tandem to advance scientific knowledge (Figure 1.7). In recent years a new approach of testing hypotheses has developed as a result of an exponential growth of data deposited in various databases. Using computer algorithms and statistical analyses of data in databases, a new field of so-called "data research" (also referred to as "in silico" research) provides new methods of data analyses and their interpretation. This will increase the demand for specialists in both biology and computer science, a promising career opportunity.
Visual Connection
Visual Connection
Figure 1.6 The scientific method consists of a series of well-defined steps. If a hypothesis is not supported by experimental data, one can propose a new hypothesis.
In the example below, the scientific method is used to solve an everyday problem. Match the scientific method steps (numbered items) with the process of solving the everyday problem (lettered items). Based on the results of the experiment, is the hypothesis correct? If it is incorrect, propose some alternative hypotheses.
1. Observation a. There is something wrong with the electrical outlet.
2. Question b. If something is wrong with the outlet, my coffeemaker also won’t work when plugged into it.
3. Hypothesis (answer) c. My toaster doesn’t toast my bread.
4. Prediction d. I plug my coffee maker into the outlet.
5. Experiment e. My coffeemaker works.
6. Result f. Why doesn’t my toaster work?
Visual Connection
Visual Connection
Figure 1.7 Scientists use two types of reasoning, inductive and deductive reasoning, to advance scientific knowledge. As is the case in this example, the conclusion from inductive reasoning can often become the premise for deductive reasoning.
Decide if each of the following is an example of inductive or deductive reasoning.
1. All flying birds and insects have wings. Birds and insects flap their wings as they move through the air. Therefore, wings enable flight.
2. Insects generally survive mild winters better than harsh ones. Therefore, insect pests will become more problematic if global temperatures increase.
3. Chromosomes, the carriers of DNA, are distributed evenly between the daughter cells during cell division. Therefore, each daughter cell will have the same chromosome set as the mother cell.
4. Animals as diverse as humans, insects, and wolves all exhibit social behavior. Therefore, social behavior must have an evolutionary advantage.
The scientific method may seem too rigid and structured. It is important to keep in mind that, although scientists often follow this sequence, there is flexibility. Sometimes an experiment leads to conclusions that favor a change in approach. Often, an experiment brings entirely new scientific questions to the puzzle. Many times, science does not operate in a linear fashion. Instead, scientists continually draw inferences and make generalizations, finding patterns as their research proceeds. Scientific reasoning is more complex than the scientific method alone suggests. Notice, too, that we can apply the scientific method to solving problems that aren’t necessarily scientific in nature.
Two Types of Science: Basic Science and Applied Science
The scientific community has been debating for the last few decades about the value of different types of science. Is it valuable to pursue science for the sake of simply gaining knowledge, or does scientific knowledge only have worth if we can apply it to solving a specific problem or to bettering our lives? This question focuses on the differences between two types of science: basic science and applied science.
Basic science or “pure” science seeks to expand knowledge regardless of the short-term application of that knowledge. It is not focused on developing a product or a service of immediate public or commercial value. The immediate goal of basic science is knowledge for knowledge’s sake, although this does not mean that, in the end, it may not result in a practical application.
In contrast, applied science or “technology,” aims to use science to solve real-world problems, making it possible, for example, to improve a crop yield, find a cure for a particular disease, or save animals threatened by a natural disaster (Figure 1.8). In applied science, the problem is usually defined for the researcher.
Figure 1.8 After Hurricane Irma struck the Caribbean and Florida in 2017, thousands of baby squirrels like this one were thrown from their nests. Thanks to applied science, scientists knew how to rehabilitate the squirrel. (credit: audreyjm529, Flickr)
Some individuals may perceive applied science as “useful” and basic science as “useless.” A question these people might pose to a scientist advocating knowledge acquisition would be, “What for?” However, a careful look at the history of science reveals that basic knowledge has resulted in many remarkable applications of great value. Many scientists think that a basic understanding of science is necessary before researchers develop an application, therefore, applied science relies on the results that researchers generate through basic science. Other scientists think that it is time to move on from basic science in order to find solutions to actual problems. Both approaches are valid. It is true that there are problems that demand immediate attention; however, scientists would find few solutions without the help of the wide knowledge foundation that basic science generates.
One example of how basic and applied science can work together to solve practical problems occurred after the discovery of DNA structure led to an understanding of the molecular mechanisms governing DNA replication. DNA strands, unique in every human, are in our cells, where they provide the instructions necessary for life. When DNA replicates, it produces new copies of itself, shortly before a cell divides. Understanding DNA replication mechanisms enabled scientists to develop laboratory techniques that researchers now use to identify genetic diseases, pinpoint individuals who were at a crime scene, and determine paternity. Without basic science, it is unlikely that applied science could exist.
Another example of the link between basic and applied research is the Human Genome Project, a study in which researchers analyzed and mapped each human chromosome to determine the precise sequence of DNA subunits and each gene's exact location. (The gene is the basic unit of heredity represented by a specific DNA segment that codes for a functional molecule. An individual’s complete collection of genes is their genome.) Researchers have studied other less complex organisms as part of this project in order to gain a better understanding of human chromosomes. The Human Genome Project (Figure 1.9) relied on basic research with simple organisms and, later, with the human genome. An important end goal eventually became using the data for applied research, seeking cures and early diagnoses for genetically related diseases.
Figure 1.9 The Human Genome Project was a 13-year collaborative effort among researchers working in several different science fields. Researchers completed the project, which sequenced the entire human genome, in 2003. (credit: the U.S. Department of Energy Genome Programs (http://genomics.energy.gov)
While scientists usually carefully plan research efforts in both basic science and applied science, note that some discoveries are made by serendipity, that is, by means of a fortunate accident or a lucky surprise. Scottish biologist Alexander Fleming discovered penicillin when he accidentally left a petri dish of Staphylococcus bacteria open. An unwanted mold grew on the dish, killing the bacteria. Fleming's curiosity to investigate the reason behind the bacterial death, followed by his experiments, led to the discovery of the antibiotic penicillin, which is produced by the fungus Penicillium. Even in the highly organized world of science, luck—when combined with an observant, curious mind—can lead to unexpected breakthroughs.
Reporting Scientific Work
Whether scientific research is basic science or applied science, scientists must share their findings in order for other researchers to expand and build upon their discoveries. Collaboration with other scientists—when planning, conducting, and analyzing results—is important for scientific research. For this reason, important aspects of a scientist’s work are communicating with peers and disseminating results to peers. Scientists can share results by presenting them at a scientific meeting or conference, but this approach can reach only the select few who are present. Instead, most scientists present their results in peer-reviewed manuscripts that are published in scientific journals. Peer-reviewed manuscripts are scientific papers that a scientist’s colleagues or peers review. These colleagues are qualified individuals, often experts in the same research area, who judge whether or not the scientist’s work is suitable for publication. The process of peer review helps to ensure that the research in a scientific paper or grant proposal is original, significant, logical, and thorough. Grant proposals, which are requests for research funding, are also subject to peer review. Scientists publish their work so other scientists can reproduce their experiments under similar or different conditions to expand on the findings.
A scientific paper is very different from creative writing. Although creativity is required to design experiments, there are fixed guidelines when it comes to presenting scientific results. First, scientific writing must be brief, concise, and accurate. A scientific paper needs to be succinct but detailed enough to allow peers to reproduce the experiments.
The scientific paper consists of several specific sections—introduction, materials and methods, results, and discussion. This structure is sometimes called the “IMRaD” format. There are usually acknowledgment and reference sections as well as an abstract (a concise summary) at the beginning of the paper. There might be additional sections depending on the type of paper and the journal where it will be published. For example, some review papers require an outline.
The introduction starts with brief, but broad, background information about what is known in the field. A good introduction also gives the rationale of the work. It justifies the work carried out and also briefly mentions the end of the paper, where the researcher will present the hypothesis or research question driving the research. The introduction refers to the published scientific work of others and therefore requires citations following the style of the journal. Using the work or ideas of others without proper citation is plagiarism.
The materials and methods section includes a complete and accurate description of the substances the researchers use, and the method and techniques they use to gather data. The description should be thorough enough to allow another researcher to repeat the experiment and obtain similar results, but it does not have to be verbose. This section will also include information on how the researchers made measurements and the types of calculations and statistical analyses they used to examine raw data. Although the materials and methods section gives an accurate description of the experiments, it does not discuss them.
Some journals require a results section followed by a discussion section, but it is more common to combine both. If the journal does not allow combining both sections, the results section simply narrates the findings without any further interpretation. The researchers present results with tables or graphs, but they do not present duplicate information. In the discussion section, the researchers will interpret the results, describe how variables may be related, and attempt to explain the observations. It is indispensable to conduct an extensive literature search to put the results in the context of previously published scientific research. Therefore, researchers include proper citations in this section as well.
Finally, the conclusion section summarizes the importance of the experimental findings. While the scientific paper almost certainly answers one or more scientific questions that the researchers stated, any good research should lead to more questions. Therefore, a well-done scientific paper allows the researchers and others to continue and expand on the findings.
Review articles do not follow the IMRAD format because they do not present original scientific findings, or primary literature. Instead, they summarize and comment on findings that were published as primary literature and typically include extensive reference sections.
Scientific Ethics
Scientists must ensure that their efforts do not cause undue damage to humans, animals, or the environment. They also must ensure that their research and communications are free of bias and that they properly balance financial, legal, safety, replicability, and other considerations. All scientists -- and many people in other fields -- have these ethical obligations, but those in the life sciences have a particular obligation because their research may involve people or other living things. Bioethics is thus an important and continually evolving field, in which researchers collaborate with other thinkers and organizations. They work to define guidelines for current practice, and also continually consider new developments and emerging technologies in order to form answers for the years and decades to come.
For example, bioethicists may examine the implications of gene editing technologies, including the ability to create organisms that may displace others in the environment, as well as the ability to “design” human beings. In that effort, ethicists will likely seek to balance the positive outcomes -- such as improved therapies or prevention of certain illnesses -- with negative outcomes.
Unfortunately, the emergence of bioethics as a field came after a number of clearly unethical practices, where biologists did not treat research subjects with dignity and in some cases did them harm. In the 1932 Tuskegee syphilis study, 399 African American men were diagnosed with syphilis but were never informed that they had the disease, leaving them to live with and pass on the illness to others. Doctors even withheld proven medications because the goal of the study was to understand the impact of untreated syphilis on Black men.
While the decisions made in the Tuskegee study are unjustifiable, some decisions are genuinely difficult to make. Bioethicists work to establish moral and dignifying approaches before such decisions come to pass. For example, doctors rely on artificial intelligence and robotics for medical diagnosis and treatment; in the near future, even more responsibility will lie with machines. Who will be responsible for medical decisions? Who will explain to families if a procedure doesn’t go as planned? And, since such treatments will likely be expensive, who will decide who has access to them and who does not? These are all questions bioethicists seek to answer, and are the types of considerations that all scientific researchers take into account when designing and conducting studies.
Bioethics are not simple, and often leave scientists balancing benefits with harm. In this text and course, you will discuss medical discoveries, vaccines, and research that, at their core, have an ethical complexity or, in the view of many, an ethical lapse. In 1951, Henrietta Lacks, a 30-year-old African American woman, was diagnosed with cervical cancer at Johns Hopkins Hospital. Unique characteristics of her illnesses gave her cells the ability to divide continuously, essentially making them “immortal.” Without her knowledge or permission, researchers took samples of her cells and with them created the immortal HeLa cell line. These cells have contributed to major medical discoveries, including the polio vaccine. Many researchers mentioned in subsequent sections of the text relied on HeLa cell research as at least a component of their work related to cancer, AIDS, cell aging, and even very recently in COVID-19 research.
Today, harvesting tissue or organs from a dying patient without consent is not only considered unethical but illegal, regardless of whether such an act could save other patients’ lives. Is it ethical, then, for scientists to continue to use Lacks’s tissues for research, even though they were obtained illegally by today’s standards? Should Lacks be mentioned as a contributor to the research based on her cells, and should she be cited in the several Nobel Prizes that have been awarded through such work? Finally, should medical companies be obligated to pay Lacks’ family (which had financial difficulties) a portion of the billions of dollars in revenue earned through medicines that benefited from HeLa cell research? How would Henrietta Lacks feel about this? Because she was never asked, we will never know.
To avoid such situations, the role of ethics in scientific research is to ask such questions before, during, and after research or practice takes place, as well as to adhere to established professional principles and consider the dignity and safety of all organisms involved or affected by the work. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/01%3A_Unit_I-_The_Chemistry_of_Life/1.01%3A_The_Study_of_Life/1.1.02%3A_The_Science_of_Biology.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Identify and describe the properties of life
• Describe the levels of organization among living things
• Recognize and interpret a phylogenetic tree
• List examples of different subdisciplines in biology
Biology is the science that studies life, but what exactly is life? This may sound like a silly question with an obvious response, but it is not always easy to define life. For example, a branch of biology called virology studies viruses, which exhibit some of the characteristics of living entities but lack others. Although viruses can attack living organisms, cause diseases, and even reproduce, they do not meet the criteria that biologists use to define life. Consequently, virologists are not biologists, strictly speaking. Similarly, some biologists study the early molecular evolution that gave rise to life. Since the events that preceded life are not biological events, these scientists are also excluded from biology in the strict sense of the term.
From its earliest beginnings, biology has wrestled with three questions: What are the shared properties that make something “alive”? Once we know something is alive, how do we find meaningful levels of organization in its structure? Finally, when faced with the remarkable diversity of life, how do we organize the different kinds of organisms so that we can better understand them? As scientists discover new organisms every day, biologists continue to seek answers to these and other questions.
Properties of Life
All living organisms share several key characteristics or functions: order, sensitivity or response to the environment, reproduction, adaptation, growth and development, regulation/homeostasis, energy processing, and evolution. When viewed together, these eight characteristics serve to define life.
Order
Figure 1.10 A toad represents a highly organized structure consisting of cells, tissues, organs, and organ systems. (credit: “Ivengo”/Wikimedia Commons)
Organisms are highly organized, coordinated structures that consist of one or more cells. Even very simple, single-celled organisms are remarkably complex: inside each cell, atoms comprise molecules. These in turn comprise cell organelles and other cellular inclusions. In multicellular organisms (Figure 1.10), similar cells form tissues. Tissues, in turn, collaborate to create organs (body structures with a distinct function). Organs work together to form organ systems.
Sensitivity or Response to Stimuli
Figure 1.11 The leaves of this sensitive plant (Mimosa pudica) will instantly droop and fold when touched. After a few minutes, the plant returns to normal. (credit: Alex Lomas)
Organisms respond to diverse stimuli. For example, plants can bend toward a source of light, climb on fences and walls, or respond to touch (Figure 1.11). Even tiny bacteria can move toward or away from chemicals (a process called chemotaxis) or light (phototaxis). Movement toward a stimulus is a positive response, while movement away from a stimulus is a negative response.
Link to Learning
Link to Learning
Watch this video to see how plants respond to a stimulus—from opening to light, to wrapping a tendril around a branch, to capturing prey.
Reproduction
Single-celled organisms reproduce by first duplicating their DNA, and then dividing it equally as the cell prepares to divide to form two new cells. Multicellular organisms often produce specialized reproductive cells—gametes and oocyte and sperm cells. After fertilization (the fusion of an oocyte and a sperm cell), a new individual develops. When reproduction occurs, DNA containing genes are passed along to an organism’s offspring. These genes ensure that the offspring will belong to the same species and will have similar characteristics, such as size and shape.
Adaptation
All living organisms exhibit a “fit” to their environment. Biologists refer to this fit as adaptation, and it is a consequence of evolution by natural selection, which operates in every lineage of reproducing organisms. Examples of adaptations are diverse and unique, from heat-resistant Archaea that live in boiling hotsprings to the tongue length of a nectar-feeding moth that matches the size of the flower from which it feeds. Adaptations enhance the reproductive potential of the individuals exhibiting them, including their ability to survive to reproduce. Adaptations are not constant. As an environment changes, natural selection causes the characteristics of the individuals in a population to track those changes.
Growth and Development
Organisms grow and develop as a result of genes providing specific instructions that will direct cellular growth and development. This ensures that a species’ young (Figure 1.12) will grow up to exhibit many of the same characteristics as its parents.
Figure 1.12 Although no two look alike, these kittens have inherited genes from both parents and share many of the same characteristics. (credit: Rocky Mountain Feline Rescue)
Regulation/Homeostasis
Even the smallest organisms are complex and require multiple regulatory mechanisms to coordinate internal functions, respond to stimuli, and cope with environmental stresses. Homeostasis (literally, “steady state”) refers to the relatively stable internal environment required to maintain life. Two examples of internal functions regulated in an organism are nutrient transport and blood flow. Organs (groups of tissues working together) perform specific functions, such as carrying oxygen throughout the body, removing wastes, delivering nutrients to every cell, and cooling the body.
Figure 1.13 Polar bears (Ursus maritimus) and other mammals living in ice-covered regions maintain their body temperature by generating heat and reducing heat loss through thick fur and a dense layer of fat under their skin. (credit: “longhorndave”/Flickr)
In order to function properly, cells require appropriate conditions such as proper temperature, pH, and appropriate concentration of diverse chemicals. These conditions may, however, change from one moment to the next. Organisms are able to maintain homeostatic internal conditions within a narrow range almost constantly, despite environmental changes, by activation of regulatory mechanisms. For example, an organism needs to regulate body temperature through the thermoregulation process. Organisms that live in cold climates, such as the polar bear (Figure 1.13), have body structures that help them withstand low temperatures and conserve body heat. Structures that aid in this type of insulation include fur, feathers, blubber, and fat. In hot climates, organisms have methods (such as perspiration in humans or panting in dogs) that help them to shed excess body heat.
Energy Processing
Figure 1.14 The California condor (Gymnogyps californianus) uses chemical energy derived from food to power flight. California condors are an endangered species. This bird has a wing tag that helps biologists identify the individual. (credit: Pacific Southwest Region U.S. Fish and Wildlife Service)
All organisms use a source of energy for their metabolic activities. Some organisms capture energy from the sun and convert it into chemical energy in food. Others use chemical energy in molecules they take in as food (Figure 1.14).
Evolution
The diversity of life on Earth is a result of mutations, or random changes in hereditary material over time. These mutations allow the possibility for organisms to adapt to a changing environment. An organism that evolves characteristics fit for the environment will have greater reproductive success, subject to the forces of natural selection.
Levels of Organization of Living Things
Living things are highly organized and structured, following a hierarchy that we can examine on a scale from small to large. The atom is the smallest and most fundamental unit of matter that retains the properties of an element. It consists of a nucleus surrounded by electrons. Atoms form molecules. A molecule is a chemical structure consisting of at least two atoms held together by one or more chemical bonds. Many molecules that are biologically important are macromolecules, large molecules that are typically formed by polymerization (a polymer is a large molecule that is made by combining smaller units called monomers, which are simpler than macromolecules). An example of a macromolecule is deoxyribonucleic acid (DNA) (Figure 1.15), which contains the instructions for the structure and functioning of all living organisms.
Figure 1.15 All molecules, including this DNA molecule, are comprised of atoms. (credit: “brian0918”/Wikimedia Commons)
Link to Learning
Link to Learning
Watch this video that animates the three-dimensional structure of the DNA molecule in Figure 1.15.
Some cells contain aggregates of macromolecules surrounded by membranes. We call these organelles. Organelles are small structures that exist within cells. Examples of organelles include mitochondria and chloroplasts, which carry out indispensable functions: mitochondria produce energy to power the cell, while chloroplasts enable green plants to utilize the energy in sunlight to make sugars. All living things are made of cells. The cell itself is the smallest fundamental unit of structure and function in living organisms. (This requirement is why scientists do not consider viruses living: they are not made of cells. To make new viruses, they have to invade and hijack the reproductive mechanism of a living cell. Only then can they obtain the materials they need to reproduce.) Some organisms consist of a single cell and others are multicellular. Scientists classify cells as prokaryotic or eukaryotic. Prokaryotes are single-celled or colonial organisms that do not have membrane-bound nuclei. In contrast, the cells of eukaryotes do have membrane-bound organelles and a membrane-bound nucleus.
In larger organisms, cells combine to make tissues, which are groups of similar cells carrying out similar or related functions. Organs are collections of tissues grouped together performing a common function. Organs are present not only in animals but also in plants. An organ system is a higher level of organization that consists of functionally related organs. Mammals have many organ systems. For instance, the circulatory system transports blood through the body and to and from the lungs. It includes organs such as the heart and blood vessels. Organisms are individual living entities. For example, each tree in a forest is an organism. Single-celled prokaryotes and single-celled eukaryotes are also organisms, which biologists typically call microorganisms.
Biologists collectively call all the individuals of a species living within a specific area a population. For example, a forest may include many pine trees, which represent the population of pine trees in this forest. Different populations may live in the same specific area. For example, the forest with the pine trees includes populations of flowering plants, insects, and microbial populations. A community is the sum of populations inhabiting a particular area. For instance, all of the trees, flowers, insects, and other populations in a forest form the forest’s community. The forest itself is an ecosystem. An ecosystem consists of all the living things in a particular area together with the abiotic, nonliving parts of that environment such as nitrogen in the soil or rain water. At the highest level of organization (Figure 1.16), the biosphere is the collection of all ecosystems, and it represents the zones of life on Earth. It includes land, water, and even the atmosphere to a certain extent.
Visual Connection
Visual Connection
Figure 1.16 shows the biological levels of organization of living things. From a single organelle to the entire biosphere, living organisms are parts of a highly structured hierarchy. (credit “organelles”: modification of work by Umberto Salvagnin; credit “cells”: modification of work by Bruce Wetzel, Harry Schaefer/ National Cancer Institute; credit “tissues”: modification of work by Kilbad; Fama Clamosa; Mikael Häggström; credit “organs”: modification of work by Mariana Ruiz Villareal; credit “organisms”: modification of work by "Crystal"/Flickr; credit “ecosystems”: modification of work by US Fish and Wildlife Service Headquarters; credit “biosphere”: modification of work by NASA)
Which of the following statements is false?
1. Tissues exist within organs which exist within organ systems.
2. Communities exist within populations which exist within ecosystems.
3. Organelles exist within cells which exist within tissues.
4. Communities exist within ecosystems which exist in the biosphere.
The Diversity of Life
The fact that biology, as a science, has such a broad scope has to do with the tremendous diversity of life on earth. The source of this diversity is evolution, the process of gradual change in a population or species over time. Evolutionary biologists study the evolution of living things in everything from the microscopic world to ecosystems.
A phylogenetic tree (Figure 1.17) can summarize the evolution of various life forms on Earth. It is a diagram showing the evolutionary relationships among biological species based on similarities and differences in genetic or physical traits or both. Nodes and branches comprise a phylogenetic tree. The internal nodes represent ancestors and are points in evolution when, based on scientific evidence, researchers believe an ancestor has diverged to form two new species. The length of each branch is proportional to the time elapsed since the split.
Figure 1.17 Microbiologist Carl Woese constructed this phylogenetic tree using data that he obtained from sequencing ribosomal RNA genes. The tree shows the separation of living organisms into three domains: Bacteria, Archaea, and Eukarya. Bacteria and Archaea are prokaryotes, single-celled organisms lacking intracellular organelles. (credit: Eric Gaba; NASA Astrobiology Institute)
Evolution Connection
Evolution Connection
Carl Woese and the Phylogenetic TreeIn the past, biologists grouped living organisms into five kingdoms: animals, plants, fungi, protists, and bacteria. They based the organizational scheme mainly on physical features, as opposed to physiology, biochemistry, or molecular biology, all of which modern systematics use. American microbiologist Carl Woese's pioneering work in the early 1970s has shown, however, that life on Earth has evolved along three lineages, now called domains—Bacteria, Archaea, and Eukarya. The first two are prokaryotic cells with microbes that lack membrane-enclosed nuclei and organelles. The third domain contains the eukaryotes and includes unicellular microorganisms (protists), together with the three remaining kingdoms (fungi, plants, and animals). Woese defined Archaea as a new domain, and this resulted in a new taxonomic tree (Figure 1.17). Many organisms belonging to the Archaea domain live under extreme conditions and are called extremophiles. To construct his tree, Woese used genetic relationships rather than similarities based on morphology (shape).
Woese constructed his tree from universally distributed comparative gene sequencing that are present in every organism, and conserved (meaning that these genes have remained essentially unchanged throughout evolution). Woese’s approach was revolutionary because comparing physical features are insufficient to differentiate between the prokaryotes that appear fairly similar in spite of their tremendous biochemical diversity and genetic variability (Figure 1.18). Comparing rRNA sequences provided Woese with a sensitive device that revealed the extensive variability of prokaryotes, and which justified separating the prokaryotes into two domains: bacteria and archaea.
Figure 1.18 These images represent different domains. The (a) bacteria in this micrograph belong to Domain Bacteria, while the (b) extremophiles (not visible) living in this hot vent belong to Domain Archaea. Both the (c) sunflower and (d) lion are part of Domain Eukarya. (credit a: modification of work by Drew March; credit b: modification of work by Steve Jurvetson; credit c: modification of work by Michael Arrighi; credit d: modification of work by Leszek Leszcynski)
Branches of Biological Study
The scope of biology is broad and therefore contains many branches and subdisciplines. Biologists may pursue one of those subdisciplines and work in a more focused field. For instance, molecular biology and biochemistry study biological processes at the molecular and chemical level, including interactions among molecules such as DNA, RNA, and proteins, as well as the way they are regulated. Microbiology, the study of microorganisms, is the study of the structure and function of single-celled organisms. It is quite a broad branch itself, and depending on the subject of study, there are also microbial physiologists, ecologists, and geneticists, among others.
Career Connection
Career Connection
Forensic ScientistForensic science is the application of science to answer questions related to the law. Biologists as well as chemists and biochemists can be forensic scientists. Forensic scientists provide scientific evidence for use in courts, and their job involves examining trace materials associated with crimes. Interest in forensic science has increased in the last few years, possibly because of popular television shows that feature forensic scientists on the job. Also, developing molecular techniques and establishing DNA databases have expanded the types of work that forensic scientists can do. Their job activities are primarily related to crimes against people such as murder, rape, and assault. Their work involves analyzing samples such as hair, blood, and other body fluids and also processing DNA (Figure 1.19) found in many different environments and materials. Forensic scientists also analyze other biological evidence left at crime scenes, such as insect larvae or pollen grains. Students who want to pursue careers in forensic science will most likely have to take chemistry and biology courses as well as some intensive math courses.
Figure 1.19 This forensic scientist works in a DNA extraction room at the U.S. Army Criminal Investigation Laboratory at Fort Gillem, GA. (credit: United States Army CID Command Public Affairs)
Another field of biological study, neurobiology, studies the biology of the nervous system, and although it is a branch of biology, it is also an interdisciplinary field of study known as neuroscience. Because of its interdisciplinary nature, this subdiscipline studies different nervous system functions using molecular, cellular, developmental, medical, and computational approaches.
Figure 1.20 Researchers work on excavating dinosaur fossils at a site in Castellón, Spain. (credit: Mario Modesto)
Paleontology, another branch of biology, uses fossils to study life’s history (Figure 1.20). Zoology and botany are the study of animals and plants, respectively. Biologists can also specialize as biotechnologists, ecologists, or physiologists, to name just a few areas. This is just a small sample of the many fields that biologists can pursue.
Biology is the culmination of the achievements of the natural sciences from their inception to today. Excitingly, it is the cradle of emerging sciences, such as the biology of brain activity, genetic engineering of custom organisms, and the biology of evolution that uses the laboratory tools of molecular biology to retrace the earliest stages of life on Earth. A scan of news headlines—whether reporting on immunizations, a newly discovered species, sports doping, or a genetically-modified food—demonstrates the way biology is active in and important to our everyday world. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/01%3A_Unit_I-_The_Chemistry_of_Life/1.01%3A_The_Study_of_Life/1.1.03%3A_Themes_and_Concepts_of_Biology.txt |
abstract
opening section of a scientific paper that summarizes the research and conclusions
applied science
form of science that aims to solve real-world problems
atom
smallest and most fundamental unit of matter that retains the properties of an element
basic science
science that seeks to expand knowledge and understanding regardless of the short-term application of that knowledge
biochemistry
study of the chemistry of biological organisms
biology
the study of life
biosphere
collection of all the ecosystems on Earth
botany
study of plants
cell
smallest fundamental unit of structure and function in living things
community
set of populations inhabiting a particular area
conclusion
section of a scientific paper that summarizes the importance of the experimental findings
control
part of an experiment that does not change during the experiment
deductive reasoning
form of logical thinking that uses a general inclusive statement to predict specific results
descriptive science
(also, discovery science) form of science that aims to observe, explore, and investigate
discussion
section of a scientific paper in which the author interprets experimental results, describes how variables may be related, and attempts to explain the phenomenon in question
ecosystem
all the living things in a particular area together with the abiotic, nonliving parts of that environment
eukaryote
organism with cells that have nuclei and membrane-bound organelles
evolution
the process of gradual change in a population or species over time
falsifiable
able to be disproven by experimental results
homeostasis
ability of an organism to maintain constant internal conditions
hypothesis
suggested explanation for an observation, which one can test
hypothesis-based science
form of science that begins with a specific question and potential testable answers
inductive reasoning
form of logical thinking that uses related observations to arrive at a general conclusion
introduction
opening section of a scientific paper, which provides background information about what was known in the field prior to the research reported in the paper
life science
field of science, such as biology, that studies living things
macromolecule
large molecule, typically formed by the joining of smaller molecules
materials and methods
section of a scientific paper that includes a complete description of the substances, methods, and techniques that the researchers used to gather data
microbiology
study of the structure and function of microorganisms
molecular biology
study of biological processes and their regulation at the molecular level, including interactions among molecules such as DNA, RNA, and proteins
molecule
chemical structure consisting of at least two atoms held together by one or more chemical bonds
natural science
field of science that is related to the physical world and its phenomena and processes
neurobiology
study of the biology of the nervous system
organ
collection of related tissues grouped together performing a common function
organ system
level of organization that consists of functionally related interacting organs
organelle
small structures that exist within cells and carry out cellular functions
organism
individual living entity
paleontology
study of life’s history by means of fossils
peer-reviewed manuscript
scientific paper that a scientist’s colleagues review who are experts in the field of study
phylogenetic tree
diagram showing the evolutionary relationships among various biological species based on similarities and differences in genetic or physical traits or both; in essence, a hypothesis concerning evolutionary connections
physical science
field of science, such as geology, astronomy, physics, and chemistry, that studies nonliving matter
plagiarism
using other people’s work or ideas without proper citation, creating the false impression that those are the author’s original ideas
population
all of the individuals of a species living within a specific area
prokaryote
single-celled organism that lacks organelles and does not have nuclei surrounded by a nuclear membrane
results
section of a scientific paper in which the author narrates the experimental findings and presents relevant figures, pictures, diagrams, graphs, and tables, without any further interpretation
review article
paper that summarizes and comments on findings that were published as primary literature
science
knowledge that covers general truths or the operation of general laws, especially when acquired and tested by the scientific method
scientific method
method of research with defined steps that include observation, formulation of a hypothesis, testing, and confirming or falsifying the hypothesis
serendipity
fortunate accident or a lucky surprise
theory
tested and confirmed explanation for observations or phenomena
tissue
group of similar cells carrying out related functions
variable
part of an experiment that the experimenter can vary or change
zoology
study of animals | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/01%3A_Unit_I-_The_Chemistry_of_Life/1.01%3A_The_Study_of_Life/1.1.04%3A_Key_Terms.txt |
1.1 The Science of Biology
Biology is the science that studies living organisms and their interactions with one another and their environments. Science attempts to describe and understand the nature of the universe in whole or in part by rational means. Science has many fields. Those fields related to the physical world and its phenomena are natural sciences.
Science can be basic or applied. The main goal of basic science is to expand knowledge without any expectation of short-term practical application of that knowledge. The primary goal of applied research, however, is to solve practical problems.
Science uses two types of logical reasoning. Inductive reasoning uses particular results to produce general scientific principles. Deductive reasoning is a form of logical thinking that predicts results by applying general principles. The common thread throughout scientific research is using the scientific method, a step-based process that consists of making observations, defining a problem, posing hypotheses, testing these hypotheses, and drawing one or more conclusions. The testing uses proper controls. Scientists present their results in peer-reviewed scientific papers published in scientific journals. A scientific research paper consists of several well-defined sections: introduction, materials and methods, results, and, finally, a concluding discussion. Review papers summarize the conducted research in a particular field over a period of time.
1.2 Themes and Concepts of Biology
Biology is the science of life. All living organisms share several key properties such as order, sensitivity or response to stimuli, reproduction, growth and development, regulation, homeostasis, and energy processing. Living things are highly organized parts of a hierarchy that includes atoms, molecules, organelles, cells, tissues, organs, and organ systems. In turn, biologists group organisms as populations, communities, ecosystems, and the biosphere. The great diversity of life today evolved from less-diverse ancestral organisms over billions of years. We can use a phylogenetic tree to show evolutionary relationships among organisms.
Biology is very broad and includes many branches and subdisciplines. Examples include molecular biology, microbiology, neurobiology, zoology, and botany, among others.
1.1.06: Visual Connection Questions
1.
Figure 1.6 In the example below, the scientific method is used to solve an everyday problem. Match the scientific method steps (numbered items) with the process of solving the everyday problem (lettered items). Based on the results of the experiment, is the hypothesis correct? If it is incorrect, propose some alternative hypotheses.
1. Observation a. There is something wrong with the electrical outlet.
2. Question b. If something is wrong with the outlet, my coffeemaker also won’t work when plugged into it.
3. Hypothesis (answer) c. My toaster doesn’t toast my bread.
4. Prediction d. I plug my coffee maker into the outlet.
5. Experiment e. My coffeemaker works.
6. Result f. Why doesn’t my toaster work?
2.
Figure 1.7 Decide if each of the following is an example of inductive or deductive reasoning.
1. All flying birds and insects have wings. Birds and insects flap their wings as they move through the air. Therefore, wings enable flight.
2. Insects generally survive mild winters better than harsh ones. Therefore, insect pests will become more problematic if global temperatures increase.
3. Chromosomes, the carriers of DNA, separate into daughter cells during cell division. Therefore, each daughter cell will have the same chromosome set as the mother cell.
4. Animals as diverse as humans, insects, and wolves all exhibit social behavior. Therefore, social behavior must have an evolutionary advantage.
3.
Figure 1.16 Which of the following statements is false?
1. Tissues exist within organs which exist within organ systems.
2. Communities exist within populations which exist within ecosystems.
3. Organelles exist within cells which exist within tissues.
4. Communities exist within ecosystems which exist in the biosphere. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/01%3A_Unit_I-_The_Chemistry_of_Life/1.01%3A_The_Study_of_Life/1.1.05%3A_Chapter_Summary.txt |
4.
The first forms of life on Earth were ________.
1. plants
2. microorganisms
3. birds
4. dinosaurs
5.
A suggested and testable explanation for an event is called a ________.
1. hypothesis
2. variable
3. theory
4. control
6.
Which of the following sciences is not considered a natural science?
1. biology
2. astronomy
3. physics
4. computer science
7.
The type of logical thinking that uses related observations to arrive at a general conclusion is called ________.
1. deductive reasoning
2. the scientific method
3. hypothesis-based science
4. inductive reasoning
8.
The process of ________ helps to ensure that a scientist’s research is original, significant, logical, and thorough.
1. publication
2. public speaking
3. peer review
4. the scientific method
9.
A person notices that her houseplants that are regularly exposed to music seem to grow more quickly than those in rooms with no music. As a result, she determines that plants grow better when exposed to music. This example most closely resembles which type of reasoning?
1. inductive reasoning
2. deductive reasoning
3. neither, because no hypothesis was made
4. both inductive and deductive reasoning
10.
The smallest unit of biological structure that meets the functional requirements of “living” is the ________.
1. organ
2. organelle
3. cell
4. macromolecule
11.
Viruses are not considered living because they ________.
1. are not made of cells
2. lack cell nuclei
3. do not contain DNA or RNA
4. cannot reproduce
12.
The presence of a membrane-enclosed nucleus is a characteristic of ________.
1. prokaryotic cells
2. eukaryotic cells
3. living organisms
4. bacteria
13.
A group of individuals of the same species living in the same area is called a(n) ________.
1. family
2. community
3. population
4. ecosystem
14.
Which of the following sequences represents the hierarchy of biological organization from the most inclusive to the least complex level?
1. organelle, tissue, biosphere, ecosystem, population
2. organ, organism, tissue, organelle, molecule
3. organism, community, biosphere, molecule, tissue, organ
4. biosphere, ecosystem, community, population, organism
15.
Where in a phylogenetic tree would you expect to find the organism that had evolved most recently?
1. at the base
2. within the branches
3. at the nodes
4. at the branch tips
1.1.08: Critical Thinking Questions
16.
Although the scientific method is used by most of the sciences, it can also be applied to everyday situations. Think about a problem that you may have at home, at school, or with your car, and apply the scientific method to solve it.
17.
Give an example of how applied science has had a direct effect on your daily life.
18.
Name two topics that are likely to be studied by biologists, and two areas of scientific study that would fall outside the realm of biology.
19.
Thinking about the topic of cancer, write a basic science question and an applied science question that a researcher interested in this topic might ask.
20.
Select two items that biologists agree are necessary in order to consider an organism “alive.” For each, give an example of a nonliving object that otherwise fits the definition of “alive.”
21.
Consider the levels of organization of the biological world, and place each of these items in order from smallest level of organization to most encompassing: skin cell, elephant, water molecule, planet Earth, tropical rainforest, hydrogen atom, wolf pack, liver.
22.
You go for a long walk on a hot day. Give an example of a way in which homeostasis keeps your body healthy.
23.
Using examples, explain how biology can be studied from a microscopic approach to a global approach. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/01%3A_Unit_I-_The_Chemistry_of_Life/1.01%3A_The_Study_of_Life/1.1.07%3A_Review_Questions.txt |
Elements in various combinations comprise all matter, including living things. Some of the most abundant elements in living organisms include carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. These form the nucleic acids, proteins, carbohydrates, and lipids that are the fundamental components of living matter. Biologists must understand these important building blocks and the unique structures of the atoms that make up molecules, allowing for the formation of cells, tissues, organ systems, and entire organisms.
• 1.2.1: Introduction
All biological processes follow the laws of physics and chemistry, so in order to understand how biological systems work, it is important to understand the underlying physics and chemistry. For example, the flow of blood within the circulatory system follows the laws of physics that regulate the modes of fluid flow. The breakdown of the large, complex molecules of food into smaller molecules is a series of chemical reactions that follow chemical laws.
• 1.2.2: Atoms, Isotopes, Ions, and Molecules - The Building Blocks
At its most fundamental level, life is made up of matter. Matter is any substance that occupies space and has mass. Elements are unique forms of matter with specific chemical and physical properties that cannot be broken down into smaller substances by ordinary chemical reactions. There are 118 elements, but only 92 occur naturally. The remaining elements are synthesized in laboratories and are unstable.
• 1.2.3: Water
The polarity of the water molecule and its resulting hydrogen bonding make water a unique substance with special properties that are intimately tied to the processes of life. Life originally evolved in a watery environment, and most of an organism’s cellular chemistry and metabolism occur inside the watery contents of the cell’s cytoplasm. Understanding the characteristics of water helps to elucidate its importance in maintaining life.
• 1.2.4: Carbon
Cells are made of many complex molecules called macromolecules, such as proteins, nucleic acids (RNA and DNA), carbohydrates, and lipids. The macromolecules are a subset of organic molecules (any carbon-containing liquid, solid, or gas) that are especially important for life. The fundamental component for all of these macromolecules is carbon.
• 1.2.5: Key Terms
• 1.2.6: Chapter Summary
• 1.2.7: Visual Connection Questions
• 1.2.8: Review Questions
• 1.2.9: Critical Thinking Questions
Thumbnail: Fatty acid molecules with cis and trans configurations. (CC BY 4.0 / modified from original; OpenStax).
1.02: The Chemical Foundation of Life
Figure 2.1 Atoms are the building blocks of molecules in the universe—air, soil, water, rocks . . . and also the cells of all living organisms. In this model of an organic molecule, the atoms of carbon (black), hydrogen (white), nitrogen (blue), oxygen (red), and phosphorus (yellow) are in proportional atomic size. The silver rods indicate chemical bonds. (credit: modification of work by Christian Guthier)
Elements in various combinations comprise all matter, including living things. Some of the most abundant elements in living organisms include carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. These form the nucleic acids, proteins, carbohydrates, and lipids that are the fundamental components of living matter. Biologists must understand these important building blocks and the unique structures of the atoms that comprise molecules, allowing for cells, tissues, organ systems, and entire organisms to form.
All biological processes follow the laws of physics and chemistry, so in order to understand how biological systems work, it is important to understand the underlying physics and chemistry. For example, the flow of blood within the circulatory system follows the laws of physics that regulate the modes of fluid flow. The breakdown of the large, complex molecules of food into smaller molecules—and the conversion of these to release energy to be stored in adenosine triphosphate (ATP)—is a series of chemical reactions that follow chemical laws. The properties of water and the formation of hydrogen bonds are key to understanding living processes. Recognizing the properties of acids and bases is important, for example, to our understanding of the digestive process. Therefore, the fundamentals of physics and chemistry are important for gaining insight into biological processes. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/01%3A_Unit_I-_The_Chemistry_of_Life/1.02%3A_The_Chemical_Foundation_of_Life/1.2.01%3A_Introduction.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Define matter and elements
• Describe the interrelationship between protons, neutrons, and electrons
• Compare the ways in which electrons can be donated or shared between atoms
• Explain the ways in which naturally occurring elements combine to create molecules, cells, tissues, organ systems, and organisms
At its most fundamental level, life is made up of matter. Matter is any substance that occupies space and has mass. Elements are unique forms of matter with specific chemical and physical properties that cannot break down into smaller substances by ordinary chemical reactions. There are 118 elements, but only 98 occur naturally. The remaining elements are unstable and require scientists to synthesize them in laboratories.
Each element is designated by its chemical symbol, which is a single capital letter or, when the first letter is already “taken” by another element, a combination of two letters. Some elements follow the English term for the element, such as C for carbon and Ca for calcium. Other elements’ chemical symbols derive from their Latin names. For example, the symbol for sodium is Na, referring to natrium, the Latin word for sodium.
The four elements common to all living organisms are oxygen (O), carbon (C), hydrogen (H), and nitrogen (N). In the nonliving world, elements are found in different proportions, and some elements common to living organisms are relatively rare on the earth as a whole, as Table 2.1 shows. For example, the atmosphere is rich in nitrogen and oxygen but contains little carbon and hydrogen, while the earth’s crust, although it contains oxygen and a small amount of hydrogen, has little nitrogen and carbon. In spite of their differences in abundance, all elements and the chemical reactions between them obey the same chemical and physical laws regardless of whether they are a part of the living or nonliving world.
Approximate Percentage of Elements in Living Organisms (Humans) Compared to the Nonliving World
Element Life (Humans) Atmosphere Earth’s Crust
Oxygen (O) 65% 21% 46%
Carbon (C) 18% trace trace
Hydrogen (H) 10% trace 0.1%
Nitrogen (N) 3% 78% trace
Table 2.1
The Structure of the Atom
To understand how elements come together, we must first discuss the element's smallest component or building block, the atom. An atom is the smallest unit of matter that retains all of the element's chemical properties. For example, one gold atom has all of the properties of gold, like its chemical reactivity. A gold coin is simply a very large number of gold atoms molded into the shape of a coin and contains small amounts of other elements known as impurities. We cannot break down gold atoms into anything smaller while still retaining the properties of gold.
An atom is composed of two regions: the nucleus, which is in the atom's center and contains protons and neutrons. The atom's outermost region holds its electrons in orbit around the nucleus, as Figure 2.2 illustrates. Atoms contain protons, electrons, and neutrons, among other subatomic particles. The most common isotope of hydrogen (H) is the only exception and is made of one proton and one electron with no neutrons.
Figure 2.2 Elements, such as helium, depicted here, are made up of atoms. Atoms are made up of protons and neutrons located within the nucleus, with electrons in orbitals surrounding the nucleus.
Protons and neutrons have approximately the same mass, about 1.67 × 10-24 grams. Scientists arbitrarily define this amount of mass as one atomic mass unit (amu) or one Dalton, as Table 2.2 shows. Although similar in mass, protons and neutrons differ in their electric charge. A proton is positively charged; whereas, a neutron is uncharged. Therefore, the number of neutrons in an atom contributes significantly to its mass, but not to its charge. Electrons are much smaller in mass than protons, weighing only 9.11 × 10-28 grams, or about 1/1800 of an atomic mass unit. Hence, they do not contribute much to an element’s overall atomic mass. Therefore, when considering atomic mass, it is customary to ignore the mass of any electrons and calculate the atom’s mass based on the number of protons and neutrons alone. Although not significant contributors to mass, electrons do contribute greatly to the atom’s charge, as each electron has a negative charge equal to the proton's positive charge. In uncharged, neutral atoms, the number of electrons orbiting the nucleus is equal to the number of protons inside the nucleus. In these atoms, the positive and negative charges cancel each other out, leading to an atom with no net charge.
Accounting for the sizes of protons, neutrons, and electrons, most of the atom's volume—greater than 99 percent—is empty space. With all this empty space, one might ask why so-called solid objects do not just pass through one another. The reason they do not is that the electrons that surround all atoms are negatively charged and negative charges repel each other.
Protons, Neutrons, and Electrons
Charge Mass (amu) Location
Proton +1 1 nucleus
Neutron 0 1 nucleus
Electron –1 0 orbitals
Table 2.2
Atomic Number and Mass
Atoms of each element contain a characteristic number of protons and electrons. The number of protons determines an element’s atomic number, which scientists use to distinguish one element from another. The number of neutrons is variable, resulting in isotopes, which are different forms of the same atom that vary only in the number of neutrons they possess. Together, the number of protons and neutrons determine an element’s mass number, as Figure 2.3 illustrates. Note that we disregard the small contribution of mass from electrons in calculating the mass number. We can use this approximation of mass to easily calculate how many neutrons an element has by simply subtracting the number of protons from the mass number. Since an element’s isotopes will have slightly different mass numbers, scientists also determine the atomic mass, which is the calculated mean of the mass number for its naturally occurring isotopes. Often, the resulting number contains a fraction. For example, the atomic mass of chlorine (Cl) is 35.45 because chlorine is composed of several isotopes, some (the majority) with atomic mass 35 (17 protons and 18 neutrons) and some with atomic mass 37 (17 protons and 20 neutrons).
Visual Connection
Visual Connection
Figure 2.3 Carbon has an atomic number of six, and two stable isotopes with mass numbers of twelve and thirteen, respectively. Its relative atomic mass is 12.011
How many neutrons do carbon-12 and carbon-13 have, respectively?
Isotopes
Isotopes are different forms of an element that have the same number of protons but a different number of neutrons. Some elements—such as carbon, potassium, and uranium—have naturally occurring isotopes. Carbon-12 contains six protons, six neutrons, and six electrons; therefore, it has a mass number of 12 (six protons and six neutrons). Carbon-14 contains six protons, eight neutrons, and six electrons; its atomic mass is 14 (six protons and eight neutrons). These two alternate forms of carbon are isotopes. Some isotopes may emit neutrons, protons, and electrons, and attain a more stable atomic configuration (lower level of potential energy); these are radioactive isotopes, or radioisotopes. Radioactive decay (carbon-14 decaying to eventually become nitrogen-14) describes the energy loss that occurs when an unstable atom’s nucleus releases radiation.
Evolution Connection
Evolution Connection
Carbon Dating Carbon is normally present in the atmosphere in the form of gaseous compounds like carbon dioxide and methane. Carbon-14 (14C) is a naturally occurring radioisotope that is created in the atmosphere from atmospheric 14N (nitrogen) by the addition of a neutron and the loss of a proton because of cosmic rays. This is a continuous process, so more 14C is always being created. As a living organism incorporates 14C initially as carbon dioxide fixed in the process of photosynthesis, the relative amount of 14C in its body is equal to the concentration of 14C in the atmosphere. When an organism dies, it is no longer ingesting 14C, so the ratio between 14C and 12C will decline as 14C decays gradually to 14N by a process called beta decay—electrons or positrons emission. This decay emits energy in a slow process.
After approximately 5,730 years, half of the starting concentration of 14C will convert back to 14N. We call the time it takes for half of the original concentration of an isotope to decay back to its more stable form its half-life. Because the half-life of 14C is long, scientists use it to date formerly living objects such as old bones or wood. Comparing the ratio of the 14C concentration in an object to the amount of 14C in the atmosphere, scientists can determine the amount of the isotope that has not yet decayed. On the basis of this amount, Figure 2.4 shows that we can calculate the age of the material, such as the pygmy mammoth, with accuracy if it is not much older than about 50,000 years. Other elements have isotopes with different half lives. For example, 40K (potassium-40) has a half-life of 1.25 billion years, and 235U (Uranium 235) has a half-life of about 700 million years. Through the use of radiometric dating, scientists can study the age of fossils or other remains of extinct organisms to understand how organisms have evolved from earlier species.
Figure 2.4 Scientists can determine the age of carbon-containing remains less than about 50,000 years old, such as this pygmy mammoth, using carbon dating. (credit: Bill Faulkner, NPS)
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To learn more about atoms, isotopes, and how to tell one isotope from another, run the simulation.
The Periodic Table
The periodic table organizes and displays different elements. Devised by Russian chemist Dmitri Mendeleev (1834–1907) in 1869, the table groups elements that, although unique, share certain chemical properties with other elements. The properties of elements are responsible for their physical state at room temperature: they may be gases, solids, or liquids. Elements also have specific chemical reactivity, the ability to combine and to chemically bond with each other.
In the periodic table in Figure 2.5, the elements are organized and displayed according to their atomic number and are arranged in a series of rows and columns based on shared chemical and physical properties. In addition to providing the atomic number for each element, the periodic table also displays the element’s atomic mass. Looking at carbon, for example, its symbol (C) and name appear, as well as its atomic number of six (in the upper left-hand corner) and its atomic mass of 12.01.
Figure 2.5 The periodic table shows each element's atomic mass and atomic number. The atomic number appears above the symbol for the element and the approximate atomic mass appears below it.
The periodic table groups elements according to chemical properties. Scientists base the differences in chemical reactivity between the elements on the number and spatial distribution of an atom’s electrons. Atoms that chemically react and bond to each other form molecules. Molecules are simply two or more atoms chemically bonded together. Logically, when two atoms chemically bond to form a molecule, their electrons, which form the outermost region of each atom, come together first as the atoms form a chemical bond.
Electron Shells and the Bohr Model
Note that there is a connection between the number of protons in an element, the atomic number that distinguishes one element from another, and the number of electrons it has. In all electrically neutral atoms, the number of electrons is the same as the number of protons. Thus, each element, at least when electrically neutral, has a characteristic number of electrons equal to its atomic number.
In 1913, Danish scientist Niels Bohr (1885–1962) developed an early model of the atom. The Bohr model shows the atom as a central nucleus containing protons and neutrons, with the electrons in circular orbitals at specific distances from the nucleus, as Figure 2.6 illustrates. These orbits form electron shells or energy levels, which are a way of visualizing the number of electrons in the outermost shells. These energy levels are designated by a number and the symbol “n.” For example, 1n represents the first energy level located closest to the nucleus.
Figure 2.6 In 1913, Niels Bohrs developed the Bohr model in which electrons exist within principal shells. An electron normally exists in the lowest energy shell available, which is the one closest to the nucleus. Energy from a photon of light can bump it up to a higher energy shell, but this situation is unstable, and the electron quickly decays back to the ground state. In the process, it releases a photon of light.
Electrons fill orbitals in a consistent order: they first fill the orbitals closest to the nucleus, then they continue to fill orbitals of increasing energy further from the nucleus. If there are multiple orbitals of equal energy, they fill with one electron in each energy level before adding a second electron. The electrons of the outermost energy level determine the atom's energetic stability and its tendency to form chemical bonds with other atoms to form molecules.
Under standard conditions, atoms fill the inner shells first, often resulting in a variable number of electrons in the outermost shell. The innermost shell has a maximum of two electrons but the next two electron shells can each have a maximum of eight electrons. This is known as the octet rule, which states, with the exception of the innermost shell, that atoms are more stable energetically when they have eight electrons in their valence shell, the outermost electron shell. Figure 2.7 shows examples of some neutral atoms and their electron configurations. Notice that in Figure 2.7, helium has a complete outer electron shell, with two electrons filling its first and only shell. Similarly, neon has a complete outer 2n shell containing eight electrons. In contrast, chlorine and sodium have seven and one in their outer shells, respectively, but theoretically they would be more energetically stable if they followed the octet rule and had eight.
Visual Connection
Visual Connection
Figure 2.7 Bohr diagrams indicate how many electrons fill each principal shell. Group 18 elements (helium, neon, and argon) have a full outer, or valence, shell. A full valence shell is the most stable electron configuration. Elements in other groups have partially filled valence shells and gain or lose electrons to achieve a stable electron configuration.
An atom may give, take, or share electrons with another atom to achieve a full valence shell, the most stable electron configuration. Looking at this figure, how many electrons do elements in group 1 need to lose in order to achieve a stable electron configuration? How many electrons do elements in groups 14 and 17 need to gain to achieve a stable configuration?
Understanding that the periodic table's organization is based on the total number of protons (and electrons) helps us know how electrons distribute themselves among the shells. The periodic table is arranged in columns and rows based on the number of electrons and their location. Examine more closely some of the elements in the table’s far right column in Figure 2.5. The group 18 atoms helium (He), neon (Ne), and argon (Ar) all have filled outer electron shells, making it unnecessary for them to share electrons with other atoms to attain stability. They are highly stable as single atoms. Because they are non reactive, scientists coin them inert (or noble gases). Compare this to the group 1 elements in the left-hand column. These elements, including hydrogen (H), lithium (Li), and sodium (Na), all have one electron in their outermost shells. That means that they can achieve a stable configuration and a filled outer shell by donating or sharing one electron with another atom or a molecule such as water. Hydrogen will donate or share its electron to achieve this configuration, while lithium and sodium will donate their electron to become stable. As a result of losing a negatively charged electron, they become positively charged ions. Group 17 elements, including fluorine and chlorine, have seven electrons in their outmost shells, so they tend to fill this shell with an electron from other atoms or molecules, making them negatively charged ions. Group 14 elements, of which carbon is the most important to living systems, have four electrons in their outer shell allowing them to make several covalent bonds (discussed below) with other atoms. Thus, the periodic table's columns represent the potential shared state of these elements’ outer electron shells that is responsible for their similar chemical characteristics.
Electron Orbitals
Although useful to explain the reactivity and chemical bonding of certain elements, the Bohr model does not accurately reflect how electrons spatially distribute themselves around the nucleus. They do not circle the nucleus like the earth orbits the sun, but we find them in electron orbitals. These relatively complex shapes result from the fact that electrons behave not just like particles, but also like waves. Mathematical equations from quantum mechanics, which scientists call wave functions, can predict within a certain level of probability where an electron might be at any given time. Scientists call the area where an electron is most likely to be found its orbital.
Recall that the Bohr model depicts an atom’s electron shell configuration. Within each electron shell are subshells, and each subshell has a specified number of orbitals containing electrons. While it is impossible to calculate exactly an electron's location, scientists know that it is most probably located within its orbital path. The letter s, p, d, and f designate the subshells. The s subshell is spherical in shape and has one orbital. Principal shell 1n has only a single s orbital, which can hold two electrons. Principal shell 2n has one s and one p subshell, and can hold a total of eight electrons. The p subshell has three dumbbell-shaped orbitals, as Figure 2.8 illustrates. Subshells d and f have more complex shapes and contain five and seven orbitals, respectively. We do not show these in the illustration. Principal shell 3n has s, p, and d subshells and can hold 18 electrons. Principal shell 4n has s, p, d and f orbitals and can hold 32 electrons. Moving away from the nucleus, the number of electrons and orbitals in the energy levels increases. Progressing from one atom to the next in the periodic table, we can determine the electron structure by fitting an extra electron into the next available orbital.
Figure 2.8 The s subshells are shaped like spheres. Both the 1n and 2n principal shells have an s orbital, but the size of the sphere is larger in the 2n orbital. Each sphere is a single orbital. Three dumbbell-shaped orbitals comprise p subshells. Principal shell 2n has a p subshell, but shell 1 does not.
The closest orbital to the nucleus, the 1s orbital, can hold up to two electrons. This orbital is equivalent to the Bohr model's innermost electron shell. The 1s orbital is the closest orbital to the nucleus, and it is always filled first, before any other orbital fills. Hydrogen has one electron; therefore, it occupies only one spot within the 1s orbital. We designate this as 1s1, where the superscripted 1 refers to the one electron within the 1s orbital. Helium has two electrons; therefore, it can completely fill the 1s orbital with its two electrons. We designate this as 1s2, referring to the two electrons of helium in the 1s orbital. On the periodic table Figure 2.5, hydrogen and helium are the only two elements in the first row (period). This is because they only have electrons in their first shell, the 1s orbital. Hydrogen and helium are the only two elements that have the 1s and no other electron orbitals in the electrically neutral state.
The second electron shell may contain eight electrons. This shell contains another spherical s orbital and three “dumbbell” shaped p orbitals, each of which can hold two electrons, as Figure 2.8 shows. After the 1s orbital fills, the second electron shell fills, first filling its 2s orbital and then its three p orbitals. When filling the p orbitals, each takes a single electron. Once each p orbital has an electron, it may add a second. Lithium (Li) contains three electrons that occupy the first and second shells. Two electrons fill the 1s orbital, and the third electron then fills the 2s orbital. Its electron configuration is 1s22s1. Neon (Ne), alternatively, has a total of ten electrons: two are in its innermost 1s orbital and eight fill its second shell (two each in the 2s and three p orbitals). Thus it is an inert gas and energetically stable as a single atom that will rarely form a chemical bond with other atoms. Larger elements have additional orbitals, comprising the third electron shell. While the concepts of electron shells and orbitals are closely related, orbitals provide a more accurate depiction of an atom's electron configuration because the orbital model specifies the different shapes and special orientations of all the places that electrons may occupy.
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Watch this visual animation to see the spatial arrangement of the p and s orbitals.
Chemical Reactions and Molecules
All elements are most stable when their outermost shell is filled with electrons according to the octet rule. This is because it is energetically favorable for atoms to be in that configuration and it makes them stable. However, since not all elements have enough electrons to fill their outermost shells, atoms form chemical bonds with other atoms thereby obtaining the electrons they need to attain a stable electron configuration. When two or more atoms chemically bond with each other, the resultant chemical structure is a molecule. The familiar water molecule, H2O, consists of two hydrogen atoms and one oxygen atom. These bond together to form water, as Figure 2.9 illustrates. Atoms can form molecules by donating, accepting, or sharing electrons to fill their outer shells.
Figure 2.9 Two or more atoms may bond with each other to form a molecule. When two hydrogens and an oxygen share electrons via covalent bonds it forms a water molecule.
Chemical reactions occur when two or more atoms bond together to form molecules or when bonded atoms break apart. Scientists call the substances used in the beginning of a chemical reaction reactants (usually on the left side of a chemical equation), and we call the substances at the end of the reaction products (usually on the right side of a chemical equation). We typically draw an arrow between the reactants and products to indicate the chemical reaction's direction. This direction is not always a “one-way street.” To create the water molecule above, the chemical equation would be:
$2H + O → H 2 O 2H + O → H 2 O$
An example of a simple chemical reaction is breaking down hydrogen peroxide molecules, each of which consists of two hydrogen atoms bonded to two oxygen atoms (H2O2). The reactant hydrogen peroxide breaks down into water, containing one oxygen atom bound to two hydrogen atoms (H2O), and oxygen, which consists of two bonded oxygen atoms (O2). In the equation below, the reaction includes two hydrogen peroxide molecules and two water molecules. This is an example of a balanced chemical equation, wherein each element's number of atoms is the same on each side of the equation. According to the law of conservation of matter, the number of atoms before and after a chemical reaction should be equal, such that no atoms are, under normal circumstances, created or destroyed.
$2H 2 O 2 (hydrogen peroxide) → 2H 2 O (water) + O 2 (oxygen) 2H 2 O 2 (hydrogen peroxide) → 2H 2 O (water) + O 2 (oxygen)$
Even though all of the reactants and products of this reaction are molecules (each atom remains bonded to at least one other atom), in this reaction only hydrogen peroxide and water are representatives of compounds: they contain atoms of more than one type of element. Molecular oxygen, alternatively, as Figure 2.10 shows, consists of two doubly bonded oxygen atoms and is not classified as a compound but as a homonuclear molecule.
Figure 2.10 A double bond joins the oxygen atoms in an O2 molecule.
Some chemical reactions, such as the one above, can proceed in one direction until they expend all the reactants. The equations that describe these reactions contain a unidirectional arrow and are irreversible. Reversible reactions are those that can go in either direction. In reversible reactions, reactants turn into products, but when the product's concentration goes beyond a certain threshold (characteristic of the particular reaction), some of these products convert back into reactants. At this point, product and reactant designations reverse. This back and forth continues until a certain relative balance between reactants and products occurs—a state called equilibrium. A chemical equation with a double headed arrow pointing towards both the reactants and products often denote these reversible reaction situations.
For example, in human blood, excess hydrogen ions (H+) bind to bicarbonate ions (HCO3-) forming an equilibrium state with carbonic acid (H2CO3). If we added carbonic acid to this system, some of it would convert to bicarbonate and hydrogen ions.
$HCO 3 − + H + ↔ H 2 CO 3 HCO 3 − + H + ↔ H 2 CO 3$
However, biological reactions rarely obtain equilibrium because the concentrations of the reactants or products or both are constantly changing, often with one reaction's product a reactant for another. To return to the example of excess hydrogen ions in the blood, forming carbonic acid will be the reaction's major direction. However, the carbonic acid can also leave the body as carbon dioxide gas (via exhalation) instead of converting back to bicarbonate ion, thus driving the reaction to the right by the law of mass action. These reactions are important for maintaining homeostasis in our blood.
$HCO 3 − + H + ↔ H 2 CO 3 ↔ CO 2 + H 2 O HCO 3 − + H + ↔ H 2 CO 3 ↔ CO 2 + H 2 O$
Ions and Ionic Bonds
Some atoms are more stable when they gain or lose an electron (or possibly two) and form ions. This fills their outermost electron shell and makes them energetically more stable. Because the number of electrons does not equal the number of protons, each ion has a net charge. Cations are positive ions that form by losing electrons. Negative ions form by gaining electrons, which we call anions. We designate anions by their elemental name and change the ending to “-ide”, thus the anion of chlorine is chloride, and the anion of sulfur is sulfide.
Scientists refer to this movement of electrons from one element to another as electron transfer. As Figure 2.11 illustrates, sodium (Na) only has one electron in its outer electron shell. It takes less energy for sodium to donate that one electron than it does to accept seven more electrons to fill the outer shell. If sodium loses an electron, it now has 11 protons, 11 neutrons, and only 10 electrons, leaving it with an overall charge of +1. We now refer to it as a sodium ion. Chlorine (Cl) in its lowest energy state (called the ground state) has seven electrons in its outer shell. Again, it is more energy-efficient for chlorine to gain one electron than to lose seven. Therefore, it tends to gain an electron to create an ion with 17 protons, 17 neutrons, and 18 electrons, giving it a net negative (–1) charge. We now refer to it as a chloride ion. In this example, sodium will donate its one electron to empty its shell, and chlorine will accept that electron to fill its shell. Both ions now satisfy the octet rule and have complete outermost shells. Because the number of electrons is no longer equal to the number of protons, each is now an ion and has a +1 (sodium cation) or –1 (chloride anion) charge. Note that these transactions can normally only take place simultaneously: in order for a sodium atom to lose an electron, it must be in the presence of a suitable recipient like a chlorine atom.
Figure 2.11 In the formation of an ionic compound, metals lose electrons and nonmetals gain electrons to achieve an octet.
Ionic bonds form between ions with opposite charges. For instance, positively charged sodium ions and negatively charged chloride ions bond together to make crystals of sodium chloride, or table salt, creating a crystalline molecule with zero net charge.
Physiologists refer to certain salts as electrolytes (including sodium, potassium, and calcium), ions necessary for nerve impulse conduction, muscle contractions, and water balance. Many sports drinks and dietary supplements provide these ions to replace those lost from the body via sweating during exercise.
Covalent Bonds and Other Bonds and Interactions
Another way to satisfy the octet rule is by sharing electrons between atoms to form covalent bonds. These bonds are stronger and much more common than ionic bonds in the molecules of living organisms. We commonly find covalent bonds in carbon-based organic molecules, such as our DNA and proteins. We also find covalent bonds in inorganic molecules like H2O, CO2, and O2. The bonds may share one, two, or three pairs of electrons, making single, double, and triple bonds, respectively. The more covalent bonds between two atoms, the stronger their connection. Thus, triple bonds are the strongest.
The strength of different levels of covalent bonding is one of the main reasons living organisms have a difficult time in acquiring nitrogen for use in constructing their molecules, even though molecular nitrogen, N2, is the most abundant gas in the atmosphere. Molecular nitrogen consists of two nitrogen atoms triple bonded to each other and, as with all molecules, sharing these three pairs of electrons between the two nitrogen atoms allows for filling their outer electron shells, making the molecule more stable than the individual nitrogen atoms. This strong triple bond makes it difficult for living systems to break apart this nitrogen in order to use it as constituents of proteins and DNA.
Forming water molecules provides an example of covalent bonding. Covalent bonds bind the hydrogen and oxygen atoms that combine to form water molecules as Figure 2.9 shows. The electron from the hydrogen splits its time between the hydrogen atoms' incomplete outer shell and the oxygen atoms' incomplete outer shell. To completely fill the oxygen's outer shell, which has six electrons but which would be more stable with eight, two electrons (one from each hydrogen atom) are needed: hence, the well-known formula H2O. The two elements share the electrons to fill the outer shell of each, making both elements more stable.
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View this short video to see an animation of ionic and covalent bonding.
Polar Covalent Bonds
There are two types of covalent bonds: polar and nonpolar. In a polar covalent bond, Figure 2.12 shows atoms unequally share the electrons and are attracted more to one nucleus than the other. Because of the unequal electron distribution between the atoms of different elements, a slightly positive (δ+) or slightly negative (δ–) charge develops. This partial charge is an important property of water and accounts for many of its characteristics.
Water is a polar molecule, with the hydrogen atoms acquiring a partial positive charge and the oxygen a partial negative charge. This occurs because the oxygen atom's nucleus is more attractive to the hydrogen atoms' electrons than the hydrogen nucleus is to the oxygen’s electrons. Thus, oxygen has a higher electronegativity than hydrogen and the shared electrons spend more time near the oxygen nucleus than the hydrogen atoms' nucleus, giving the oxygen and hydrogen atoms slightly negative and positive charges, respectively. Another way of stating this is that the probability of finding a shared electron near an oxygen nucleus is more likely than finding it near a hydrogen nucleus. Either way, the atom’s relative electronegativity contributes to developing partial charges whenever one element is significantly more electronegative than the other, and the charges that these polar bonds generate may then be used to form hydrogen bonds based on the attraction of opposite partial charges. (Hydrogen bonds, which we discuss in detail below, are weak bonds between slightly positively charged hydrogen atoms to slightly negatively charged atoms in other molecules.) Since macromolecules often have atoms within them that differ in electronegativity, polar bonds are often present in organic molecules.
Nonpolar Covalent Bonds
Nonpolar covalent bonds form between two atoms of the same element or between different elements that share electrons equally. For example, molecular oxygen (O2) is nonpolar because the electrons distribute equally between the two oxygen atoms.
Figure 2.12 also shows another example of a nonpolar covalent bond—methane (CH4). Carbon has four electrons in its outermost shell and needs four more to fill it. It obtains these four from four hydrogen atoms, each atom providing one, making a stable outer shell of eight electrons. Carbon and hydrogen do not have the same electronegativity but are similar; thus, nonpolar bonds form. The hydrogen atoms each need one electron for their outermost shell, which is filled when it contains two electrons. These elements share the electrons equally among the carbons and the hydrogen atoms, creating a nonpolar covalent molecule.
Figure 2.12 Whether a molecule is polar or nonpolar depends both on bond type and molecular shape. Both water and carbon dioxide have polar covalent bonds, but carbon dioxide is linear, so the partial charges on the molecule cancel each other out.
Hydrogen Bonds and Van Der Waals Interactions
Ionic and covalent bonds between elements require energy to break. Ionic bonds are not as strong as covalent, which determines their behavior in biological systems. However, not all bonds are ionic or covalent bonds. Weaker bonds can also form between molecules. Two weak bonds that occur frequently are hydrogen bonds and van der Waals interactions. Without these two types of bonds, life as we know it would not exist. Hydrogen bonds provide many of the critical, life-sustaining properties of water and also stabilize the structures of proteins and DNA, the building block of cells.
When polar covalent bonds containing hydrogen form, the hydrogen in that bond has a slightly positive charge because hydrogen’s electron is pulled more strongly toward the other element and away from the hydrogen. Because the hydrogen is slightly positive, it will be attracted to neighboring negative charges. When this happens, a weak interaction occurs between the hydrogen's δ+ from one molecule and the molecule's δ charge on another molecule with the more electronegative atoms, usually oxygen. Scientists call this interaction a hydrogen bond. This type of bond is common and occurs regularly between water molecules. Individual hydrogen bonds are weak and easily broken; however, they occur in very large numbers in water and in organic polymers, creating a major force in combination. Hydrogen bonds are also responsible for zipping together the DNA double helix.
Like hydrogen bonds, van der Waals interactions are weak attractions or interactions between molecules. Van der Waals attractions can occur between any two or more molecules and are dependent on slight fluctuations of the electron densities, which are not always symmetrical around an atom. For these attractions to happen, the molecules need to be very close to one another. These bonds—along with ionic, covalent, and hydrogen bonds—contribute to the proteins' three-dimensional structure in our cells that is necessary for their proper function.
Career Connection
Career Connection
Pharmaceutical Chemist Pharmaceutical chemists are responsible for developing new drugs and trying to determine the mode of action of both old and new drugs. They are involved in every step of the drug development process. We can find drugs in the natural environment or we can synthesize them in the laboratory. In many cases, chemists change potential drugs from nature chemically in the laboratory to make them safer and more effective, and sometimes synthetic versions of drugs substitute for the version we find in nature.
After a drug's initial discovery or synthesis, the chemist then develops the drug, perhaps chemically altering it, testing it to see if it is toxic, and then designing methods for efficient large-scale production. Then, the process of approving the drug for human use begins. In the United States, the Food and Drug Administration (FDA) handles drug approval. This involves a series of large-scale experiments using human subjects to ensure the drug is not harmful and effectively treats the condition for which it is intended. This process often takes several years and requires the participation of physicians and scientists, in addition to chemists, to complete testing and gain approval.
An example of a drug that was originally discovered in a living organism is Paclitaxel (Taxol), an anti-cancer drug used to treat breast cancer. This drug was discovered in the bark of the pacific yew tree. Another example is aspirin, originally isolated from willow tree bark. Finding drugs often means testing hundreds of samples of plants, fungi, and other forms of life to see if they contain any biologically active compounds. Sometimes, traditional medicine can give modern medicine clues as to where to find an active compound. For example, mankind has used willow bark to make medicine for thousands of years, dating back to ancient Egypt. However, it was not until the late 1800s that scientists and pharmaceutical companies purified and marketed the aspirin molecule, acetylsalicylic acid, for human use.
Occasionally, drugs developed for one use have unforeseen effects that allow usage in other, unrelated ways. For example, scientists originally developed the drug minoxidil (Rogaine) to treat high blood pressure. When tested on humans, researchers noticed that individuals taking the drug would grow new hair. Eventually the pharmaceutical company marketed the drug to people with baldness to restore lost hair.
Finally, a pharmaceutical chemist may discover negative effects or even lack of effects. In the early 1960s, inventors, doctors, and even a U.S. senator claimed anti-cancer properties of a new drug, Krebiozen, and began to market and sell it aggressively. Through the process of infrared spectrometry, FDA chemist Alma Levant Hayden and her team discovered that the "miracle drug" was nothing more than a common compound called creatine. A pharmaceutical chemist's career may involve detective work, experimentation, and drug development, all with the goal of making human beings healthier. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/01%3A_Unit_I-_The_Chemistry_of_Life/1.02%3A_The_Chemical_Foundation_of_Life/1.2.02%3A_Atoms_Isotopes_Ions_and_Molecules_-_The_Building_Blocks.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Describe the properties of water that are critical to maintaining life
• Explain why water is an excellent solvent
• Provide examples of water’s cohesive and adhesive properties
• Discuss the role of acids, bases, and buffers in homeostasis
Why do scientists spend time looking for water on other planets? Why is water so important? It is because water is essential to life as we know it. Water is one of the more abundant molecules and the one most critical to life on Earth. Water comprises approximately 60–70 percent of the human body. Without it, life as we know it simply would not exist.
The polarity of the water molecule and its resulting hydrogen bonding make water a unique substance with special properties that are intimately tied to the processes of life. Life originally evolved in a watery environment, and most of an organism’s cellular chemistry and metabolism occur inside the watery contents of the cell’s cytoplasm. Special properties of water are its high heat capacity and heat of vaporization, its ability to dissolve polar molecules, its cohesive and adhesive properties, and its dissociation into ions that leads to generating pH. Understanding these characteristics of water helps to elucidate its importance in maintaining life.
Water’s Polarity
One of water’s important properties is that it is composed of polar molecules: the hydrogen and oxygen within water molecules (H2O) form polar covalent bonds. While there is no net charge to a water molecule, water's polarity creates a slightly positive charge on hydrogen and a slightly negative charge on oxygen, contributing to water’s properties of attraction. Water generates charges because oxygen is more electronegative than hydrogen, making it more likely that a shared electron would be near the oxygen nucleus than the hydrogen nucleus, thus generating the partial negative charge near the oxygen.
As a result of water’s polarity, each water molecule attracts other water molecules because of the opposite charges between water molecules, forming hydrogen bonds. Water also attracts or is attracted to other polar molecules and ions. We call a polar substance that interacts readily with or dissolves in water hydrophilic (hydro- = “water”; -philic = “loving”). In contrast, nonpolar molecules such as oils and fats do not interact well with water, as Figure 2.13 shows. A good example of this is vinegar and oil salad dressing (an acidic water solution). We call such nonpolar compounds hydrophobic (hydro- = “water”; -phobic = “fearing”).
Figure 2.13 The polarity of water. The polarity of water is due to the differing electronegativities of hydrogen and oxygen. As a consequence, hydrogen bonds are formed when the slightly negative oxygen on one water molecule is attracted to the slightly positive hydrogen of another water molecule. Credit: Rao, A., Fletcher, S., Ryan, K., Tag, A. and Hawkins, A. Department of Biology, Texas A&M University
Water’s States: Gas, Liquid, and Solid
The formation of hydrogen bonds is an important quality of the liquid water that is crucial to life as we know it. As water molecules make hydrogen bonds with each other, water takes on some unique chemical characteristics compared to other liquids and, since living things have a high water content, understanding these chemical features is key to understanding life. In liquid water, hydrogen bonds constantly form and break as the water molecules slide past each other. The water molecules' motion (kinetic energy) causes the bonds to break due to the heat contained in the system. When the heat rises as water boils, the water molecules' higher kinetic energy causes the hydrogen bonds to break completely and allows water molecules to escape into the air as gas (steam or water vapor). Alternatively, when water temperature reduces and water freezes, the water molecules form a crystalline structure maintained by hydrogen bonding (there is not enough energy to break the hydrogen bonds) that makes ice less dense than liquid water, a phenomenon that we do not see when other liquids solidify.
Water’s lower density in its solid form is due to the way hydrogen bonds orient as they freeze: the water molecules push farther apart compared to liquid water. With most other liquids, solidification when the temperature drops includes lowering kinetic energy between molecules, allowing them to pack even more tightly than in liquid form and giving the solid a greater density than the liquid.
The lower density of ice, as Figure 2.14 depicts, an anomaly causes it to float at the surface of liquid water, such as in an iceberg or ice cubes in a glass of water. In lakes and ponds, ice will form on the water's surface creating an insulating barrier that protects the animals and plant life in the pond from freezing. Without this insulating ice layer, plants and animals living in the pond would freeze in the solid block of ice and could not survive. The expansion of ice relative to liquid water causes the detrimental effect of freezing on living organisms. The ice crystals that form upon freezing rupture the delicate membranes essential for living cells to function, irreversibly damaging them. Cells can only survive freezing if another liquid like glycerol temporarily replaces the water in them.
Figure 2.14 Hydrogen bonding makes ice less dense than liquid water. The (a) lattice structure of ice makes it less dense than the liquid water's freely flowing molecules, enabling it to (b) float on water. (credit a: modification of work by Jane Whitney, image created using Visual Molecular Dynamics (VMD) software1; credit b: modification of work by Carlos Ponte)
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Click here to see a 3-D animation of an ice lattice structure.
Water’s High Heat Capacity
Water’s high heat capacity is a property that hydrogen bonding among water molecules causes. Water has the highest specific heat capacity of any liquid. We define specific heat as the amount of heat one gram of a substance must absorb or lose to change its temperature by one degree Celsius. For water, this amount is one calorie. It therefore takes water a long time to heat and a long time to cool. In fact, water's specific heat capacity is about five times more than that of sand. This explains why the land cools faster than the sea. Due to its high heat capacity, warm blooded animals use water to more evenly disperse heat in their bodies: it acts in a similar manner to a car’s cooling system, transporting heat from warm places to cool places, causing the body to maintain a more even temperature.
Water’s Heat of Vaporization
Water also has a high heat of vaporization, the amount of energy required to change one gram of a liquid substance to a gas. A considerable amount of heat energy (586 cal) is required to accomplish this change in water. This process occurs on the water's surface. As liquid water heats up, hydrogen bonding makes it difficult to separate the liquid water molecules from each other, which is required for it to enter its gaseous phase (steam). As a result, water acts as a heat sink or heat reservoir and requires much more heat to boil than does a liquid such as ethanol (grain alcohol), whose hydrogen bonding with other ethanol molecules is weaker than water’s hydrogen bonding. Eventually, as water reaches its boiling point of 100° Celsius (212° Fahrenheit), the heat is able to break the hydrogen bonds between the water molecules, and the kinetic energy (motion) between the water molecules allows them to escape from the liquid as a gas. Even when below its boiling point, water’s individual molecules acquire enough energy from other water molecules such that some surface water molecules can escape and vaporize: we call this process evaporation.
The fact that hydrogen bonds need to be broken for water to evaporate means that bonds use a substantial amount of energy in the process. As the water evaporates, energy is taken up by the process, cooling the environment where the evaporation is taking place. In many living organisms, including in humans, the evaporation of sweat, which is 90 percent water, allows the organism to cool so that it can maintain homeostasis of body temperature.
Water’s Solvent Properties
Since water is a polar molecule with slightly positive and slightly negative charges, ions and polar molecules can readily dissolve in it. Therefore, we refer to water as a solvent, a substance capable of dissolving other polar molecules and ionic compounds. The charges associated with these molecules will form hydrogen bonds with water, surrounding the particle with water molecules. We refer to this as a sphere of hydration, or a hydration shell, as Figure 2.15 illustrates and serves to keep the particles separated or dispersed in the water.
When we add ionic compounds to water, the individual ions react with the water molecules' polar regions and their ionic bonds are disrupted in the process of dissociation. Dissociation occurs when atoms or groups of atoms break off from molecules and form ions. Consider table salt (NaCl, or sodium chloride): when we add NaCl crystals to water, the NaCl molecules dissociate into Na+ and Cl ions, and spheres of hydration form around the ions, as Figure 2.15 illustrates. The partially negative charge of the water molecule’s oxygen surrounds the positively charged sodium ion. The hydrogen's partially positive charge on the water molecule surrounds the negatively charged chloride ion.
Figure 2.15 When we mix table salt (NaCl) in water, it forms spheres of hydration around the ions.
Water’s Cohesive and Adhesive Properties
Have you ever filled a glass of water to the very top and then slowly added a few more drops? Before it overflows, the water forms a dome-like shape above the rim of the glass. This water can stay above the glass because of the property of cohesion. In cohesion, water molecules are attracted to each other (because of hydrogen bonding), keeping the molecules together at the liquid-gas (water-air) interface, although there is no more room in the glass.
Cohesion allows for surface tension, the capacity of a substance to withstand rupturing when placed under tension or stress. This is also why water forms droplets when on a dry surface rather than flattening by gravity. When we place a small scrap of paper onto a water droplet, the paper floats on top even though paper is denser (heavier) than the water. Cohesion and surface tension keep the water molecules' hydrogen bonds intact and support the item floating on the top. It’s even possible to “float” a needle on top of a glass of water if you place it gently without breaking the surface tension, as Figure 2.16 shows.
Figure 2.16 A needle's weight pulls the surface downward. At the same time, the surface tension pulls it up, suspending it on the water's surface preventing it from sinking. Notice the indentation in the water around the needle. (credit: Cory Zanker)
These cohesive forces are related to water’s property of adhesion, or the attraction between water molecules and other molecules. This attraction is sometimes stronger than water’s cohesive forces, especially when the water is exposed to charged surfaces such as those on the inside of thin glass tubes known as capillary tubes. We observe adhesion when water “climbs” up the tube placed in a glass of water: notice that the water appears to be higher on the tube's sides than in the middle. This is because the water molecules are attracted to the capillary's charged glass walls more than they are to each other and therefore adhere to it. We call this type of adhesion capillary action, as Figure 2.17 illustrates.
Figure 2.17 The adhesive forces exerted by the glass' internal surface exceeding the cohesive forces between the water molecules themselves causes capillary action in a glass tube. (credit: modification of work by Pearson-Scott Foresman, donated to the Wikimedia Foundation)
Why are cohesive and adhesive forces important for life? Cohesive and adhesive forces are important for transporting water from the roots to the leaves in plants. These forces create a “pull” on the water column. This pull results from the tendency of water molecules evaporating on the plant's surface to stay connected to water molecules below them, and so they are pulled along. Plants use this natural phenomenon to help transport water from their roots to their leaves. Without these properties of water, plants would be unable to receive the water and the dissolved minerals they require. In another example, insects such as the water strider, as Figure 2.18 shows, use the water's surface tension to stay afloat on the water's surface layer and even mate there.
Figure 2.18 Water’s cohesive and adhesive properties allow this water strider (Gerris sp.) to stay afloat. (credit: Tim Vickers)
pH, Buffers, Acids, and Bases
The pH of a solution indicates its acidity or basicity.
$H 2 O ( I ) ↔ H + ( aq ) + O H - ( aq ) H 2 O ( I ) ↔ H + ( aq ) + O H - ( aq )$
You may have used litmus or pH paper, filter paper treated with a natural water-soluble dye for use as a pH indicator. It tests how much acid (acidity) or base (basicity) exists in a solution. You might have even used some to test whether the water in a swimming pool is properly treated. In both cases, the pH test measures hydrogen ions' concentration in a given solution.
Hydrogen ions spontaneously generate in pure water by the dissociation (ionization) of a small percentage of water molecules into equal numbers of hydrogen (H+) ions and hydroxide (OH-) ions. While the hydroxide ions are kept in solution by their hydrogen bonding with other water molecules, the hydrogen ions, consisting of naked protons, immediately attract to un-ionized water molecules, forming hydronium ions (H3O+). Still, by convention, scientists refer to hydrogen ions and their concentration as if they were free in this state in liquid water.
The concentration of hydrogen ions dissociating from pure water is 1 × 10-7 moles H+ ions per liter of water. Moles (mol) are a way to express the amount of a substance (which can be atoms, molecules, ions, etc.). One mole represents the atomic weight of a substance, expressed in grams, which equals the amount of the substance containing as many units as there are atoms in 12 grams of 12C. Mathematically, one mole is equal to 6.02 × 1023 particles of the substance. Therefore, 1 mole of water is equal to 6.02 × 1023 water molecules. We calculate the pH as the negative of the base 10 logarithm of this concentration. The log10 of 1 × 10-7 is -7.0, and the negative of this number (indicated by the “p” of “pH”) yields a pH of 7.0, which is also a neutral pH. The pH inside of human cells and blood are examples of two body areas where near-neutral pH is maintained.
Non-neutral pH readings result from dissolving acids or bases in water. Using the negative logarithm to generate positive integers, high concentrations of hydrogen ions yield a low pH number; whereas, low levels of hydrogen ions result in a high pH. An acid is a substance that increases hydrogen ions' (H+) concentration in a solution, usually by having one of its hydrogen atoms dissociate. A base provides either hydroxide ions (OH) or other negatively charged ions that combine with hydrogen ions, reducing their concentration in the solution and thereby raising the pH. In cases where the base releases hydroxide ions, these ions bind to free hydrogen ions, generating new water molecules.
The stronger the acid, the more readily it donates H+. For example, hydrochloric acid (HCl) completely dissociates into hydrogen and chloride ions and is highly acidic; whereas the acids in tomato juice or vinegar do not completely dissociate and are weak acids. Conversely, strong bases are those substances that readily donate OHor take up hydrogen ions. Sodium hydroxide (NaOH) and many household cleaners are highly alkaline and give up OH rapidly when we place them in water, thereby raising the pH. An example of a weak basic solution is seawater, which has a pH near 8.0 This is close enough to a neutral pH that marine organisms have adapted in order to live and thrive in a saline environment.
The pH scale is, as we previously mentioned, an inverse logarithm and ranges from 0 to 14 (Figure 2.19). Anything below 7.0 (ranging from 0.0 to 6.9) is acidic, and anything above 7.0 (from 7.1 to 14.0) is alkaline. Extremes in pH in either direction from 7.0 are usually inhospitable to life. The pH inside cells (6.8) and the pH in the blood (7.4) are both very close to neutral. However, the environment in the stomach is highly acidic, with a pH of 1 to 2. As a result, how do stomach cells survive in such an acidic environment? How do they homeostatically maintain the near neutral pH inside them? The answer is that they cannot do it and are constantly dying. The stomach constantly produces new cells to replace dead ones, which stomach acids digest. Scientists estimate that the human body completely replaces the stomach lining every seven to ten days.
Figure 2.19 The pH scale measures hydrogen ions' (H+) concentration in a solution. (credit: modification of work by Edward Stevens)
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Watch this video for a straightforward explanation of pH and its logarithmic scale.
How can organisms whose bodies require a near-neutral pH ingest acidic and basic substances (a human drinking orange juice, for example) and survive? Buffers are the key. Buffers readily absorb excess H+ or OH, keeping the body's pH carefully maintained in the narrow range required for survival. Maintaining a constant blood pH is critical to a person’s well-being. The buffer maintaining the pH of human blood involves carbonic acid (H2CO3), bicarbonate ion (HCO3), and carbon dioxide (CO2). When bicarbonate ions combine with free hydrogen ions and become carbonic acid, it removes hydrogen ions and moderates pH changes. Similarly, as Figure 2.20 shows, excess carbonic acid can convert to carbon dioxide gas which we exhale through the lungs. This prevents too many free hydrogen ions from building up in the blood and dangerously reducing the blood’s pH. Likewise, if too much OH enters into the system, carbonic acid will combine with it to create bicarbonate, lowering the pH. Without this buffer system, the body’s pH would fluctuate enough to put survival in jeopardy.
Figure 2.20 This diagram shows the body’s buffering of blood pH levels. The blue arrows show the process of raising pH as more CO2 is made. The purple arrows indicate the reverse process: the lowering of pH as more bicarbonate is created.
Other examples of buffers are antacids that some people use to combat excess stomach acid. Many of these over-the-counter medications work in the same way as blood buffers, usually with at least one ion capable of absorbing hydrogen and moderating pH, bringing relief to those who suffer “heartburn” after eating. Water's unique properties that contribute to this capacity to balance pH—as well as water’s other characteristics—are essential to sustaining life on Earth.
Link to Learning
Link to Learning
To learn more about water, visit the U.S. Geological Survey Water Science for Schools All About Water! website.
Footnotes
• 1W. Humphrey W., A. Dalke, and K. Schulten, “VMD—Visual Molecular Dynamics,” Journal of Molecular Graphics 14 (1996): 33-38. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/01%3A_Unit_I-_The_Chemistry_of_Life/1.02%3A_The_Chemical_Foundation_of_Life/1.2.03%3A_Water.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Explain why carbon is important for life
• Describe the role of functional groups in biological molecules
Many complex molecules called macromolecules, such as proteins, nucleic acids (RNA and DNA), carbohydrates, and lipids comprise cells. The macromolecules are a subset of organic molecules (any carbon-containing liquid, solid, or gas) that are especially important for life. The fundamental component for all of these macromolecules is carbon. The carbon atom has unique properties that allow it to form covalent bonds to as many as four different atoms, making this versatile element ideal to serve as the basic structural component, or “backbone,” of the macromolecules.
Individual carbon atoms have an incomplete outermost electron shell. With an atomic number of 6 (six electrons and six protons), the first two electrons fill the inner shell, leaving four in the second shell. Therefore, carbon atoms can form up to four covalent bonds with other atoms to satisfy the octet rule. The methane molecule provides an example: it has the chemical formula CH4. Each of its four hydrogen atoms forms a single covalent bond with the carbon atom by sharing a pair of electrons. This results in a filled outermost shell.
Hydrocarbons
Hydrocarbons are organic molecules consisting entirely of carbon and hydrogen, such as methane (CH4) described above. We often use hydrocarbons in our daily lives as fuels—like the propane in a gas grill or the butane in a lighter. The many covalent bonds between the atoms in hydrocarbons store a great amount of energy, which releases when these molecules burn (oxidize). Methane, an excellent fuel, is the simplest hydrocarbon molecule, with a central carbon atom bonded to four different hydrogen atoms, as Figure 2.21 illustrates. The shape of its electron orbitals determines the shape of the methane molecule's geometry, where the atoms reside in three dimensions. The carbons and the four hydrogen atoms form a tetrahedron, with four triangular faces. For this reason, we describe methane as having tetrahedral geometry.
Figure 2.21 Methane has a tetrahedral geometry, with each of the four hydrogen atoms spaced 109.5° apart.
As the backbone of the large molecules of living things, hydrocarbons may exist as linear carbon chains, carbon rings, or combinations of both. Furthermore, individual carbon-to-carbon bonds may be single, double, or triple covalent bonds, and each type of bond affects the molecule's geometry in a specific way. This three-dimensional shape or conformation of the large molecules of life (macromolecules) is critical to how they function.
Hydrocarbon Chains
Successive bonds between carbon atoms form hydrocarbon chains. These may be branched or unbranched. Furthermore, a molecule's different geometries of single, double, and triple covalent bonds alter the overall molecule's geometry as Figure 2.22 illustrates. The hydrocarbons ethane, ethene, and ethyne serve as examples of how different carbon-to-carbon bonds affect the molecule's geometry. The names of all three molecules start with the prefix “eth-,” which is the prefix for two carbon hydrocarbons. The suffixes “-ane,” “-ene,” and “-yne” refer to the presence of single, double, or triple carbon-carbon bonds, respectively. Thus, propane, propene, and propyne follow the same pattern with three carbon molecules, butane, butene, and butyne for four carbon molecules, and so on. Double and triple bonds change the molecule's geometry: single bonds allow rotation along the bond's axis; whereas, double bonds lead to a planar configuration and triple bonds to a linear one. These geometries have a significant impact on the shape a particular molecule can assume.
Figure 2.22 When carbon forms single bonds with other atoms, the shape is tetrahedral. When two carbon atoms form a double bond, the shape is planar, or flat. Single bonds, like those in ethane, are able to rotate. Double bonds, like those in ethene, cannot rotate, so the atoms on either side are locked in place.
Hydrocarbon Rings
So far, the hydrocarbons we have discussed have been aliphatic hydrocarbons, which consist of linear chains of carbon atoms, and sometimes they can form rings with all single bonds, as shown in Figure 2.23 in the examples of cyclopentane and cyclohexane. Another type of hydrocarbon, aromatic hydrocarbons, consists of closed rings of carbon atoms with alternating single and double bonds. We find ring structures in aliphatic hydrocarbons, sometimes with the presence of double bonds, which we can see by comparing cyclohexane's structure (aliphatic) to benzene (aromatic) in Figure 2.23. Examples of biological molecules that incorporate the benzene ring include some amino acids and cholesterol and its derivatives, including the hormones estrogen and testosterone. We also find the benzene ring in the herbicide 2,4-D. Benzene is a natural component of crude oil and has been classified as a carcinogen. Some hydrocarbons have both aliphatic and aromatic portions. Beta-carotene is an example of such a hydrocarbon.
Figure 2.23 Carbon can form five- and six-membered rings. Single or double bonds may connect the carbons in the ring, and nitrogen may be substituted for carbon.
Isomers
The three-dimensional placement of atoms and chemical bonds within organic molecules is central to understanding their chemistry. We call molecules that share the same chemical formula but differ in the placement (structure) of their atoms and/or chemical bonds isomers. Structural isomers (like butane and isobutane in Figure 2.24a) differ in the placement of their covalent bonds: both molecules have four carbons and ten hydrogens (C4H10), but the different atom arrangement within the molecules leads to differences in their chemical properties. For example, butane is suited for use as a fuel for cigarette lighters and torches; whereas, isobutane is suited for use as a refrigerant and a propellant in spray cans.
Geometric isomers, alternatively have similar placements of their covalent bonds but differ in how these bonds are made to the surrounding atoms, especially in carbon-to-carbon double bonds. In the simple molecule butene (C4H8), the two methyl groups (CH3) can be on either side of the double covalent bond central to the molecule, as Figure 2.24b illustrates. When the carbons are bound on the same side of the double bond, this is the cis configuration. If they are on opposite sides of the double bond, it is a trans configuration. In the trans configuration, the carbons form a more or less linear structure; whereas, the carbons in the cis configuration make a bend (change in direction) of the carbon backbone.
Visual Connection
Visual Connection
Figure 2.24 We call molecules that have the same number and type of atoms arranged differently isomers. (a) Structural isomers have a different covalent arrangement of atoms. (b) Geometric isomers have a different arrangement of atoms around a double bond. (c) Enantiomers are mirror images of each other.
Which of the following statements is false?
1. Molecules with the formulas CH3CH2COOH and C3H6O2 could be structural isomers.
2. Molecules must have a double bond to be cis-trans isomers.
3. To be enantiomers, a molecule must have at least three different atoms or groups connected to a central carbon.
4. To be enantiomers, a molecule must have at least four different atoms or groups connected to a central carbon.
In triglycerides (fats and oils), long carbon chains known as fatty acids may contain double bonds, which can be in either the cis or trans configuration, as Figure 2.25 illustrates. Fats with at least one double bond between carbon atoms are unsaturated fats. When some of these bonds are in the cis configuration, the resulting bend in the chain's carbon backbone means that triglyceride molecules cannot pack tightly, so they remain liquid (oil) at room temperature. Alternatively, triglycerides with trans double bonds (popularly called trans fats), have relatively linear fatty acids that are able to pack tightly together at room temperature and form solid fats. In the human diet, trans fats are linked to an increased risk of cardiovascular disease, so many food manufacturers have reduced or eliminated their use in recent years. In contrast to unsaturated fats, we call triglycerides without double bonds between carbon atoms saturated fats, meaning that they contain all the hydrogen atoms available. Saturated fats are a solid at room temperature and usually of animal origin.
Figure 2.25 These space-filling models show a cis (oleic acid) and a trans (eliadic acid) fatty acid. Notice the bend in the molecule caused by the cis configuration.
Enantiomers
Enantiomers are molecules that share the same chemical structure and chemical bonds but differ in the three-dimensional placement of atoms so that they are non-superimposable mirror images. Figure 2.26 shows an amino acid alanine example, where the two structures are nonsuperimposable. In nature, the L-forms of amino acids are predominant in proteins. Some D forms of amino acids are seen in the cell walls of bacteria and polypeptides in other organisms. Similarly, the D-form of glucose is the main product of photosynthesis and we rarely see the molecule's L-form in nature.
Figure 2.26 Enantiomers are molecules that are mirror images of each other and are non-superimposable. The L/D naming system is from the Latin words for left and right: laevus and dexter, respectively. This example shows the L and D isomers of the amino acid alanine. Credit: Rao, A., Hawkins, A., Fletcher, S. and Ryan K. Department of Biology, Texas A&M University.
Functional Groups
Functional groups are groups of atoms that occur within molecules and confer specific chemical properties to those molecules. We find them along the “carbon backbone” of macromolecules. Chains and/or rings of carbon atoms with the occasional substitution of an element such as nitrogen or oxygen form this carbon backbone. Molecules with other elements in their carbon backbone are substituted hydrocarbons.
The functional groups in a macromolecule are usually attached to the carbon backbone at one or several different places along its chain and/or ring structure. Each of the four types of macromolecules—proteins, lipids, carbohydrates, and nucleic acids—has its own characteristic set of functional groups that contributes greatly to its differing chemical properties and its function in living organisms.
A functional group can participate in specific chemical reactions. Figure 2.27 shows some of the important functional groups in biological molecules. They include: hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl. These groups play an important role in forming molecules like DNA, proteins, carbohydrates, and lipids. We usually classify functional groups as hydrophobic or hydrophilic depending on their charge or polarity characteristics. An example of a hydrophobic group is the nonpolar methyl molecule. Among the hydrophilic functional groups is the carboxyl group in amino acids, some amino acid side chains, and the fatty acids that form triglycerides and phospholipids. This carboxyl group ionizes to release hydrogen ions (H+) from the COOH group resulting in the negatively charged COO- group. This contributes to the hydrophilic nature of whatever molecule on which it is found. Other functional groups, such as the carbonyl group, have a partially negatively charged oxygen atom that may form hydrogen bonds with water molecules, again making the molecule more hydrophilic.
Figure 2.27 These functional groups are in many different biological molecules. R, also known as R-group, is an abbreviation for any group in which a carbon or hydrogen atom is attached to the rest of the molecule.
Hydrogen bonds between functional groups (within the same molecule or between different molecules) are important to the function of many macromolecules and help them to fold properly into and maintain the appropriate shape for functioning. Hydrogen bonds are also involved in various recognition processes, such as DNA complementary base pairing and the binding of an enzyme to its substrate, as Figure 2.28 illustrates.
Figure 2.28 Hydrogen bonds connect two strands of DNA together to create the double-helix structure. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/01%3A_Unit_I-_The_Chemistry_of_Life/1.02%3A_The_Chemical_Foundation_of_Life/1.2.04%3A_Carbon.txt |
acid
molecule that donates hydrogen ions and increases the concentration of hydrogen ions in a solution
adhesion
attraction between water molecules and other molecules
aliphatic hydrocarbon
hydrocarbon consisting of a linear chain of carbon atoms
anion
negative ion that is formed by an atom gaining one or more electrons
aromatic hydrocarbon
hydrocarbon consisting of closed rings of carbon atoms
atom
the smallest unit of matter that retains all of the chemical properties of an element
atomic mass
calculated mean of the mass number for an element’s isotopes
atomic number
total number of protons in an atom
balanced chemical equation
statement of a chemical reaction with the number of each type of atom equalized for both the products and reactants
base
molecule that donates hydroxide ions or otherwise binds excess hydrogen ions and decreases the hydrogen ions' concentration in a solution
buffer
substance that resists a change in pH by absorbing or releasing hydrogen or hydroxide ions
calorie
amount of heat required to change the temperature of one gram of water by one degree Celsius
capillary action
occurs because water molecules are attracted to charges on the inner surfaces of narrow tubular structures such as glass tubes, drawing the water molecules to the tubes' sides
cation
positive ion that is formed by an atom losing one or more electrons
chemical bond
interaction between two or more of the same or different atoms that results in forming molecules
chemical reaction
process leading to rearranging atoms in molecules
chemical reactivity
the ability to combine and to chemically bond with each other
cohesion
intermolecular forces between water molecules caused by the polar nature of water; responsible for surface tension
compound
substance composed of molecules consisting of atoms of at least two different elements
covalent bond
type of strong bond formed between two atoms of the same or different elements; forms when electrons are shared between atoms
dissociation
release of an ion from a molecule such that the original molecule now consists of an ion and the charged remains of the original, such as when water dissociates into H+ and OH-
electrolyte
ion necessary for nerve impulse conduction, muscle contractions, and water balance
electron
negatively charged subatomic particle that resides outside of the nucleus in the electron orbital; lacks functional mass and has a negative charge of –1 unit
electron configuration
arrangement of electrons in an atom’s electron shell (for example, 1s22s22p6)
electron orbital
how electrons are spatially distributed surrounding the nucleus; the area where we are most likely to find an electron
electron transfer
movement of electrons from one element to another; important in creating ionic bonds
electronegativity
ability of some elements to attract electrons (often of hydrogen atoms), acquiring partial negative charges in molecules and creating partial positive charges on the hydrogen atoms
element
one of 118 unique substances that cannot break down into smaller substances; each element has unique properties and a specified number of protons
enantiomers
molecules that share overall structure and bonding patterns, but differ in how the atoms are three dimensionally placed such that they are mirror images of each other
equilibrium
steady state of relative reactant and product concentration in reversible chemical reactions in a closed system
evaporation
change from liquid to gaseous state at a body of water's surface, plant leaves, or an organism's skin
functional group
group of atoms that provides or imparts a specific function to a carbon skeleton
geometric isomer
isomer with similar bonding patterns differing in the placement of atoms alongside a double covalent bond
heat of vaporization of water
high amount of energy required for liquid water to turn into water vapor
hydrocarbon
molecule that consists only of carbon and hydrogen
hydrogen bond
weak bond between slightly positively charged hydrogen atoms and slightly negatively charged atoms in other molecules
hydrophilic
describes ions or polar molecules that interact well with other polar molecules such as water
hydrophobic
describes uncharged nonpolar molecules that do not interact well with polar molecules such as water
inert gas
(also, noble gas) element with filled outer electron shell that is unreactive with other atoms
ion
atom or chemical group that does not contain equal numbers of protons and electrons
ionic bond
chemical bond that forms between ions with opposite charges (cations and anions)
irreversible chemical reaction
chemical reaction where reactants proceed unidirectionally to form products
isomers
molecules that differ from one another even though they share the same chemical formula
isotope
one or more forms of an element that have different numbers of neutrons
law of mass action
chemical law stating that the rate of a reaction is proportional to the concentration of the reacting substances
litmus paper
(also, pH paper) filter paper treated with a natural water-soluble dye that changes its color as the pH of the environment changes in order to use it as a pH indicator
mass number
total number of protons and neutrons in an atom
matter
anything that has mass and occupies space
molecule
two or more atoms chemically bonded together
neutron
uncharged particle that resides in an atom's nucleus; has a mass of one amu
noble gas
see inert gas
nonpolar covalent bond
type of covalent bond that forms between atoms when electrons are shared equally between them
nucleus
core of an atom; contains protons and neutrons
octet rule
rule that atoms are most stable when they hold eight electrons in their outermost shells
orbital
region surrounding the nucleus; contains electron(s)
organic molecule
any molecule containing carbon (except carbon dioxide)
periodic table
organizational chart of elements indicating each element's atomic number and atomic mass; provides key information about the elements' properties
pH paper
see litmus paper
pH scale
scale ranging from zero to 14 that is inversely proportional to the hydrogen ions' concentration in a solution
polar covalent bond
type of covalent bond that forms as a result of unequal electron sharing, resulting in creating slightly positive and negative charged molecule regions
product
molecule that is result of chemical reaction
proton
positively charged particle that resides in the atom's nucleus; has a mass of one amu and a charge of +1
radioisotope
isotope that emits radiation comprised of subatomic particles to form more stable elements
reactant
molecule that takes part in a chemical reaction
reversible chemical reaction
chemical reaction that functions bidirectionally, where products may turn into reactants if their concentration is great enough
solvent
substance capable of dissolving another substance
specific heat capacity
the amount of heat one gram of a substance must absorb or lose to change its temperature by one degree Celsius
sphere of hydration
when a polar water molecule surrounds charged or polar molecules thus keeping them dissolved and in solution
structural isomers
molecules that share a chemical formula but differ in the placement of their chemical bonds
substituted hydrocarbon
hydrocarbon chain or ring containing an atom of another element in place of one of the backbone carbons
surface tension
tension at the surface of a body of liquid that prevents the molecules from separating; created by the attractive cohesive forces between the liquid's molecules
valence shell
outermost shell of an atom
van der Waals interaction
very weak interaction between molecules due to temporary charges attracting atoms that are very close together | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/01%3A_Unit_I-_The_Chemistry_of_Life/1.02%3A_The_Chemical_Foundation_of_Life/1.2.05%3A_Key_Terms.txt |
2.1 Atoms, Isotopes, Ions, and Molecules: The Building Blocks
Matter is anything that occupies space and has mass. It is comprised of elements. All of the 98 elements that occur naturally have unique qualities that allow them to combine in various ways to create molecules, which in turn combine to form cells, tissues, organ systems, and organisms. Atoms, which consist of protons, neutrons, and electrons, are the smallest units of an element that retain all of the properties of that element. Electrons can transfer, share, or cause charge disparities between atoms to create bonds, including ionic, covalent, and hydrogen bonds, as well as van der Waals interactions.
2.2 Water
Water has many properties that are critical to maintaining life. It is a polar molecule, allowing for forming hydrogen bonds. Hydrogen bonds allow ions and other polar molecules to dissolve in water. Therefore, water is an excellent solvent. The hydrogen bonds between water molecules cause the water to have a high heat capacity, meaning it takes considerable added heat to raise its temperature. As the temperature rises, the hydrogen bonds between water continually break and form anew. This allows for the overall temperature to remain stable, although energy is added to the system. Water also exhibits a high heat of vaporization, which is key to how organisms cool themselves by evaporating sweat. Water’s cohesive forces allow for the property of surface tension; whereas, we see its adhesive properties as water rises inside capillary tubes. The pH value is a measure of hydrogen ion concentration in a solution and is one of many chemical characteristics that is highly regulated in living organisms through homeostasis. Acids and bases can change pH values, but buffers tend to moderate the changes they cause. These properties of water are intimately connected to the biochemical and physical processes performed by living organisms, and life would be very different if these properties were altered, if it could exist at all.
2.3 Carbon
The unique properties of carbon make it a central part of biological molecules. Carbon binds to oxygen, hydrogen, and nitrogen covalently to form the many molecules important for cellular function. Carbon has four electrons in its outermost shell and can form four bonds. Carbon and hydrogen can form hydrocarbon chains or rings. Functional groups are groups of atoms that confer specific properties to hydrocarbon (or substituted hydrocarbon) chains or rings that define their overall chemical characteristics and function.
1.2.07: Visual Connection Questions
1.
Figure 2.3 How many neutrons do carbon-12 and carbon-13 have, respectively?
2.
Figure 2.7 An atom may give, take, or share electrons with another atom to achieve a full valence shell, the most stable electron configuration. Looking at this figure, how many electrons do elements in group 1 need to lose in order to achieve a stable electron configuration? How many electrons do elements in groups 14 and 17 need to gain to achieve a stable configuration?
3.
Figure 2.24 Which of the following statements is false?
1. Molecules with the formulas CH3CH2COOH and C3H6O2 could be structural isomers.
2. Molecules must have a double bond to be cis-trans isomers.
3. To be enantiomers, a molecule must have at least three different atoms or groups connected to a central carbon.
4. To be enantiomers, a molecule must have at least four different atoms or groups connected to a central carbon.
1.2.08: Review Questions
4.
If xenon has an atomic number of 54 and a mass number of 108, how many neutrons does it have?
1. 54
2. 27
3. 100
4. 108
5.
Atoms that vary in the number of neutrons found in their nuclei are called ________.
1. ions
2. neutrons
3. neutral atoms
4. isotopes
6.
Potassium has an atomic number of 19. What is its electron configuration?
1. shells 1 and 2 are full, and shell 3 has nine electrons
2. shells 1, 2 and 3 are full and shell 4 has three electrons
3. shells 1, 2 and 3 are full and shell 4 has one electron
4. shells 1, 2 and 3 are full and no other electrons are present
7.
Which type of bond represents a weak chemical bond?
1. hydrogen bond
2. atomic bond
3. covalent bond
4. nonpolar covalent bond
8.
Which of the following statements is not true?
1. Water is polar.
2. Water stabilizes temperature.
3. Water is essential for life.
4. Water is the most abundant molecule in the Earth’s atmosphere.
9.
When acids are added to a solution, the pH should ________.
1. decrease
2. increase
3. stay the same
4. cannot tell without testing
10.
We call a molecule that binds up excess hydrogen ions in a solution a(n) ________.
1. acid
2. isotope
3. base
4. donator
11.
Which of the following statements is true?
1. Acids and bases cannot mix together.
2. Acids and bases will neutralize each other.
3. Acids, but not bases, can change the pH of a solution.
4. Acids donate hydroxide ions (OH); bases donate hydrogen ions (H+).
12.
Each carbon atom can bond with as many as________ other atom(s) or molecule(s).
1. one
2. two
3. six
4. four
13.
Which of the following is not a functional group that can bond with carbon?
1. sodium
2. hydroxyl
3. phosphate
4. carbonyl
1.2.09: Critical Thinking Questions
14.
What makes ionic bonds different from covalent bonds?
15.
Why are hydrogen bonds and van der Waals interactions necessary for cells?
16.
Discuss how buffers help prevent drastic swings in pH.
17.
Why can some insects walk on water?
18.
What property of carbon makes it essential for organic life?
19.
Compare and contrast saturated and unsaturated triglycerides. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/01%3A_Unit_I-_The_Chemistry_of_Life/1.02%3A_The_Chemical_Foundation_of_Life/1.2.06%3A_Chapter_Summary.txt |
Food provides the body with the nutrients it needs to survive. Many of these critical nutrients are biological macromolecules, or large molecules, necessary for life. These macromolecules (polymers) are built from different combinations of smaller organic molecules (monomers). What specific types of biological macromolecules do living things require? How are these molecules formed? What functions do they serve? In this chapter, these questions will be explored.
• 1.3.1: Introduction
Food provides the body with the nutrients it needs to survive. Many of these critical nutrients are biological macromolecules, or large molecules, necessary for life. These macromolecules (polymers) are built from different combinations of smaller organic molecules (monomers). What specific types of biological macromolecules do living things require? How are these molecules formed? What functions do they serve? In this chapter, these questions will be explored.
• 1.3.2: Synthesis of Biological Macromolecules
Biological macromolecules are large molecules, necessary for life, that are built from smaller organic molecules. There are four major classes of biological macromolecules (carbohydrates, lipids, proteins, and nucleic acids); each is an important cell component and performs a wide array of functions. Combined, these molecules make up the majority of a cell’s dry mass (recall that water makes up the majority of its complete mass).
• 1.3.3: Carbohydrates
Carbohydrates are, in fact, an essential part of our diet; grains, fruits, and vegetables are all natural sources of carbohydrates. Carbohydrates provide energy to the body, particularly through glucose, a simple sugar that is a component of starch and an ingredient in many staple foods. Carbohydrates also have other important functions in humans, animals, and plants.
• 1.3.4: Lipids
Lipids include a diverse group of compounds that are largely nonpolar in nature. This is because they are hydrocarbons that include mostly nonpolar carbon–carbon or carbon–hydrogen bonds. Non-polar molecules are hydrophobic (“water fearing”), or insoluble in water. Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of fats. Lipids also provide insulation from the environment for plants and animals.
• 1.3.5: Proteins
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective; they may serve in transport, storage, or membranes; or they may be toxins or enzymes. Each cell in a living system may contain thousands of proteins, each with a unique function. Their structures, like their functions, vary greatly.
• 1.3.6: Nucleic Acids
Nucleic acids are the most important macromolecules for the continuity of life. They carry the genetic blueprint of a cell and carry instructions for the functioning of the cell.
• 1.3.7: Key Terms
• 1.3.8: Chapter Summary
• 1.3.9: Visual Connection Questions
• 1.3.10: Review Questions
• 1.3.11: Critical Thinking Questions
Thumbnail: 1K6F_Crystal Structure Of The Collagen Triple Helix Model Pro- Pro-Gly103. (CC-SA-BY-3.0; Nevit Dilmen)
1.03: Biological Macromolecules
Figure 3.1 Foods such as bread, fruit, and cheese are rich sources of biological macromolecules. (credit: modification of work by Bengt Nyman)
Food provides the body with the nutrients it needs to survive. Many of these critical nutrients are biological macromolecules, or large molecules, necessary for life. Different smaller organic molecule (monomer) combinations build these macromolecules (polymers). What specific biological macromolecules do living things require? How do these molecules form? What functions do they serve? We explore these questions in this chapter. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/01%3A_Unit_I-_The_Chemistry_of_Life/1.03%3A_Biological_Macromolecules/1.3.01%3A_Introduction.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Understand macromolecule synthesis
• Explain dehydration (or condensation) and hydrolysis reactions
As you’ve learned, biological macromolecules are large molecules, necessary for life, that are built from smaller organic molecules. There are four major biological macromolecule classes (carbohydrates, lipids, proteins, and nucleic acids). Each is an important cell component and performs a wide array of functions. Combined, these molecules make up the majority of a cell’s dry mass (recall that water makes up the majority of its complete mass). Biological macromolecules are organic, meaning they contain carbon. In addition, they may contain hydrogen, oxygen, nitrogen, and additional minor elements.
Dehydration Synthesis
Most macromolecules are made from single subunits, or building blocks, called monomers. The monomers combine with each other using covalent bonds to form larger molecules known as polymers. In doing so, monomers release water molecules as byproducts. This type of reaction is dehydration synthesis, which means “to put together while losing water.”
Figure 3.2 In the dehydration synthesis reaction above, two glucose molecules link to form the disaccharide maltose. In the process, it forms a water molecule.
In a dehydration synthesis reaction (Figure 3.2), the hydrogen of one monomer combines with the hydroxyl group of another monomer, releasing a water molecule. At the same time, the monomers share electrons and form covalent bonds. As additional monomers join, this chain of repeating monomers forms a polymer. Different monomer types can combine in many configurations, giving rise to a diverse group of macromolecules. Even one kind of monomer can combine in a variety of ways to form several different polymers. For example, glucose monomers are the constituents of starch, glycogen, and cellulose.
Hydrolysis
Polymers break down into monomers during hydrolysis. A chemical reaction occurs when inserting a water molecule across the bond. Breaking a covalent bond with this water molecule in the compound achieves this (Figure 3.3). During these reactions, the polymer breaks into two components: one part gains a hydrogen atom (H+) and the other gains a hydroxyl molecule (OH–) from a split water molecule.
Figure 3.3 In the hydrolysis reaction here, the disaccharide maltose breaks down to form two glucose monomers by adding a water molecule. Note that this reaction is the reverse of the synthesis reaction in Figure 3.2.
Dehydration and hydrolysis reactions are catalyzed, or “sped up,” by specific enzymes; dehydration reactions involve the formation of new bonds, requiring energy, while hydrolysis reactions break bonds and release energy. These reactions are similar for most macromolecules, but each monomer and polymer reaction is specific for its class. For example, catalytic enzymes in the digestive system hydrolyze or break down the food we ingest into smaller molecules. This allows cells in our body to easily absorb nutrients in the intestine. A specific enzyme breaks down each macromolecule. For instance, amylase, sucrase, lactase, or maltase break down carbohydrates. Enzymes called proteases, such as pepsin and peptidase, and hydrochloric acid break down proteins. Lipases break down lipids. These broken down macromolecules provide energy for cellular activities.
Link to Learning
Link to Learning
Visit this site to see visual representations of dehydration synthesis and hydrolysis. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/01%3A_Unit_I-_The_Chemistry_of_Life/1.03%3A_Biological_Macromolecules/1.3.02%3A_Synthesis_of_Biological_Macromolecules.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Discuss the role of carbohydrates in cells and in the extracellular materials of animals and plants
• Explain carbohydrate classifications
• List common monosaccharides, disaccharides, and polysaccharides
Most people are familiar with carbohydrates, one type of macromolecule, especially when it comes to what we eat. To lose weight, some individuals adhere to “low-carb” diets. Athletes, in contrast, often “carb-load” before important competitions to ensure that they have enough energy to compete at a high level. Carbohydrates are, in fact, an essential part of our diet. Grains, fruits, and vegetables are all natural carbohydrate sources that provide energy to the body, particularly through glucose, a simple sugar that is a component of starch and an ingredient in many staple foods. Carbohydrates also have other important functions in humans, animals, and plants.
Molecular Structures
The stoichiometric formula (CH2O)n, where n is the number of carbons in the molecule represents carbohydrates. In other words, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. This formula also explains the origin of the term “carbohydrate”: the components are carbon (“carbo”) and the components of water (hence, “hydrate”). Scientists classify carbohydrates into three subtypes: monosaccharides, disaccharides, and polysaccharides.
Monosaccharides
Monosaccharides (mono- = “one”; sacchar- = “sweet”) are simple sugars, the most common of which is glucose. In monosaccharides, the number of carbons usually ranges from three to seven. Most monosaccharide names end with the suffix -ose. If the sugar has an aldehyde group (the functional group with the structure R-CHO), it is an aldose, and if it has a ketone group (the functional group with the structure RC(=O)R'), it is a ketose. Depending on the number of carbons in the sugar, they can be trioses (three carbons), pentoses (five carbons), and/or hexoses (six carbons). Figure 3.4 illustrates monosaccharides.
Figure 3.4 Scientists classify monosaccharides based on the position of their carbonyl group and the number of carbons in the backbone. Aldoses have a carbonyl group (indicated in green) at the end of the carbon chain, and ketoses have a carbonyl group in the middle of the carbon chain. Trioses, pentoses, and hexoses have three-, five-, and six- carbon backbones, respectively.
The chemical formula for glucose is C6H12O6. In humans, glucose is an important source of energy. During cellular respiration, energy releases from glucose, and that energy helps make adenosine triphosphate (ATP). Plants synthesize glucose using carbon dioxide and water, and glucose in turn provides energy requirements for the plant. Humans and other animals that feed on plants often obtain glucose from catabolized (cell breakdown of larger molecules) starch.
Galactose (part of lactose, or milk sugar) and fructose (found in sucrose, in fruit) are other common monosaccharides. Although glucose, galactose, and fructose all have the same chemical formula (C6H12O6), they differ structurally and chemically (and are isomers) because of the different arrangement of functional groups around the asymmetric carbon. All these monosaccharides have more than one asymmetric carbon (Figure 3.5).
Visual Connection
Visual Connection
Figure 3.5 Glucose, galactose, and fructose are all hexoses. They are structural isomers, meaning they have the same chemical formula (C6H12O6) but a different atom arrangement.
What kind of sugars are these, aldose or ketose?
Glucose, galactose, and fructose are isomeric monosaccharides (hexoses), meaning they have the same chemical formula but have slightly different structures. Glucose and galactose are aldoses, and fructose is a ketose.
Monosaccharides can exist as a linear chain or as ring-shaped molecules. In aqueous solutions they are usually in ring forms (Figure 3.6). Glucose in a ring form can have two different hydroxyl group arrangements (OH) around the anomeric carbon (carbon 1 that becomes asymmetric in the ring formation process). If the hydroxyl group is below carbon number 1 in the sugar, it is in the alpha (α) position, and if it is above the plane, it is in the beta (β) position.
Figure 3.6 Five and six carbon monosaccharides exist in equilibrium between linear and ring forms. When the ring forms, the side chain it closes on locks into an α or β position. Fructose and ribose also form rings, although they form five-membered rings as opposed to the six-membered ring of glucose.
Disaccharides
Disaccharides (di- = “two”) form when two monosaccharides undergo a dehydration reaction (or a condensation reaction or dehydration synthesis). During this process, one monosaccharide's hydroxyl group combines with another monosaccharide's hydrogen, releasing a water molecule and forming a covalent bond. A covalent bond forms between a carbohydrate molecule and another molecule (in this case, between two monosaccharides). Scientists call this a glycosidic bond (Figure 3.7). Glycosidic bonds (or glycosidic linkages) can be an alpha or beta type. An alpha bond is formed when the OH group on the carbon-1 of the first glucose is below the ring plane, and a beta bond is formed when the OH group on the carbon-1 is above the ring plane.
Figure 3.7 Sucrose forms when a glucose monomer and a fructose monomer join in a dehydration reaction to form a glycosidic bond. In the process, a water molecule is lost. By convention, the carbon atoms in a monosaccharide are numbered from the terminal carbon closest to the carbonyl group. In sucrose, a glycosidic linkage forms between carbon 1 in glucose and carbon 2 in fructose.
Common disaccharides include lactose, maltose, and sucrose (Figure 3.8). Lactose is a disaccharide consisting of the monomers glucose and galactose. It is naturally in milk. Maltose, or malt sugar, is a disaccharide formed by a dehydration reaction between two glucose molecules. The most common disaccharide is sucrose, or table sugar, which is comprised of glucose and fructose monomers.
Figure 3.8 Common disaccharides include maltose (grain sugar), lactose (milk sugar), and sucrose (table sugar).
Polysaccharides
A long chain of monosaccharides linked by glycosidic bonds is a polysaccharide (poly- = “many”). The chain may be branched or unbranched, and it may contain different types of monosaccharides. The molecular weight may be 100,000 daltons or more depending on the number of joined monomers. Starch, glycogen, cellulose, and chitin are primary examples of polysaccharides.
Plants store sugars in the form of starch. In plants, an amylose and amylopectin mixture (both glucose polymers) comprise these sugars. Plants are able to synthesize glucose, and they store the excess glucose, beyond their immediate energy needs, as starch in different plant parts, including roots and seeds. The starch in the seeds provides food for the embryo as it germinates and can also act as a food source for humans and animals. Enzymes break down the starch that humans consume. For example, an amylase present in saliva catalyzes, or breaks down this starch into smaller molecules, such as maltose and glucose. The cells can then absorb the glucose.
Glucose starch comprises monomers that are joined by α 1-4 or α 1-6 glycosidic bonds. The numbers 1-4 and 1-6 refer to the carbon number of the two residues that have joined to form the bond. As Figure 3.9 illustrates, unbranched glucose monomer chains (only α 1-4 linkages) form the starch; whereas, amylopectin is a branched polysaccharide (α 1-6 linkages at the branch points).
Figure 3.9 Amylose and amylopectin are two different starch forms. Unbranched glucose monomer chains comprise amylose by α 1-4 glycosidic linkages. Branched glucose monomer chains comprise amylopectin by α 1-4 and α 1-6 glycosidic linkages. Because of the way the subunits are joined, the glucose chains have a helical structure. Glycogen (not shown) is similar in structure to amylopectin but more highly branched.
Glycogen is the storage form of glucose in humans and other vertebrates and is comprised of monomers of glucose. Glycogen is the animal equivalent of starch and is a highly branched molecule usually stored in liver and muscle cells. Whenever blood glucose levels decrease, glycogen breaks down to release glucose in a process scientists call glycogenolysis.
Cellulose is the most abundant natural biopolymer. Cellulose mostly comprises a plant's cell wall. This provides the cell structural support. Wood and paper are mostly cellulosic in nature. Glucose monomers comprise cellulose that β 1-4 glycosidic bonds link (Figure 3.10).
Figure 3.10 Cellulose is an organic compound composed of linear chains of hundreds to thousands of linked glucose molecules. The glucose monomers form hydrogen bonds, holding the chains firmly together side-by-side and form strong microfibrils. This rigidity is an important structural component of the cell walls found in plants. Credit: Ryan, K. Rao, A. and Hawkins, A. Department of Biology, Texas A&M University.
As Figure 3.10 shows, every other glucose monomer in cellulose is flipped over, and the monomers are packed tightly as extended long chains. This gives cellulose its rigidity and high tensile strength—which is so important to plant cells. While human digestive enzymes cannot break down the β 1-4 linkage, herbivores such as cows, koalas, and buffalos are able, with the help of the specialized flora in their stomach, to digest plant material that is rich in cellulose and use it as a food source. In some of these animals, certain species of bacteria and protists reside in the rumen (part of the herbivore's digestive system) and secrete the enzyme cellulase. The appendix of grazing animals also contains bacteria that digest cellulose, giving it an important role in ruminants' digestive systems. Cellulases can break down cellulose into glucose monomers that animals use as an energy source. Termites are also able to break down cellulose because of the presence of other organisms in their bodies that secrete cellulases.
Carbohydrates serve various functions in different animals. Arthropods (insects, crustaceans, and others) have an outer skeleton, the exoskeleton, which protects their internal body parts (as we see in the bee in Figure 3.11). This exoskeleton is made of the biological macromolecule chitin, which is a nitrogen-containing polysaccharide. It is made of repeating N-acetyl-β-d-glucosamine units, which are a modified sugar. Chitin is also a major component of fungal cell walls. Fungi are neither animals nor plants and form a kingdom of their own in the domain Eukarya.
Figure 3.11 Insects have a hard outer exoskeleton made of chitin, a type of polysaccharide. (credit: Louise Docker)
Career Connection
Career Connections
Registered DietitianObesity is a worldwide health concern, and many diseases such as diabetes and heart disease are becoming more prevalent because of obesity. This is one of the reasons why people increasingly seek out registered dietitians for advice. Registered dietitians help plan nutrition programs for individuals in various settings. They often work with patients in health care facilities, designing nutrition plans to treat and prevent diseases. For example, dietitians may teach a patient with diabetes how to manage blood sugar levels by eating the correct types and amounts of carbohydrates. Dietitians may also work in nursing homes, schools, and private practices.
To become a registered dietitian, one needs to earn at least a bachelor’s degree in dietetics, nutrition, food technology, or a related field. In addition, registered dietitians must complete a supervised internship program and pass a national exam. Those who pursue careers in dietetics take courses in nutrition, chemistry, biochemistry, biology, microbiology, and human physiology. Dietitians must become experts in the chemistry and physiology (biological functions) of food (proteins, carbohydrates, and fats).
Benefits of Carbohydrates
Are carbohydrates good for you? Some people believe that carbohydrates are bad and they should avoid them. Some diets completely forbid carbohydrate consumption, claiming that a low-carbohydrate diet helps people to lose weight faster. However, carbohydrates have been an important part of the human diet for thousands of years. Artifacts from ancient civilizations show the presence of wheat, rice, and corn in our ancestors’ storage areas.
As part of a well balanced diet, we should supplement carbohydrates with proteins, vitamins, and fats. Calorie-wise, a gram of carbohydrate provides 4.3 Kcal. For comparison, fats provide 9 Kcal/g, a less desirable ratio. Carbohydrates contain soluble and insoluble elements. The insoluble part, fiber, is mostly cellulose. Fiber has many uses. It promotes regular bowel movement by adding bulk, and it regulates the blood glucose consumption rate. Fiber also helps to remove excess cholesterol from the body. Fiber binds to the cholesterol in the small intestine, then attaches to the cholesterol and prevents the cholesterol particles from entering the bloodstream. Cholesterol then exits the body via the feces. Fiber-rich diets also have a protective role in reducing the occurrence of colon cancer. In addition, a meal containing whole grains and vegetables gives a feeling of fullness. As an immediate source of energy, glucose breaks down during the cellular respiration process, which produces ATP, the cell's energy currency. Without consuming carbohydrates, we reduce the availability of “instant energy”. Eliminating carbohydrates from the diet may be necessary for some people, but such a step may not be healthy for everyone.
Link to Learning
Link to Learning
For an additional perspective on carbohydrates, explore “Biomolecules: the Carbohydrates” through this interactive animation. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/01%3A_Unit_I-_The_Chemistry_of_Life/1.03%3A_Biological_Macromolecules/1.3.03%3A_Carbohydrates.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Describe the four major types of lipids
• Explain the role of fats in storing energy
• Differentiate between saturated and unsaturated fatty acids
• Describe phospholipids and their role in cells
• Define the basic structure of a steroid and some steroid functions
• Explain how cholesterol helps maintain the plasma membrane's fluid nature
Lipids include a diverse group of compounds that are largely nonpolar in nature. This is because they are hydrocarbons that include mostly nonpolar carbon–carbon or carbon–hydrogen bonds. Non-polar molecules are hydrophobic (“water fearing”), or insoluble in water. Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of fats. Lipids also provide insulation from the environment for plants and animals (Figure 3.12). For example, they help keep aquatic birds and mammals dry when forming a protective layer over fur or feathers because of their water-repellant hydrophobic nature. Lipids are also the building blocks of many hormones and are an important constituent of all cellular membranes. Lipids include fats, oils, waxes, phospholipids, and steroids.
Figure 3.12 Hydrophobic lipids in aquatic mammals' fur, such as this river otter, protect them from the elements. (credit: Ken Bosma)
Fats and Oils
A fat molecule consists of two main components—glycerol and fatty acids. Glycerol is an organic compound (alcohol) with three carbons, five hydrogens, and three hydroxyl (OH) groups. Fatty acids have a long chain of hydrocarbons to which a carboxyl group is attached, hence the name “fatty acid.” The number of carbons in the fatty acid may range from 4 to 36. The most common are those containing 12–18 carbons. In a fat molecule, the fatty acids attach to each of the glycerol molecule's three carbons with an ester bond through an oxygen atom (Figure 3.13).
Figure 3.13 Joining three fatty acids to a glycerol backbone in a dehydration reaction forms triacylglycerol. Three water molecules release in the process.
During this ester bond formation, three water molecules are released. The three fatty acids in the triacylglycerol may be similar or dissimilar. We also call fats triacylglycerols or triglycerides because of their chemical structure. Some fatty acids have common names that specify their origin. For example, palmitic acid, a saturated fatty acid, is derived from the palm tree. Arachidic acid is derived from Arachis hypogea, the scientific name for groundnuts or peanuts.
Fatty acids may be saturated or unsaturated. In a fatty acid chain, if there are only single bonds between neighboring carbons in the hydrocarbon chain, the fatty acid is saturated. Saturated fatty acids are saturated with hydrogen. In other words, the number of hydrogen atoms attached to the carbon skeleton is maximized. Stearic acid is an example of a saturated fatty acid (Figure 3.14).
Figure 3.14 Stearic acid is a common saturated fatty acid.
When the hydrocarbon chain contains a double bond, the fatty acid is unsaturated. Oleic acid is an example of an unsaturated fatty acid (Figure 3.15).
Figure 3.15 Oleic acid is a common unsaturated fatty acid.
Most unsaturated fats are liquid at room temperature. We call these oils. If there is one double bond in the molecule, then it is a monounsaturated fat (e.g., olive oil), and if there is more than one double bond, then it is a polyunsaturated fat (e.g., canola oil).
When a fatty acid has no double bonds, it is a saturated fatty acid because it is not possible to add more hydrogen to the chain's carbon atoms. A fat may contain similar or different fatty acids attached to glycerol. Long straight fatty acids with single bonds generally pack tightly and are solid at room temperature. Animal fats with stearic acid and palmitic acid (common in meat) and the fat with butyric acid (common in butter) are examples of saturated fats. Mammals store fats in specialized cells, or adipocytes, where fat globules occupy most of the cell’s volume. Plants store fat or oil in many seeds and use them as a source of energy during seedling development. Unsaturated fats or oils are usually of plant origin and contain cis unsaturated fatty acids. Cis and trans indicate the configuration of the molecule around the double bond. If hydrogens are present in the same plane, it is a cis fat. If the hydrogen atoms are on two different planes, it is a trans fat. The cis double bond causes a bend or a “kink” that prevents the fatty acids from packing tightly, keeping them liquid at room temperature (Figure 3.16). Olive oil, corn oil, canola oil, and cod liver oil are examples of unsaturated fats. Unsaturated fats help to lower blood cholesterol levels; whereas, saturated fats contribute to plaque formation in the arteries.
Figure 3.16 Saturated fatty acids have hydrocarbon chains connected by single bonds only. Unsaturated fatty acids have one or more double bonds. Each double bond may be in a cis or trans configuration. In the cis configuration, both hydrogens are on the same side of the hydrocarbon chain. In the trans configuration, the hydrogens are on opposite sides. A cis double bond causes a kink in the chain.
Trans Fats
The food industry artificially hydrogenates oils to make them semi-solid and of a consistency desirable for many processed food products. Simply speaking, hydrogen gas is bubbled through oils to solidify them. During this hydrogenation process, double bonds of the cis- conformation in the hydrocarbon chain may convert to double bonds in the trans- conformation.
Margarine, some types of peanut butter, and shortening are examples of artificially hydrogenated trans fats. Recent studies have shown that an increase in trans fats in the human diet may lead to higher levels of low-density lipoproteins (LDL), or “bad” cholesterol, which in turn may lead to plaque deposition in the arteries, resulting in heart disease. Many fast food restaurants have recently banned using trans fats, and food labels are required to display the trans fat content.
Omega Fatty Acids
Essential fatty acids are those that the human body requires but does not synthesize. Consequently, they have to be supplemented through ingestion via the diet. Omega-3 fatty acids (like those in Figure 3.17) fall into this category and are one of only two known for humans (the other is omega-6 fatty acid). These are polyunsaturated fatty acids and are omega-3 because a double bond connects the third carbon from the hydrocarbon chain's end to its neighboring carbon.
Figure 3.17 Alpha-linolenic acid is an example of an omega-3 fatty acid. It has three cis double bonds and, as a result, a curved shape. For clarity, the diagram does not show the carbons. Each singly bonded carbon has two hydrogens associated with it, which the diagram also does not show.
The farthest carbon away from the carboxyl group is numbered as the omega (ω) carbon, and if the double bond is between the third and fourth carbon from that end, it is an omega-3 fatty acid. Nutritionally important because the body does not make them, omega-3 fatty acids include alpha-linoleic acid (ALA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA), all of which are polyunsaturated. Salmon, trout, and tuna are good sources of omega-3 fatty acids. Research indicates that omega-3 fatty acids reduce the risk of sudden death from heart attacks, lower triglycerides in the blood, decrease blood pressure, and prevent thrombosis by inhibiting blood clotting. They also reduce inflammation, and may help lower the risk of some cancers in animals.
Like carbohydrates, fats have received considerable bad publicity. It is true that eating an excess of fried foods and other “fatty” foods leads to weight gain. However, fats do have important functions. Many vitamins are fat soluble, and fats serve as a long-term storage form of fatty acids: a source of energy. They also provide insulation for the body. Therefore, we should consume “healthy” fats in moderate amounts on a regular basis.
Waxes
Wax covers some aquatic birds' feathers and some plants' leaf surfaces. Because of waxes' hydrophobic nature, they prevent water from sticking on the surface (Figure 3.18). Long fatty acid chains esterified to long-chain alcohols comprise waxes.
Figure 3.18 Lipids comprise waxy coverings on some leaves. (credit: Roger Griffith)
Phospholipids
Phospholipids are major plasma membrane constituents that comprise cells' outermost layer. Like fats, they are comprised of fatty acid chains attached to a glycerol or sphingosine backbone. However, instead of three fatty acids attached as in triglycerides, there are two fatty acids forming diacylglycerol, and a modified phosphate group occupies the glycerol backbone's third carbon (Figure 3.19). A phosphate group alone attached to a diacylglycerol does not qualify as a phospholipid. It is phosphatidate (diacylglycerol 3-phosphate), the precursor of phospholipids. An alcohol modifies the phosphate group. Phosphatidylcholine and phosphatidylserine are two important phospholipids that are in plasma membranes.
Figure 3.19 A phospholipid is a molecule with two fatty acids and a modified phosphate group attached to a glycerol backbone. Adding a charged or polar chemical group may modify the phosphate.
A phospholipid is an amphipathic molecule, meaning it has a hydrophobic and a hydrophilic part. The fatty acid chains are hydrophobic and cannot interact with water; whereas, the phosphate-containing group is hydrophilic and interacts with water (Figure 3.20).
Figure 3.20 The phospholipid bilayer is the major component of all cellular membranes. The hydrophilic head groups of the phospholipids face the aqueous solution. The hydrophobic tails are sequestered in the middle of the bilayer.
The head is the hydrophilic part, and the tail contains the hydrophobic fatty acids. In a membrane, a bilayer of phospholipids forms the structure's matrix, phospholipids' fatty acid tails face inside, away from water; whereas, the phosphate group faces the outside, aqueous side (Figure 3.20).
Phospholipids are responsible for the plasma membrane's dynamic nature. If a drop of phospholipids is placed in water, it spontaneously forms a structure that scientists call a micelle, where the hydrophilic phosphate heads face the outside and the fatty acids face the structure's interior.
Steroids
Unlike the phospholipids and fats that we discussed earlier, steroids have a fused ring structure. Although they do not resemble the other lipids, scientists group them with them because they are also hydrophobic and insoluble in water. All steroids have four linked carbon rings and several of them, like cholesterol, have a short tail (Figure 3.21). Many steroids also have the –OH functional group, which puts them in the alcohol classification (sterols).
Figure 3.21 Four fused hydrocarbon rings comprise steroids such as cholesterol and cortisol.
Cholesterol is the most common steroid. The liver synthesizes cholesterol and is the precursor to many steroid hormones such as testosterone and estradiol, which gonads and endocrine glands secrete. It is also the precursor to Vitamin D. Cholesterol is also the precursor of bile salts, which help emulsifying fats and their subsequent absorption by cells. Although lay people often speak negatively about cholesterol, it is necessary for the body's proper functioning. Sterols (cholesterol in animal cells, phytosterol in plants) are components of the plasma membrane of cells and are found within the phospholipid bilayer.
Link to Learning
Link to Learning
For an additional perspective on lipids, watch this video about types of fat. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/01%3A_Unit_I-_The_Chemistry_of_Life/1.03%3A_Biological_Macromolecules/1.3.04%3A_Lipids.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Describe the functions proteins perform in the cell and in tissues
• Discuss the relationship between amino acids and proteins
• Explain the four levels of protein organization
• Describe the ways in which protein shape and function are linked
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Each cell in a living system may contain thousands of proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
Types and Functions of Proteins
Enzymes, which living cells produce, are catalysts in biochemical reactions (like digestion) and are usually complex or conjugated proteins. Each enzyme is specific for the substrate (a reactant that binds to an enzyme) upon which it acts. The enzyme may help in breakdown, rearrangement, or synthesis reactions. We call enzymes that break down their substrates catabolic enzymes. Those that build more complex molecules from their substrates are anabolic enzymes, and enzymes that affect the rate of reaction are catalytic enzymes. Note that all enzymes increase the reaction rate and, therefore, are organic catalysts. An example of an enzyme is salivary amylase, which hydrolyzes its substrate amylose, a component of starch.
Hormones are chemical-signaling molecules, usually small proteins or steroids, secreted by endocrine cells that act to control or regulate specific physiological processes, including growth, development, metabolism, and reproduction. For example, insulin is a protein hormone that helps regulate the blood glucose level. Table 3.1 lists the primary types and functions of proteins.
Protein Types and Functions
TypeExamplesFunctions
Digestive EnzymesAmylase, lipase, pepsin, trypsinHelp in food by catabolizing nutrients into monomeric units
TransportHemoglobin, albuminCarry substances in the blood or lymph throughout the body
StructuralActin, tubulin, keratinConstruct different structures, like the cytoskeleton
HormonesInsulin, thyroxineCoordinate different body systems' activity
DefenseImmunoglobulinsProtect the body from foreign pathogens
ContractileActin, myosinEffect muscle contraction
StorageLegume storage proteins, egg white (albumin)Provide nourishment in early embryo development and the seedling
Table 3.1
Proteins have different shapes and molecular weights. Some proteins are globular in shape; whereas, others are fibrous in nature. For example, hemoglobin is a globular protein, but collagen, located in our skin, is a fibrous protein. Protein shape is critical to its function, and many different types of chemical bonds maintain this shape. Changes in temperature, pH, and exposure to chemicals may lead to permanent changes in the protein's shape, leading to loss of function, or denaturation. Different arrangements of the same 20 types of amino acids comprise all proteins. Two rare new amino acids were discovered recently (selenocystein and pirrolysine), and additional new discoveries may be added to the list.
Amino Acids
Amino acids are the monomers that comprise proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, or the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group (Figure 3.22).
Figure 3.22 Amino acids have a central asymmetric carbon to which an amino group, a carboxyl group, a hydrogen atom, and a side chain (R group) are attached.
Scientists use the name "amino acid" because these acids contain both amino group and carboxyl-acid-group in their basic structure. As we mentioned, there are 20 common amino acids present in proteins. Nine of these are essential amino acids in humans because the human body cannot produce them and we obtain them from our diet. For each amino acid, the R group (or side chain) is different (Figure 3.23).
Visual Connection
Visual Connection
Figure 3.23 There are 20 common amino acids commonly found in proteins, each with a different R group (variant group) that determines its chemical nature.
Which categories of amino acid would you expect to find on a soluble protein's surface and which would you expect to find in the interior? What distribution of amino acids would you expect to find in a protein embedded in a lipid bilayer?
The chemical nature of the side chain determines the amino acid's nature (that is, whether it is acidic, basic, polar, or nonpolar). For example, the amino acid glycine has a hydrogen atom as the R group. Amino acids such as valine, methionine, and alanine are nonpolar or hydrophobic in nature, while amino acids such as serine, threonine, and cysteine are polar and have hydrophilic side chains. The side chains of lysine and arginine are positively charged, and therefore these amino acids are also basic amino acids. Proline has an R group that is linked to the amino group, forming a ring-like structure. Proline is an exception to the amino acid's standard structure since its amino group is not separate from the side chain (Figure 3.23).
A single upper case letter or a three-letter abbreviation represents amino acids. For example, the letter V or the three-letter symbol val represent valine. Just as some fatty acids are essential to a diet, some amino acids also are necessary. These essential amino acids in humans include isoleucine, leucine, and cysteine. Essential amino acids refer to those necessary to build proteins in the body, but not those that the body produces. Which amino acids are essential varies from organism to organism.
The sequence and the number of amino acids ultimately determine the protein's shape, size, and function. A covalent bond, or peptide bond, attaches to each amino acid, which a dehydration reaction forms. One amino acid's carboxyl group and the incoming amino acid's amino group combine, releasing a water molecule. The resulting bond is the peptide bond (Figure 3.24).
Figure 3.24 Peptide bond formation is a dehydration synthesis reaction. The carboxyl group of one amino acid is linked to the incoming amino acid's amino group. In the process, it releases a water molecule.
The products that such linkages form are peptides. As more amino acids join to this growing chain, the resulting chain is a polypeptide. Each polypeptide has a free amino group at one end. This end the N terminal, or the amino terminal, and the other end has a free carboxyl group, also the C or carboxyl terminal. While the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically a polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have combined together, often have bound non-peptide prosthetic groups, have a distinct shape, and have a unique function. After protein synthesis (translation), most proteins are modified. These are known as post-translational modifications. They may undergo cleavage, phosphorylation, or may require adding other chemical groups. Only after these modifications is the protein completely functional.
Link to Learning
Link to Learning
Click through the steps of protein synthesis in this interactive tutorial.
Evolution Connection
Evolution Connection
The Evolutionary Significance of Cytochrome cCytochrome c is an important component of the electron transport chain, a part of cellular respiration, and it is normally located in the cellular organelle, the mitochondrion. This protein has a heme prosthetic group, and the heme's central ion alternately reduces and oxidizes during electron transfer. Because this essential protein’s role in producing cellular energy is crucial, it has changed very little over millions of years. Protein sequencing has shown that there is a considerable amount of cytochrome c amino acid sequence homology among different species. In other words, we can assess evolutionary kinship by measuring the similarities or differences among various species’ DNA or protein sequences.
Scientists have determined that human cytochrome c contains 104 amino acids. For each cytochrome c molecule from different organisms that scientists have sequenced to date, 37 of these amino acids appear in the same position in all cytochrome c samples. This indicates that there may have been a common ancestor. On comparing the human and chimpanzee protein sequences, scientists did not find a sequence difference. When researchers compared human and rhesus monkey sequences, the single difference was in one amino acid. In another comparison, human to yeast sequencing shows a difference in the 44th position.
Protein Structure
As we discussed earlier, a protein's shape is critical to its function. For example, an enzyme can bind to a specific substrate at an active site. If this active site is altered because of local changes or changes in overall protein structure, the enzyme may be unable to bind to the substrate. To understand how the protein gets its final shape or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary.
Primary Structure
Amino acids' unique sequence in a polypeptide chain is its primary structure. For example, the pancreatic hormone insulin has two polypeptide chains, A and B, and they are linked together by disulfide bonds. The N terminal amino acid of the A chain is glycine; whereas, the C terminal amino acid is asparagine (Figure 3.25). The amino acid sequences in the A and B chains are unique to insulin.
Figure 3.25 Bovine serum insulin is a protein hormone comprised of two peptide chains, A (21 amino acids long) and B (30 amino acids long). In each chain, three-letter abbreviations that represent the amino acids' names in the order they are present indicate primary structure. The amino acid cysteine (cys) has a sulfhydryl (SH) group as a side chain. Two sulfhydryl groups can react in the presence of oxygen to form a disulfide (S-S) bond. Two disulfide bonds connect the A and B chains together, and a third helps the A chain fold into the correct shape. Note that all disulfide bonds are the same length, but we have drawn them different sizes for clarity.
The gene encoding the protein ultimately determines the unique sequence for every protein. A change in nucleotide sequence of the gene’s coding region may lead to adding a different amino acid to the growing polypeptide chain, causing a change in protein structure and function. In sickle cell anemia, the hemoglobin β chain (a small portion of which we show in Figure 3.26) has a single amino acid substitution, causing a change in protein structure and function. Specifically, valine in the β chain substitutes the amino acid glutamic. What is most remarkable to consider is that a hemoglobin molecule is comprised of two alpha and two beta chains that each consist of about 150 amino acids. The molecule, therefore, has about 600 amino acids. The structural difference between a normal hemoglobin molecule and a sickle cell molecule—which dramatically decreases life expectancy—is a single amino acid of the 600. What is even more remarkable is that three nucleotides each encode those 600 amino acids, and a single base change (point mutation), 1 in 1800 bases causes the mutation.
Figure 3.26 Because of this change of one amino acid in the chain, hemoglobin molecules form long fibers that distort the biconcave, or disc-shaped, red blood cells and causes them to assume a crescent or “sickle” shape, which clogs blood vessels (Figure 3.27). .his 3.4 • Proteins 81 The beta (β)- chain of hemoglobin is 147 amino acids in length, yet a single amino acid substitution in the primary sequence leads changes in secondary, tertiary and quaternary structures and sickle cell anemia. In normal hemoglobin, the amino acid at position six is glutamate. In sickle cell hemoglobin glutamate is replaced by valine. Credit: Rao, A., Tag, A. Ryan, K. and Fletcher, S. Department of Biology, Texas A&M University.
Because of this change of one amino acid in the chain, hemoglobin molecules form long fibers that distort the biconcave, or disc-shaped, red blood cells and causes them to assume a crescent or “sickle” shape, which clogs blood vessels (Figure 3.27). This can lead to myriad serious health problems such as breathlessness, dizziness, headaches, and abdominal pain for those affected by this disease. William Warrick Cardozo showed that sickle-cell anemia is an inherited disorder, meaning that the difference in the specific gene's encoding region is passed down from parents to children. As you will learn in the genetics unit, the inheritance of such traits is determined by a combination of genes from both parents, and these very small differences can have significant impacts on organisms.
Figure 3.27 In this blood smear, visualized at 535x magnification using bright field microscopy, sickle cells are crescent shaped, while normal cells are disc-shaped. (credit: modification of work by Ed Uthman; scale-bar data from Matt Russell)
Secondary Structure
The local folding of the polypeptide in some regions gives rise to the secondary structure of the protein. The most common are the α-helix and β-pleated sheet structures (Figure 3.28). Both structures are held in shape by hydrogen bonds. The hydrogen bonds form between the oxygen atom in the carbonyl group in one amino acid and another amino acid that is four amino acids farther along the chain.
Figure 3.28 The α-helix and β-pleated sheet are secondary protein structures formed when hydrogen bonds form between the carbonyl oxygen and the amino hydrogen in the peptide backbone. Certain amino acids have a propensity to form an α-helix while others favor β-pleated sheet formation. Black = carbon, White = hydrogen, Blue = nitrogen, and Red = oxygen. Credit: Rao, A., Ryan, K. Fletcher, S. and Tag, A. Department of Biology, Texas A&M University.
Every helical turn in an alpha helix has 3.6 amino acid residues. The polypeptide's R groups (the variant groups) protrude out from the α-helix chain. In the β-pleated sheet, hydrogen bonding between atoms on the polypeptide chain's backbone form the "pleats". The R groups are attached to the carbons and extend above and below the pleat's folds. The pleated segments align parallel or antiparallel to each other, and hydrogen bonds form between the partially positive hydrogen atom in the amino group and the partially negative oxygen atom in the peptide backbone's carbonyl group. The α-helix and β-pleated sheet structures are in most globular and fibrous proteins and they play an important structural role.
Tertiary Structure
The polypeptide's unique three-dimensional structure is its tertiary structure (Figure 3.29). This structure is in part due to chemical interactions at work on the polypeptide chain. Primarily, the interactions among R groups create the protein's complex three-dimensional tertiary structure. The nature of the R groups in the amino acids involved can counteract forming the hydrogen bonds we described for standard secondary structures. For example, R groups with like charges repel each other and those with unlike charges are attracted to each other (ionic bonds). When protein folding takes place, the nonpolar amino acids' hydrophobic R groups lie in the protein's interior; whereas, the hydrophilic R groups lie on the outside. Scientists also call the former interaction types hydrophobic interactions. Interaction between cysteine side chains forms disulfide linkages in the presence of oxygen, the only covalent bond that forms during protein folding.
Figure 3.29 A variety of chemical interactions determine the proteins' tertiary structure. These include hydrophobic interactions, ionic bonding, hydrogen bonding, and disulfide linkages.
All of these interactions, weak and strong, determine the protein's final three-dimensional shape. When a protein loses its three-dimensional shape, it may no longer be functional.
Quaternary Structure
In nature, some proteins form from several polypeptides, or subunits, and the interaction of these subunits forms the quaternary structure. Weak interactions between the subunits help to stabilize the overall structure. For example, insulin (a globular protein) has a combination of hydrogen and disulfide bonds that cause it to mostly clump into a ball shape. Insulin starts out as a single polypeptide and loses some internal sequences in the presence of post-translational modification after forming the disulfide linkages that hold the remaining chains together. Silk (a fibrous protein), however, has a β-pleated sheet structure that is the result of hydrogen bonding between different chains.
Figure 3.30 illustrates the four levels of protein structure (primary, secondary, tertiary, and quaternary).
Figure 3.30 Observe the four levels of protein structure in these illustrations. Credit: Rao, A. Ryan, K. and Tag, A. Department of Biology, Texas A&M University.
Denaturation and Protein Folding
Each protein has its own unique sequence and shape that chemical interactions hold together. If the protein is subject to changes in temperature, pH, or exposure to chemicals, the protein structure may change, losing its shape without losing its primary sequence in what scientists call denaturation. Denaturation is often reversible because the polypeptide's primary structure is conserved in the process if the denaturing agent is removed, allowing the protein to resume its function. Sometimes denaturation is irreversible, leading to loss of function. One example of irreversible protein denaturation is frying an egg. The albumin protein in the liquid egg white denatures when placed in a hot pan. Not all proteins denature at high temperatures. For instance, bacteria that survive in hot springs have proteins that function at temperatures close to boiling. The stomach is also very acidic, has a low pH, and denatures proteins as part of the digestion process; however, the stomach's digestive enzymes retain their activity under these conditions.
Protein folding is critical to its function. Scientists originally thought that the proteins themselves were responsible for the folding process. Only recently researchers discovered that often they receive assistance in the folding process from protein helpers, or chaperones (or chaperonins) that associate with the target protein during the folding process. They act by preventing polypeptide aggregation that comprise the complete protein structure, and they disassociate from the protein once the target protein is folded.
Link to Learning
Link to Learning
For an additional perspective on proteins, view this animation called “Biomolecules: The Proteins.” | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/01%3A_Unit_I-_The_Chemistry_of_Life/1.03%3A_Biological_Macromolecules/1.3.05%3A_Proteins.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Describe nucleic acids' structure and define the two types of nucleic acids
• Explain DNA's structure and role
• Explain RNA's structure and roles
Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the DNA is not enclosed in a membranous envelope.
The cell's entire genetic content is its genome, and the study of genomes is genomics. In eukaryotic cells but not in prokaryotes, DNA forms a complex with histone proteins to form chromatin, the substance of eukaryotic chromosomes. A chromosome may contain tens of thousands of genes. Many genes contain the information to make protein products. Other genes code for RNA products. DNA controls all of the cellular activities by turning the genes “on” or “off.”
The other type of nucleic acid, RNA, is mostly involved in protein synthesis. The DNA molecules never leave the nucleus but instead use an intermediary to communicate with the rest of the cell. This intermediary is the messenger RNA (mRNA). Other types of RNA—like rRNA, tRNA, and microRNA—are involved in protein synthesis and its regulation.
DNA and RNA are comprised of monomers that scientists call nucleotides. The nucleotides combine with each other to form a polynucleotide, DNA or RNA. Three components comprise each nucleotide: a nitrogenous base, a pentose (five-carbon) sugar, and a phosphate group (Figure 3.31). Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to one or more phosphate groups.
Figure 3.31 Three components comprise a nucleotide: a nitrogenous base, a pentose sugar, and one or more phosphate groups. Carbon residues in the pentose are numbered 1′ through 5′ (the prime distinguishes these residues from those in the base, which are numbered without using a prime notation). The base is attached to the ribose's 1′ position, and the phosphate is attached to the 5′ position. When a polynucleotide forms, the incoming nucleotide's 5′ phosphate attaches to the 3′ hydroxyl group at the end of the growing chain. Two types of pentose are in nucleotides, deoxyribose (found in DNA) and ribose (found in RNA). Deoxyribose is similar in structure to ribose, but it has an H instead of an OH at the 2′ position. We can divide bases into two categories: purines and pyrimidines. Purines have a double ring structure, and pyrimidines have a single ring.
The nitrogenous bases, important components of nucleotides, are organic molecules and are so named because they contain carbon and nitrogen. They are bases because they contain an amino group that has the potential of binding an extra hydrogen, and thus decreasing the hydrogen ion concentration in its environment, making it more basic. Each nucleotide in DNA contains one of four possible nitrogenous bases: adenine (A), guanine (G) cytosine (C), and thymine (T).
Scientists classify adenine and guanine as purines. The purine's primary structure is two carbon-nitrogen rings. Scientists classify cytosine, thymine, and uracil as pyrimidines which have a single carbon-nitrogen ring as their primary structure (Figure 3.31). Each of these basic carbon-nitrogen rings has different functional groups attached to it. In molecular biology shorthand, we know the nitrogenous bases by their symbols A, T, G, C, and U. DNA contains A, T, G, and C; whereas, RNA contains A, U, G, and C.
The pentose sugar in DNA is deoxyribose, and in RNA, the sugar is ribose (Figure 3.31). The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and hydrogen on the deoxyribose's second carbon. The carbon atoms of the sugar molecule are numbered as 1′, 2′, 3′, 4′, and 5′ (1′ is read as “one prime”). The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′–3′ phosphodiester linkage. A simple dehydration reaction like the other linkages connecting monomers in macromolecules does not form the phosphodiester linkage. Its formation involves removing two phosphate groups. A polynucleotide may have thousands of such phosphodiester linkages.
DNA Double-Helix Structure
DNA has a double-helix structure (Figure 3.32). The sugar and phosphate lie on the outside of the helix, forming the DNA's backbone. The nitrogenous bases are stacked in the interior, like a pair of staircase steps. Hydrogen bonds bind the pairs to each other. Every base pair in the double helix is separated from the next base pair by 0.34 nm. The helix's two strands run in opposite directions, meaning that the 5′ carbon end of one strand will face the 3′ carbon end of its matching strand. (Scientists call this an antiparallel orientation and is important to DNA replication and in many nucleic acid interactions.)
Figure 3.32 Native DNA is an antiparallel double helix. The phosphate backbone (indicated by the curvy lines) is on the outside, and the bases are on the inside. Each base from one strand interacts via hydrogen bonding with a base from the opposing strand. (credit: Jerome Walker/Dennis Myts)
Only certain types of base pairing are allowed. For example, a certain purine can only pair with a certain pyrimidine. This means A can pair with T, and G can pair with C, as Figure 3.33 shows. This is the base complementary rule. In other words, the DNA strands are complementary to each other. If the sequence of one strand is AATTGGCC, the complementary strand would have the sequence TTAACCGG. During DNA replication, each strand copies itself, resulting in a daughter DNA double helix containing one parental DNA strand and a newly synthesized strand.
Visual Connection
Visual Connection
Figure 3.33 In a double stranded DNA molecule, the two strands run antiparallel to one another so that one strand runs 5′ to 3′ and the other 3′ to 5′. The phosphate backbone is located on the outside, and the bases are in the middle. Adenine forms hydrogen bonds (or base pairs) with thymine, and guanine base pairs with cytosine.
A mutation occurs, and adenine replaces cytosine. What impact do you think this will have on the DNA structure?
RNA
Ribonucleic acid, or RNA, is mainly involved in the process of protein synthesis under the direction of DNA. RNA is usually single-stranded and is comprised of ribonucleotides that are linked by phosphodiester bonds. A ribonucleotide in the RNA chain contains ribose (the pentose sugar), one of the four nitrogenous bases (A, U, G, and C), and the phosphate group.
There are four major types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), and microRNA (miRNA). The first, mRNA, carries the message from DNA, which controls all of the cellular activities in a cell. If a cell requires synthesizing a certain protein, the gene for this product turns “on” and the messenger RNA synthesizes in the nucleus. The RNA base sequence is complementary to the DNA's coding sequence from which it has been copied. However, in RNA, the base T is absent and U is present instead. If the DNA strand has a sequence AATTGCGC, the sequence of the complementary RNA is UUAACGCG. In the cytoplasm, the mRNA interacts with ribosomes and other cellular machinery (Figure 3.34).
Figure 3.34 A ribosome has two parts: a large subunit and a small subunit. The mRNA sits in between the two subunits. A tRNA molecule recognizes a codon on the mRNA, binds to it by complementary base pairing, and adds the correct amino acid to the growing peptide chain.
The mRNA is read in sets of three bases known as codons. Each codon codes for a single amino acid. In this way, the mRNA is read and the protein product is made. Ribosomal RNA (rRNA) is a major constituent of ribosomes on which the mRNA binds. The rRNA ensures the proper alignment of the mRNA and the Ribosomes. The ribosome's rRNA also has an enzymatic activity (peptidyl transferase) and catalyzes peptide bond formation between two aligned amino acids. Transfer RNA (tRNA) is one of the smallest of the four types of RNA, usually 70–90 nucleotides long. It carries the correct amino acid to the protein synthesis site. It is the base pairing between the tRNA and mRNA that allows for the correct amino acid to insert itself in the polypeptide chain. MicroRNAs are the smallest RNA molecules and their role involves regulating gene expression by interfering with the expression of certain mRNA messages. Table 3.2 summarizes DNA and RNA features.
DNA and RNA Features
DNA RNA
FunctionCarries genetic informationInvolved in protein synthesis
LocationRemains in the nucleusLeaves the nucleus
StructureDouble helixUsually single-stranded
SugarDeoxyriboseRibose
PyrimidinesCytosine, thymineCytosine, uracil
PurinesAdenine, guanineAdenine, guanine
Table 3.2
Even though the RNA is single stranded, most RNA types show extensive intramolecular base pairing between complementary sequences, creating a predictable three-dimensional structure essential for their function.
As you have learned, information flow in an organism takes place from DNA to RNA to protein. DNA dictates the structure of mRNA in a process scientists call transcription, and RNA dictates the protein's structure in a process scientists call translation. This is the Central Dogma of Life, which holds true for all organisms; however, exceptions to the rule occur in connection with viral infections.
Link to Learning
Link to Learning
To learn more about DNA, explore the Howard Hughes Medical Institute BioInteractive animations on the topic of DNA. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/01%3A_Unit_I-_The_Chemistry_of_Life/1.03%3A_Biological_Macromolecules/1.3.06%3A_Nucleic_Acids.txt |
alpha-helix structure (α-helix)
type of secondary protein structure formed by folding the polypeptide into a helix shape with hydrogen bonds stabilizing the structure
amino acid
a protein's monomer; has a central carbon or alpha carbon to which an amino group, a carboxyl group, a hydrogen, and an R group or side chain is attached; the R group is different for all 20 common amino acids
beta-pleated sheet (β-pleated)
secondary structure in proteins in which hydrogen bonding forms “pleats” between atoms on the polypeptide chain's backbone
biological macromolecule
large molecule necessary for life that is built from smaller organic molecules
carbohydrate
biological macromolecule in which the ratio of carbon to hydrogen and to oxygen is 1:2:1; carbohydrates serve as energy sources and structural support in cells and form arthropods' cellular exoskeleton
cellulose
polysaccharide that comprises the plants' cell wall; provides structural support to the cell
chaperone
(also, chaperonin) protein that helps nascent protein in the folding process
chitin
type of carbohydrate that forms the outer skeleton of all arthropods that include crustaceans and insects; it also forms fungi cell walls
dehydration synthesis
(also, condensation) reaction that links monomer molecules, releasing a water molecule for each bond formed
denaturation
loss of shape in a protein as a result of changes in temperature, pH, or chemical exposure
deoxyribonucleic acid (DNA)
double-helical molecule that carries the cell's hereditary information
disaccharide
two sugar monomers that a glycosidic bond links
enzyme
catalyst in a biochemical reaction that is usually a complex or conjugated protein
glycogen
storage carbohydrate in animals
glycosidic bond
bond formed by a dehydration reaction between two monosaccharides with eliminating a water molecule
hormone
chemical signaling molecule, usually protein or steroid, secreted by endocrine cells that act to control or regulate specific physiological processes
hydrolysis
reaction that causes breakdown of larger molecules into smaller molecules by utilizing water
lipid
macromolecule that is nonpolar and insoluble in water
messenger RNA (mRNA)
RNA that carries information from DNA to ribosomes during protein synthesis
monomer
smallest unit of larger molecules that are polymers
monosaccharide
single unit or monomer of carbohydrates
nucleic acid
biological macromolecule that carries the cell's genetic blueprint and carries instructions for the cell's functioning
nucleotide
monomer of nucleic acids; contains a pentose sugar, one or more phosphate groups, and a nitrogenous base
omega fat
type of polyunsaturated fat that the body requires; numbering the carbon omega starts from the methyl end or the end that is farthest from the carboxylic end
peptide bond
bond formed between two amino acids by a dehydration reaction
phosphodiester
linkage covalent chemical bond that holds together the polynucleotide chains with a phosphate group linking neighboring nucleotides' two pentose sugars
phospholipid
membranes' major constituent; comprised of two fatty acids and a phosphate-containing group attached to a glycerol backbone
polymer
chain of monomer residues that covalent bonds link; polymerization is the process of polymer formation from monomers by condensation
polynucleotide
long chain of nucleotides
polypeptide
long chain of amino acids that peptide bonds link
polysaccharide
long chain of monosaccharides; may be branched or unbranched
primary structure
linear sequence of amino acids in a protein
protein
biological macromolecule comprised of one or more amino acid chains
purine
type of nitrogenous base in DNA and RNA; adenine and guanine are purines
pyrimidine
type of nitrogenous base in DNA and RNA; cytosine, thymine, and uracil are pyrimidines
quaternary structure
association of discrete polypeptide subunits in a protein
ribonucleic acid (RNA)
single-stranded, often internally base paired, molecule that is involved in protein synthesis
ribosomal RNA (rRNA)
RNA that ensures the proper alignment of the mRNA and the ribosomes during protein synthesis and catalyzes forming the peptide linkage
saturated fatty acid
long-chain hydrocarbon with single covalent bonds in the carbon chain; the number of hydrogen atoms attached to the carbon skeleton is maximized
secondary structure
regular structure that proteins form by intramolecular hydrogen bonding between the oxygen atom of one amino acid residue and the hydrogen attached to the nitrogen atom of another amino acid residue
starch
storage carbohydrate in plants
steroid
type of lipid comprised of four fused hydrocarbon rings forming a planar structure
tertiary structure
a protein's three-dimensional conformation, including interactions between secondary structural elements; formed from interactions between amino acid side chains
trans fat
fat formed artificially by hydrogenating oils, leading to a different arrangement of double bond(s) than those in naturally occurring lipids
transcription
process through which messenger RNA forms on a template of DNA
transfer RNA (tRNA)
RNA that carries activated amino acids to the site of protein synthesis on the ribosome
translation
process through which RNA directs the protein's formation
triacylglycerol (also, triglyceride)
fat molecule; consists of three fatty acids linked to a glycerol molecule
unsaturated fatty acid
long-chain hydrocarbon that has one or more double bonds in the hydrocarbon chain
wax
lipid comprised of a long-chain fatty acid that is esterified to a long-chain alcohol; serves as a protective coating on some feathers, aquatic mammal fur, and leaves | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/01%3A_Unit_I-_The_Chemistry_of_Life/1.03%3A_Biological_Macromolecules/1.3.07%3A_Key_Terms.txt |
3.1 Synthesis of Biological Macromolecules
Proteins, carbohydrates, nucleic acids, and lipids are the four major classes of biological macromolecules—large molecules necessary for life that are built from smaller organic molecules. Macromolecules are comprised of single units scientists call monomers that are joined by covalent bonds to form larger polymers. The polymer is more than the sum of its parts: it acquires new characteristics, and leads to an osmotic pressure that is much lower than that formed by its ingredients. This is an important advantage in maintaining cellular osmotic conditions. A monomer joins with another monomer with water molecule release, leading to a covalent bond forming. Scientists call these dehydration or condensation reactions. When polymers break down into smaller units (monomers), they use a water molecule for each bond broken by these reactions. Such reactions are hydrolysis reactions. Dehydration and hydrolysis reactions are similar for all macromolecules, but each monomer and polymer reaction is specific to its class. Dehydration reactions typically require an investment of energy for new bond formation, while hydrolysis reactions typically release energy by breaking bonds.
3.2 Carbohydrates
Carbohydrates are a group of macromolecules that are a vital energy source for the cell and provide structural support to plant cells, fungi, and all of the arthropods that include lobsters, crabs, shrimp, insects, and spiders. Scientists classify carbohydrates as monosaccharides, disaccharides, and polysaccharides depending on the number of monomers in the molecule. Monosaccharides are linked by glycosidic bonds that form as a result of dehydration reactions, forming disaccharides and polysaccharides with eliminating a water molecule for each bond formed. Glucose, galactose, and fructose are common monosaccharides; whereas, common disaccharides include lactose, maltose, and sucrose. Starch and glycogen, examples of polysaccharides, are the storage forms of glucose in plants and animals, respectively. The long polysaccharide chains may be branched or unbranched. Cellulose is an example of an unbranched polysaccharide; whereas, amylopectin, a constituent of starch, is a highly branched molecule. Glucose storage, in the form of polymers like starch of glycogen, makes it slightly less accessible for metabolism; however, this prevents it from leaking out of the cell or creating a high osmotic pressure that could cause the cell to uptake excessive water.
3.3 Lipids
Lipids are a class of macromolecules that are nonpolar and hydrophobic in nature. Major types include fats and oils, waxes, phospholipids, and steroids. Fats are a stored form of energy and are also known as triacylglycerols or triglycerides. Fats are comprised of fatty acids and either glycerol or sphingosine. Fatty acids may be unsaturated or saturated, depending on the presence or absence of double bonds in the hydrocarbon chain. If only single bonds are present, they are saturated fatty acids. Unsaturated fatty acids may have one or more double bonds in the hydrocarbon chain. Phospholipids comprise the membrane's matrix. They have a glycerol or sphingosine backbone to which two fatty acid chains and a phosphate-containing group are attached. Steroids are another class of lipids. Their basic structure has four fused carbon rings. Cholesterol is a type of steroid and is an important constituent of the plasma membrane, where it helps to maintain the membrane's fluid nature. It is also the precursor of steroid hormones such as testosterone.
3.4 Proteins
Proteins are a class of macromolecules that perform a diverse range of functions for the cell. They help in metabolism by acting as enzymes, carriers, or hormones, and provide structural support. The building blocks of proteins (monomers) are amino acids. Each amino acid has a central carbon that bonds to an amino group, a carboxyl group, a hydrogen atom, and an R group or side chain. There are 20 commonly occurring amino acids, each of which differs in the R group. A peptide bond links each amino acid to its neighbors. A long amino acid chain is a polypeptide.
Proteins are organized at four levels: primary, secondary, tertiary, and (optional) quaternary. The primary structure is the amino acids' unique sequence. The polypeptide's local folding to form structures such as the α-helix and β-pleated sheet constitutes the secondary structure. The overall three-dimensional structure is the tertiary structure. When two or more polypeptides combine to form the complete protein structure, the configuration is the protein's quaternary structure. Protein shape and function are intricately linked. Any change in shape caused by changes in temperature or pH may lead to protein denaturation and a loss in function.
3.5 Nucleic Acids
Nucleic acids are molecules comprised of nucleotides that direct cellular activities such as cell division and protein synthesis. Pentose sugar, a nitrogenous base, and a phosphate group comprise each nucleotide. There are two types of nucleic acids: DNA and RNA. DNA carries the cell's genetic blueprint and passes it on from parents to offspring (in the form of chromosomes). It has a double-helical structure with the two strands running in opposite directions, connected by hydrogen bonds, and complementary to each other. RNA is a single-stranded polymer composed of linked nucleotides made up of a pentose sugar (ribose), a nitrogenous base, and a phosphate group. RNA is involved in protein synthesis and its regulation. Messenger RNA (mRNA) copies from the DNA, exports itself from the nucleus to the cytoplasm, and contains information for constructing proteins. Ribosomal RNA (rRNA) is a part of the ribosomes at the site of protein synthesis; whereas, transfer RNA (tRNA) carries the amino acid to the site of protein synthesis. The microRNA regulates using mRNA for protein synthesis. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/01%3A_Unit_I-_The_Chemistry_of_Life/1.03%3A_Biological_Macromolecules/1.3.08%3A_Chapter_Summary.txt |
1.
Figure 3.5 What kind of sugars are these, aldose or ketose?
2.
Figure 3.23 Which categories of amino acid would you expect to find on the surface of a soluble protein, and which would you expect to find in the interior? What distribution of amino acids would you expect to find in a protein embedded in a lipid bilayer?
3.
Figure 3.33 A mutation occurs, and cytosine is replaced with adenine. What impact do you think this will have on the DNA structure?
1.3.10: Review Questions
4.
Dehydration synthesis leads to formation of
1. monomers
2. polymers
3. water and polymers
4. none of the above
5.
During the breakdown of polymers, which of the following reactions takes place?
1. hydrolysis
2. dehydration
3. condensation
4. covalent bond
6.
The following chemical reactants produce the ester ethyl ethanoate (C4H8O2):
C2H6O + CH3COOH
What type of reaction occurs to make ethyl ethanoate?
1. condensation
2. hydrolysis
3. combustion
4. acid-base reaction
7.
An example of a monosaccharide is ________.
1. fructose
2. glucose
3. galactose
4. all of the above
8.
Cellulose and starch are examples of:
1. monosaccharides
2. disaccharides
3. lipids
4. polysaccharides
9.
Plant cell walls contain which of the following in abundance?
1. starch
2. cellulose
3. glycogen
4. lactose
10.
Lactose is a disaccharide formed by the formation of a ________ bond between glucose and ________.
1. glycosidic; lactose
2. glycosidic; galactose
3. hydrogen; sucrose
4. hydrogen; fructose
11.
Which of the following is not an extracellular matrix role of carbohydrates?
1. protect an insect’s internal organs from external trauma
2. prevent plant cells from lysing after the plant is watered
3. maintain the shape of a fungal spore
4. provide energy for muscle movement
12.
Saturated fats have all of the following characteristics except:
1. they are solid at room temperature
2. they have single bonds within the carbon chain
3. they are usually obtained from animal sources
4. they tend to dissolve in water easily
13.
Phospholipids are important components of ________.
1. the plasma membrane of cells
2. the ring structure of steroids
3. the waxy covering on leaves
4. the double bond in hydrocarbon chains
14.
Cholesterol is an integral part of plasma membranes. Based on its structure, where is it found in the membrane?
1. on the extracellular surface
2. embedded with the phospholipid heads
3. within the tail bilayer
4. attached to the intracellular surface
15.
The monomers that make up proteins are called ________.
1. nucleotides
2. disaccharides
3. amino acids
4. chaperones
16.
The α-helix and the β-pleated sheet are part of which protein structure?
1. primary
2. secondary
3. tertiary
4. quaternary
17.
Mad cow disease is an infectious disease where one misfolded protein causes all other copies of the protein to begin misfolding. This is an example of a disease impacting ____ structure.
1. primary
2. secondary
3. tertiary
4. quaternary
18.
A nucleotide of DNA may contain ________.
1. ribose, uracil, and a phosphate group
2. deoxyribose, uracil, and a phosphate group
3. deoxyribose, thymine, and a phosphate group
4. ribose, thymine, and a phosphate group
19.
The building blocks of nucleic acids are ________.
1. sugars
2. nitrogenous bases
3. peptides
4. nucleotides
20.
How does the double helix structure of DNA support its role in encoding the genome?
1. The sugar-phosphate backbone provides a template for DNA replication.
2. tRNA pairing with the template strand creates proteins encoded by the genome.
3. Complementary base pairing creates a very stable structure.
4. Complementary base pairing allows for easy editing of both strands of DNA.
1.3.11: Critical Thinking Questions
21.
Why are biological macromolecules considered organic?
22.
What role do electrons play in dehydration synthesis and hydrolysis?
23.
Amino acids have the generic structure seen below, where R represents different carbon-based side chains.
Describe how the structure of amino acids allows them to be linked into long peptide chains to form proteins.
24.
Describe the similarities and differences between glycogen and starch.
25.
Why is it impossible for humans to digest food that contains cellulose?
26.
Draw the ketose and aldose forms of a monosaccharide with the chemical formula C3H6O3. How is the structure of the monosaccharide changed from one form to the other in the human body?
27.
Explain at least three functions that lipids serve in plants and/or animals.
28.
Why have trans fats been banned from some restaurants? How are they created?
29.
Why are fatty acids better than glycogen for storing large amounts of chemical energy?
30.
Part of cortisol’s role in the body involves passing through the plasma membrane to initiate signaling inside a cell. Describe how the structures of cortisol and the plasma membrane allow this to occur.
31.
Explain what happens if even one amino acid is substituted for another in a polypeptide chain. Provide a specific example.
32.
Describe the differences in the four protein structures.
33.
Aquaporins are proteins embedded in the plasma membrane that allow water molecules to move between the extracellular matrix and the intracellular space. Based on its function and location, describe the key features of the protein’s shape and the chemical characteristics of its amino acids.
34.
What are the structural differences between RNA and DNA?
35.
What are the four types of RNA and how do they function? | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/01%3A_Unit_I-_The_Chemistry_of_Life/1.03%3A_Biological_Macromolecules/1.3.09%3A_Visual_Connection_Questions.txt |
Unit 2: Students will gain solid understanding of the structures, functions, and processes of the most basic unit of life: the cell.
• 2.1: Cell Structure
Your body has many kinds of cells, each specialized for a specific purpose. Just as a home is made from a variety of building materials, the human body is constructed from many cell types. For example, epithelial cells protect the surface of the body and cover the organs and body cavities within.
• 2.2: Structure and Function of Plasma Membranes
The plasma membrane, which is also called the cell membrane, has many functions, but the most basic one is to define the borders of the cell and keep the cell functional. The plasma membrane is selectively permeable. This means that the membrane allows some materials to freely enter or leave the cell, while other materials cannot move freely, but require the use of a specialized structure, and occasionally, even energy investment for crossing.
• 2.3: Metabolism
Cellular processes require a steady supply of energy. From where, and in what form, does this energy come? How do living cells obtain energy, and how do they use it? This chapter will discuss different forms of energy and the physical laws that govern energy transfer. This chapter will also describe how cells use energy and replenish it, and how chemical reactions in the cell are performed with great efficiency.
• 2.4: Cellular Respiration
• 2.5: Photosynthesis
The processes in all organisms—from bacteria to humans—require energy. To get this energy, many organisms access stored energy by eating, that is, by ingesting other organisms. But where does the stored energy in food originate? All of this energy can be traced back to photosynthesis.
• 2.6: Cell Communication
• 2.7: Cell Reproduction
Thumbnail: A diagram of a typical prokaryotic cell. (Public Domain; LadyofHats).
02: Unit II- The Cell
Your body has many kinds of cells, each specialized for a specific purpose. Just as a home is made from a variety of building materials, the human body is constructed from many cell types. For example, epithelial cells protect the surface of the body and cover the organs and body cavities within. Bone cells help to support and protect the body. Cells of the immune system fight invading bacteria. Additionally, blood and blood cells carry nutrients and oxygen throughout the body while removing carbon dioxide. Each of these cell types plays a vital role during the growth, development, and day-to-day maintenance of the body. In spite of their enormous variety, however, cells from all organisms—even ones as diverse as bacteria, onion, and human—share certain fundamental characteristics.
• 2.1.1: Introduction
Your body has many kinds of cells, each specialized for a specific purpose. Just as a home is made from a variety of building materials, the human body is constructed from many cell types. For example, epithelial cells protect the surface of the body and cover the organs and body cavities within. Bone cells help to support and protect the body. Cells of the immune system fight invading bacteria. Additionally, blood and blood cells carry nutrients and oxygen throughout the body while removing CO2
• 2.1.2: Studying Cells
A cell is the smallest unit of a living thing. A living thing, whether made of one cell (like bacteria) or many cells (like a human), is called an organism. Thus, cells are the basic building blocks of all organisms. There are many types of cells, all grouped into one of two broad categories: prokaryotic and eukaryotic. For example, both animal and plant cells are classified as eukaryotic cells, whereas bacterial cells are classified as prokaryotic.
• 2.1.3: Prokaryotic Cells
Cells fall into one of two broad categories: prokaryotic and eukaryotic. Only the predominantly single-celled organisms of the domains Bacteria and Archaea are classified as prokaryotes (pro- = “before”; -kary- = “nucleus”). Cells of animals, plants, fungi, and protists are all eukaryotes (eu- = “true”) and are made up of eukaryotic cells.
• 2.1.4: Eukaryotic Cells
Our natural world also utilizes the principle of form following function, especially in cell biology, and this will become clear as we explore eukaryotic cells. Unlike prokaryotic cells, eukaryotic cells have: 1) a membrane-bound nucleus; 2) numerous membrane-bound organelles such as the endoplasmic reticulum, Golgi apparatus, chloroplasts, mitochondria, and others; and 3) several, rod-shaped chromosomes. Because a eukaryotic cell’s nucleus is surrounded by a membrane, it is has “true nucleus.”
• 2.1.5: The Endomembrane System and Proteins
The endomembrane system is a group of membranes and organelles in eukaryotic cells that works together to modify, package, and transport lipids and proteins. It includes the nuclear envelope, lysosomes, and vesicles, which we’ve already mentioned, and the endoplasmic reticulum and Golgi apparatus. Although not technically within the cell, the plasma membrane is included in the endomembrane system because, as you will see, it interacts with the other endomembranous organelles.
• 2.1.6: The Cytoskeleton
Within the cytoplasm, there are ions and organic molecules, plus a network of protein fibers that help maintain the shape of the cell, secure some organelles in specific positions, allow cytoplasm and vesicles to move within the cell, and enable cells within multicellular organisms to move. Collectively, this network of protein fibers is known as the cytoskeleton. There are three types of fibers within the cytoskeleton: microfilaments, intermediate filaments, and microtubules.
• 2.1.7: Connections between Cells and Cellular Activities
You already know that a group of similar cells working together is called a tissue. As you might expect, if cells are to work together, they must communicate with each other, just as you need to communicate with others if you work on a group project. Let’s take a look at how cells communicate with each other.
• 2.1.8: Key Terms
• 2.1.9: Chapter Summary
• 2.1.10: Visual Connection Questions
• 2.1.11: Review Questions
• 2.1.12: Critical Thinking Questions
Thumbnail: The generalized structure of a prokaryotic cell. (CC BY 4.0; OpenStax).
2.01: Cell Structure
Figure 4.1 (a) Nasal sinus cells (viewed with a light microscope), (b) onion cells (viewed with a light microscope), and (c) Vibrio tasmaniensis bacterial cells (seen through a scanning electron microscope) are from very different organisms, yet all share certain basic cell structure characteristics. (credit a: modification of work by Ed Uthman, MD; credit b: modification of work by Umberto Salvagnin; credit c: modification of work by Anthony D'Onofrio, William H. Fowle, Eric J. Stewart, and Kim Lewis of the Lewis Lab at Northeastern University; scale-bar data from Matt Russell)
Close your eyes and picture a brick wall. What is the wall's basic building block? It is a single brick. Like a brick wall, cells are the building blocks that make up your body.
Your body has many kinds of cells, each specialized for a specific purpose. Just as we use a variety of materials to build a home, the human body is constructed from many cell types. For example, epithelial cells protect the body's surface and cover the organs and body cavities within. Bone cells help to support and protect the body. Immune system cells fight invading bacteria. Additionally, blood and blood cells carry nutrients and oxygen throughout the body while removing carbon dioxide. Each of these cell types plays a vital role during the body's growth, development, and day-to-day maintenance. In spite of their enormous variety, however, cells from all organisms—even ones as diverse as bacteria, onion, and human—share certain fundamental characteristics. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.01%3A_Cell_Structure/2.1.01%3A_Introduction.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Describe the role of cells in organisms
• Compare and contrast light microscopy and electron microscopy
• Summarize cell theory
A cell is the smallest unit of a living thing. Whether comprised of one cell (like bacteria) or many cells (like a human), we call it an organism. Thus, cells are the basic building blocks of all organisms.
Several cells of one kind that interconnect with each other and perform a shared function form tissues. These tissues combine to form an organ (your stomach, heart, or brain), and several organs comprise an organ system (such as the digestive system, circulatory system, or nervous system). Several systems that function together form an organism (like a human being). Here, we will examine the structure and function of cells.
There are many types of cells, which scientists group into one of two broad categories: prokaryotic and eukaryotic. For example, we classify both animal and plant cells as eukaryotic cells; whereas, we classify bacterial cells as prokaryotic. Before discussing the criteria for determining whether a cell is prokaryotic or eukaryotic, we will first examine how biologists study cells.
Microscopy
Cells vary in size. With few exceptions, we cannot see individual cells with the naked eye, so scientists use microscopes (micro- = “small”; -scope = “to look at”) to study them. A microscope is an instrument that magnifies an object. We photograph most cells with a microscope, so we can call these images micrographs.
The optics of a microscope’s lenses change the image orientation that the user sees. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa. Similarly, if one moves the slide left while looking through the microscope, it will appear to move right, and if one moves it down, it will seem to move up. This occurs because microscopes use two sets of lenses to magnify the image. Because of the manner by which light travels through the lenses, this two lens system produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but include an additional magnification system that makes the final image appear to be upright).
Light Microscopes
To give you a sense of cell size, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as eight μm) in diameter. A pin head is about two thousandths of a meter (two mm) in diameter. That means about 250 red blood cells could fit on a pinhead.
Most student microscopes are light microscopes (Figure 4.2a). Visible light passes and bends through the lens system to enable the user to see the specimen. Light microscopes are advantageous for viewing living organisms, but since individual cells are generally transparent, their components are not distinguishable unless they are colored with special stains. Staining, however, usually kills the cells.
Light microscopes that undergraduates commonly use in the laboratory magnify up to approximately 400 times. Two parameters that are important in microscopy are magnification and resolving power. Magnification is the process of enlarging an object in appearance. Resolving power is the microscope's ability to distinguish two adjacent structures as separate: the higher the resolution, the better the image's clarity and detail. When one uses oil immersion lenses to study small objects, magnification usually increases to 1,000 times. In order to gain a better understanding of cellular structure and function, scientists typically use electron microscopes.
Figure 4.2 (a) Most light microscopes in a college biology lab can magnify cells up to approximately 400 times and have a resolution of about 200 nanometers. (b) Electron microscopes provide a much higher magnification, 100,000x, and have a resolution of 50 picometers. (credit a: modification of work by "GcG"/Wikimedia Commons; credit b: modification of work by Evan Bench)
Electron Microscopes
In contrast to light microscopes, electron microscopes (Figure 4.2b) use a beam of electrons instead of a beam of light. Not only does this allow for higher magnification and, thus, more detail (Figure 4.3), it also provides higher resolving power. The method to prepare the specimen for viewing with an electron microscope kills the specimen. Electrons have short wavelengths (shorter than photons) that move best in a vacuum, so we cannot view living cells with an electron microscope.
In a scanning electron microscope, a beam of electrons moves back and forth across a cell’s surface, creating details of cell surface characteristics. In a transmission electron microscope, the electron beam penetrates the cell and provides details of a cell’s internal structures. As you might imagine, electron microscopes are significantly more bulky and expensive than light microscopes.
Figure 4.3 (a) These Salmonella bacteria appear as tiny purple dots when viewed with a light microscope. (b) This scanning electron microscope micrograph shows Salmonella bacteria (in red) invading human cells (yellow). Even though subfigure (b) shows a different Salmonella specimen than subfigure (a), you can still observe the comparative increase in magnification and detail. (credit a: modification of work by CDC/Armed Forces Institute of Pathology, Charles N. Farmer, Rocky Mountain Laboratories; credit b: modification of work by NIAID, NIH; scale-bar data from Matt Russell)
Link to Learning
Link to Learning
For another perspective on cell size, try the HowBig interactive at this site.
Cell Theory
The microscopes we use today are far more complex than those that Dutch shopkeeper Antony van Leeuwenhoek, used in the 1600s. Skilled in crafting lenses, van Leeuwenhoek observed the movements of single-celled organisms, which he collectively termed “animalcules.”
In the 1665 publication Micrographia, experimental scientist Robert Hooke coined the term “cell” for the box-like structures he observed when viewing cork tissue through a lens. In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells.
By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that one or more cells comprise all living things, the cell is the basic unit of life, and new cells arise from existing cells. Rudolf Virchow later made important contributions to this theory.
Career Connection
Career Connection
CytotechnologistHave you ever heard of a medical test called a Pap smear (Figure 4.4)? In this test, a doctor takes a small sample of cells from the patient's uterine cervix and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection.
Cytotechnologists (cyto- = “cell”) are professionals who study cells via microscopic examinations and other laboratory tests. They are trained to determine which cellular changes are within normal limits and which are abnormal. Their focus is not limited to cervical cells. They study cellular specimens that come from all organs. When they notice abnormalities, they consult a pathologist, a medical doctor who interprets and diagnoses changes that disease in body tissue and fluids cause.
Cytotechnologists play a vital role in saving people’s lives. When doctors discover abnormalities early, a patient’s treatment can begin sooner, which usually increases the chances of a successful outcome.
Figure 4.4 These uterine cervix cells, viewed through a light microscope, are from a Pap smear. Normal cells are on the left. The cells on the right are infected with human papillomavirus (HPV). Notice that the infected cells are larger. Also, two of these cells each have two nuclei instead of one, the normal number. (credit: modification of work by Ed Uthman, MD; scale-bar data from Matt Russell) | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.01%3A_Cell_Structure/2.1.02%3A_Studying_Cells.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Name examples of prokaryotic and eukaryotic organisms
• Compare and contrast prokaryotic and eukaryotic cells
• Describe the relative sizes of different cells
• Explain why cells must be small
Cells fall into one of two broad categories: prokaryotic and eukaryotic. We classify only the predominantly single-celled organisms Bacteria and Archaea as prokaryotes (pro- = “before”; -kary- = “nucleus”). Animal cells, plants, fungi, and protists are all eukaryotes (eu- = “true”).
Components of Prokaryotic Cells
All cells share four common components: 1) a plasma membrane, an outer covering that separates the cell’s interior from its surrounding environment; 2) cytoplasm, consisting of a jelly-like cytosol within the cell in which there are other cellular components; 3) DNA, the cell's genetic material; and 4) ribosomes, which synthesize proteins. However, prokaryotes differ from eukaryotic cells in several ways.
A prokaryote is a simple, mostly single-celled (unicellular) organism that lacks a nucleus, or any other membrane-bound organelle. We will shortly come to see that this is significantly different in eukaryotes. Prokaryotic DNA is in the cell's central part: the nucleoid (Figure 4.5).
Figure 4.5 This figure shows the generalized structure of a prokaryotic cell. All prokaryotes have chromosomal DNA localized in a nucleoid, ribosomes, a cell membrane, and a cell wall. The other structures shown are present in some, but not all, bacteria.
Most prokaryotes have a peptidoglycan cell wall and many have a polysaccharide capsule (Figure 4.5). The cell wall acts as an extra layer of protection, helps the cell maintain its shape, and prevents dehydration. The capsule enables the cell to attach to surfaces in its environment. Some prokaryotes have flagella, pili, or fimbriae. Flagella are used for locomotion. Pili exchange genetic material during conjugation, the process by which one bacterium transfers genetic material to another through direct contact. Bacteria use fimbriae to attach to a host cell.
Career Connection
Career Connection
MicrobiologistThe most effective action anyone can take to prevent the spread of contagious illnesses is to wash their hands. Why? Because microbes (organisms so tiny that they can only be seen with microscopes) are ubiquitous. They live on doorknobs, money, your hands, and many other surfaces. If someone sneezes into his hand and touches a doorknob, and afterwards you touch that same doorknob, the microbes from the sneezer’s mucus are now on your hands. If you touch your hands to your mouth, nose, or eyes, those microbes can enter your body and could make you sick.
However, not all microbes (also called microorganisms) cause disease; most are actually beneficial. You have microbes in your gut that make vitamin K. Other microorganisms are used to ferment beer and wine.
Microbiologists are scientists who study microbes. Microbiologists can pursue a number of careers. Not only do they work in the food industry, they are also employed in the veterinary and medical fields. They can work in the pharmaceutical sector, serving key roles in research and development by identifying new antibiotic sources that can treat bacterial infections.
Environmental microbiologists may look for new ways to use specially selected or genetically engineered microbes to remove pollutants from soil or groundwater, as well as hazardous elements from contaminated sites. We call using these microbes bioremediation technologies. Microbiologists can also work in the bioinformatics field, providing specialized knowledge and insight for designing, developing, and specificity of computer models of, for example, bacterial epidemics.
Cell Size
At 0.1 to 5.0 μm in diameter, prokaryotic cells are significantly smaller than eukaryotic cells, which have diameters ranging from 10 to 100 μm (Figure 4.6). The prokaryotes' small size allows ions and organic molecules that enter them to quickly diffuse to other parts of the cell. Similarly, any wastes produced within a prokaryotic cell can quickly diffuse. This is not the case in eukaryotic cells, which have developed different structural adaptations to enhance intracellular transport.
Figure 4.6 This figure shows relative sizes of microbes on a logarithmic scale (recall that each unit of increase in a logarithmic scale represents a 10-fold increase in the quantity measured).
Small size, in general, is necessary for all cells, whether prokaryotic or eukaryotic. Let’s examine why that is so. First, we’ll consider the area and volume of a typical cell. Not all cells are spherical in shape, but most tend to approximate a sphere. You may remember from your high school geometry course that the formula for the surface area of a sphere is 4πr2, while the formula for its volume is 4πr3/3. Thus, as the radius of a cell increases, its surface area increases as the square of its radius, but its volume increases as the cube of its radius (much more rapidly). Therefore, as a cell increases in size, its surface area-to-volume ratio decreases. This same principle would apply if the cell had a cube shape (Figure 4.7). If the cell grows too large, the plasma membrane will not have sufficient surface area to support the rate of diffusion required for the increased volume. In other words, as a cell grows, it becomes less efficient. One way to become more efficient is to divide. Other ways are to increase surface area by foldings of the cell membrane, become flat or thin and elongated, or develop organelles that perform specific tasks. These adaptations lead to developing more sophisticated cells, which we call eukaryotic cells.
Visual Connection
Visual Connection
Figure 4.7 Notice that as a cell increases in size, its surface area-to-volume ratio decreases. When there is insufficient surface area to support a cell’s increasing volume, a cell will either divide or die. The cell on the left has a volume of 1 mm3 and a surface area of 6 mm2, with a surface area-to-volume ratio of 6 to 1; whereas, the cell on the right has a volume of 8 mm3 and a surface area of 24 mm2, with a surface area-to-volume ratio of 3 to 1.
Prokaryotic cells are much smaller than eukaryotic cells. What advantages might small cell size confer on a cell? What advantages might large cell size have? | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.01%3A_Cell_Structure/2.1.03%3A_Prokaryotic_Cells.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Describe the structure of eukaryotic cells
• Compare animal cells with plant cells
• State the role of the plasma membrane
• Summarize the functions of the major cell organelles
Have you ever heard the phrase “form follows function?” It’s a philosophy that many industries follow. In architecture, this means that buildings should be constructed to support the activities that will be carried out inside them. For example, a skyscraper should include several elevator banks. A hospital should have its emergency room easily accessible.
Our natural world also utilizes the principle of form following function, especially in cell biology, and this will become clear as we explore eukaryotic cells (Figure 4.8). Unlike prokaryotic cells, eukaryotic cells have: 1) a membrane-bound nucleus; 2) numerous membrane-bound organelles such as the endoplasmic reticulum, Golgi apparatus, chloroplasts, mitochondria, and others; and 3) several, rod-shaped chromosomes. Because a membrane surrounds eukaryotic cell’s nucleus, it has a “true nucleus.” The word “organelle” means “little organ,” and, as we already mentioned, organelles have specialized cellular functions, just as your body's organs have specialized functions.
At this point, it should be clear to you that eukaryotic cells have a more complex structure than prokaryotic cells. Organelles allow different functions to be compartmentalized in different areas of the cell. Before turning to organelles, let’s first examine two important components of the cell: the plasma membrane and the cytoplasm.
Visual Connection
Visual Connection
Figure 4.8 These figures show the major organelles and other cell components of (a) a typical animal cell and (b) a typical eukaryotic plant cell. The plant cell has a cell wall, chloroplasts, plastids, and a central vacuole—structures not in animal cells. Most cells do not have lysosomes or centrosomes.
If the nucleolus were not able to carry out its function, what other cellular organelles would be affected?
The Plasma Membrane
Like prokaryotes, eukaryotic cells have a plasma membrane (Figure 4.9), a phospholipid bilayer with embedded proteins that separates the internal contents of the cell from its surrounding environment. A phospholipid is a lipid molecule with two fatty acid chains and a phosphate-containing group. The plasma membrane controls the passage of organic molecules, ions, water, and oxygen into and out of the cell. Wastes (such as carbon dioxide and ammonia) also leave the cell by passing through the plasma membrane.
Figure 4.9 The eukaryotic plasma membrane is a phospholipid bilayer with proteins and cholesterol embedded in it.
The plasma membranes of cells that specialize in absorption fold into fingerlike projections that we call microvilli (singular = microvillus); (Figure 4.10). Such cells typically line the small intestine, the organ that absorbs nutrients from digested food. This is an excellent example of form following function. People with celiac disease have an immune response to gluten, which is a protein in wheat, barley, and rye. The immune response damages microvilli, and thus, afflicted individuals cannot absorb nutrients. This leads to malnutrition, cramping, and diarrhea. Patients suffering from celiac disease must follow a gluten-free diet.
Figure 4.10 Microvilli, as they appear on cells lining the small intestine, increase the surface area available for absorption. These microvilli are only on the area of the plasma membrane that faces the cavity from which substances will be absorbed. (credit "micrograph": modification of work by Louisa Howard)
The Cytoplasm
The cytoplasm is the cell's entire region between the plasma membrane and the nuclear envelope (a structure we will discuss shortly). It is comprised of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals (Figure 4.8). Even though the cytoplasm consists of 70 to 80 percent water, it has a semi-solid consistency, which comes from the proteins within it. However, proteins are not the only organic molecules in the cytoplasm. Glucose and other simple sugars, polysaccharides, amino acids, nucleic acids, fatty acids, and derivatives of glycerol are also there. Ions of sodium, potassium, calcium, and many other elements also dissolve in the cytoplasm. Many metabolic reactions, including protein synthesis, take place in the cytoplasm.
The Nucleus
Typically, the nucleus is the most prominent organelle in a cell (Figure 4.8). The nucleus (plural = nuclei) houses the cell’s DNA and directs the synthesis of ribosomes and proteins. Let’s look at it in more detail (Figure 4.11).
Figure 4.11 The nucleus stores chromatin (DNA plus proteins) in a gel-like substance called the nucleoplasm. The nucleolus is a condensed chromatin region where ribosome synthesis occurs. We call the nucleus' boundary the nuclear envelope. It consists of two phospholipid bilayers: an outer and an inner membrane. The nuclear membrane is continuous with the endoplasmic reticulum. Nuclear pores allow substances to enter and exit the nucleus.
The Nuclear Envelope
The nuclear envelope is a double-membrane structure that constitutes the nucleus' outermost portion (Figure 4.11). Both the nuclear envelope's inner and outer membranes are phospholipid bilayers.
The nuclear envelope is punctuated with pores that control the passage of ions, molecules, and RNA between the nucleoplasm and cytoplasm. The nucleoplasm is the semi-solid fluid inside the nucleus, where we find the chromatin and the nucleolus.
Chromatin and Chromosomes
To understand chromatin, it is helpful to first explore chromosomes, structures within the nucleus that are made up of DNA, the hereditary material. You may remember that in prokaryotes, DNA is organized into a single circular chromosome. In eukaryotes, chromosomes are linear structures. Every eukaryotic species has a specific number of chromosomes in the nucleus of each cell. For example, in humans, the chromosome number is 46, while in fruit flies, it is eight. Chromosomes are only visible and distinguishable from one another when the cell is getting ready to divide. When the cell is in the growth and maintenance phases of its life cycle, proteins attach to chromosomes, and they resemble an unwound, jumbled bunch of threads. We call these unwound protein-chromosome complexes chromatin (Figure 4.12). Chromatin describes the material that makes up the chromosomes both when condensed and decondensed.
Figure 4.12 (a) This image shows various levels of chromatin's organization (DNA and protein). (b) This image shows paired chromosomes. (credit b: modification of work by NIH; scale-bar data from Matt Russell)
The Nucleolus
We already know that the nucleus directs the synthesis of ribosomes, but how does it do this? Some chromosomes have sections of DNA that encode ribosomal RNA. A darkly staining area within the nucleus called the nucleolus (plural = nucleoli) aggregates the ribosomal RNA with associated proteins to assemble the ribosomal subunits that are then transported out through the pores in the nuclear envelope to the cytoplasm.
Ribosomes
Ribosomes are the cellular structures responsible for protein synthesis. When we view them through an electron microscope, ribosomes appear either as clusters (polyribosomes) or single, tiny dots that float freely in the cytoplasm. They may be attached to the plasma membrane's cytoplasmic side or the endoplasmic reticulum's cytoplasmic side and the nuclear envelope's outer membrane (Figure 4.8). Electron microscopy shows us that ribosomes, which are large protein and RNA complexes, consist of two subunits, large and small (Figure 4.13). Ribosomes receive their “orders” for protein synthesis from the nucleus where the DNA transcribes into messenger RNA (mRNA). The mRNA travels to the ribosomes, which translate the code provided by the sequence of the nitrogenous bases in the mRNA into a specific order of amino acids in a protein. Amino acids are the building blocks of proteins.
Figure 4.13 A large subunit (top) and a small subunit (bottom) comprise ribosomes. During protein synthesis, ribosomes assemble amino acids into proteins.
Because protein synthesis is an essential function of all cells (including enzymes, hormones, antibodies, pigments, structural components, and surface receptors), there are ribosomes in practically every cell. Ribosomes are particularly abundant in cells that synthesize large amounts of protein. For example, the pancreas is responsible for creating several digestive enzymes and the cells that produce these enzymes contain many ribosomes. Thus, we see another example of form following function.
Mitochondria
Scientists often call mitochondria (singular = mitochondrion) “powerhouses” or “energy factories” of both plant and animal cells because they are responsible for making adenosine triphosphate (ATP), the cell’s main energy-carrying molecule. ATP represents the cell's short-term stored energy. Cellular respiration is the process of making ATP using the chemical energy in glucose and other nutrients. In mitochondria, this process uses oxygen and produces carbon dioxide as a waste product. In fact, the carbon dioxide that you exhale with every breath comes from the cellular reactions that produce carbon dioxide as a byproduct.
In keeping with our theme of form following function, it is important to point out that muscle cells have a very high concentration of mitochondria that produce ATP. Your muscle cells need considerable energy to keep your body moving. When your cells don’t get enough oxygen, they do not make much ATP. Instead, producing lactic acid accompanies the small amount of ATP they make in the absence of oxygen.
Mitochondria are oval-shaped, double membrane organelles (Figure 4.14) that have their own ribosomes and DNA. Each membrane is a phospholipid bilayer embedded with proteins. The inner layer has folds called cristae. We call the area surrounded by the folds the mitochondrial matrix. The cristae and the matrix have different roles in cellular respiration.
Figure 4.14 This electron micrograph shows a mitochondrion through an electron microscope. This organelle has an outer membrane and an inner membrane. The inner membrane contains folds, called cristae, which increase its surface area. We call the space between the two membranes the intermembrane space, and the space inside the inner membrane the mitochondrial matrix. ATP synthesis takes place on the inner membrane. (credit: modification of work by Matthew Britton; scale-bar data from Matt Russell)
Peroxisomes
Peroxisomes are small, round organelles enclosed by single membranes. They carry out oxidation reactions that break down fatty acids and amino acids. They also detoxify many poisons that may enter the body. (Many of these oxidation reactions release hydrogen peroxide, H2O2, which would be damaging to cells; however, when these reactions are confined to peroxisomes, enzymes safely break down the H2O2 into oxygen and water.) For example, peroxisomes in liver cells detoxify alcohol. Glyoxysomes, which are specialized peroxisomes in plants, are responsible for converting stored fats into sugars. Plant cells contain many different types of peroxisomes that play a role in metabolism, pathogene defense, and stress response, to mention a few.
Vesicles and Vacuoles
Vesicles and vacuoles are membrane-bound sacs that function in storage and transport. Other than the fact that vacuoles are somewhat larger than vesicles, there is a very subtle distinction between them. Vesicle membranes can fuse with either the plasma membrane or other membrane systems within the cell. Additionally, some agents such as enzymes within plant vacuoles break down macromolecules. The vacuole's membrane does not fuse with the membranes of other cellular components.
Animal Cells versus Plant Cells
At this point, you know that each eukaryotic cell has a plasma membrane, cytoplasm, a nucleus, ribosomes, mitochondria, peroxisomes, and in some, vacuoles, but there are some striking differences between animal and plant cells. While both animal and plant cells have microtubule organizing centers (MTOCs), animal cells also have centrioles associated with the MTOC: a complex we call the centrosome. Animal cells each have a centrosome and lysosomes; whereas, most plant cells do not. Plant cells have a cell wall, chloroplasts and other specialized plastids, and a large central vacuole; whereas, animal cells do not.
The Centrosome
The centrosome is a microtubule-organizing center found near the nuclei of animal cells. It contains a pair of centrioles, two structures that lie perpendicular to each other (Figure 4.15). Each centriole is a cylinder of nine triplets of microtubules.
Figure 4.15 The centrosome consists of two centrioles that lie at right angles to each other. Each centriole is a cylinder comprised of nine triplets of microtubules. Nontubulin proteins (indicated by the green lines) hold the microtubule triplets together.
The centrosome (the organelle where all microtubules originate) replicates itself before a cell divides, and the centrioles appear to have some role in pulling the duplicated chromosomes to opposite ends of the dividing cell. However, the centriole's exact function in cell division isn’t clear, because cells that have had the centrosome removed can still divide, and plant cells, which lack centrosomes, are capable of cell division.
Lysosomes
Animal cells have another set of organelles that most plant cells do not: lysosomes. The lysosomes are the cell’s “garbage disposal.” In plant cells, the digestive processes take place in vacuoles. Enzymes within the lysosomes aid in breaking down proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles. These enzymes are active at a much lower pH than the cytoplasm's. Therefore, the pH within lysosomes is more acidic than the cytoplasm's pH. Many reactions that take place in the cytoplasm could not occur at a low pH, so again, the advantage of compartmentalizing the eukaryotic cell into organelles is apparent.
The Cell Wall
If you examine Figure 4.8, the plant cell diagram, you will see a structure external to the plasma membrane. This is the cell wall, a rigid covering that protects the cell, provides structural support, and gives shape to the cell. Fungal and some protistan cells also have cell walls. While the prokaryotic cell walls' chief component is peptidoglycan, the major organic molecule in the plant (and some protists') cell wall is cellulose (Figure 4.16), a polysaccharide comprised of glucose units. Have you ever noticed that when you bite into a raw vegetable, like celery, it crunches? That’s because you are tearing the celery cells' rigid cell walls with your teeth.
Figure 4.16 Cellulose is a long chain of β-glucose molecules connected by a 1-4 linkage. The dashed lines at each end of the figure indicate a series of many more glucose units. The size of the page makes it impossible to portray an entire cellulose molecule.
Chloroplasts
Like the mitochondria, chloroplasts have their own DNA and ribosomes, but chloroplasts have an entirely different function. Chloroplasts are plant cell organelles that carry out photosynthesis. Photosynthesis is the series of reactions that use carbon dioxide, water, and light energy to make glucose and oxygen. This is a major difference between plants and animals. Plants (autotrophs) are able to make their own food, like sugars used in cellular respiration to provide ATP energy generated in the plant mitochondria. Animals (heterotrophs) must ingest their food.
Like mitochondria, chloroplasts have outer and inner membranes, but within the space enclosed by a chloroplast’s inner membrane is a set of interconnected and stacked fluid-filled membrane sacs we call thylakoids (Figure 4.17). Each thylakoid stack is a granum (plural = grana). We call the fluid enclosed by the inner membrane that surrounds the grana the stroma.
Figure 4.17 The chloroplast has an outer membrane, an inner membrane, and membrane structures - thylakoids that are stacked into grana. We call the space inside the thylakoid membranes the thylakoid space. The light harvesting reactions take place in the thylakoid membranes, and sugar synthesis takes place in the fluid inside the inner membrane, which we call the stroma. Chloroplasts also have their own genome, which is contained on a single circular chromosome.
The chloroplasts contain a green pigment, chlorophyll, which captures the light energy that drives the reactions of photosynthesis. Like plant cells, photosynthetic protists also have chloroplasts. Some bacteria perform photosynthesis, but their chlorophyll is not relegated to an organelle.
Evolution Connection
Evolution Connection
EndosymbiosisWe have mentioned that both mitochondria and chloroplasts contain DNA and ribosomes. Have you wondered why? Strong evidence points to endosymbiosis as the explanation.
Symbiosis is a relationship in which organisms from two separate species depend on each other for their survival. Endosymbiosis (endo- = “within”) is a mutually beneficial relationship in which one organism lives inside the other. Endosymbiotic relationships abound in nature. We have already mentioned that microbes that produce vitamin K live inside the human gut. This relationship is beneficial for us because we are unable to synthesize vitamin K. It is also beneficial for the microbes because they are protected from other organisms and from drying out, and they receive abundant food from the environment of the large intestine.
Scientists have long noticed that bacteria, mitochondria, and chloroplasts are similar in size. We also know that bacteria have DNA and ribosomes, just like mitochondria and chloroplasts. Scientists believe that host cells and bacteria formed an endosymbiotic relationship when the host cells ingested both aerobic and autotrophic bacteria (cyanobacteria) but did not destroy them. Through many millions of years of evolution, these ingested bacteria became more specialized in their functions, with the aerobic bacteria becoming mitochondria and the autotrophic bacteria becoming chloroplasts.
The Central Vacuole
Previously, we mentioned vacuoles as essential components of plant cells. If you look at Figure 4.8b, you will see that plant cells each have a large central vacuole that occupies most of the cell's area. The central vacuole plays a key role in regulating the cell’s concentration of water in changing environmental conditions. Have you ever noticed that if you forget to water a plant for a few days, it wilts? That’s because as the water concentration in the soil becomes lower than the water concentration in the plant, water moves out of the central vacuoles and cytoplasm. As the central vacuole shrinks, it leaves the cell wall unsupported. This loss of support to the plant's cell walls results in the wilted appearance.
The central vacuole also supports the cell's expansion. When the central vacuole holds more water, the cell becomes larger without having to invest considerable energy in synthesizing new cytoplasm. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.01%3A_Cell_Structure/2.1.04%3A_Eukaryotic_Cells.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• List the components of the endomembrane system
• Recognize the relationship between the endomembrane system and its functions
The endomembrane system (endo = “within”) is a group of membranes and organelles (Figure 4.18) in eukaryotic cells that works together to modify, package, and transport lipids and proteins. It includes the nuclear envelope, lysosomes, and vesicles, which we have already mentioned, and the endoplasmic reticulum and Golgi apparatus, which we will cover shortly. Although not technically within the cell, the plasma membrane is included in the endomembrane system because, as you will see, it interacts with the other endomembranous organelles. The endomembrane system does not include either mitochondria or chloroplast membranes.
Visual Connection
Visual Connection
Figure 4.18 Membrane and secretory proteins are synthesized in the rough endoplasmic reticulum (RER). The RER also sometimes modifies proteins. In this illustration, a (green) integral membrane protein is modified by attachment of a (purple) carbohydrate in the ER. Vesicles with the integral protein bud from the ER and fuse with the Golgi apparatus' cis face. As the protein passes along the Golgi’s cisternae, the addition of more carbohydrates further modifies it. After its synthesis is complete, it exits as an integral membrane protein of the vesicle that buds from the Golgi’s trans face. When the vesicle fuses with the cell membrane, the protein becomes an integral portion of that cell membrane. (credit: modification of work by Magnus Manske)
If a peripheral membrane protein were synthesized in the lumen (inside) of the ER, would it end up on the inside or outside of the plasma membrane?
The Endoplasmic Reticulum
The endoplasmic reticulum (ER) (Figure 4.18) is a series of interconnected membranous sacs and tubules that collectively modifies proteins and synthesizes lipids. However, these two functions take place in separate areas of the ER: the rough ER and the smooth ER, respectively.
We call the ER tubules' hollow portion the lumen or cisternal space. The ER's membrane, which is a phospholipid bilayer embedded with proteins, is continuous with the nuclear envelope.
Rough ER
Scientists have named the rough endoplasmic reticulum (RER) as such because the ribosomes attached to its cytoplasmic surface give it a studded appearance when viewing it through an electron microscope (Figure 4.19).
Figure 4.19 This transmission electron micrograph shows the rough endoplasmic reticulum and other organelles in a pancreatic cell. (credit: modification of work by Louisa Howard)
Ribosomes transfer their newly synthesized proteins into the RER's lumen where they undergo structural modifications, such as folding or acquiring side chains. These modified proteins incorporate into cellular membranes—the ER or the ER's or other organelles' membranes. The proteins can also secrete from the cell (such as protein hormones, enzymes). The RER also makes phospholipids for cellular membranes.
If the phospholipids or modified proteins are not destined to stay in the RER, they will reach their destinations via transport vesicles that bud from the RER’s membrane (Figure 4.18).
Since the RER is engaged in modifying proteins (such as enzymes, for example) that secrete from the cell, you would be correct in assuming that the RER is abundant in cells that secrete proteins. This is the case with liver cells, for example.
Smooth ER
The smooth endoplasmic reticulum (SER) is continuous with the RER but has few or no ribosomes on its cytoplasmic surface (Figure 4.18). SER functions include synthesis of carbohydrates, lipids, and steroid hormones; detoxification of medications and poisons; and storing calcium ions.
In muscle cells, a specialized SER, the sarcoplasmic reticulum, is responsible for storing calcium ions that are needed to trigger the muscle cells' coordinated contractions.
Link to Learning
Link to Learning
You can watch an excellent animation of the endomembrane system here. At the end of the animation, there is a short self-assessment.
Career Connection
Career Connection
CardiologistHeart disease is the leading cause of death in the United States. This is primarily due to our sedentary lifestyle and our high trans-fat diets.
Heart failure is just one of many disabling heart conditions. Heart failure does not mean that the heart has stopped working. Rather, it means that the heart can’t pump with sufficient force to transport oxygenated blood to all the vital organs. Left untreated, heart failure can lead to kidney failure and other organ failure.
Cardiac muscle tissue comprises the heart's wall. Heart failure occurs when cardiac muscle cells' endoplasmic reticula do not function properly. As a result, an insufficient number of calcium ions are available to trigger a sufficient contractile force.
Cardiologists (cardi- = “heart”; -ologist = “one who studies”) are doctors who specialize in treating heart diseases, including heart failure. Cardiologists can diagnose heart failure via a physical examination, results from an electrocardiogram (ECG, a test that measures the heart's electrical activity), a chest X-ray to see whether the heart is enlarged, and other tests. If the cardiologist diagnoses heart failure, they will typically prescribe appropriate medications and recommend a reduced table salt intake and a supervised exercise program.
The Golgi Apparatus
We have already mentioned that vesicles can bud from the ER and transport their contents elsewhere, but where do the vesicles go? Before reaching their final destination, the lipids or proteins within the transport vesicles still need sorting, packaging, and tagging so that they end up in the right place. Sorting, tagging, packaging, and distributing lipids and proteins takes place in the Golgi apparatus (also called the Golgi body), a series of flattened membranous sacs (Figure 4.20).
Figure 4.20 The Golgi apparatus in this white blood cell is visible as a stack of semicircular, flattened rings in the lower portion of the image. You can see several vesicles near the Golgi apparatus. (credit: modification of work by Louisa Howard)
The side of the Golgi apparatus that is closer to the ER is called the cis face. The opposite side is the trans face. The transport vesicles that formed from the ER travel to the cis face, fuse with it, and empty their contents into the Golgi apparatus' lumen. As the proteins and lipids travel through the Golgi, they undergo further modifications that allow them to be sorted. The most frequent modification is adding short sugar molecule chains. These newly modified proteins and lipids then tag with phosphate groups or other small molecules in order to travel to their proper destinations.
Finally, the modified and tagged proteins are packaged into secretory vesicles that bud from the Golgi's trans face. While some of these vesicles deposit their contents into other cell parts where they will be used, other secretory vesicles fuse with the plasma membrane and release their contents outside the cell.
In another example of form following function, cells that engage in a great deal of secretory activity (such as salivary gland cells that secrete digestive enzymes or immune system cells that secrete antibodies) have an abundance of Golgi.
In plant cells, the Golgi apparatus has the additional role of synthesizing polysaccharides, some of which are incorporated into the cell wall and some of which other cell parts use.
Career Connection
Career Connection
GeneticistMany diseases arise from genetic mutations that prevent synthesizing critical proteins. One such disease is Lowe disease (or oculocerebrorenal syndrome, because it affects the eyes, brain, and kidneys). In Lowe disease, there is a deficiency in an enzyme localized to the Golgi apparatus. Children with Lowe disease are born with cataracts, typically develop kidney disease after the first year of life, and may have intellectual disabilities.
A mutation on the X chromosome causes Lowe disease. The X chromosome is one of the two human sex chromosomes, as these chromosomes determine a person's sex. Females possess two X chromosomes while males possess one X and one Y chromosome. In females, the genes on only one of the two X chromosomes are expressed. Females who carry the Lowe disease gene on one of their X chromosomes are carriers and do not show symptoms of the disease. However, males only have one X chromosome and the genes on this chromosome are always expressed. Therefore, males will always have Lowe disease if their X chromosome carries the Lowe disease gene. Geneticists have identified the mutated gene's location, as well as many other mutation locations that cause genetic diseases. Through prenatal testing, a pregnant person can find out if the fetus they are carrying may be afflicted with one of several genetic diseases.
Geneticists analyze prenatal genetic test results and may counsel pregnant people on available options. They may also conduct genetic research that leads to new drugs or foods, or perform DNA analyses for forensic investigations.
Lysosomes
In addition to their role as the digestive component and organelle-recycling facility of animal cells, lysosomes are part of the endomembrane system. Lysosomes also use their hydrolytic enzymes to destroy pathogens (disease-causing organisms) that might enter the cell. A good example of this occurs in macrophages, a group of white blood cells which are part of your body’s immune system. In a process that scientists call phagocytosis or endocytosis, a section of the macrophage's plasma membrane invaginates (folds in) and engulfs a pathogen. The invaginated section, with the pathogen inside, then pinches itself off from the plasma membrane and becomes a vesicle. The vesicle fuses with a lysosome. The lysosome’s hydrolytic enzymes then destroy the pathogen (Figure 4.21).
Figure 4.21 A macrophage has engulfed (phagocytized) a potentially pathogenic bacterium and then fuses with lysosomes within the cell to destroy the pathogen. Other organelles are present in the cell but for simplicity we do not show them. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.01%3A_Cell_Structure/2.1.05%3A_The_Endomembrane_System_and_Proteins.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Describe the cytoskeleton
• Compare the roles of microfilaments, intermediate filaments, and microtubules
• Compare and contrast cilia and flagella
• Summarize the differences among the components of prokaryotic cells, animal cells, and plant cells
If you were to remove all the organelles from a cell, would the plasma membrane and the cytoplasm be the only components left? No. Within the cytoplasm, there would still be ions and organic molecules, plus a network of protein fibers that help maintain the cell's shape, secure some organelles in specific positions, allow cytoplasm and vesicles to move within the cell, and enable cells within multicellular organisms to move. Collectively, scientists call this network of protein fibers the cytoskeleton. There are three types of fibers within the cytoskeleton: microfilaments, intermediate filaments, and microtubules (Figure 4.22). Here, we will examine each.
Figure 4.22 Microfilaments thicken the cortex around the cell's inner edge. Like rubber bands, they resist tension. There are microtubules in the cell's interior where they maintain their shape by resisting compressive forces. There are intermediate filaments throughout the cell that hold organelles in place.
Microfilaments
Of the three types of protein fibers in the cytoskeleton, microfilaments are the narrowest. They function in cellular movement, have a diameter of about 7 nm, and are comprised of two globular protein intertwined strands, which we call actin (Figure 4.23). For this reason, we also call microfilaments actin filaments.
Figure 4.23 Two intertwined actin strands comprise microfilaments.
ATP powers actin to assemble its filamentous form, which serves as a track for the movement of a motor protein we call myosin. This enables actin to engage in cellular events requiring motion, such as cell division in eukaryotic cells and cytoplasmic streaming, which is the cell cytoplasm's circular movement in plant cells. Actin and myosin are plentiful in muscle cells. When your actin and myosin filaments slide past each other, your muscles contract.
Microfilaments also provide some rigidity and shape to the cell. They can depolymerize (disassemble) and reform quickly, thus enabling a cell to change its shape and move. White blood cells (your body’s infection-fighting cells) make good use of this ability. They can move to an infection site and phagocytize the pathogen.
Link to Learning
Link to Learning
To see an example of a white blood cell in action, watch a short time-lapse video of the cell capturing two bacteria. It engulfs one and then moves on to the other.
Intermediate Filaments
Several strands of fibrous proteins that are wound together comprise intermediate filaments (Figure 4.24). Cytoskeleton elements get their name from the fact that their diameter, 8 to 10 nm, is between those of microfilaments and microtubules.
Figure 4.24 Intermediate filaments consist of several intertwined strands of fibrous proteins.
Intermediate filaments have no role in cell movement. Their function is purely structural. They bear tension, thus maintaining the cell's shape, and anchor the nucleus and other organelles in place. Figure 4.22 shows how intermediate filaments create a supportive scaffolding inside the cell.
The intermediate filaments are the most diverse group of cytoskeletal elements. Several fibrous protein types are in the intermediate filaments. You are probably most familiar with keratin, the fibrous protein that strengthens your hair, nails, and the skin's epidermis.
Microtubules
As their name implies, microtubules are small hollow tubes. Polymerized dimers of α-tubulin and β-tubulin, two globular proteins, comprise the microtubule's walls (Figure 4.25). With a diameter of about 25 nm, microtubules are cytoskeletons' widest components. They help the cell resist compression, provide a track along which vesicles move through the cell, and pull replicated chromosomes to opposite ends of a dividing cell. Like microfilaments, microtubules can disassemble and reform quickly.
Figure 4.25 Microtubules are hollow. Their walls consist of 13 polymerized dimers of α-tubulin and β-tubulin (right image). The left image shows the tube's molecular structure.
Microtubules are also the structural elements of flagella, cilia, and centrioles (the latter are the centrosome's two perpendicular bodies). In animal cells, the centrosome is the microtubule-organizing center. In eukaryotic cells, flagella and cilia are quite different structurally from their counterparts in prokaryotes, as we discuss below.
Flagella and Cilia
The flagella (singular = flagellum) are long, hair-like structures that extend from the plasma membrane and enable an entire cell to move (for example, sperm, Euglena, and some prokaryotes). When present, the cell has just one flagellum or a few flagella. However, when cilia (singular = cilium) are present, many of them extend along the plasma membrane's entire surface. They are short, hair-like structures that move entire cells (such as paramecia) or substances along the cell's outer surface (for example, the cilia of cells lining the Fallopian tubes that move the ovum toward the uterus, or cilia lining the cells of the respiratory tract that trap particulate matter and move it toward your nostrils.)
Despite their differences in length and number, flagella and cilia share a common structural arrangement of microtubules called a “9 + 2 array.” This is an appropriate name because a single flagellum or cilium is made of a ring of nine microtubule doublets, surrounding a single microtubule doublet in the center (Figure 4.26).
Figure 4.26 This transmission electron micrograph of two flagella shows the microtubules' 9 + 2 array: nine microtubule doublets surround a single microtubule doublet. (credit: modification of work by Dartmouth Electron Microscope Facility, Dartmouth College; scale-bar data from Matt Russell)
You have now completed a broad survey of prokaryotic and eukaryotic cell components. For a summary of cellular components in prokaryotic and eukaryotic cells, see Table 4.1.
Components of Prokaryotic and Eukaryotic Cells
Cell Component Function Present in Prokaryotes? Present in Animal Cells? Present in Plant Cells?
Plasma membrane Separates cell from external environment; controls passage of organic molecules, ions, water, oxygen, and wastes into and out of cell Yes Yes Yes
Cytoplasm Provides turgor pressure to plant cells as fluid inside the central vacuole; site of many metabolic reactions; medium in which organelles are found Yes Yes Yes
Nucleolus Darkened area within the nucleus where ribosomal subunits are synthesized. No Yes Yes
Nucleus Cell organelle that houses DNA and directs synthesis of ribosomes and proteins No Yes Yes
Ribosomes Protein synthesis Yes Yes Yes
Mitochondria ATP production/cellular respiration No Yes Yes
Peroxisomes Oxidize and thus break down fatty acids and amino acids, and detoxify poisons No Yes Yes
Vesicles and vacuoles Storage and transport; digestive function in plant cells No Yes Yes
Centrosome Unspecified role in cell division in animal cells; microtubule source in animal cells No Yes No
Lysosomes Digestion of macromolecules; recycling of worn-out organelles No Yes Some
Cell wall Protection, structural support, and maintenance of cell shape Yes, primarily peptidoglycan No Yes, primarily cellulose
Chloroplasts Photosynthesis No No Yes
Endoplasmic reticulum Modifies proteins and synthesizes lipids No Yes Yes
Golgi apparatus Modifies, sorts, tags, packages, and distributes lipids and proteins No Yes Yes
Cytoskeleton Maintains cell’s shape, secures organelles in specific positions, allows cytoplasm and vesicles to move within cell, and enables unicellular organisms to move independently Yes Yes Yes
Flagella Cellular locomotion Some Some No, except for some plant sperm cells
Cilia Cellular locomotion, movement of particles along plasma membrane's extracellular surface, and filtration Some Some No
Table 4.1 | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.01%3A_Cell_Structure/2.1.06%3A_The_Cytoskeleton.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Describe the extracellular matrix
• List examples of the ways that plant cells and animal cells communicate with adjacent cells
• Summarize the roles of tight junctions, desmosomes, gap junctions, and plasmodesmata
You already know that tissue is a group of similar cells working together. As you might expect, if cells are to work together, they must communicate with each other, just as you need to communicate with others if you work on a group project. Let’s take a look at how cells communicate with each other.
Extracellular Matrix of Animal Cells
While cells in most multicellular organisms release materials into the extracellular space, animal cells will be discussed as an example. The primary components of these materials are proteins, and the most abundant protein is collagen. Collagen fibers are interwoven with proteoglycans, which are carbohydrate-containing protein molecules. Collectively, we call these materials the extracellular matrix (Figure 4.27). Not only does the extracellular matrix hold the cells together to form a tissue, but it also allows the cells within the tissue to communicate with each other. How can this happen?
Figure 4.27 The extracellular matrix consists of a network of proteins and carbohydrates.
Cells have protein receptors on their plasma membranes' extracellular surfaces. When a molecule within the matrix binds to the receptor, it changes the receptor's molecular structure. The receptor, in turn, changes the microfilaments' conformation positioned just inside the plasma membrane. These conformational changes induce chemical signals inside the cell that reach the nucleus and turn “on” or “off” the transcription of specific DNA sections, which affects the associated protein production, thus changing the activities within the cell.
Blood clotting provides an example of the extracellular matrix's role in cell communication. When the cells lining a blood vessel are damaged, they display a protein receptor, which we call tissue factor. When tissue factor binds with another factor in the extracellular matrix, it causes platelets to adhere to the damaged blood vessel's wall, stimulates the adjacent smooth muscle cells in the blood vessel to contract (thus constricting the blood vessel), and initiates a series of steps that stimulate the platelets to produce clotting factors.
Intercellular Junctions
Cells can also communicate with each other via direct contact, or intercellular junctions. There are differences in the ways that plant and animal and fungal cells communicate. Plasmodesmata are junctions between plant cells; whereas, animal cell contacts include tight junctions, gap junctions, and desmosomes.
Plasmodesmata
In general, long stretches of the plasma membranes of neighboring plant cells cannot touch one another because the cell wall that surrounds each cell separates them (Figure 4.8). How then, can a plant transfer water and other soil nutrients from its roots, through its stems, and to its leaves? Such transport uses the vascular tissues (xylem and phloem) primarily. There also exist structural modifications, which we call plasmodesmata (singular = plasmodesma). Numerous channels that pass between adjacent plant cells' cell walls connect their cytoplasm, and enable transport of materials from cell to cell, and thus throughout the plant (Figure 4.28).
Figure 4.28 A plasmodesma is a channel between two adjacent plant cells' cell walls. Plasmodesmata allow materials to pass from one plant cell's cytoplasm to an adjacent cell's cytoplasm.
Tight Junctions
A tight junction is a watertight seal between two adjacent animal cells (Figure 4.29). Proteins (predominantly two proteins called claudins and occludins) tightly hold the cells against each other.
Figure 4.29 Tight junctions form watertight connections between adjacent animal cells. Proteins create tight junction adherence. (credit: modification of work by Mariana Ruiz Villareal)
This tight adherence prevents materials from leaking between the cells; tight junctions are typically found in epithelial tissues that line internal organs and cavities, and comprise most of the skin. For example, the tight junctions of the epithelial cells lining your urinary bladder prevent urine from leaking out into the extracellular space.
Desmosomes
Also only in animal cells are desmosomes, which act like spot welds between adjacent epithelial cells (Figure 4.30). Cadherins, short proteins in the plasma membrane connect to intermediate filaments to create desmosomes. The cadherins connect two adjacent cells and maintain the cells in a sheet-like formation in organs and tissues that stretch, like the skin, heart, and muscles.
Figure 4.30 A desmosome forms a very strong spot weld between cells. Linking cadherins and intermediate filaments create it. (credit: modification of work by Mariana Ruiz Villareal)
Gap Junctions
Gap junctions in animal cells are like plasmodesmata in plant cells in that they are channels between adjacent cells that allow for transporting ions, nutrients, and other substances that enable cells to communicate (Figure 4.31). Structurally, however, gap junctions and plasmodesmata differ.
Figure 4.31 A gap junction is a protein-lined pore that allows water and small molecules to pass between adjacent animal cells. (credit: modification of work by Mariana Ruiz Villareal)
Gap junctions develop when a set of six proteins (connexins) in the plasma membrane arrange themselves in an elongated donut-like configuration - a connexon. When the connexon's pores (“doughnut holes”) in adjacent animal cells align, a channel between the two cells forms. Gap junctions are particularly important in cardiac muscle. The electrical signal for the muscle to contract passes efficiently through gap junctions, allowing the heart muscle cells to contract in tandem.
Link to Learning
Link to Learning
To conduct a virtual microscopy lab and review the parts of a cell, work through the steps of this interactive assignment. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.01%3A_Cell_Structure/2.1.07%3A__Connections_between_Cells_and_Cellular_Activities.txt |
cell theory
see unified cell theory
cell wall
rigid cell covering comprised of various molecules that protects the cell, provides structural support, and gives shape to the cell
central vacuole
large plant cell organelle that regulates the cell’s storage compartment, holds water, and plays a significant role in cell growth as the site of macromolecule degradation
centrosome
region in animal cells made of two centrioles that serves as an organizing center for microtubules
chlorophyll
green pigment that captures the light energy that drives the light reactions of photosynthesis
chloroplast
plant cell organelle that carries out photosynthesis
chromatin
protein-DNA complex that serves as the chromosomes' building material
chromosome
structure within the nucleus that comprises chromatin that contains DNA, the hereditary material
cilium
(plural = cilia) short, hair-like structure that extends from the plasma membrane in large numbers and functions to move an entire cell or move substances along the cell's outer surface
cytoplasm
entire region between the plasma membrane and the nuclear envelope, consisting of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals
cytoskeleton
protein fiber network that collectively maintains the cell's shape, secures some organelles in specific positions, allows cytoplasm and vesicles to move within the cell, and enables unicellular organisms to move independently
cytosol
the cytoplasm's gel-like material in which cell structures are suspended
desmosome
linkages between adjacent epithelial cells that form when cadherins in the plasma membrane attach to intermediate filaments
electron microscope
an instrument that magnifies an object using an electron beam that passes and bends through a lens system to visualize a specimen
endomembrane system
group of organelles and membranes in eukaryotic cells that work together modifying, packaging, and transporting lipids and proteins
endoplasmic reticulum (ER)
series of interconnected membranous structures within eukaryotic cells that collectively modify proteins and synthesize lipids
eukaryotic cell
cell that has a membrane-bound nucleus and several other membrane-bound compartments or sacs
extracellular matrix
material secreted from animal or fungal cells that provides mechanical protection and anchoring for the cells in the tissue
flagellum
(plural = flagella) long, hair-like structure that extends from the plasma membrane and moves the cell
gap junction
channel between two adjacent animal cells that allows ions, nutrients, and low molecular weight substances to pass between cells, enabling the cells to communicate
Golgi apparatus
eukaryotic organelle comprised of a series of stacked membranes that sorts, tags, and packages lipids and proteins for distribution
intermediate filament
cytoskeletal component, comprised of several fibrous protein intertwined strands, that bears tension, supports cell-cell junctions, and anchors cells to extracellular structures
light microscope
an instrument that magnifies an object using a beam of visible light that passes and bends through a lens system to visualize a specimen
lysosome
organelle in an animal cell that functions as the cell’s digestive component; it breaks down proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles
microfilament
the cytoskeleton system's narrowest element; it provides rigidity and shape to the cell and enables cellular movements
microscope
an instrument that magnifies an object
microtubule
the cytoskeleton system's widest element; it helps the cell resist compression, provides a track along which vesicles move through the cell, pulls replicated chromosomes to opposite ends of a dividing cell, and is the structural element of centrioles, flagella, and cilia
mitochondria
(singular = mitochondrion) cellular organelles responsible for carrying out cellular respiration, resulting in producing ATP, the cell’s main energy-carrying molecule
nuclear envelope
double-membrane structure that constitutes the nucleus' outermost portion
nucleoid
central part of a prokaryotic cell's central part where the chromosome is located
nucleolus
darkly staining body within the nucleus that is responsible for assembling ribosome subunits
nucleoplasm
semi-solid fluid inside the nucleus that contains the chromatin and nucleolus
nucleus
cell organelle that houses the cell’s DNA and directs ribosome and protein synthesis
organelle
compartment or sac within a cell
peroxisome
small, round organelle that contains hydrogen peroxide, oxidizes fatty acids and amino acids, and detoxifies many poisons
plasma membrane
phospholipid bilayer with embedded (integral) or attached (peripheral) proteins, and separates the cell's internal content from its surrounding environment
plasmodesma
(plural = plasmodesmata) channel that passes between adjacent plant cells' cell walls, connects their cytoplasm, and allows transporting of materials from cell to cell
prokaryote
unicellular organism that lacks a nucleus or any other membrane-bound organelle
ribosome
cellular structure that carries out protein synthesis
rough endoplasmic reticulum (RER)
region of the endoplasmic reticulum that is studded with ribosomes and engages in protein modification and phospholipid synthesis
smooth endoplasmic reticulum (SER)
region of the endoplasmic reticulum that has few or no ribosomes on its cytoplasmic surface and synthesizes carbohydrates, lipids, and steroid hormones; detoxifies certain chemicals (like pesticides, preservatives, medications, and environmental pollutants), and stores calcium ions
tight junction
protein adherence that creates a firm seal between two adjacent animal cells
unified cell theory
a biological concept that states that one or more cells comprise all organisms; the cell is the basic unit of life; and new cells arise from existing cells
vacuole
membrane-bound sac, somewhat larger than a vesicle, which functions in cellular storage and transport
vesicle
small, membrane-bound sac that functions in cellular storage and transport; its membrane is capable of fusing with the plasma membrane and the membranes of the endoplasmic reticulum and Golgi apparatus | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.01%3A_Cell_Structure/2.1.08%3A_Key_Terms.txt |
4.1 Studying Cells
A cell is the smallest unit of life. Most cells are so tiny that we cannot see them with the naked eye. Therefore, scientists use microscopes to study cells. Electron microscopes provide higher magnification, higher resolution, and more detail than light microscopes. The unified cell theory states that one or more cells comprise all organisms, the cell is the basic unit of life, and new cells arise from existing cells.
4.2 Prokaryotic Cells
Prokaryotes are single-celled organisms of the domains Bacteria and Archaea. All prokaryotes have plasma membranes, cytoplasm, ribosomes, and DNA that is not membrane-bound. Most have peptidoglycan cell walls and many have polysaccharide capsules. Prokaryotic cells range in diameter from 0.1 to 5.0 μm.
As a cell increases in size, its surface area-to-volume ratio decreases. If the cell grows too large, the plasma membrane will not have sufficient surface area to support the rate of diffusion required for the increased volume.
4.3 Eukaryotic Cells
Like a prokaryotic cell, a eukaryotic cell has a plasma membrane, cytoplasm, and ribosomes, but a eukaryotic cell is typically larger than a prokaryotic cell, has a true nucleus (meaning a membrane surrounds its DNA), and has other membrane-bound organelles that allow for compartmentalizing functions. The plasma membrane is a phospholipid bilayer embedded with proteins. The nucleus’s nucleolus is the site of ribosome assembly. We find ribosomes either in the cytoplasm or attached to the cytoplasmic side of the plasma membrane or endoplasmic reticulum. They perform protein synthesis. Mitochondria participate in cellular respiration. They are responsible for the majority of ATP produced in the cell. Peroxisomes hydrolyze fatty acids, amino acids, and some toxins. Vesicles and vacuoles are storage and transport compartments. In plant cells, vacuoles also help break down macromolecules.
Animal cells also have a centrosome and lysosomes. The centrosome has two bodies perpendicular to each other, the centrioles, and has an unknown purpose in cell division. Lysosomes are the digestive organelles of animal cells.
Plant cells and plant-like cells each have a cell wall, chloroplasts, and a central vacuole. The plant cell wall, whose primary component is cellulose, protects the cell, provides structural support, and gives the cell shape. Photosynthesis takes place in chloroplasts. The central vacuole can expand without having to produce more cytoplasm.
4.4 The Endomembrane System and Proteins
The endomembrane system includes the nuclear envelope, lysosomes, vesicles, the ER, and Golgi apparatus, as well as the plasma membrane. These cellular components work together to modify, package, tag, and transport proteins and lipids that form the membranes.
The RER modifies proteins and synthesizes phospholipids in cell membranes. The SER synthesizes carbohydrates, lipids, and steroid hormones; engages in the detoxification of medications and poisons; and stores calcium ions. Sorting, tagging, packaging, and distributing lipids and proteins take place in the Golgi apparatus. Budding RER and Golgi membranes create lysosomes. Lysosomes digest macromolecules, recycle worn-out organelles, and destroy pathogens.
4.5 The Cytoskeleton
The cytoskeleton has three different protein element types. From narrowest to widest, they are the microfilaments (actin filaments), intermediate filaments, and microtubules. Biologists often associate microfilaments with myosin. They provide rigidity and shape to the cell and facilitate cellular movements. Intermediate filaments bear tension and anchor the nucleus and other organelles in place. Microtubules help the cell resist compression, serve as tracks for motor proteins that move vesicles through the cell, and pull replicated chromosomes to opposite ends of a dividing cell. They are also the structural element of centrioles, flagella, and cilia.
4.6 Connections between Cells and Cellular Activities
Animal cells communicate via their extracellular matrices and are connected to each other via tight junctions, desmosomes, and gap junctions. Plant cells are connected and communicate with each other via plasmodesmata.
When protein receptors on the plasma membrane's surface of an animal cell bind to a substance in the extracellular matrix, a chain of reactions begins that changes activities taking place within the cell. Plasmodesmata are channels between adjacent plant cells, while gap junctions are channels between adjacent animal cells. However, their structures are quite different. A tight junction is a watertight seal between two adjacent cells, while a desmosome acts like a spot weld.
2.1.10: Visual Connection Questions
1.
Figure 4.7 Prokaryotic cells are much smaller than eukaryotic cells. What advantages might small cell size confer on a cell? What advantages might large cell size have?
2.
Figure 4.8 If the nucleolus were not able to carry out its function, what other cellular organelles would be affected?
3.
Figure 4.18 If a peripheral membrane protein were synthesized in the lumen (inside) of the ER, would it end up on the inside or outside of the plasma membrane? | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.01%3A_Cell_Structure/2.1.09%3A_Chapter_Summary.txt |
4.
When viewing a specimen through a light microscope, scientists use ________ to distinguish the individual components of cells.
1. a beam of electrons
2. radioactive isotopes
3. special stains
4. high temperatures
5.
The ________ is the basic unit of life.
1. organism
2. cell
3. tissue
4. organ
6.
Prokaryotes depend on ________ to obtain some materials and to get rid of wastes.
1. ribosomes
2. flagella
3. cell division
4. diffusion
7.
Bacteria that lack fimbriae are less likely to ________.
1. adhere to cell surfaces
2. swim through bodily fluids
3. synthesize proteins
4. retain the ability to divide
8.
Which of the following organisms is a prokaryote?
1. amoeba
2. influenza A virus
3. charophyte algae
4. E. coli
9.
Which of the following is surrounded by two phospholipid bilayers?
1. the ribosomes
2. the vesicles
3. the cytoplasm
4. the nucleoplasm
10.
Peroxisomes got their name because hydrogen peroxide is:
1. used in their detoxification reactions
2. produced during their oxidation reactions
3. incorporated into their membranes
4. a cofactor for the organelles’ enzymes
11.
In plant cells, the function of the lysosomes is carried out by __________.
1. vacuoles
2. peroxisomes
3. ribosomes
4. nuclei
12.
Which of the following is both in eukaryotic and prokaryotic cells?
1. nucleus
2. mitochondrion
3. vacuole
4. ribosomes
13.
Tay-Sachs disease is a genetic disorder that results in the destruction of neurons due to a buildup of sphingolipids in the cells. Which organelle is malfunctioning in Tay-Sachs?
1. lysosome
2. endoplasmic reticulum
3. peroxisome
4. mitochondria
14.
Which of the following is not a component of the endomembrane system?
1. mitochondrion
2. Golgi apparatus
3. endoplasmic reticulum
4. lysosome
15.
The process by which a cell engulfs a foreign particle is known as:
1. endosymbiosis
2. phagocytosis
3. hydrolysis
4. membrane synthesis
16.
Which of the following is most likely to have the greatest concentration of smooth endoplasmic reticulum?
1. a cell that secretes enzymes
2. a cell that destroys pathogens
3. a cell that makes steroid hormones
4. a cell that engages in photosynthesis
17.
Which of the following sequences correctly lists in order the steps involved in the incorporation of a proteinaceous molecule within a cell?
1. protein synthesis of the protein on the ribosome; modification in the Golgi apparatus; packaging in the endoplasmic reticulum; tagging in the vesicle
2. synthesis of the protein on the lysosome; tagging in the Golgi; packaging in the vesicle; distribution in the endoplasmic reticulum
3. synthesis of the protein on the ribosome; modification in the endoplasmic reticulum; tagging in the Golgi; distribution via the vesicle
4. synthesis of the protein on the lysosome; packaging in the vesicle; distribution via the Golgi; tagging in the endoplasmic reticulum
18.
Congenital disorders of glycosylation are a growing class of rare diseases. Which organelle would be most commonly involved in the glycoprotein disorder portion of the group?
1. RER
2. ribosomes
3. endosomes
4. Golgi apparatus
19.
Which of the following have the ability to disassemble and reform quickly?
1. microfilaments and intermediate filaments
2. microfilaments and microtubules
3. intermediate filaments and microtubules
4. only intermediate filaments
20.
Which of the following do not play a role in intracellular movement?
1. microfilaments and intermediate filaments
2. microfilaments and microtubules
3. intermediate filaments and microtubules
4. only intermediate filaments
21.
In humans, _____ are used to move a cell within its environment while _____ are used to move the environment relative to the cell.
1. cilia, pseudopodia
2. flagella; cilia
3. microtubules; flagella
4. microfilaments; microtubules
22.
Which of the following are only in plant cells?
1. gap junctions
2. desmosomes
3. plasmodesmata
4. tight junctions
23.
The key components of desmosomes are cadherins and __________.
1. actin
2. microfilaments
3. intermediate filaments
4. microtubules
24.
Diseased animal cells may produce molecules that activate death cascades to kill the cells in a controlled manner. Why would neighboring healthy cells also die?
1. The death molecule is passed through desmosomes.
2. The death molecule is passed through plasmodesmata.
3. The death molecule disrupts the extracellular matrix.
4. The death molecule passes through gap junctions.
2.1.12: Critical Thinking Questions
25.
In your everyday life, you have probably noticed that certain instruments are ideal for certain situations. For example, you would use a spoon rather than a fork to eat soup because a spoon is shaped for scooping, while soup would slip between the tines of a fork. The use of ideal instruments also applies in science. In what situation(s) would the use of a light microscope be ideal, and why?
26.
In what situation(s) would the use of a scanning electron microscope be ideal, and why?
27.
In what situation(s) would a transmission electron microscope be ideal, and why?
28.
What are the advantages and disadvantages of each of these types of microscopes?
29.
Explain how the formation of an adult human follows the cell theory.
30.
Antibiotics are medicines that are used to fight bacterial infections. These medicines kill prokaryotic cells without harming human cells. What part or parts of the bacterial cell do you think antibiotics target? Why?
31.
Explain why not all microbes are harmful.
32.
You already know that ribosomes are abundant in red blood cells. In what other cells of the body would you find them in great abundance? Why?
33.
What are the structural and functional similarities and differences between mitochondria and chloroplasts?
34.
Why are plasma membranes arranged as a bilayer rather than a monolayer?
35.
In the context of cell biology, what do we mean by form follows function? What are at least two examples of this concept?
36.
In your opinion, is the nuclear membrane part of the endomembrane system? Why or why not? Defend your answer.
37.
What are the similarities and differences between the structures of centrioles and flagella?
38.
How do cilia and flagella differ?
39.
Describe how microfilaments and microtubules are involved in the phagocytosis and destruction of a pathogen by a macrophage.
40.
Compare and contrast the boundaries that plant, animal, and bacteria cells use to separate themselves from their surrounding environment.
41.
How does the structure of a plasmodesma differ from that of a gap junction?
42.
Explain how the extracellular matrix functions.
43.
Pathogenic E. coli have recently been shown to degrade tight junction proteins during infection. How would this provide an advantage to the bacteria? | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.01%3A_Cell_Structure/2.1.11%3A_Review_Questions.txt |
The plasma membrane, which is also called the cell membrane, has many functions, but the most basic one is to define the borders of the cell and keep the cell functional. The plasma membrane is selectively permeable. This means that the membrane allows some materials to freely enter or leave the cell, while other materials cannot move freely, but require the use of a specialized structure, and occasionally, even energy investment for crossing.
• 2.2.1: Introduction
Despite its seeming hustle and bustle, Grand Central Station functions with a high level of organization: People and objects move from one location to another, they cross or are contained within certain boundaries, and they provide a constant flow as part of larger activity. Analogously, a plasma membrane’s functions involve movement within the cell and across boundaries in the process of intracellular and intercellular activities.
• 2.2.2: Components and Structure
Among the most sophisticated functions of the plasma membrane is the ability to transmit signals by means of complex, integral proteins known as receptors. These proteins act both as receivers of extracellular inputs and as activators of intracellular processes. These membrane receptors provide extracellular attachment sites for effectors like hormones and growth factors, and they activate intracellular response cascades when their effectors are bound.
• 2.2.3: Passive Transport
Plasma membranes must allow certain substances to enter and leave a cell, and prevent some harmful materials from entering and some essential materials from leaving. In other words, plasma membranes are selectively permeable—they allow some substances to pass through, but not others. If they were to lose this selectivity, the cell would no longer be able to sustain itself, and it would be destroyed. Some cells require larger amounts of specific substances than do other cells.
• 2.2.4: Active Transport
Active transport mechanisms require the use of the cell’s energy, usually in the form of adenosine triphosphate (ATP). If a substance must move into the cell against its concentration gradient—that is, if the concentration of the substance inside the cell is greater than its concentration in the extracellular fluid (and vice versa)—the cell must use energy to move the substance. Some active transport mechanisms move small-molecular weight materials, such as ions, through the membrane.
• 2.2.5: Bulk Transport
In addition to moving small ions and molecules through the membrane, cells also need to remove and take in larger molecules and particles. Some cells are even capable of engulfing entire unicellular microorganisms. You might have correctly hypothesized that the uptake and release of large particles by the cell requires energy. A large particle, however, cannot pass through the membrane, even with energy supplied by the cell.
• 2.2.6: Key Terms
• 2.2.7: Chapter Summary
• 2.2.8: Visual Connection Questions
• 2.2.9: Review Questions
• 2.2.10: Critical Thinking Questions
Thumbnail: The cell membrane. (Public Domain; LadyofHats via Wikimedia Commons).
2.02: Structure and Function of Plasma Membranes
Figure 5.1 Despite its seeming hustle and bustle, Grand Central Station functions with a high level of organization: People and objects move from one location to another, they cross or are contained within certain boundaries, and they provide a constant flow as part of larger activity. Analogously, a plasma membrane’s functions involve movement within the cell and across boundaries' activities. (credit: modification of work by Randy Le’Moine)
The plasma membrane, the cell membrane, has many functions, but the most basic one is to define the cell's borders and keep the cell functional. The plasma membrane is selectively permeable. This means that the membrane allows some materials to freely enter or leave the cell, while other materials cannot move freely, but require a specialized structure, and occasionally, even energy investment for crossing. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.02%3A_Structure_and_Function_of_Plasma_Membranes/2.2.01%3A_Introduction.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Understand the cell membrane fluid mosaic model
• Describe phospholipid, protein, and carbohydrate functions in membranes
• Discuss membrane fluidity
A cell’s plasma membrane defines the cell, outlines its borders, and determines the nature of its interaction with its environment (see Table 5.1 for a summary). Cells exclude some substances, take in others, and excrete still others, all in controlled quantities. The plasma membrane must be very flexible to allow certain cells, such as red and white blood cells, to change shape as they pass through narrow capillaries. These are the more obvious plasma membrane functions. In addition, the plasma membrane's surface carries markers that allow cells to recognize one another, which is vital for tissue and organ formation during early development, and which later plays a role in the immune response's “self” versus “non-self” distinction.
Among the most sophisticated plasma membrane functions is the ability for complex, integral proteins, receptors to transmit signals. These proteins act both as extracellular input receivers and as intracellular processing activators. These membrane receptors provide extracellular attachment sites for effectors like hormones and growth factors, and they activate intracellular response cascades when their effectors are bound. Occasionally, viruses hijack receptors (HIV, human immunodeficiency virus, is one example) that use them to gain entry into cells, and at times, the genes encoding receptors become mutated, causing the signal transduction process to malfunction with disastrous consequences.
Fluid Mosaic Model
Scientists identified the plasma membrane in the 1890s, and its chemical components in 1915. The principal components they identified were lipids and proteins. In 1935, Hugh Davson and James Danielli proposed the plasma membrane's structure. This was the first model that others in the scientific community widely accepted. It was based on the plasma membrane's “railroad track” appearance in early electron micrographs. Davson and Danielli theorized that the plasma membrane's structure resembles a sandwich. They made the analogy of proteins to bread, and lipids to the filling. In the 1950s, advances in microscopy, notably transmission electron microscopy (TEM), allowed researchers to see that the plasma membrane's core consisted of a double, rather than a single, layer. In 1972, S.J. Singer and Garth L. Nicolson proposed a new model that provides microscopic observations and better explains plasma membrane function.
The explanation, the fluid mosaic model, has evolved somewhat over time, but it still best accounts for plasma membrane structure and function as we now understand them. The fluid mosaic model describes the plasma membrane structure as a mosaic of components—including phospholipids, cholesterol, proteins, and carbohydrates—that gives the membrane a fluid character. Plasma membranes range from 5 to 10 nm in thickness. For comparison, human red blood cells, visible via light microscopy, are approximately 8 µm wide, or approximately 1,000 times wider than a plasma membrane. The membrane does look a bit like a sandwich (Figure 5.2).
Figure 5.2 The plasma membrane fluid mosaic model describes the plasma membrane as a fluid combination of phospholipids, cholesterol, and proteins. Carbohydrates attached to lipids (glycolipids) and to proteins (glycoproteins) extend from the membrane's outward-facing surface. Credit: Rao, A., Ryan, K., Fletcher, S., Hawkins, A. and Tag, A. Department of Biology, Texas A&M University.
A plasma membrane's principal components are lipids (phospholipids and cholesterol), proteins, and carbohydrates attached to some of the lipids and proteins. A phospholipid is a molecule consisting of glycerol, two fatty acids, and a phosphate-linked head group. Cholesterol, another lipid comprised of four fused carbon rings, is situated alongside the phospholipids in the membrane's core. The protein, lipid, and carbohydrate proportions in the plasma membrane vary with cell type, but for a typical human cell, protein accounts for about 50 percent of the composition by mass, lipids (of all types) account for about 40 percent, and carbohydrates comprise the remaining 10 percent. However, protein and lipid concentration varies with different cell membranes. For example, myelin, an outgrowth of specialized cells' membrane that insulates the peripheral nerves' axons, contains only 18 percent protein and 76 percent lipid. The mitochondrial inner membrane contains 76 percent protein and only 24 percent lipid. The plasma membrane of human red blood cells is 30 percent lipid. Carbohydrates are present only on the plasma membrane's exterior surface and are attached to proteins, forming glycoproteins, or attached to lipids, forming glycolipids.
Phospholipids
The membrane's main fabric comprises amphiphilic, phospholipid molecules. The hydrophilic or “water-loving” areas of these molecules (which look like a collection of balls in an artist’s rendition of the model) (Figure 5.2) are in contact with the aqueous fluid both inside and outside the cell. Hydrophobic, or water-hating molecules, tend to be non-polar. They interact with other non-polar molecules in chemical reactions, but generally do not interact with polar molecules. When placed in water, hydrophobic molecules tend to form a ball or cluster. The phospholipids' hydrophilic regions form hydrogen bonds with water and other polar molecules on both the cell's exterior and interior. Thus, the membrane surfaces that face the cell's interior and exterior are hydrophilic. In contrast, the cell membrane's interior is hydrophobic and will not interact with water. Therefore, phospholipids form an excellent two-layer cell membrane that separates fluid within the cell from the fluid outside the cell.
A phospholipid molecule (Figure 5.3) consists of a three-carbon glycerol backbone with two fatty acid molecules attached to carbons 1 and 2, and a phosphate-containing group attached to the third carbon. This arrangement gives the overall molecule a head area (the phosphate-containing group), which has a polar character or negative charge, and a tail area (the fatty acids), which has no charge. The head can form hydrogen bonds, but the tail cannot. Scientists call a molecule with a positively or negatively charged area and an uncharged, or non-polar, area amphiphilic or “dual-loving.”
Figure 5.3 A hydrophilic head and two hydrophobic tails comprise this phospholipid molecule. The hydrophilic head group consists of a phosphate-containing group attached to a glycerol molecule. The hydrophobic tails, each containing either a saturated or an unsaturated fatty acid, are long hydrocarbon chains.
This characteristic is vital to the plasma membrane's structure because, in water, phospholipids arrange themselves with their hydrophobic tails facing each other and their hydrophilic heads facing out. In this way, they form a lipid bilayer—a double layered phospholipid barrier that separates the water and other materials on one side from the water and other materials on the other side. Phospholipids heated in an aqueous solution usually spontaneously form small spheres or droplets (micelles or liposomes), with their hydrophilic heads forming the exterior and their hydrophobic tails on the inside (Figure 5.4).
Figure 5.4 In an aqueous solution, phospholipids usually arrange themselves with their polar heads facing outward and their hydrophobic tails facing inward. (credit: modification of work by Mariana Ruiz Villareal)
Proteins
Proteins comprise the plasma membranes' second major component. Integral proteins, or integrins, as their name suggests, integrate completely into the membrane structure, and their hydrophobic membrane-spanning regions interact with the phospholipid bilayer's hydrophobic region (Figure 5.2). Single-pass integral membrane proteins usually have a hydrophobic transmembrane segment that consists of 20–25 amino acids. Some span only part of the membrane—associating with a single layer—while others stretch from one side to the other, and are exposed on either side. Up to 12 single protein segments comprise some complex proteins, which are extensively folded and embedded in the membrane (Figure 5.5). This protein type has a hydrophilic region or regions, and one or several mildly hydrophobic regions. This arrangement of protein regions orients the protein alongside the phospholipids, with the protein's hydrophobic region adjacent to the phospholipids' tails and the protein's hydrophilic region or regions protruding from the membrane and in contact with the cytosol or extracellular fluid.
Figure 5.5 Integral membrane proteins may have one or more alpha-helices that span the membrane (examples 1 and 2), or they may have beta-sheets that span the membrane (example 3). (credit: “Foobar”/Wikimedia Commons)
Peripheral proteins are on the membranes' exterior and interior surfaces, attached either to integral proteins or to phospholipids. Peripheral proteins, along with integral proteins, may serve as enzymes, as structural attachments for the cytoskeleton's fibers, or as part of the cell’s recognition sites. Scientists sometimes refer to these as “cell-specific” proteins. The body recognizes its own proteins and attacks foreign proteins associated with invasive pathogens.
Carbohydrates
Carbohydrates are the third major plasma membrane component. They are always on the cells' exterior surface and are bound either to proteins (forming glycoproteins) or to lipids (forming glycolipids) (Figure 5.2). These carbohydrate chains may consist of 2–60 monosaccharide units and can be either straight or branched. Along with peripheral proteins, carbohydrates form specialized sites on the cell surface that allow cells to recognize each other. These sites have unique patterns that allow for cell recognition, much the way that the facial features unique to each person allow individuals to recognize him or her. This recognition function is very important to cells, as it allows the immune system to differentiate between body cells (“self”) and foreign cells or tissues (“non-self”). Similar glycoprotein and glycolipid types are on the surfaces of viruses and may change frequently, preventing immune cells from recognizing and attacking them.
We collectively refer to these carbohydrates on the cell's exterior surface—the carbohydrate components of both glycoproteins and glycolipids—as the glycocalyx (meaning “sugar coating”). The glycocalyx is highly hydrophilic and attracts large amounts of water to the cell's surface. This aids in the cell's interaction with its watery environment and in the cell’s ability to obtain substances dissolved in the water. As we discussed above, the glycocalyx is also important for cell identification, self/non-self determination, and embryonic development, and is used in cell to cell attachments to form tissues.
Evolution Connection
Evolution Connection
How Viruses Infect Specific OrgansGlycoprotein and glycolipid patterns on the cells' surfaces give many viruses an opportunity for infection. HIV and hepatitis viruses infect only specific organs or cells in the human body. HIV is able to penetrate the plasma membranes of a subtype of lymphocytes called T-helper cells, as well as some monocytes and central nervous system cells. The hepatitis virus attacks liver cells.
These viruses are able to invade these cells, because the cells have binding sites on their surfaces that are specific to and compatible with certain viruses (Figure 5.6). Other recognition sites on the virus’s surface interact with the human immune system, prompting the body to produce antibodies. Antibodies are made in response to the antigens or proteins associated with invasive pathogens, or in response to foreign cells, such as might occur with an organ transplant. These same sites serve as places for antibodies to attach and either destroy or inhibit the virus' activity. Unfortunately, these recognition sites on HIV change at a rapid rate because of mutations, making an effective vaccine against the virus very difficult, as the virus evolves and adapts. A person infected with HIV will quickly develop different populations, or variants, of the virus that differences in these recognition sites distinguish. This rapid change of surface markers decreases the effectiveness of the person’s immune system in attacking the virus, because the antibodies will not recognize the surface patterns' new variations. In the case of HIV, the problem is compounded because the virus specifically infects and destroys cells involved in the immune response, further incapacitating the host.
Figure 5.6 HIV binds to the CD4 receptor, a glycoprotein on T cell surfaces. (credit: modification of work by NIH, NIAID)
Membrane Fluidity
The membrane's mosaic characteristic helps to illustrate its nature. The integral proteins and lipids exist in the membrane as separate but loosely attached molecules. These resemble the separate, multicolored tiles of a mosaic picture, and they float, moving somewhat with respect to one another. The membrane is not like a balloon, however, that can expand and contract; rather, it is fairly rigid and can burst if penetrated or if a cell takes in too much water. However, because of its mosaic nature, a very fine needle can easily penetrate a plasma membrane without causing it to burst, and the membrane will flow and self-seal when one extracts the needle.
The membrane's mosaic characteristics explain some but not all of its fluidity. There are two other factors that help maintain this fluid characteristic. One factor is the nature of the phospholipids themselves. In their saturated form, the fatty acids in phospholipid tails are saturated with bound hydrogen atoms. There are no double bonds between adjacent carbon atoms. This results in tails that are relatively straight. In contrast, unsaturated fatty acids do not contain a maximal number of hydrogen atoms, but they do contain some double bonds between adjacent carbon atoms. A double bond results in a bend in the carbon string of approximately 30 degrees (Figure 5.3).
Thus, if decreasing temperatures compress saturated fatty acids with their straight tails, they press in on each other, making a dense and fairly rigid membrane. If unsaturated fatty acids are compressed, the “kinks” in their tails elbow adjacent phospholipid molecules away, maintaining some space between the phospholipid molecules. This “elbow room” helps to maintain fluidity in the membrane at temperatures at which membranes with saturated fatty acid tails in their phospholipids would “freeze” or solidify. The membrane's relative fluidity is particularly important in a cold environment. A cold environment usually compresses membranes comprised largely of saturated fatty acids, making them less fluid and more susceptible to rupturing. Many organisms (fish are one example) are capable of adapting to cold environments by changing the proportion of unsaturated fatty acids in their membranes in response to lower temperature.
Link to Learning
Link to Learning
Visit this site to see animations of the membranes' fluidity and mosaic quality.
Animals have an additional membrane constituent that assists in maintaining fluidity. Cholesterol, which lies alongside the phospholipids in the membrane, tends to dampen temperature effects on the membrane. Thus, this lipid functions as a buffer, preventing lower temperatures from inhibiting fluidity and preventing increased temperatures from increasing fluidity too much. Thus, cholesterol extends, in both directions, the temperature range in which the membrane is appropriately fluid and consequently functional. Cholesterol also serves other functions, such as organizing clusters of transmembrane proteins into lipid rafts.
Plasma Membrane Components and Functions
Component Location
Phospholipid Main membrane fabric
Cholesterol Attached between phospholipids and between the two phospholipid layers
Integral proteins (for example, integrins) Embedded within the phospholipid layer(s); may or may not penetrate through both layers
Peripheral proteins On the phospholipid bilayer's inner or outer surface; not embedded within the phospholipids
Carbohydrates (components of glycoproteins and glycolipids) Generally attached to proteins on the outside membrane layer
Table 5.1
Career Connection
Career Connection
ImmunologistThe variations in peripheral proteins and carbohydrates that affect a cell’s recognition sites are of prime interest in immunology. In developing vaccines, researchers have been able to conquer many infectious diseases, such as smallpox, polio, diphtheria, and tetanus.
Immunologists are the physicians and scientists who research and develop vaccines, as well as treat and study allergies or other immune problems. Some immunologists study and treat autoimmune problems (diseases in which a person’s immune system attacks their own cells or tissues, such as lupus) and immunodeficiencies, whether acquired (such as acquired immunodeficiency syndrome, or AIDS) or hereditary (such as severe combined immunodeficiency, or SCID). Immunologists also help treat organ transplantation patients, who must have their immune systems suppressed so that their bodies will not reject a transplanted organ. Some immunologists work to understand natural immunity and the effects of a person’s environment on it. Others work on questions about how the immune system affects diseases such as cancer. In the past, researchers did not understand the importance of having a healthy immune system in preventing cancer.
Immunologists who focus on certain types of diseases or pathogens can play an important role in saving lives during specific outbreaks and pandemics. Kizzmekia S. Corbett, for example, was a research fellow and scientific lead working specifically on coronaviruses. When the COVID-19 pandemic occurred, Corbett's deep experience and knowledge was instrumental in developing one of the main vaccines (Moderna). She is now applying that experience to other respiratory diseases and vaccine development processes.
To work as an immunologist, one must have a PhD or MD. In addition, immunologists undertake at least two to three years of training in an accredited program and must pass the American Board of Allergy and Immunology exam. Immunologists must possess knowledge of the human body's function as they relate to issues beyond immunization, and knowledge of pharmacology and medical technology, such as medications, therapies, test materials, and surgical procedures. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.02%3A_Structure_and_Function_of_Plasma_Membranes/2.2.02%3A_Components_and_Structure.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Explain why and how passive transport occurs
• Understand the osmosis and diffusion processes
• Define tonicity and its relevance to passive transport
Plasma membranes must allow certain substances to enter and leave a cell, and prevent some harmful materials from entering and some essential materials from leaving. In other words, plasma membranes are selectively permeable (semipermeable)—they allow some substances to pass through, but not others. If they were to lose this selectivity, the cell would no longer be able to sustain itself, and it would be destroyed. Some cells require larger amounts of specific substances. They must have a way of obtaining these materials from extracellular fluids. This may happen passively, as certain materials move back and forth, or the cell may have special mechanisms that facilitate transport. Some materials are so important to a cell that it spends some of its energy, hydrolyzing adenosine triphosphate (ATP), to obtain these materials. Red blood cells use some of their energy doing just that. Most cells spend the majority of their energy to maintain an imbalance of sodium and potassium ions between the cell's interior and exterior, as well as on protein synthesis.
The most direct forms of membrane transport are passive. Passive transport is a naturally occurring phenomenon and does not require the cell to exert any of its energy to accomplish the movement. In passive transport, substances move from an area of higher concentration to an area of lower concentration. A physical space in which there is a single substance concentration range has a concentration gradient.
Selective Permeability
Plasma membranes are asymmetric: the membrane's interior is not identical to its exterior. There is a considerable difference between the array of phospholipids and proteins between the two leaflets that form a membrane. On the membrane's interior, some proteins serve to anchor the membrane to cytoskeleton's fibers. There are peripheral proteins on the membrane's exterior that bind extracellular matrix elements. Carbohydrates, attached to lipids or proteins, are also on the plasma membrane's exterior surface. These carbohydrate complexes help the cell bind required substances in the extracellular fluid. This adds considerably to plasma membrane's selective nature (Figure 5.7).
Figure 5.7 The plasma membrane's exterior surface is not identical to its interior surface. Credit: Rao, A., Ryan, K., Fletcher, S., Hawkins, A. and Tag, A. Department of Biology, Texas A&M University.
Recall that plasma membranes are amphiphilic: They have hydrophilic and hydrophobic regions. This characteristic helps move some materials through the membrane and hinders the movement of others. Non-polar and lipid-soluble material with a low molecular weight can easily slip through the membrane's hydrophobic lipid core. Substances such as the fat-soluble vitamins A, D, E, and K readily pass through the plasma membranes in the digestive tract and other tissues. Fat-soluble drugs and hormones also gain easy entry into cells and readily transport themselves into the body’s tissues and organs. Oxygen and carbon dioxide molecules have no charge and pass through membranes by simple diffusion.
Polar substances present problems for the membrane. While some polar molecules connect easily with the cell's outside, they cannot readily pass through the plasma membrane's lipid core. Additionally, while small ions could easily slip through the spaces in the membrane's mosaic, their charge prevents them from doing so. Ions such as sodium, potassium, calcium, and chloride must have special means of penetrating plasma membranes. Simple sugars and amino acids also need the help of various transmembrane proteins (channels) to transport themselves across plasma membranes.
Diffusion
Diffusion is a passive process of transport. A single substance moves from a high concentration to a low concentration area until the concentration is equal across a space. You are familiar with diffusion of substances through the air. For example, think about someone opening a bottle of ammonia in a room filled with people. The ammonia gas is at its highest concentration in the bottle. Its lowest concentration is at the room's edges. The ammonia vapor will diffuse, or spread away, from the bottle, and gradually, increasingly more people will smell the ammonia as it spreads. Materials move within the cell’s cytosol by diffusion, and certain materials move through the plasma membrane by diffusion (Figure 5.8). Diffusion expends no energy. On the contrary, concentration gradients are a form of potential energy, which dissipates as the gradient is eliminated.
Figure 5.8 Diffusion through a permeable membrane moves a substance from a high concentration area (extracellular fluid, in this case) down its concentration gradient (into the cytoplasm). (credit: modification of work by Mariana Ruiz Villareal)
Each separate substance in a medium, such as the extracellular fluid, has its own concentration gradient, independent of other materials' concentration gradients. In addition, each substance will diffuse according to that gradient. Within a system, there will be different diffusion rates of various substances in the medium.
Factors That Affect Diffusion
Molecules move constantly in a random manner, at a rate that depends on their mass, their environment, and the amount of thermal energy they possess, which in turn is a function of temperature. This movement accounts for molecule diffusion through whatever medium in which they are localized. A substance moves into any space available to it until it evenly distributes itself throughout. After a substance has diffused completely through a space, removing its concentration gradient, molecules will still move around in the space, but there will be no net movement of the number of molecules from one area to another. We call this lack of a concentration gradient in which the substance has no net movement dynamic equilibrium. While diffusion will go forward in the presence of a substance's concentration gradient, several factors affect the diffusion rate.
• Extent of the concentration gradient: The greater the difference in concentration, the more rapid the diffusion. The closer the distribution of the material gets to equilibrium, the slower the diffusion rate.
• Mass of the molecules diffusing: Heavier molecules move more slowly; therefore, they diffuse more slowly. The reverse is true for lighter molecules.
• Temperature: Higher temperatures increase the energy and therefore the molecules' movement, increasing the diffusion rate. Lower temperatures decrease the molecules' energy, thus decreasing the diffusion rate.
• Solvent density: As the density of a solvent increases, the diffusion rate decreases. The molecules slow down because they have a more difficult time passing through the denser medium. If the medium is less dense, diffusion increases. Because cells primarily use diffusion to move materials within the cytoplasm, any increase in the cytoplasm’s density will inhibit the movement of the materials. An example of this is a person experiencing dehydration. As the body’s cells lose water, the diffusion rate decreases in the cytoplasm, and the cells’ functions deteriorate. Neurons tend to be very sensitive to this effect. Dehydration frequently leads to unconsciousness and possibly coma because of the decrease in diffusion rate within the cells.
• Solubility: As we discussed earlier, nonpolar or lipid-soluble materials pass through plasma membranes more easily than polar materials, allowing a faster diffusion rate.
• Surface area and plasma membrane thickness: Increased surface area increases the diffusion rate; whereas, a thicker membrane reduces it.
• Distance travelled: The greater the distance that a substance must travel, the slower the diffusion rate. This places an upper limitation on cell size. A large, spherical cell will die because nutrients or waste cannot reach or leave the cell's center, respectively. Therefore, cells must either be small in size, as in the case of many prokaryotes, or be flattened, as with many single-celled eukaryotes.
A variation of diffusion is the process of filtration. In filtration, material moves according to its concentration gradient through a membrane. Sometimes pressure enhances the diffusion rate, causing the substances to filter more rapidly. This occurs in the kidney, where blood pressure forces large amounts of water and accompanying dissolved substances, or solutes, out of the blood and into the renal tubules. The diffusion rate in this instance is almost totally dependent on pressure. One of the effects of high blood pressure is the appearance of protein in the urine, which abnormally high pressure "squeezes through".
Facilitated transport
In facilitated transport, or facilitated diffusion, materials diffuse across the plasma membrane with the help of membrane proteins. A concentration gradient exists that would allow these materials to diffuse into the cell without expending cellular energy. However, these materials are polar molecule ions that the cell membrane's hydrophobic parts repel. Facilitated transport proteins shield these materials from the membrane's repulsive force, allowing them to diffuse into the cell.
The transported material first attaches to protein or glycoprotein receptors on the plasma membrane's exterior surface. This allows removal of material from the extracellular fluid that the cell needs. The substances then pass to specific integral proteins that facilitate their passage. Some of these integral proteins are collections of beta-pleated sheets that form a pore or channel through the phospholipid bilayer. Others are carrier proteins which bind with the substance and aid its diffusion through the membrane.
Channels
The integral proteins involved in facilitated transport are transport proteins, and they function as either channels for the material or carriers. In both cases, they are transmembrane proteins. Channels are specific for the transported substance. Channel proteins have hydrophilic domains exposed to the intracellular and extracellular fluids. In addition, they have a hydrophilic channel through their core that provides a hydrated opening through the membrane layers (Figure 5.9). Passage through the channel allows polar compounds to avoid the plasma membrane's nonpolar central layer that would otherwise slow or prevent their entry into the cell. Aquaporins are channel proteins that allow water to pass through the membrane at a very high rate.
Figure 5.9 Ion Channel Proteins. Ion channel proteins are gated. When they are closed, no ions can pass through them. However, when a channel opens, select ions diffuse through the channel. Channel proteins are highly specific, letting only a specific ion or subset of ions pass. Credit: Rao, A., Ryan, K., Tag, A. and Fletcher, S. Department of Biology, Texas A&M University.
Channel proteins are either open at all times or they are “gated,” which controls the channel's opening. When a particular ion attaches to the channel protein it may control the opening, or other mechanisms or substances may be involved. In some tissues, sodium and chloride ions pass freely through open channels; whereas, in other tissues a gate must open to allow passage. An example of this occurs in the kidney, where there are both channel forms in different parts of the renal tubules. Cells involved in transmitting electrical impulses, such as nerve and muscle cells, have gated channels for sodium, potassium, and calcium in their membranes. Opening and closing these channels changes the relative concentrations on opposing sides of the membrane of these ions, resulting in facilitating electrical transmission along membranes (in the case of nerve cells) or in muscle contraction (in the case of muscle cells).
Carrier Proteins
Another type of protein embedded in the plasma membrane is a carrier protein. This aptly named protein binds a substance and, thus triggers a change of its own shape, moving the bound molecule from the cell's outside to its interior (Figure 5.10). Depending on the gradient, the material may move in the opposite direction. Carrier proteins are typically specific for a single substance. This selectivity adds to the plasma membrane's overall selectivity. Scientists poorly understand the exact mechanism for the change of shape. Proteins can change shape when their hydrogen bonds are affected, but this may not fully explain this mechanism. Each carrier protein is specific to one substance, and there are a finite number of these proteins in any membrane. This can cause problems in transporting enough material for the cell to function properly. When all of the proteins are bound to their ligands, they are saturated and the rate of transport is at its maximum. Increasing the concentration gradient at this point will not result in an increased transport rate.
Figure 5.10 Some substances are able to move down their concentration gradient across the plasma membrane with the aid of carrier proteins. Carrier proteins change shape as they move molecules across the membrane. Credit: Rao, A., Tag, A. and Fletcher, S. Department of Biology, Texas A&M University.
An example of this process occurs in the kidney. In one part, the kidney filters glucose, water, salts, ions, and amino acids that the body requires. This filtrate, which includes glucose, then reabsorbs in another part of the kidney. Because there are only a finite number of carrier proteins for glucose, if more glucose is present than the proteins can handle, the excess is not transported and the body excretes this through urine. In a diabetic individual, the term is “spilling glucose into the urine.” A different group of carrier proteins, glucose transport proteins, or GLUTs, are involved in transporting glucose and other hexose sugars through plasma membranes within the body.
Channel and carrier proteins transport material at different rates. Channel proteins transport much more quickly than carrier proteins. Channel proteins facilitate diffusion at a rate of tens of millions of molecules per second; whereas, carrier proteins work at a rate of a thousand to a million molecules per second.
Osmosis
Osmosis is the movement of free water molecules through a semipermeable membrane according to the water's concentration gradient across the membrane, which is inversely proportional to the solutes' concentration. While diffusion transports material across membranes and within cells, osmosis transports only water across a membrane and the membrane limits the solutes' diffusion in the water. Not surprisingly, the aquaporins that facilitate water movement play a large role in osmosis, most prominently in red blood cells and the membranes of kidney tubules.
Mechanism
Osmosis is a special case of diffusion. Water, like other substances, moves from an area of high concentration of free water molecules to one of low free water molecule concentration. An obvious question is what makes water move at all? Imagine a beaker with a semipermeable membrane separating the two sides or halves (Figure 5.11). On both sides of the membrane the water level is the same, but there are different dissolved substance concentrations, or solute, that cannot cross the membrane (otherwise the solute crossing the membrane would balance concentrations on each side). If the solution's volume on both sides of the membrane is the same, but the solute's concentrations are different, then there are different amounts of water, the solvent, on either side of the membrane.
Figure 5.11 In osmosis, water always moves from an area of higher water concentration to one of lower concentration. In the diagram, the solute cannot pass through the selectively permeable membrane, but the water can.
To illustrate this, imagine two full water glasses. One has a single teaspoon of sugar in it; whereas, the second one contains one-quarter cup of sugar. If the total volume of the solutions in both cups is the same, which cup contains more water? Because the large sugar amount in the second cup takes up much more space than the teaspoon of sugar in the first cup, the first cup has more water in it.
Returning to the beaker example, recall that it has a solute mixture on either side of the membrane. A principle of diffusion is that the molecules move around and will spread evenly throughout the medium if they can. However, only the material capable of getting through the membrane will diffuse through it. In this example, the solute cannot diffuse through the membrane, but the water can. Water has a concentration gradient in this system. Thus, water will diffuse down its concentration gradient, crossing the membrane to the side where it is less concentrated. This diffusion of water through the membrane—osmosis—will continue until the water's concentration gradient goes to zero or until the water's hydrostatic pressure balances the osmotic pressure. Osmosis proceeds constantly in living systems.
Tonicity
Tonicity describes how an extracellular solution can change a cell's volume by affecting osmosis. A solution's tonicity often directly correlates with the solution's osmolarity. Osmolarity describes the solution's total solute concentration. A solution with low osmolarity has a greater number of water molecules relative to the number of solute particles. A solution with high osmolarity has fewer water molecules with respect to solute particles. In a situation in which a membrane permeable to water, though not to the solute separates two different osmolarities, water will move from the membrane's side with lower osmolarity (and more water) to the side with higher osmolarity (and less water). This effect makes sense if you remember that the solute cannot move across the membrane, and thus the only component in the system that can move—the water—moves along its own concentration gradient. An important distinction that concerns living systems is that osmolarity measures the number of particles (which may be molecules) in a solution. Therefore, a solution that is cloudy with cells may have a lower osmolarity than a solution that is clear, if the second solution contains more dissolved molecules than there are cells.
Hypotonic Solutions
Scientists use three terms—hypotonic, isotonic, and hypertonic—to relate the cell's osmolarity to the extracellular fluid's osmolarity that contains the cells. In a hypotonic situation, the extracellular fluid has lower osmolarity than the fluid inside the cell, and water enters the cell. (In living systems, the point of reference is always the cytoplasm, so the prefix hypo- means that the extracellular fluid has a lower solute concentration, or a lower osmolarity, than the cell cytoplasm.) It also means that the extracellular fluid has a higher water concentration in the solution than does the cell. In this situation, water will follow its concentration gradient and enter the cell.
Hypertonic Solutions
As for a hypertonic solution, the prefix hyper- refers to the extracellular fluid having a higher osmolarity than the cell’s cytoplasm; therefore, the fluid contains less water than the cell does. Because the cell has a relatively higher water concentration, water will leave the cell.
Isotonic Solutions
In an isotonic solution, the extracellular fluid has the same osmolarity as the cell. If the cell's osmolarity matches that of the extracellular fluid, there will be no net movement of water into or out of the cell, although water will still move in and out. Blood cells and plant cells in hypertonic, isotonic, and hypotonic solutions take on characteristic appearances (Figure 5.12).
Visual Connection
Visual Connection
Figure 5.12 Three different scenarios involving red blood cells (RBC) are shown. Left: A RBC placed in a hypotonic solution, where the concentration of solutes in the surrounding fluid is lower than those in the cell, will cause water to rush into the RBC and lead to lysis of the cell. Middle: there is no net water movement into or out of the cell as the concentration of the solutes inside the cell equal or is isotonic to that of the surrounding fluid. Right: a RBC placed in a hypertonic solution, where the concentration of solutes in the surrounding fluid is greater than that in the cell will cause water to rush out of the cell and into the surrounding fluid. This will cause the RBC to shrivel. Credit: Tag, A., Rao, A., Hawkins, A and Fletcher, S. Department of Biology, Texas A&M University.
A doctor injects a patient with what the doctor thinks is an isotonic saline solution. The patient dies, and an autopsy reveals that many red blood cells have been destroyed. Do you think the solution the doctor injected was really isotonic?
Link to Learning
Link to Learning
For a video illustrating the diffusion process in solutions, visit this site.
Tonicity in Living Systems
In a hypotonic environment, water enters a cell, and the cell swells. In an isotonic condition, the relative solute and solvent concentrations are equal on both membrane sides. There is no net water movement; therefore, there is no change in the cell's size. In a hypertonic solution, water leaves a cell and the cell shrinks. If either the hypo- or hyper- condition goes to excess, the cell’s functions become compromised, and the cell may be destroyed.
A red blood cell will burst, or lyse, when it swells beyond the plasma membrane’s capability to expand. Remember, the membrane resembles a mosaic, with discrete spaces between the molecules comprising it. If the cell swells, and the spaces between the lipids and proteins become too large, the cell will break apart.
In contrast, when excessive water amounts leave a red blood cell, the cell shrinks, or crenates. This has the effect of concentrating the solutes left in the cell, making the cytosol denser and interfering with diffusion within the cell. The cell’s ability to function will be compromised and may also result in the cell's death.
Various living things have ways of controlling the effects of osmosis—a mechanism we call osmoregulation. Some organisms, such as plants, fungi, bacteria, and some protists, have cell walls that surround the plasma membrane and prevent cell lysis in a hypotonic solution. The plasma membrane can only expand to the cell wall's limit, so the cell will not lyse. The cytoplasm in plants is always slightly hypertonic to the cellular environment, and water will always enter a cell if water is available. This water inflow produces turgor pressure, which stiffens the plant's cell walls (Figure 5.13). In nonwoody plants, turgor pressure supports the plant. Conversely, if you do not water the plant, the extracellular fluid will become hypertonic, causing water to leave the cell. In this condition, the cell does not shrink because the cell wall is not flexible. However, the cell membrane detaches from the wall and constricts the cytoplasm. We call this plasmolysis. Plants lose turgor pressure in this condition and wilt (Figure 5.14).
Figure 5.13 The turgor pressure within a plant cell depends on the solution's tonicity in which it is bathed. (credit: modification of work by Mariana Ruiz Villareal)
Figure 5.14 Without adequate water, the plant on the left has lost turgor pressure, visible in its wilting. Watering the plant (right) will restore the turgor pressure. (credit: Victor M. Vicente Selvas)
Tonicity is a concern for all living things. For example, paramecia and amoebas, which are protists that lack cell walls, have contractile vacuoles. This vesicle collects excess water from the cell and pumps it out, keeping the cell from lysing as it takes on water from its environment (Figure 5.15).
Figure 5.15 A paramecium’s contractile vacuole, here visualized using bright field light microscopy at 480x magnification, continuously pumps water out of the organism’s body to keep it from bursting in a hypotonic medium. (credit: modification of work by NIH; scale-bar data from Matt Russell)
Many marine invertebrates have internal salt levels matched to their environments, making them isotonic with the water in which they live. Fish, however, must spend approximately five percent of their metabolic energy maintaining osmotic homeostasis. Freshwater fish live in an environment that is hypotonic to their cells. These fish actively take in salt through their gills and excrete diluted urine to rid themselves of excess water. Saltwater fish live in the reverse environment, which is hypertonic to their cells, and they secrete salt through their gills and excrete highly concentrated urine.
In vertebrates, the kidneys regulate the water amount in the body. Osmoreceptors are specialized cells in the brain that monitor solute concentration in the blood. If the solute levels increase beyond a certain range, a hormone releases that slows water loss through the kidney and dilutes the blood to safer levels. Animals also have high albumin concentrations, which the liver produces, in their blood. This protein is too large to pass easily through plasma membranes and is a major factor in controlling the osmotic pressures applied to tissues. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.02%3A_Structure_and_Function_of_Plasma_Membranes/2.2.03%3A_Passive_Transport.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Understand how electrochemical gradients affect ions
• Distinguish between primary active transport and secondary active transport
Active transport mechanisms require the cell’s energy, usually in the form of adenosine triphosphate (ATP). If a substance must move into the cell against its concentration gradient—that is, if the substance's concentration inside the cell is greater than its concentration in the extracellular fluid (and vice versa)—the cell must use energy to move the substance. Some active transport mechanisms move small-molecular weight materials, such as ions, through the membrane. Other mechanisms transport much larger molecules.
Electrochemical Gradient
We have discussed simple concentration gradients—a substance's differential concentrations across a space or a membrane—but in living systems, gradients are more complex. Because ions move into and out of cells and because cells contain proteins that do not move across the membrane and are mostly negatively charged, there is also an electrical gradient, a difference of charge, across the plasma membrane. The interior of living cells is electrically negative with respect to the extracellular fluid in which they are bathed, and at the same time, cells have higher concentrations of potassium (K+) and lower concentrations of sodium (Na+) than the extracellular fluid. Thus in a living cell, the concentration gradient of Na+ tends to drive it into the cell, and its electrical gradient (a positive ion) also drives it inward to the negatively charged interior. However, the situation is more complex for other elements such as potassium. The electrical gradient of K+, a positive ion, also drives it into the cell, but the concentration gradient of K+ drives K+ out of the cell (Figure 5.16). We call the combined concentration gradient and electrical charge that affects an ion its electrochemical gradient.
Visual Connection
Visual Connection
Figure 5.16 Electrochemical gradients arise from the combined effects of concentration gradients and electrical gradients. Structures labeled A represent proteins. (credit: “Synaptitude”/Wikimedia Commons)
Injecting a potassium solution into a person’s blood is lethal. This is how capital punishment and euthanasia subjects die. Why do you think a potassium solution injection is lethal?
Figure 5.17 Proton Gradient provides energy for a secondary active transporter. The proton pump creates an electrochemical gradient of protons (hydrogen ions, H+) using ATP to drive primary active transport. This gradient allows for cotransport/secondary transport of sucrose against its concentration gradient as protons come down their concentration gradient via their membrane cotransporter protein. Credit: Rao, A. Tag, A. and Ryan, K. Department of Biology, Texas A&M University.
Moving Against a Gradient
To move substances against a concentration or electrochemical gradient, the cell must use energy. This energy comes from ATP generated through the cell’s metabolism. Active transport mechanisms, or pumps, work against electrochemical gradients. Small substances constantly pass through plasma membranes. Active transport maintains concentrations of ions and other substances that living cells require in the face of these passive movements. A cell may spend much of its metabolic energy supply maintaining these processes. (A red blood cell uses most of its metabolic energy to maintain the imbalance between exterior and interior sodium and potassium levels that the cell requires.) Because active transport mechanisms depend on a cell’s metabolism for energy, they are sensitive to many metabolic poisons that interfere with the ATP supply.
Two mechanisms exist for transporting small-molecular weight material and small molecules. Primary active transport moves ions across a membrane and creates a difference in charge across that membrane, which is directly dependent on ATP. Secondary active transport does not directly require ATP: instead, it is the movement of material due to the electrochemical gradient established by primary active transport.
Carrier Proteins for Active Transport
An important membrane adaptation for active transport is the presence of specific carrier proteins or pumps to facilitate movement: there are three protein types or transporters (Figure 5.18). A uniporter carries one specific ion or molecule. A symporter carries two different ions or molecules, both in the same direction. An antiporter also carries two different ions or molecules, but in different directions. All of these transporters can also transport small, uncharged organic molecules like glucose. These three types of carrier proteins are also in facilitated diffusion, but they do not require ATP to work in that process. Some examples of pumps for active transport are Na+-K+ ATPase, which carries sodium and potassium ions, and H+-K+ ATPase, which carries hydrogen and potassium ions. Both of these are antiporter carrier proteins. Two other carrier proteins are Ca2+ ATPase and H+ ATPase, which carry only calcium and only hydrogen ions, respectively. Both are pumps.
Figure 5.18 A uniporter carries one molecule or ion. A symporter carries two different molecules or ions, both in the same direction. An antiporter also carries two different molecules or ions, but in different directions. (credit: modification of work by “Lupask”/Wikimedia Commons)
Primary Active Transport
The primary active transport that functions with the active transport of sodium and potassium allows secondary active transport to occur. The second transport method is still active because it depends on using energy as does primary transport (Figure 5.19).
Figure 5.19 The sodium-potassium pump is an example of primary active transport that moves ions, sodium and potassium ions in this instance, across a membrane against their concentration gradients. The energy is provided by the hydrolysis of ATP. Three sodium ions are moved out of the cell for every 2 potassium ions that are brought into the cell. This creates an electrochemical gradient that is crucial for living cells. Credit: Rao, A., Ryan, K. and Fletcher, S. Department of Biology, Texas A&M University.
One of the most important pumps in animal cells is the sodium-potassium pump (Na+-K+ ATPase), which maintains the electrochemical gradient (and the correct concentrations of Na+ and K+) in living cells. The sodium-potassium pump moves K+ into the cell while moving Na+ out at the same time, at a ratio of three Na+ for every two K+ ions moved in. The Na+-K+ ATPase exists in two forms, depending on its orientation to the cell's interior or exterior and its affinity for either sodium or potassium ions. The process consists of the following six steps.
1. With the enzyme oriented towards the cell's interior, the carrier has a high affinity for sodium ions. Three ions bind to the protein.
2. The protein carrier hydrolyzes ATP and a low-energy phosphate group attaches to it.
3. As a result, the carrier changes shape and reorients itself towards the membrane's exterior. The protein’s affinity for sodium decreases and the three sodium ions leave the carrier.
4. The shape change increases the carrier’s affinity for potassium ions, and two such ions attach to the protein. Subsequently, the low-energy phosphate group detaches from the carrier.
5. With the phosphate group removed and potassium ions attached, the carrier protein repositions itself towards the cell's interior.
6. The carrier protein, in its new configuration, has a decreased affinity for potassium, and the two ions moves into the cytoplasm. The protein now has a higher affinity for sodium ions, and the process starts again.
Several things have happened as a result of this process. At this point, there are more sodium ions outside the cell than inside and more potassium ions inside than out. For every three sodium ions that move out, two potassium ions move in. This results in the interior being slightly more negative relative to the exterior. This difference in charge is important in creating the conditions necessary for the secondary process. The sodium-potassium pump is, therefore, an electrogenic pump (a pump that creates a charge imbalance), creating an electrical imbalance across the membrane and contributing to the membrane potential.
Link to Learning
Link to Learning
Watch this video to see an active transport simulation in a sodium-potassium ATPase.
Secondary Active Transport (Co-transport)
Secondary active transport uses the kinetic energy of the sodium ions to bring other compounds, against their concentration gradient into the cell. As sodium ion concentrations build outside of the plasma membrane because of the primary active transport process, this creates an electrochemical gradient. If a channel protein exists and is open, the sodium ions will move down its concentration gradient across the membrane. This movement transports other substances that must be attached to the same transport protein in order for the sodium ions to move across the membrane (Figure 5.20). Many amino acids, as well as glucose, enter a cell this way. This secondary process also stores high-energy hydrogen ions in the mitochondria of plant and animal cells in order to produce ATP. The potential energy that accumulates in the stored hydrogen ions translates into kinetic energy as the ions surge through the channel protein ATP synthase, and that energy then converts ADP into ATP.
Visual Connection
Visual Connection
Figure 5.20 An electrochemical gradient (Na+ concentration - green), is generated by primary active transport. The energy stored in the Na+ gradient provides the energy to move other substances against their concentration gradients (Glucose - blue), a process called co-transport or secondary active transport. Credit: Rao, A., Ryan, K., Tag, A. and Fletcher, S. Department of Biology, Texas A&M University.
If the pH outside the cell decreases, would you expect the amount of amino acids transported into the cell to increase or decrease? | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.02%3A_Structure_and_Function_of_Plasma_Membranes/2.2.04%3A_Active_Transport.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Describe endocytosis, including phagocytosis, pinocytosis, and receptor-mediated endocytosis
• Understand the process of exocytosis
In addition to moving small ions and molecules through the membrane, cells also need to remove and take in larger molecules and particles (see Table 5.2 for examples). Some cells are even capable of engulfing entire unicellular microorganisms. You might have correctly hypothesized that when a cell uptakes and releases large particles, it requires energy. A large particle, however, cannot pass through the membrane, even with energy that the cell supplies.
Endocytosis
Endocytosis is a type of active transport that moves particles, such as large molecules, parts of cells, and even whole cells, into a cell. There are different endocytosis variations, but all share a common characteristic: the cell's plasma membrane invaginates, forming a pocket around the target particle. The pocket pinches off, resulting in the particle containing itself in a newly created intracellular vesicle formed from the plasma membrane.
Phagocytosis
Phagocytosis (the condition of “cell eating”) is the process by which a cell takes in large particles, such as other cells or relatively large particles. For example, when microorganisms invade the human body, a type of white blood cell, a neutrophil, will remove the invaders through this process, surrounding and engulfing the microorganism, which the neutrophil then destroys (Figure 5.21).
Figure 5.21 In phagocytosis, the cell membrane surrounds the particle and engulfs it. (credit: modification of work by Mariana Ruiz Villareal)
In preparation for phagocytosis, a portion of the plasma membrane's inward-facing surface becomes coated with the protein clathrin, which stabilizes this membrane's section. The membrane's coated portion then extends from the cell's body and surrounds the particle, eventually enclosing it. Once the vesicle containing the particle is enclosed within the cell, the clathrin disengages from the membrane and the vesicle merges with a lysosome for breaking down the material in the newly formed compartment (endosome). When accessible nutrients from the vesicular contents' degradation have been extracted, the newly formed endosome merges with the plasma membrane and releases its contents into the extracellular fluid. The endosomal membrane again becomes part of the plasma membrane.
Pinocytosis
A variation of endocytosis is pinocytosis. This literally means “cell drinking”. Discovered by Warren Lewis in 1929, this American embryologist and cell biologist described a process whereby he assumed that the cell was purposefully taking in extracellular fluid. In reality, this is a process that takes in molecules, including water, which the cell needs from the extracellular fluid. Pinocytosis results in a much smaller vesicle than does phagocytosis, and the vesicle does not need to merge with a lysosome (Figure 5.22).
Figure 5.22 In pinocytosis, the cell membrane invaginates, surrounds a small volume of fluid, and pinches off. (credit: modification of work by Mariana Ruiz Villareal)
A variation of pinocytosis is potocytosis. This process uses a coating protein, caveolin, on the plasma membrane's cytoplasmic side, which performs a similar function to clathrin. The cavities in the plasma membrane that form the vacuoles have membrane receptors and lipid rafts in addition to caveolin. The vacuoles or vesicles formed in caveolae (singular caveola) are smaller than those in pinocytosis. Potocytosis brings small molecules into the cell and transports them through the cell for their release on the other side, a process we call transcytosis. In some cases, the caveolae deliver their cargo to membranous organelles like the ER.
Receptor-mediated Endocytosis
A targeted variation of endocytosis employs receptor proteins in the plasma membrane that have a specific binding affinity for certain substances (Figure 5.23).
Figure 5.23 In receptor-mediated endocytosis, the cell's uptake of substances targets a single type of substance that binds to the receptor on the cell membrane's external surface. (credit: modification of work by Mariana Ruiz Villareal)
In receptor-mediated endocytosis, as in phagocytosis, clathrin attaches to the plasma membrane's cytoplasmic side. If a compound's uptake is dependent on receptor-mediated endocytosis and the process is ineffective, the material will not be removed from the tissue fluids or blood. Instead, it will stay in those fluids and increase in concentration. The failure of receptor-mediated endocytosis causes some human diseases. For example, receptor mediated endocytosis removes low density lipoprotein or LDL (or "bad" cholesterol) from the blood. In the human genetic disease familial hypercholesterolemia, the LDL receptors are defective or missing entirely. People with this condition have life-threatening levels of cholesterol in their blood, because their cells cannot clear LDL particles.
Although receptor-mediated endocytosis is designed to bring specific substances that are normally in the extracellular fluid into the cell, other substances may gain entry into the cell at the same site. Flu viruses, diphtheria, and cholera toxin all have sites that cross-react with normal receptor-binding sites and gain entry into cells.
Link to Learning
Link to Learning
See receptor-mediated endocytosis in action, and click on different parts for a focused animation.
Exocytosis
The reverse process of moving material into a cell is the process of exocytosis. Exocytosis is the opposite of the processes we discussed above in that its purpose is to expel material from the cell into the extracellular fluid. Waste material is enveloped in a membrane and fuses with the plasma membrane's interior. This fusion opens the membranous envelope on the cell's exterior, and the waste material expels into the extracellular space (Figure 5.24). Other examples of cells releasing molecules via exocytosis include extracellular matrix protein secretion and neurotransmitter secretion into the synaptic cleft by synaptic vesicles.
Figure 5.24 In exocytosis, vesicles containing substances fuse with the plasma membrane. The contents then release to the cell's exterior. (credit: modification of work by Mariana Ruiz Villareal)
Methods of Transport, Energy Requirements, and Types of Transported Material
Transport MethodActive/PassiveMaterial Transported
DiffusionPassiveSmall-molecular weight material
OsmosisPassiveWater
Facilitated transport/diffusionPassiveSodium, potassium, calcium, glucose
Primary active transportActiveSodium, potassium, calcium
Secondary active transportActiveAmino acids, lactose
PhagocytosisActiveLarge macromolecules, whole cells, or cellular structures
Pinocytosis and potocytosisActiveSmall molecules (liquids/water)
Receptor-mediated endocytosisActiveLarge quantities of macromolecules
Table 5.2 | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.02%3A_Structure_and_Function_of_Plasma_Membranes/2.2.05%3A_Bulk_Transport.txt |
active transport
method of transporting material that requires energy
amphiphilic
molecule possessing a polar or charged area and a nonpolar or uncharged area capable of interacting with both hydrophilic and hydrophobic environments
antiporter
transporter that carries two ions or small molecules in different directions
aquaporin
channel protein that allows water through the membrane at a very high rate
carrier protein
membrane protein that moves a substance across the plasma membrane by changing its own shape
caveolin
protein that coats the plasma membrane's cytoplasmic side and participates in the liquid uptake process by potocytosis
channel protein
membrane protein that allows a substance to pass through its hollow core across the plasma membrane
clathrin
protein that coats the plasma membrane's inward-facing surface and assists in forming specialized structures, like coated pits, for phagocytosis
concentration gradient
area of high concentration adjacent to an area of low concentration
diffusion
passive transport process of low-molecular weight material according to its concentration gradient
electrochemical gradient
a combined electrical and chemical force that produces a gradient
electrogenic pump
pump that creates a charge imbalance
endocytosis
type of active transport that moves substances, including fluids and particles, into a cell
exocytosis
process of passing bulk material out of a cell
facilitated transport
process by which material moves down a concentration gradient (from high to low concentration) using integral membrane proteins
fluid mosaic model
describes the plasma membrane's structure as a mosaic of components including phospholipids, cholesterol, proteins, glycoproteins, and glycolipids (sugar chains attached to proteins or lipids, respectively), resulting in a fluid character (fluidity)
glycolipid
combination of carbohydrates and lipids
glycoprotein
combination of carbohydrates and proteins
hydrophilic
molecule with the ability to bond with water; “water-loving”
hydrophobic
molecule that does not have the ability to bond with water; “water-hating”
hypertonic
situation in which extracellular fluid has a higher osmolarity than the fluid inside the cell, resulting in water moving out of the cell
hypotonic
situation in which extracellular fluid has a lower osmolarity than the fluid inside the cell, resulting in water moving into the cell
integral protein
protein integrated into the membrane structure that interacts extensively with the membrane lipids' hydrocarbon chains and often spans the membrane
isotonic
situation in which the extracellular fluid has the same osmolarity as the fluid inside the cell, resulting in no net water movement into or out of the cell
osmolarity
total amount of solutes dissolved in a specific amount of solution
osmosis
transport of water through a semipermeable membrane according to the water's concentration gradient across the membrane that results from the presence of solute that cannot pass through the membrane
passive transport
method of transporting material through a membrane that does not require energy
peripheral protein
protein at the plasma membrane's surface either on its exterior or interior side
pinocytosis
a variation of endocytosis that imports macromolecules that the cell needs from the extracellular fluid
plasmolysis
detaching the cell membrane from the cell wall and constricting the cell membrane when a plant cell is in a hypertonic solution
potocytosis
variation of pinocytosis that uses a different coating protein (caveolin) on the plasma membrane's cytoplasmic side
primary active transport
active transport that moves ions or small molecules across a membrane and may create a difference in charge across that membrane
pump
active transport mechanism that works against electrochemical gradients
receptor-mediated endocytosis
variation of endocytosis that involves using specific binding proteins in the plasma membrane for specific molecules or particles, and clathrin-coated pits that become clathrin-coated vesicles
secondary active transport
movement of material that results from primary active transport to the electrochemical gradient
selectively permeable
membrane characteristic that allows some substances through (also known as semipermeable)
solute
substance dissolved in a liquid to form a solution
symporter
transporter that carries two different ions or small molecules, both in the same direction
tonicity
amount of solute in a solution
transport protein
membrane protein that facilitates a substance's passage across a membrane by binding it
transporter
specific carrier proteins or pumps that facilitate movement
uniporter
transporter that carries one specific ion or molecule | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.02%3A_Structure_and_Function_of_Plasma_Membranes/2.2.06%3A_Key_Terms.txt |
5.1 Components and Structure
Modern scientists refer to the plasma membrane as the fluid mosaic model. A phospholipid bilayer comprises the plasma membrane, with hydrophobic, fatty acid tails in contact with each other. The membrane's landscape is studded with proteins, some which span the membrane. Some of these proteins serve to transport materials into or out of the cell. Carbohydrates are attached to some of the proteins and lipids on the membrane's outward-facing surface, forming complexes that function to identify the cell to other cells. The membrane's fluid nature is due to temperature, fatty acid tail configuration (some kinked by double bonds), cholesterol presence embedded in the membrane, and the mosaic nature of the proteins and protein-carbohydrate combinations, which are not firmly fixed in place. Plasma membranes enclose and define the cells' borders. Not static, they are dynamic and constantly in flux.
5.2 Passive Transport
The passive transport forms, diffusion and osmosis, move materials of small molecular weight across membranes. Substances diffuse from high to lower concentration areas, and this process continues until the substance evenly distributes itself in a system. In solutions containing more than one substance, each molecule type diffuses according to its own concentration gradient, independent of other substances diffusing. Many factors can affect the diffusion rate, such as concentration gradient, diffusing, particle sizes, and the system's temperature.
In living systems, the plasma membrane mediates substances diffusing in and out of cells. Some materials diffuse readily through the membrane, but others are hindered and only can pass through due to specialized proteins such as channels and transporters. The chemistry of living things occurs in aqueous solutions, and balancing the concentrations of those solutions is an ongoing problem. In living systems, diffusing some substances would be slow or difficult without membrane proteins that facilitate transport.
5.3 Active Transport
The combined gradient that affects an ion includes its concentration gradient and its electrical gradient. A positive ion, for example, might diffuse into a new area, down its concentration gradient, but if it is diffusing into an area of net positive charge, its electrical gradient hampers its diffusion. When dealing with ions in aqueous solutions, one must consider electrochemical and concentration gradient combinations, rather than just the concentration gradient alone. Living cells need certain substances that exist inside the cell in concentrations greater than they exist in the extracellular space. Moving substances up their electrochemical gradients requires energy from the cell. Active transport uses energy stored in ATP to fuel this transport. Active transport of small molecular-sized materials uses integral proteins in the cell membrane to move the materials. These proteins are analogous to pumps. Some pumps, which carry out primary active transport, couple directly with ATP to drive their action. In co-transport (or secondary active transport), energy from primary transport can move another substance into the cell and up its concentration gradient.
5.4 Bulk Transport
Active transport methods require directly using ATP to fuel the transport. In a process scientists call phagocytosis, other cells can engulf large particles, such as macromolecules, cell parts, or whole cells. In phagocytosis, a portion of the membrane invaginates and flows around the particle, eventually pinching off and leaving the particle entirely enclosed by a plasma membrane's envelope. The cell breaks down vesicle contents, with the particles either used as food or dispatched. Pinocytosis is a similar process on a smaller scale. The plasma membrane invaginates and pinches off, producing a small envelope of fluid from outside the cell. Pinocytosis imports substances that the cell needs from the extracellular fluid. The cell expels waste in a similar but reverse manner. It pushes a membranous vacuole to the plasma membrane, allowing the vacuole to fuse with the membrane and incorporate itself into the membrane structure, releasing its contents to the exterior.
2.2.08: Visual Connection Questions
1.
Figure 5.12 A doctor injects a patient with what the doctor thinks is an isotonic saline solution. The patient dies, and an autopsy reveals that many red blood cells have been destroyed. Do you think the solution the doctor injected was really isotonic?
2.
Figure 5.16 Injecting a potassium solution into a person’s blood is lethal. Capital punishment and euthanasia utilize this method in their subjects. Why do you think a potassium solution injection is lethal?
3.
Figure 5.20 If the pH outside the cell decreases, would you expect the amount of amino acids transported into the cell to increase or decrease? | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.02%3A_Structure_and_Function_of_Plasma_Membranes/2.2.07%3A_Chapter_Summary.txt |
4.
Which plasma membrane component can be either found on its surface or embedded in the membrane structure?
1. protein
2. cholesterol
3. carbohydrate
4. phospholipid
5.
Which characteristic of a phospholipid contributes to the fluidity of the membrane?
1. its head
2. cholesterol
3. a saturated fatty acid tail
4. double bonds in the fatty acid tail
6.
What is the primary function of carbohydrates attached to the exterior of cell membranes?
1. identification of the cell
2. flexibility of the membrane
3. strengthening the membrane
4. channels through membrane
7.
A scientist compares the plasma membrane composition of an animal from the Mediterranean coast with one from the Mojave Desert. Which hypothesis is most likely to be correct?
1. The cells from the Mediterranean coast animal will have more fluid plasma membranes.
2. The cells from the Mojave Desert animal will have a higher cholesterol concentration in the plasma membranes.
3. The cells’ plasma membranes will be indistinguishable.
4. The cells from the Mediterranean coast animal will have a higher glycoprotein content, while the cells from the Mojave Desert animal will have a higher lipoprotein content.
8.
Water moves via osmosis _________.
1. throughout the cytoplasm
2. from an area with a high concentration of other solutes to a lower one
3. from an area with a high concentration of water to one of lower concentration
4. from an area with a low concentration of water to higher concentration
9.
The principal force driving movement in diffusion is the __________.
1. temperature
2. particle size
3. concentration gradient
4. membrane surface area
10.
What problem is faced by organisms that live in fresh water?
1. Their bodies tend to take in too much water.
2. They have no way of controlling their tonicity.
3. Only salt water poses problems for animals that live in it.
4. Their bodies tend to lose too much water to their environment.
11.
In which situation would passive transport not use a transport protein for entry into a cell?
1. water flowing into a hypertonic environment
2. glucose being absorbed from the blood
3. an ion flowing into a nerve cell to create an electrical potential
4. oxygen moving into a cell after oxygen deprivation
12.
Active transport must function continuously because __________.
1. plasma membranes wear out
2. not all membranes are amphiphilic
3. facilitated transport opposes active transport
4. diffusion is constantly moving solutes in opposite directions
13.
How does the sodium-potassium pump make the interior of the cell negatively charged?
1. by expelling anions
2. by pulling in anions
3. by expelling more cations than are taken in
4. by taking in and expelling an equal number of cations
14.
What is the combination of an electrical gradient and a concentration gradient called?
1. potential gradient
2. electrical potential
3. concentration potential
4. electrochemical gradient
15.
What happens to the membrane of a vesicle after exocytosis?
1. It leaves the cell.
2. It is disassembled by the cell.
3. It fuses with and becomes part of the plasma membrane.
4. It is used again in another exocytosis event.
16.
Which transport mechanism can bring whole cells into a cell?
1. pinocytosis
2. phagocytosis
3. facilitated transport
4. primary active transport
17.
In what important way does receptor-mediated endocytosis differ from phagocytosis?
1. It transports only small amounts of fluid.
2. It does not involve the pinching off of membrane.
3. It brings in only a specifically targeted substance.
4. It brings substances into the cell, while phagocytosis removes substances.
18.
Many viruses enter host cells through receptor-mediated endocytosis. What is an advantage of this entry strategy?
1. The virus directly enters the cytoplasm of the cell.
2. The virus is protected from recognition by white blood cells.
3. The virus only enters its target host cell type.
4. The virus can directly inject its genome into the cell’s nucleus.
19.
Which of the following organelles relies on exocytosis to complete its function?
1. Golgi apparatus
2. vacuole
3. mitochondria
4. endoplasmic reticulum
20.
Imagine a cell can perform exocytosis, but only minimal endocytosis. What would happen to the cell?
1. The cell would secrete all its intracellular proteins.
2. The plasma membrane would increase in size over time.
3. The cell would stop expressing integral receptor proteins in its plasma membrane.
4. The cell would lyse.
2.2.10: Critical Thinking Questions
21.
Why is it advantageous for the cell membrane to be fluid in nature?
22.
Why do phospholipids tend to spontaneously orient themselves into something resembling a membrane?
23.
How can a cell use an extracellular peripheral protein as the receptor to transmit a signal into the cell?
24.
Discuss why the following affect the rate of diffusion: molecular size, temperature, solution density, and the distance that must be traveled.
25.
Why does water move through a membrane?
26.
Both of the regular intravenous solutions administered in medicine, normal saline and lactated Ringer’s solution, are isotonic. Why is this important?
27.
Describe two ways that decreasing temperature would affect the rate of diffusion of molecules across a cell’s plasma membrane.
28.
A cell develops a mutation in its potassium channels that prevents the ions from leaving the cell. If the cell’s aquaporins are still active, what will happen to the cell? Be sure to describe the tonicity and osmolarity of the cell.
29.
Where does the cell get energy for active transport processes?
30.
How does the sodium-potassium pump contribute to the net negative charge of the interior of the cell?
31.
Glucose from digested food enters intestinal epithelial cells by active transport. Why would intestinal cells use active transport when most body cells use facilitated diffusion?
32.
The sodium/calcium exchanger (NCX) transports sodium into and calcium out of cardiac muscle cells. Describe why this transporter is classified as secondary active transport.
33.
Why is it important that there are different types of proteins in plasma membranes for the transport of materials into and out of a cell?
34.
Why do ions have a difficult time getting through plasma membranes despite their small size? | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.02%3A_Structure_and_Function_of_Plasma_Membranes/2.2.09%3A_Review_Questions.txt |
Cellular processes require a steady supply of energy. From where, and in what form, does this energy come? How do living cells obtain energy, and how do they use it? This chapter will discuss different forms of energy and the physical laws that govern energy transfer. This chapter will also describe how cells use energy and replenish it, and how chemical reactions in the cell are performed with great efficiency.
• 2.3.1: Introduction
Virtually every task performed by living organisms requires energy. Energy is needed to perform heavy labor and exercise, but humans also use a great deal of energy while thinking, and even during sleep. In fact, the living cells of every organism constantly use energy. Nutrients and other molecules are imported, metabolized (broken down) and possibly synthesized into new molecules, modified if needed, transported around the cell, and may be distributed to the entire organism.
• 2.3.2: Energy and Metabolism
Cellular processes such as the building and breaking down of complex molecules occur through stepwise chemical reactions. Some of these chemical reactions are spontaneous and release energy, whereas others require energy to proceed. Just as living things must continually consume food to replenish what has been used, cells must continually produce more energy to replenish that used by the many energy-requiring chemical reactions that constantly take place.
• 2.3.3: Potential, Kinetic, Free, and Activation Energy
Energy is defined as the ability to do work and exists in different forms. For example, electrical energy, light energy, and heat energy are all different types of energy. While these are all familiar types of energy that one can see or feel, there is another type of energy that is much less tangible. To appreciate the way energy flows into and out of biological systems, it is important to understand more about the different types of energy that exist in the physical world.
• 2.3.4: The Laws of Thermodynamics
Biological organisms are open systems. Energy is exchanged between them and their surroundings, as they consume energy-storing molecules and release energy to the environment by doing work. Like all things in the physical world, energy is subject to the laws of physics. The laws of thermodynamics govern the transfer of energy in and among all systems in the universe.
• 2.3.5: ATP- Adenosine Triphosphate
Even exergonic, energy-releasing reactions require a small amount of activation energy in order to proceed. However, consider endergonic reactions, which require much more energy input, because their products have more free energy than their reactants. Within the cell, where does energy to power such reactions come from? The answer lies with an energy-supplying molecule called adenosine triphosphate, or ATP.
• 2.3.6: Enzymes
A substance that helps a chemical reaction to occur is a catalyst, and the special molecules that catalyze biochemical reactions are called enzymes. Almost all enzymes are proteins, made up of chains of amino acids, and they perform the critical task of lowering the activation energies of chemical reactions inside the cell. Enzymes do this by binding to the reactant molecules, and holding them in such a way as to make the chemical bond-breaking and bond-forming processes take place more readily.
• 2.3.7: Key Terms
• 2.3.8: Chapter Summary
• 2.3.9: Visual Connection Questions
• 2.3.10: Review Questions
• 2.3.11: Critical Thinking Questions
Thumbnail: diagram showing the induced fit model in enzymes (Public Domain; LadyofHats).
2.03: Metabolism
Figure 6.1 A hummingbird needs energy to maintain prolonged periods of flight. The bird obtains its energy from taking in food and transforming the nutrients into energy through a series of biochemical reactions. The flight muscles in birds are extremely efficient in energy production. (credit: modification of work by Cory Zanker)
Virtually every task performed by living organisms requires energy. Organisms require energy to perform heavy labor and exercise, but humans also use considerable energy while thinking, and even during sleep. Every organism's living cells constantly use energy. Organisms import nutrients and other molecules. They metabolize (break down) and possibly synthesize into new molecules. If necessary, molecules modify, move around the cell and may distribute themselves to the entire organism. For example, the large proteins that make up muscles are actively built from smaller molecules. Complex carbohydrates break down into simple sugars that the cell uses for energy. Just as energy is required to both build and demolish a building, energy is required to synthesize and break down molecules. Additionally, signaling molecules such as hormones and neurotransmitters transport between cells. Cells ingest and break down bacteria and viruses. Cells must also export waste and toxins to stay healthy, and many cells must swim or move surrounding materials via the beating motion of cellular appendages like cilia and flagella.
The cellular processes that we listed above require a steady supply of energy. From where, and in what form, does this energy come? How do living cells obtain energy, and how do they use it? This chapter will discuss different forms of energy and the physical laws that govern energy transfer. This chapter will also describe how cells use energy and replenish it, and how chemical reactions in the cell perform with great efficiency. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.03%3A_Metabolism/2.3.01%3A_Introduction.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Explain metabolic pathways and describe the two major types
• Discuss how chemical reactions play a role in energy transfer
Scientists use the term bioenergetics to discuss the concept of energy flow (Figure 6.2) through living systems, such as cells. Cellular processes such as building and breaking down complex molecules occur through stepwise chemical reactions. Some of these chemical reactions are spontaneous and release energy; whereas, others require energy to proceed. Just as living things must continually consume food to replenish what they have used, cells must continually obtain more energy to replenish that which the many energy-requiring chemical reactions that constantly take place use. All of the chemical reactions that transpire inside cells, including those that use and release energy, are the cell’s metabolism.
Figure 6.2 Most life forms on earth obtain their energy from the sun. Plants use photosynthesis to capture sunlight, and herbivores eat those plants to obtain energy. Carnivores eat the herbivores, and decomposers digest plant and animal matter.
Carbohydrate Metabolism
Sugar (a simple carbohydrate) metabolism (chemical reactions) is a classic example of the many cellular processes that use and produce energy. Living things consume sugar as a major energy source, because sugar molecules have considerable energy stored within their bonds. The following equation describes the breakdown of glucose, a simple sugar:
$C 6 H 12 O 6 + 6O 2 →6 CO 2 + 6H 2 O+energy C 6 H 12 O 6 + 6O 2 →6 CO 2 + 6H 2 O+energy$
Consumed carbohydrates have their origins in photosynthesizing organisms like plants (Figure 6.3). During photosynthesis, plants use the energy of sunlight to convert carbon dioxide gas (CO2) into sugar molecules, like glucose (C6H12O6). Because this process involves synthesizing a larger, energy-storing molecule, it requires an energy input to proceed. The following equation (notice that it is the reverse of the previous equation) describes the synthesis of glucose:
$6CO 2 + 6H 2 O+energy→ C 6 H 12 O 6 + 6O 2 6CO 2 + 6H 2 O+energy→ C 6 H 12 O 6 + 6O 2$
During photosynthesis chemical reactions, energy is in the form of a very high-energy molecule scientists call ATP, or adenosine triphosphate. This is the primary energy currency of all cells. Just as the dollar is the currency we use to buy goods, cells use ATP molecules as energy currency to perform immediate work. The sugar (glucose) is stored as starch or glycogen. Energy-storing polymers like these break down into glucose to supply ATP molecules.
Solar energy is required to synthesize a glucose molecule during the photosynthesis reactions. In photosynthesis, light energy from the sun initially transforms into chemical energy that temporally stores itself in the energy carrier molecules ATP and NADPH (nicotinamide adenine dinucleotide phosphate). Photosynthesis later uses the stored energy in ATP and NADPH to build one glucose molecule from six molecules of CO2. This process is analogous to eating breakfast in the morning to acquire energy for your body that you can use later in the day. Under ideal conditions, energy from 18 molecules of ATP is required to synthesize one glucose molecule during photosynthesis reactions. Glucose molecules can also combine with and convert into other sugar types. When an organism consumes sugars, glucose molecules eventually make their way into each organism's living cell. Inside the cell, each sugar molecule breaks down through a complex series of chemical reactions. The goal of these reactions is to harvest the energy stored inside the sugar molecules. The harvested energy makes high-energy ATP molecules, which perform work, powering many chemical reactions in the cell. The amount of energy needed to make one glucose molecule from six carbon dioxide molecules is 18 ATP molecules and 12 NADPH molecules (each one of which is energetically equivalent to three ATP molecules), or a total of 54 molecule equivalents required for synthesizing one glucose molecule. This process is a fundamental and efficient way for cells to generate the molecular energy that they require.
Figure 6.3 Plants, like this oak tree and acorn, use energy from sunlight to make sugar and other organic molecules. Both plants and animals (like this squirrel) use cellular respiration to derive energy from the organic molecules that plants originally produced. (credit “acorn”: modification of work by Noel Reynolds; credit “squirrel”: modification of work by Dawn Huczek)
Metabolic Pathways
The processes of making and breaking down sugar molecules illustrate two types of metabolic pathways. A metabolic pathway is a series of interconnected biochemical reactions that convert a substrate molecule or molecules, step-by-step, through a series of metabolic intermediates, eventually yielding a final product or products. In the case of sugar metabolism, the first metabolic pathway synthesized sugar from smaller molecules, and the other pathway broke sugar down into smaller molecules. Scientists call these two opposite processes—the first requiring energy and the second producing energy—anabolic (building) and catabolic (breaking down) pathways, respectively. Consequently, building (anabolism) and degradation (catabolism) comprise metabolism.
Evolution Connection
Evolution Connection
Figure 6.4 This tree shows the evolution of the various branches of life. The vertical dimension is time. Early life forms, in blue, used anaerobic metabolism to obtain energy from their surroundings.
Evolution of Metabolic PathwaysThere is more to the complexity of metabolism than understanding the metabolic pathways alone. Metabolic complexity varies from organism to organism. Photosynthesis is the primary pathway in which photosynthetic organisms like plants (planktonic algae perform the majority of global photosynthesis) harvest the sun’s energy and convert it into carbohydrates. The by-product of photosynthesis is oxygen, which some cells require to carry out cellular respiration. During cellular respiration, oxygen aids in the catabolic breakdown of carbon compounds, like carbohydrates. Among the products are CO2 and ATP. In addition, some eukaryotes perform catabolic processes without oxygen (fermentation); that is, they perform or use anaerobic metabolism.
Organisms probably evolved anaerobic metabolism to survive (living organisms came into existence about 3.8 billion years ago, when the atmosphere lacked oxygen). Despite the differences between organisms and the complexity of metabolism, researchers have found that all branches of life share some of the same metabolic pathways, suggesting that all organisms evolved from the same ancient common ancestor (Figure 6.4). Evidence indicates that over time, the pathways diverged, adding specialized enzymes to allow organisms to better adapt to their environment, thus increasing their chance to survive. However, the underlying principle remains that all organisms must harvest energy from their environment and convert it to ATP to carry out cellular functions.
Anabolic and Catabolic Pathways
Anabolic pathways require an input of energy to synthesize complex molecules from simpler ones. Synthesizing sugar from CO2 is one example. Other examples are synthesizing large proteins from amino acid building blocks, and synthesizing new DNA strands from nucleic acid building blocks. These biosynthetic processes are critical to the cell's life, take place constantly, and demand energy that ATP and other high-energy molecules like NADH (nicotinamide adenine dinucleotide) and NADPH provide (Figure 6.5).
ATP is an important molecule for cells to have in sufficient supply at all times. The breakdown of sugars illustrates how a single glucose molecule can store enough energy to make a great deal of ATP, 36 to 38 molecules. This is a catabolic pathway. Catabolic pathways involve degrading (or breaking down) complex molecules into simpler ones. Molecular energy stored in complex molecule bonds release in catabolic pathways and harvest in such a way that it can produce ATP. Other energy-storing molecules, such as fats, also break down through similar catabolic reactions to release energy and make ATP (Figure 6.5).
It is important to know that metabolic pathway chemical reactions do not take place spontaneously. A protein called an enzyme facilitates or catalyzes each reaction step. Enzymes are important for catalyzing all types of biological reactions—those that require energy as well as those that release energy.
Figure 6.5 Anabolic pathways are those that require energy to synthesize larger molecules. Catabolic pathways are those that generate energy by breaking down larger molecules. Both types of pathways are required for maintaining the cell’s energy balance. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.03%3A_Metabolism/2.3.02%3A_Energy_and_Metabolism.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Define “energy”
• Explain the difference between kinetic and potential energy
• Discuss the concepts of free energy and activation energy
• Describe endergonic and exergonic reactions
We define energy as the ability to do work. As you’ve learned, energy exists in different forms. For example, electrical energy, light energy, and heat energy are all different energy types. While these are all familiar energy types that one can see or feel, there is another energy type that is much less tangible. Scientists associate this energy with something as simple as an object above the ground. In order to appreciate the way energy flows into and out of biological systems, it is important to understand more about the different energy types that exist in the physical world.
Energy Types
When an object is in motion, there is energy. For example, an airplane in flight produces considerable energy. This is because moving objects are capable of enacting a change, or doing work. Think of a wrecking ball. Even a slow-moving wrecking ball can do considerable damage to other objects. However, a wrecking ball that is not in motion is incapable of performing work. Energy with objects in motion is kinetic energy. A speeding bullet, a walking person, rapid molecule movement in the air (which produces heat), and electromagnetic radiation like light all have kinetic energy.
What if we lift that same motionless wrecking ball two stories above a car with a crane? If the suspended wrecking ball is unmoving, can we associate energy with it? The answer is yes. The suspended wrecking ball has associated energy that is fundamentally different from the kinetic energy of objects in motion. This energy form results from the potential for the wrecking ball to do work. If we release the ball it would do work. Because this energy type refers to the potential to do work, we call it potential energy. Objects transfer their energy between kinetic and potential in the following way: As the wrecking ball hangs motionless, it has 0 kinetic and 100 percent potential energy. Once it releases, its kinetic energy begins to increase because it builds speed due to gravity. Simultaneously, as it nears the ground, it loses potential energy. Somewhere mid-fall it has 50 percent kinetic and 50 percent potential energy. Just before it hits the ground, the ball has nearly lost its potential energy and has near-maximal kinetic energy. Other examples of potential energy include water's energy held behind a dam (Figure 6.6), or a person about to skydive from an airplane.
Figure 6.6 Water behind a dam has potential energy. Moving water, such as in a waterfall or a rapidly flowing river, has kinetic energy. (credit “dam”: modification of work by "Pascal"/Flickr; credit “waterfall”: modification of work by Frank Gualtieri)
We associate potential energy not only with the matter's location (such as a child sitting on a tree branch), but also with the matter's structure. A spring on the ground has potential energy if it is compressed; so does a tautly pulled rubber band. The very existence of living cells relies heavily on structural potential energy. On a chemical level, the bonds that hold the molecules' atoms together have potential energy. Remember that anabolic cellular pathways require energy to synthesize complex molecules from simpler ones, and catabolic pathways release energy when complex molecules break down. That certain chemical bonds' breakdown can release energy implies that those bonds have potential energy. In fact, there is potential energy stored within the bonds of all the food molecules we eat, which we eventually harness for use. This is because these bonds can release energy when broken. Scientists call the potential energy type that exists within chemical bonds that releases when those bonds break chemical energy (Figure 6.7). Chemical energy is responsible for providing living cells with energy from food. Breaking the molecular bonds within fuel molecules brings about the energy's release.
Figure 6.7 The molecules in gasoline contain chemical energy within the chemical bonds. This energy transforms into kinetic energy that allows a car to race on a racetrack. (credit “car”: modification of work by Russell Trow)
Link to Learning
Link to Learning
Visit this site and select “A simple pendulum” on the menu (under “Harmonic Motion”) to see the shifting kinetic (K) and potential energy (U) of a pendulum in motion.
Free Energy
After learning that chemical reactions release energy when energy-storing bonds break, an important next question is how do we quantify and express the chemical reactions with the associated energy? How can we compare the energy that releases from one reaction to that of another reaction? We use a measurement of free energy to quantitate these energy transfers. Scientists call this free energy Gibbs free energy (abbreviated with the letter G) after Josiah Willard Gibbs, the scientist who developed the measurement. According to the second law of thermodynamics, all energy transfers involve losing some energy in an unusable form such as heat, resulting in entropy. Gibbs free energy specifically refers to the energy that takes place with a chemical reaction that is available after we account for entropy. In other words, Gibbs free energy is usable energy, or energy that is available to do work.
Every chemical reaction involves a change in free energy, called delta G (∆G). We can calculate the change in free energy for any system that undergoes such a change, such as a chemical reaction. To calculate ∆G, subtract the amount of energy lost to entropy (denoted as ∆S) from the system's total energy change. The total energy in the system is enthalpy and we denote it as ∆H. The formula for calculating ∆G is as follows, where the symbol T refers to absolute temperature in Kelvin (degrees Celsius + 273):
$ΔG=ΔH−TΔS ΔG=ΔH−TΔS$
We express a chemical reaction's standard free energy change as an amount of energy per mole of the reaction product (either in kilojoules or kilocalories, kJ/mol or kcal/mol; 1 kJ = 0.239 kcal) under standard pH, temperature, and pressure conditions. We generally calculate standard pH, temperature, and pressure conditions at pH 7.0 in biological systems, 25 degrees Celsius, and 100 kilopascals (1 atm pressure), respectively. Note that cellular conditions vary considerably from these standard conditions, and so standard calculated ∆G values for biological reactions will be different inside the cell.
Endergonic Reactions and Exergonic Reactions
If energy releases during a chemical reaction, then the resulting value from the above equation will be a negative number. In other words, reactions that release energy have a ∆G < 0. A negative ∆G also means that the reaction's products have less free energy than the reactants, because they gave off some free energy during the reaction. Scientists call reactions that have a negative ∆G and consequently release free energy exergonic reactions. Think: exergonic means energy is exiting the system. We also refer to these reactions as spontaneous reactions, because they can occur without adding energy into the system. Understanding which chemical reactions are spontaneous and release free energy is extremely useful for biologists, because these reactions can be harnessed to perform work inside the cell. We must draw an important distinction between the term spontaneous and the idea of a chemical reaction that occurs immediately. Contrary to the everyday use of the term, a spontaneous reaction is not one that suddenly or quickly occurs. Rusting iron is an example of a spontaneous reaction that occurs slowly, little by little, over time.
If a chemical reaction requires an energy input rather than releasing energy, then the ∆G for that reaction will be a positive value. In this case, the products have more free energy than the reactants. Thus, we can think of the reactions' products as energy-storing molecules. We call these chemical reactions endergonic reactions, and they are non-spontaneous. An endergonic reaction will not take place on its own without adding free energy.
Let’s revisit the example of the synthesis and breakdown of the food molecule, glucose. Remember that building complex molecules, such as sugars, from simpler ones is an anabolic process and requires energy. Therefore, the chemical reactions involved in anabolic processes are endergonic reactions. Alternatively the catabolic process of breaking sugar down into simpler molecules releases energy in a series of exergonic reactions. Like the rust example above, the sugar breakdown involves spontaneous reactions, but these reactions do not occur instantaneously. Figure 6.8 shows some other examples of endergonic and exergonic reactions. Later sections will provide more information about what else is required to make even spontaneous reactions happen more efficiently.
Visual Connection
Visual Connection
Figure 6.8 This figure shows some examples of endergonic processes (ones that require energy) and exergonic processes (ones that release energy). These include (a) a compost pile decomposing, (b) a chick developing from a fertilized egg, (c) sand art destruction, and (d) a ball rolling down a hill. (credit a: modification of work by Natalie Maynor; credit b: modification of work by USDA; credit c: modification of work by “Athlex”/Flickr; credit d: modification of work by Harry Malsch)
Look at each of the processes, and decide if it is endergonic or exergonic. In each case, does enthalpy increase or decrease, and does entropy increase or decrease?
An important concept in studying metabolism and energy is that of chemical equilibrium. Most chemical reactions are reversible. They can proceed in both directions, releasing energy into their environment in one direction, and absorbing it from the environment in the other direction (Figure 6.9). The same is true for the chemical reactions involved in cell metabolism, such as the breaking down and building up of proteins into and from individual amino acids, respectively. Reactants within a closed system will undergo chemical reactions in both directions until they reach a state of equilibrium, which is one of the lowest possible free energy and a state of maximal entropy. To push the reactants and products away from a state of equilibrium requires energy. Either reactants or products must be added, removed, or changed. If a cell were a closed system, its chemical reactions would reach equilibrium, and it would die because there would be insufficient free energy left to perform the necessary work to maintain life. In a living cell, chemical reactions are constantly moving towards equilibrium, but never reach it. This is because a living cell is an open system. Materials pass in and out, the cell recycles the products of certain chemical reactions into other reactions, and there is never chemical equilibrium. In this way, living organisms are in a constant energy-requiring, uphill battle against equilibrium and entropy. This constant energy supply ultimately comes from sunlight, which produces nutrients in the photosynthesis process.
Figure 6.9 Exergonic and endergonic reactions result in changes in Gibbs free energy (G). Exergonic reactions have a net release of energy and are spontaneous reactions. Endergonic reactions require an input of energy to proceed and are nonspontaneous reactions. Both Exergonic and endergonic reactions require initial activation energy for the reaction to occur.Credit: Tag, A., Rao, A., Fletcher, S. and Ryan, A. Department of Biology, Texas A&M University.
Activation Energy
There is another important concept that we must consider regarding endergonic and exergonic reactions. Even exergonic reactions require a small amount of energy input before they can proceed with their energy-releasing steps. These reactions have a net release of energy, but still require some initial energy. Scientists call this small amount of energy input necessary for all chemical reactions to occur the activation energy (or free energy of activation) abbreviated as EA (Figure 6.10).
Why would an energy-releasing, negative ∆G reaction actually require some energy to proceed? The reason lies in the steps that take place during a chemical reaction. During chemical reactions, certain chemical bonds break and new ones form. For example, when a glucose molecule breaks down, bonds between the molecule's carbon atoms break. Since these are energy-storing bonds, they release energy when broken. However, to get them into a state that allows the bonds to break, the molecule must be somewhat contorted. A small energy input is required to achieve this contorted state. This contorted state is the transition state, and it is a high-energy, unstable state. For this reason, reactant molecules do not last long in their transition state, but very quickly proceed to the chemical reaction's next steps. Free energy diagrams illustrate the energy profiles for a given reaction. Whether the reaction is exergonic or endergonic determines whether the products in the diagram will exist at a lower or higher energy state than both the reactants and the products. However, regardless of this measure, the transition state of the reaction exists at a higher energy state than the reactants, and thus, EA is always positive.
Link to Learning
Link to Learning
Watch an animation of the move from free energy to transition state at this site.
From where does the activation energy that chemical reactants require come? The activation energy's required source to push reactions forward is typically heat energy from the surroundings. Heat energy (the total bond energy of reactants or products in a chemical reaction) speeds up the molecule's motion, increasing the frequency and force with which they collide. It also moves atoms and bonds within the molecule slightly, helping them reach their transition state. For this reason, heating a system will cause chemical reactants within that system to react more frequently. Increasing the pressure on a system has the same effect. Once reactants have absorbed enough heat energy from their surroundings to reach the transition state, the reaction will proceed.
The activation energy of a particular reaction determines the rate at which it will proceed. The higher the activation energy, the slower the chemical reaction. The example of iron rusting illustrates an inherently slow reaction. This reaction occurs slowly over time because of its high EA. Additionally, burning many fuels, which is strongly exergonic, will take place at a negligible rate unless sufficient heat from a spark overcomes their activation energy. However, once they begin to burn, the chemical reactions release enough heat to continue the burning process, supplying the activation energy for surrounding fuel molecules. Like these reactions outside of cells, the activation energy for most cellular reactions is too high for heat energy to overcome at efficient rates. In other words, in order for important cellular reactions to occur at appreciable rates (number of reactions per unit time), their activation energies must be lowered (Figure 6.10). Scientist refer to this as catalysis. This is a very good thing as far as living cells are concerned. Important macromolecules, such as proteins, DNA, and RNA, store considerable energy, and their breakdown is exergonic. If cellular temperatures alone provided enough heat energy for these exergonic reactions to overcome their activation barriers, the cell's essential components would disintegrate.
Visual Connection
Visual Connection
Figure 6.10 Activation energy is the energy required for a reaction to proceed, and it is lower if the reaction is catalyzed. This diagram's horizontal axis describes the sequence of events in time.
If no activation energy were required to break down sucrose (table sugar), would you be able to store it in a sugar bowl? | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.03%3A_Metabolism/2.3.03%3A_Potential_Kinetic_Free_and_Activation_Energy.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Discuss the concept of entropy
• Explain the first and second laws of thermodynamics
Thermodynamics refers to the study of energy and energy transfer involving physical matter. The matter and its environment relevant to a particular case of energy transfer are classified as a system, and everything outside that system is the surroundings. For instance, when heating a pot of water on the stove, the system includes the stove, the pot, and the water. Energy transfers within the system (between the stove, pot, and water). There are two types of systems: open and closed. An open system is one in which energy and matter can transfer between the system and its surroundings. The stovetop system is open because it can lose heat into the air. A closed system is one that can transfer energy but not matter to its surroundings.
Biological organisms are open systems. Energy exchanges between them and their surroundings, as they consume energy-storing molecules and release energy to the environment by doing work. Like all things in the physical world, energy is subject to the laws of physics. The laws of thermodynamics govern the transfer of energy in and among all systems in the universe.
The First Law of Thermodynamics
The first law of thermodynamics deals with the total amount of energy in the universe. It states that this total amount of energy is constant. In other words, there has always been, and always will be, exactly the same amount of energy in the universe. Energy exists in many different forms. According to the first law of thermodynamics, energy may transfer from place to place or transform into different forms, but it cannot be created or destroyed. The transfers and transformations of energy take place around us all the time. Light bulbs transform electrical energy into light energy. Gas stoves transform chemical energy from natural gas into heat energy. Plants perform one of the most biologically useful energy transformations on earth: that of converting sunlight energy into the chemical energy stored within organic molecules (Figure 6.2). Figure 6.11 examples of energy transformations.
The challenge for all living organisms is to obtain energy from their surroundings in forms that they can transfer or transform into usable energy to do work. Living cells have evolved to meet this challenge very well. Chemical energy stored within organic molecules such as sugars and fats transforms through a series of cellular chemical reactions into energy within ATP molecules. Energy in ATP molecules is easily accessible to do work. Examples of the types of work that cells need to do include building complex molecules, transporting materials, powering the beating motion of cilia or flagella, contracting muscle fibers to create movement, and reproduction.
Figure 6.11 Here are two examples of energy transferring from one system to another and transformed from one form to another. Humans can convert the chemical energy in food, like this ice cream cone, into kinetic energy (the energy of movement to ride a bicycle). Plants can convert electromagnetic radiation (light energy) from the sun into chemical energy. (credit “ice cream”: modification of work by D. Sharon Pruitt; credit “kids on bikes”: modification of work by Michelle Riggen-Ransom; credit “leaf”: modification of work by Cory Zanker)
The Second Law of Thermodynamics
A living cell’s primary tasks of obtaining, transforming, and using energy to do work may seem simple. However, the second law of thermodynamics explains why these tasks are harder than they appear. None of the energy transfers that we have discussed, along with all energy transfers and transformations in the universe, is completely efficient. In every energy transfer, some amount of energy is lost in a form that is unusable. In most cases, this form is heat energy. Thermodynamically, scientists define heat energy as energy that transfers from one system to another that is not doing work. For example, when an airplane flies through the air, it loses some of its energy as heat energy due to friction with the surrounding air. This friction actually heats the air by temporarily increasing air molecule speed. Likewise, some energy is lost as heat energy during cellular metabolic reactions. This is good for warm-blooded creatures like us, because heat energy helps to maintain our body temperature. Strictly speaking, no energy transfer is completely efficient, because some energy is lost in an unusable form.
An important concept in physical systems is that of order and disorder (or randomness). The more energy that a system loses to its surroundings, the less ordered and more random the system. Scientists refer to the measure of randomness or disorder within a system as entropy. High entropy means high disorder and low energy (Figure 6.12). To better understand entropy, think of a student’s bedroom. If no energy or work were put into it, the room would quickly become messy. It would exist in a very disordered state, one of high entropy. Energy must be put into the system, in the form of the student doing work and putting everything away, in order to bring the room back to a state of cleanliness and order. This state is one of low entropy. Similarly, a car or house must be constantly maintained with work in order to keep it in an ordered state. Left alone, a house's or car's entropy gradually increases through rust and degradation. Molecules and chemical reactions have varying amounts of entropy as well. For example, as chemical reactions reach a state of equilibrium, entropy increases, and as molecules at a high concentration in one place diffuse and spread out, entropy also increases.
Scientific Method Connection
Scientific Connection
Transfer of Energy and the Resulting EntropySet up a simple experiment to understand how energy transfers and how a change in entropy results.
1. Take a block of ice. This is water in solid form, so it has a high structural order. This means that the molecules cannot move very much and are in a fixed position. The ice's temperature is 0°C. As a result, the system's entropy is low.
2. Allow the ice to melt at room temperature. What is the state of molecules in the liquid water now? How did the energy transfer take place? Is the system's entropy higher or lower? Why?
3. Heat the water to its boiling point. What happens to the system's entropy when the water is heated?
Think of all physical systems of in this way: Living things are highly ordered, requiring constant energy input to maintain themselves in a state of low entropy. As living systems take in energy-storing molecules and transform them through chemical reactions, they lose some amount of usable energy in the process, because no reaction is completely efficient. They also produce waste and by-products that are not useful energy sources. This process increases the entropy of the system’s surroundings. Since all energy transfers result in losing some usable energy, the second law of thermodynamics states that every energy transfer or transformation increases the universe's entropy. Even though living things are highly ordered and maintain a state of low entropy, the universe's entropy in total is constantly increasing due to losing usable energy with each energy transfer that occurs. Essentially, living things are in a continuous uphill battle against this constant increase in universal entropy.
Figure 6.12 Entropy is a measure of randomness or disorder in a system. Gases have higher entropy than liquids, and liquids have higher entropy than solids. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.03%3A_Metabolism/2.3.04%3A_The_Laws_of_Thermodynamics.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Explain ATP's role as the cellular energy currency
• Describe how energy releases through ATP hydrolysis
Even exergonic, energy-releasing reactions require a small amount of activation energy in order to proceed. However, consider endergonic reactions, which require much more energy input, because their products have more free energy than their reactants. Within the cell, from where does energy to power such reactions come? The answer lies with an energy-supplying molecule scientists call adenosine triphosphate, or ATP. This is a small, relatively simple molecule (Figure 6.13), but within some of its bonds, it contains the potential for a quick burst of energy that can be harnessed to perform cellular work. Think of this molecule as the cells' primary energy currency in much the same way that money is the currency that people exchange for things they need. ATP powers the majority of energy-requiring cellular reactions.
Figure 6.13 ATP is the cell's primary energy currency. It has an adenosine backbone with three phosphate groups attached.
As its name suggests, adenosine triphosphate is comprised of adenosine bound to three phosphate groups (Figure 6.13). Adenosine is a nucleoside consisting of the nitrogenous base adenine and a five-carbon sugar, ribose. The three phosphate groups, in order of closest to furthest from the ribose sugar, are alpha, beta, and gamma. Together, these chemical groups constitute an energy powerhouse. However, not all bonds within this molecule exist in a particularly high-energy state. Both bonds that link the phosphates are equally high-energy bonds (phosphoanhydride bonds) that, when broken, release sufficient energy to power a variety of cellular reactions and processes. These high-energy bonds are the bonds between the second and third (or beta and gamma) phosphate groups and between the first and second phosphate groups. These bonds are “high-energy” because the products of such bond breaking—adenosine diphosphate (ADP) and one inorganic phosphate group (Pi)—have considerably lower free energy than the reactants: ATP and a water molecule. Because this reaction takes place using a water molecule, it is a hydrolysis reaction. In other words, ATP hydrolyzes into ADP in the following reaction:
$ATP+ H 2 O→ADP+ P i +free energy ATP+ H 2 O→ADP+ P i +free energy$
Like most chemical reactions, ATP to ADP hydrolysis is reversible. The reverse reaction regenerates ATP from ADP + Pi. Cells rely on ATP regeneration just as people rely on regenerating spent money through some sort of income. Since ATP hydrolysis releases energy, ATP regeneration must require an input of free energy. This equation expresses ATP formation:
$ADP+ P i +free energy→ATP+ H 2 O ADP+ P i +free energy→ATP+ H 2 O$
Two prominent questions remain with regard to using ATP as an energy source. Exactly how much free energy releases with ATP hydrolysis, and how does that free energy do cellular work? The calculated ∆G for the hydrolysis of one ATP mole into ADP and Pi is −7.3 kcal/mole (−30.5 kJ/mol). Since this calculation is true under standard conditions, one would expect a different value exists under cellular conditions. In fact, the ∆G for one ATP mole's hydrolysis in a living cell is almost double the value at standard conditions: –14 kcal/mol (−57 kJ/mol).
ATP is a highly unstable molecule. Unless quickly used to perform work, ATP spontaneously dissociates into ADP + Pi, and the free energy released during this process is lost as heat. The second question we posed above discusses how ATP hydrolysis energy release performs work inside the cell. This depends on a strategy scientists call energy coupling. Cells couple the ATP hydrolysis' exergonic reaction allowing them to proceed. One example of energy coupling using ATP involves a transmembrane ion pump that is extremely important for cellular function. This sodium-potassium pump (Na+/K+ pump) drives sodium out of the cell and potassium into the cell (Figure 6.14). A large percentage of a cell’s ATP powers this pump, because cellular processes bring considerable sodium into the cell and potassium out of it. The pump works constantly to stabilize cellular concentrations of sodium and potassium. In order for the pump to turn one cycle (exporting three Na+ ions and importing two K+ ions), one ATP molecule must hydrolyze. When ATP hydrolyzes, its gamma phosphate does not simply float away, but it actually transfers onto the pump protein. Scientists call this process of a phosphate group binding to a molecule phosphorylation. As with most ATP hydrolysis cases, a phosphate from ATP transfers onto another molecule. In a phosphorylated state, the Na+/K+ pump has more free energy and is triggered to undergo a conformational change. This change allows it to release Na+ to the cell's outside. It then binds extracellular K+, which, through another conformational change, causes the phosphate to detach from the pump. This phosphate release triggers the K+ to release to the cell's inside. Essentially, the energy released from the ATP hydrolysis couples with the energy required to power the pump and transport Na+ and K+ ions. ATP performs cellular work using this basic form of energy coupling through phosphorylation.
Visual Connection
Visual Connection
Figure 6.14 The sodium-potassium pump is an example of energy coupling. The energy derived from exergonic ATP hydrolysis pumps sodium and potassium ions across the cell membrane.
One ATP molecule's hydrolysis releases 7.3 kcal/mol of energy (∆G = −7.3 kcal/mol of energy). If it takes 2.1 kcal/mol of energy to move one Na+ across the membrane (∆G = +2.1 kcal/mol of energy), how many sodium ions could one ATP molecule's hydrolysis move?
Often during cellular metabolic reactions, such as nutrient synthesis and breakdown, certain molecules must alter slightly in their conformation to become substrates for the next step in the reaction series. One example is during the very first steps of cellular respiration, when a sugar glucose molecule breaks down in the process of glycolysis. In the first step, ATP is required to phosphorylate glucose, creating a high-energy but unstable intermediate. This phosphorylation reaction powers a conformational change that allows the phosphorylated glucose molecule to convert to the phosphorylated sugar fructose. Fructose is a necessary intermediate for glycolysis to move forward. Here, ATP hydrolysis' exergonic reaction couples with the endergonic reaction of converting glucose into a phosphorylated intermediate in the pathway. Once again, the energy released by breaking a phosphate bond within ATP was used for phosphorylyzing another molecule, creating an unstable intermediate and powering an important conformational change.
Link to Learning
Link to Learning
See an animation of the ATP-producing glycolysis process at this site. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.03%3A_Metabolism/2.3.05%3A_ATP-_Adenosine_Triphosphate.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Describe the role of enzymes in metabolic pathways
• Explain how enzymes function as molecular catalysts
• Discuss enzyme regulation by various factors
A substance that helps a chemical reaction to occur is a catalyst, and the special molecules that catalyze biochemical reactions are enzymes. Almost all enzymes are proteins, comprised of amino acid chains, and they perform the critical task of lowering the activation energies of chemical reactions inside the cell. Enzymes do this by binding to the reactant molecules, and holding them in such a way as to make the chemical bond-breaking and bond-forming processes take place more readily. It is important to remember that enzymes do not change the reaction's ∆G. In other words, they do not change whether a reaction is exergonic (spontaneous) or endergonic. This is because they do not change the reactants' or products' free energy. They only reduce the activation energy required to reach the transition state (Figure 6.15).
Figure 6.15 Enzymes lower the reaction's activation energy but do not change the reaction's free energy.
Enzyme Active Site and Substrate Specificity
The chemical reactants to which an enzyme binds are the enzyme’s substrates. There may be one or more substrates, depending on the particular chemical reaction. In some reactions, a single-reactant substrate breaks down into multiple products. In others, two substrates may come together to create one larger molecule. Two reactants might also enter a reaction, both become modified, and leave the reaction as two products. The location within the enzyme where the substrate binds is the enzyme’s active site. This is where the “action” happens. Since enzymes are proteins, there is a unique combination of amino acid residues (also side chains, or R groups) within the active site. Different properties characterize each residue. These can be large or small, weakly acidic or basic, hydrophilic or hydrophobic, positively or negatively charged, or neutral. The unique combination of amino acid residues, their positions, sequences, structures, and properties, creates a very specific chemical environment within the active site. This specific environment is suited to bind, albeit briefly, to a specific chemical substrate (or substrates). Due to this jigsaw puzzle-like match between an enzyme and its substrates (which adapts to find the best fit between the transition state and the active site), enzymes are known for their specificity. The “best fit” results from the shape and the amino acid functional group’s attraction to the substrate. There is a specifically matched enzyme for each substrate and, thus, for each chemical reaction; however, there is flexibility as well.
The fact that active sites are so perfectly suited to provide specific environmental conditions also means that they are subject to local environmental influences. It is true that increasing the environmental temperature generally increases reaction rates, enzyme-catalyzed or otherwise. However, increasing or decreasing the temperature outside of an optimal range can affect chemical bonds within the active site in such a way that they are less well suited to bind substrates. High temperatures will eventually cause enzymes, like other biological molecules, to denature, a process that changes the substance's natural properties. Likewise, the local environment's pH can also affect enzyme function. Active site amino acid residues have their own acidic or basic properties that are optimal for catalysis. These residues are sensitive to changes in pH that can impair the way substrate molecules bind. Enzymes are suited to function best within a certain pH range, and, as with temperature, extreme environmental pH values (acidic or basic) can cause enzymes to denature.
Induced Fit and Enzyme Function
For many years, scientists thought that enzyme-substrate binding took place in a simple “lock-and-key” fashion. This model asserted that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit (Figure 6.16). This model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild shift in the enzyme’s structure that confirms an ideal binding arrangement between the enzyme and the substrate's transition state. This ideal binding maximizes the enzyme’s ability to catalyze its reaction.
Link to Learning
Link to Learning
View an induced fit animation at this website.
When an enzyme binds its substrate, it forms an enzyme-substrate complex. This complex lowers the reaction's activation energy and promotes its rapid progression in one of many ways. On a basic level, enzymes promote chemical reactions that involve more than one substrate by bringing the substrates together in an optimal orientation. The appropriate region (atoms and bonds) of one molecule is juxtaposed to the other molecule's appropriate region with which it must react. Another way in which enzymes promote substrate reaction is by creating an optimal environment within the active site for the reaction to occur. Certain chemical reactions might proceed best in a slightly acidic or non-polar environment. The chemical properties that emerge from the particular arrangement of amino acid residues within an active site create the perfect environment for an enzyme’s specific substrates to react.
You have learned that the activation energy required for many reactions includes the energy involved in manipulating or slightly contorting chemical bonds so that they can easily break and allow others to reform. Enzymatic action can aid this process. The enzyme-substrate complex can lower the activation energy by contorting substrate molecules in such a way as to facilitate bond-breaking, helping to reach the transition state. Finally, enzymes can also lower activation energies by taking part in the chemical reaction itself. The amino acid residues can provide certain ions or chemical groups that actually form covalent bonds with substrate molecules as a necessary step of the reaction process. In these cases, it is important to remember that the enzyme will always return to its original state at the reaction's completion. One of enzymes' hallmark properties is that they remain ultimately unchanged by the reactions they catalyze. After an enzyme catalyzes a reaction, it releases its product(s).
Figure 6.16 According to the induced-fit model, both enzyme and substrate undergo dynamic conformational changes upon binding. The enzyme contorts the substrate into its transition state, thereby increasing the reaction's rate.
Metabolism Control Through Enzyme Regulation
It would seem ideal to have a scenario in which all the encoded enzymes in an organism’s genome existed in abundant supply and functioned optimally under all cellular conditions, in all cells, at all times. In reality, this is far from the case. A variety of mechanisms ensure that this does not happen. Cellular needs and conditions vary from cell to cell, and change within individual cells over time. The required enzymes and energetic demands of stomach cells are different from those of fat storage cells, skin cells, blood cells, and nerve cells. Furthermore, a digestive cell works much harder to process and break down nutrients during the time that closely follows a meal compared with many hours after a meal. As these cellular demands and conditions vary, so do the amounts and functionality of different enzymes.
Since the rates of biochemical reactions are controlled by activation energy, and enzymes lower and determine activation energies for chemical reactions, the relative amounts and functioning of the variety of enzymes within a cell ultimately determine which reactions will proceed and at which rates. This determination is tightly controlled. In certain cellular environments, environmental factors like pH and temperature partly control enzyme activity. There are other mechanisms through which cells control enzyme activity and determine the rates at which various biochemical reactions will occur.
Molecular Regulation of Enzymes
Enzymes can be regulated in ways that either promote or reduce their activity. There are many different kinds of molecules that inhibit or promote enzyme function, and various mechanisms exist for doing so. For example, in some cases of enzyme inhibition, an inhibitor molecule is similar enough to a substrate that it can bind to the active site and simply block the substrate from binding. When this happens, the enzyme is inhibited through competitive inhibition, because an inhibitor molecule competes with the substrate for active site binding (Figure 6.17). On the other hand, in noncompetitive inhibition, an inhibitor molecule binds to the enzyme in a location other than the active site, called an allosteric site, but still manages to prevent substrate binding to the active site. Some inhibitor molecules bind to enzymes in a location where their binding induces a conformational change that reduces the enzyme activity as it no longer effectively catalyzes the conversion of the substrate to product.
Figure 6.17 Competitive and noncompetitive inhibition affect the reaction's rate differently. Competitive inhibitors affect the initial rate but do not affect the maximal rate; whereas, noncompetitive inhibitors affect the maximal rate.
Some inhibitor molecules bind to enzymes in a location where their binding induces a conformational change that reduces the enzyme's affinity for its substrate. This type of inhibition is an allosteric inhibition (Figure 6.18). More than one polypeptide comprise most allosterically regulated enzymes, meaning that they have more than one protein subunit. When an allosteric inhibitor binds to an enzyme, all active sites on the protein subunits change slightly such that they bind their substrates with less efficiency. There are allosteric activators as well as inhibitors. Allosteric activators bind to locations on an enzyme away from the active site, inducing a conformational change that increases the affinity of the enzyme’s active site(s) for its substrate(s).
Figure 6.18 Allosteric inhibitors modify the enzyme's active site so that substrate binding is reduced or prevented. In contrast, allosteric activators modify the enzyme's active site so that the affinity for the substrate increases. Credit: Rao, A., Hawkins, A., Fletcher, S. and Tag, A. Department of Biology, Texas A&M University.
Everyday Connection
Everyday Connection
Figure 6.19 Have you ever wondered how pharmaceutical drugs are developed? (credit: Deborah Austin)
Drug Discovery by Looking for Inhibitors of Key Enzymes in Specific PathwaysEnzymes are key components of metabolic pathways. Understanding how enzymes work and how they can be regulated is a key principle behind developing many pharmaceutical drugs (Figure 6.19) on the market today. Biologists working in this field collaborate with other scientists, usually chemists, to design drugs.
Consider statins for example—which is a class of drugs that reduces cholesterol levels. These compounds are essentially inhibitors of the enzyme HMG-CoA reductase. HMG-CoA reductase is the enzyme that synthesizes cholesterol from lipids in the body. By inhibiting this enzyme, the drug reduces cholesterol levels synthesized in the body. Similarly, acetaminophen, popularly marketed under the brand name Tylenol, is an inhibitor of the enzyme cyclooxygenase. While it is effective in providing relief from fever and inflammation (pain), scientists still do not completely understand its mechanism of action.
How are drugs developed? One of the first challenges in drug development is identifying the specific molecule that the drug is intended to target. In the case of statins, HMG-CoA reductase is the drug target. Researchers identify targets through painstaking research in the laboratory. Identifying the target alone is not sufficient. Scientists also need to know how the target acts inside the cell and which reactions go awry in the case of disease. Once researchers identify the target and the pathway, then the actual drug design process begins. During this stage, chemists and biologists work together to design and synthesize molecules that can either block or activate a particular reaction. However, this is only the beginning: both if and when a drug prototype is successful in performing its function, then it must undergo many tests from in vitro experiments to clinical trials before it can obtain FDA approval to be on the market.
Many enzymes don’t work optimally, or even at all, unless bound to other specific non-protein helper molecules, either temporarily through ionic or hydrogen bonds or permanently through stronger covalent bonds. Two types of helper molecules are cofactors and coenzymes. Binding to these molecules promotes optimal conformation and function for their respective enzymes. Cofactors are inorganic ions such as iron (Fe++) and magnesium (Mg++). One example of an enzyme that requires a metal ion as a cofactor is the enzyme that builds DNA molecules, DNA polymerase, which requires a bound zinc ion (Zn++) to function. Coenzymes are organic helper molecules, with a basic atomic structure comprised of carbon and hydrogen, which are required for enzyme action. The most common sources of coenzymes are dietary vitamins (Figure 6.20). Some vitamins are precursors to coenzymes and others act directly as coenzymes. Vitamin C is a coenzyme for multiple enzymes that take part in building the important connective tissue component, collagen. An important step in breaking down glucose to yield energy is catalysis by a multi-enzyme complex scientists call pyruvate dehydrogenase. Pyruvate dehydrogenase is a complex of several enzymes that actually requires one cofactor (a magnesium ion) and five different organic coenzymes to catalyze its specific chemical reaction. Therefore, enzyme function is, in part, regulated by an abundance of various cofactors and coenzymes, which the diets of most organisms supply.
Figure 6.20 Vitamins are important coenzymes or precursors of coenzymes, and are required for enzymes to function properly. Multivitamin capsules usually contain mixtures of all the vitamins at different percentages.
Enzyme Compartmentalization
In eukaryotic cells, molecules such as enzymes are usually compartmentalized into different organelles. This allows for yet another level of regulation of enzyme activity. Enzymes required only for certain cellular processes are sometimes housed separately along with their substrates, allowing for more efficient chemical reactions. Examples of this sort of enzyme regulation based on location and proximity include the enzymes involved in the latter stages of cellular respiration, which take place exclusively in the mitochondria, and the enzymes involved in digesting cellular debris and foreign materials, located within lysosomes.
Feedback Inhibition in Metabolic Pathways
Molecules can regulate enzyme function in many ways. However, a major question remains: What are these molecules and from where do they come? Some are cofactors and coenzymes, ions, and organic molecules, as you have learned. What other molecules in the cell provide enzymatic regulation, such as allosteric modulation, and competitive and noncompetitive inhibition? The answer is that a wide variety of molecules can perform these roles. Some include pharmaceutical and non-pharmaceutical drugs, toxins, and poisons from the environment. Perhaps the most relevant sources of enzyme regulatory molecules, with respect to cellular metabolism, are cellular metabolic reaction products themselves. In a most efficient and elegant way, cells have evolved to use their own reactions' products for feedback inhibition of enzyme activity. Feedback inhibition involves using a reaction product to regulate its own further production (Figure 6.21). The cell responds to the abundance of specific products by slowing down production during anabolic or catabolic reactions. Such reaction products may inhibit the enzymes that catalyzed their production through the mechanisms that we described above.
Figure 6.21 Metabolic pathways are a series of reactions that multiple enzymes catalyze. Feedback inhibition, where the pathway's end product inhibits an upstream step, is an important regulatory mechanism in cells. Metabolic pathways are a series of reactions catalyzed by multiple enzymes (Intermediates A – D, Enzymes 1 – 5). Feedback inhibition occurs when the pathway's end product (here isoleucine) inhibits an upstream enzyme (indicated by red bar). In this example, isoleucine will bind to Threonine Deaminase (at the allosteric site) and prevent threonine from binding to this enzyme’s active site, effectively blocking this metabolic pathway. When isoleucine levels decrease, Threonine will then bind to Threonine Deaminase’s active site and the metabolic pathway will resume. This is an important regulatory mechanism in cells to inhibit the overproduction of a product. Credit: Rao, A., Ryan, K., Tag, A., Hawkins, A. and Fletcher S. Department of Biology, Texas A&M University.
Producing both amino acids and nucleotides is controlled through feedback inhibition. Additionally, ATP is an allosteric regulator of some of the enzymes involved in sugar's catabolic breakdown, the process that produces ATP. In this way, when ATP is abundant, the cell can prevent its further production. Remember that ATP is an unstable molecule that can spontaneously dissociate into ADP and inorganic phosphate. If too much ATP were present in a cell, much of it would go to waste. Alternatively, ADP serves as a positive allosteric regulator (an allosteric activator) for some of the same enzymes that ATP inhibits. Thus, when relative ADP levels are high compared to ATP, the cell is triggered to produce more ATP through sugar catabolism. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.03%3A_Metabolism/2.3.06%3A_Enzymes.txt |
activation energy
energy necessary for reactions to occur
active site
enzyme's specific region to which the substrate binds
allosteric inhibition
inhibition by a binding event at a site different from the active site, which induces a conformational change and reduces the enzyme's affinity for its substrate
anabolic
(also, anabolism) pathways that require an energy input to synthesize complex molecules from simpler ones
ATP
adenosine triphosphate, the cell’s energy currency
bioenergetics
study of energy flowing through living systems
catabolic
(also, catabolism) pathways in which complex molecules break down into simpler ones
chemical energy
potential energy in chemical bonds that releases when those bonds are broken
coenzyme
small organic molecule, such as a vitamin or its derivative, which is required to enhance an enzyme's activity
cofactor
inorganic ion, such as iron and magnesium ions, required for optimal enzyme activity regulation
competitive inhibition
type of inhibition in which the inhibitor competes with the substrate molecule by binding to the enzyme's active site
denature
process that changes a substance's natural properties
endergonic
describes chemical reactions that require energy input
energy coupling
process during which energy released by one reaction is used to drive another reaction
enthalpy
a system's total energy
entropy (S)
measure of randomness or disorder within a system
exergonic
describes chemical reactions that release free energy
feedback inhibition
a product's effect of a reaction sequence to decrease its further production by inhibiting the first enzyme's activity in the pathway that produces it
free energy
Gibbs free energy is the usable energy, or energy that is available to do work
heat
energy transferred from one system to another that is not work (energy of the molecules' motion or particles)
heat energy
total bond energy of reactants or products in a chemical reaction
induced fit
dynamic fit between the enzyme and its substrate, in which both components modify their structures to allow for ideal binding
kinetic energy
energy type that takes place with objects or particles in motion
metabolism
all the chemical reactions that take place inside cells, including anabolism and catabolism
phosphoanhydride bond
bond that connects phosphates in an ATP molecule
potential energy
energy type that has the potential to do work; stored energy
substrate
molecule on which the enzyme acts
thermodynamics
study of energy and energy transfer involving physical matter
transition state
high-energy, unstable state (an intermediate form between the substrate and the product) occurring during a chemical reaction
2.3.08: Chapter Summary
6.1 Energy and Metabolism
Cells perform the functions of life through various chemical reactions. A cell’s metabolism refers to the chemical reactions that take place within it. There are metabolic reactions that involve breaking down complex chemicals into simpler ones, such as breaking down large macromolecules. Scientists refer to this process as catabolism, and we associate such reactions an energy release. On the other end of the spectrum, anabolism refers to metabolic processes that build complex molecules out of simpler ones, such as macromolecule synthesis. Anabolic processes require energy. Glucose synthesis and glucose breakdown are examples of anabolic and catabolic pathways, respectively.
6.2 Potential, Kinetic, Free, and Activation Energy
Energy comes in many different forms. Objects in motion do physical work, and kinetic energy is the energy of objects in motion. Objects that are not in motion may have the potential to do work, and thus, have potential energy. Molecules also have potential energy because breaking molecular bonds has the potential to release energy. Living cells depend on harvesting potential energy from molecular bonds to perform work. Free energy is a measure of energy that is available to do work. A system's free energy changes during energy transfers such as chemical reactions, and scientists refer to this change as ∆G.
A reaction's ∆G can be negative or positive, meaning that the reaction releases energy or consumes energy, respectively. A reaction with a negative ∆G that gives off energy is an exergonic reaction. One with a positive ∆G that requires energy input is an endergonic reaction. Exergonic reactions are spontaneous because their products have less energy than their reactants. Endergonic reactions' products have a higher energy state than the reactants, and so these are nonspontaneous reactions. However, all reactions (including spontaneous -∆G reactions) require an initial energy input in order to reach the transition state, at which they will proceed. This initial input of energy is the activation energy.
6.3 The Laws of Thermodynamics
In studying energy, scientists use the term “system” to refer to the matter and its environment involved in energy transfers. Everything outside of the system is the surroundings. Single cells are biological systems. We can think of systems as having a certain amount of order. It takes energy to make a system more ordered. The more ordered a system, the lower its entropy. Entropy is a measure of a system's disorder. As a system becomes more disordered, the lower its energy and the higher its entropy.
The laws of thermodynamics are a series of laws that describe the properties and processes of energy transfer. The first law states that the total amount of energy in the universe is constant. This means that energy cannot be created or destroyed, only transferred or transformed. The second law of thermodynamics states that every energy transfer involves some loss of energy in an unusable form, such as heat energy, resulting in a more disordered system. In other words, no energy transfer is completely efficient, and all transfers trend toward disorder.
6.4 ATP: Adenosine Triphosphate
ATP is the primary energy-supplying molecule for living cells. ATP is comprised of a nucleotide, a five-carbon sugar, and three phosphate groups. The bonds that connect the phosphates (phosphoanhydride bonds) have high-energy content. The energy released from ATP hydrolysis into ADP + Pi performs cellular work. Cells use ATP to perform work by coupling ATP hydrolysis' exergonic reaction with endergonic reactions. ATP donates its phosphate group to another molecule via phosphorylation. The phosphorylated molecule is at a higher-energy state and is less stable than its unphosphorylated form, and this added energy from phosphate allows the molecule to undergo its endergonic reaction.
6.5 Enzymes
Enzymes are chemical catalysts that accelerate chemical reactions at physiological temperatures by lowering their activation energy. Enzymes are usually proteins consisting of one or more polypeptide chains. Enzymes have an active site that provides a unique chemical environment, comprised of certain amino acid R groups (residues). This unique environment is perfectly suited to convert particular chemical reactants for that enzyme, scientists call substrates, into unstable intermediates that they call transition states. Enzymes and substrates bind with an induced fit, which means that enzymes undergo slight conformational adjustments upon substrate contact, leading to full, optimal binding. Enzymes bind to substrates and catalyze reactions in four different ways: bringing substrates together in an optimal orientation, compromising the bond structures of substrates so that bonds can break down more easily, providing optimal environmental conditions for a reaction to occur, or participating directly in their chemical reaction by forming transient covalent bonds with the substrates.
Enzyme action must be regulated so that in a given cell at a given time, the desired reactions catalyze and the undesired reactions are not. Enzymes are regulated by cellular conditions, such as temperature and pH. They are also regulated through their location within a cell, sometimes compartmentalized so that they can only catalyze reactions under certain circumstances. Enzyme inhibition and activation via other molecules are other important ways that enzymes are regulated. Inhibitors can act competitively, noncompetitively, or allosterically. Noncompetitive inhibitors are usually allosteric. Activators can also enhance enzyme function allosterically. The most common method by which cells regulate the enzymes in metabolic pathways is through feedback inhibition. During feedback inhibition, metabolic pathway products serve as inhibitors (usually allosteric) of one or more of the enzymes (usually the first committed enzyme of the pathway) involved in the pathway that produces them. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.03%3A_Metabolism/2.3.07%3A_Key_Terms.txt |
1.
Figure 6.8 Look at each of the processes, and decide if it is endergonic or exergonic. In each case, does enthalpy increase or decrease, and does entropy increase or decrease?
2.
Figure 6.10 If no activation energy were required to break down sucrose (table sugar), would you be able to store it in a sugar bowl?
3.
Figure 6.14 One ATP molecule's hydrolysis releases 7.3 kcal/mol of energy (∆G = −7.3 kcal/mol of energy). If it takes 2.1 kcal/mol of energy to move one Na+ across the membrane (∆G = +2.1 kcal/mol of energy), how many sodium ions could one ATP molecule's hydrolysis move?
2.3.10: Review Questions
4.
Energy is stored long-term in the bonds of _____ and used short-term to perform work from a(n) _____ molecule.
1. ATP : glucose
2. an anabolic molecule : catabolic molecule
3. glucose : ATP
4. a catabolic molecule : anabolic molecule
5.
DNA replication involves unwinding two strands of parent DNA, copying each strand to synthesize complementary strands, and releasing the parent and daughter DNA. Which of the following accurately describes this process?
1. This is an anabolic process.
2. This is a catabolic process.
3. This is both anabolic and catabolic.
4. This is a metabolic process but is neither anabolic nor catabolic.
6.
Consider a pendulum swinging. Which type(s) of energy is/are associated with the pendulum in the following instances: i. the moment at which it completes one cycle, just before it begins to fall back towards the other end, ii. the moment that it is in the middle between the two ends, and iii. just before it reaches the end of one cycle (just before instant i.).
1. i. potential and kinetic, ii. potential and kinetic, iii. kinetic
2. i. potential, ii. potential and kinetic, iii. potential and kinetic
3. i. potential, ii. kinetic, iii. potential and kinetic
4. i. potential and kinetic, ii. kinetic iii. kinetic
7.
Which of the following comparisons or contrasts between endergonic and exergonic reactions is false?
1. Endergonic reactions have a positive ∆G and exergonic reactions have a negative ∆G.
2. Endergonic reactions consume energy and exergonic reactions release energy.
3. Both endergonic and exergonic reactions require a small amount of energy to overcome an activation barrier.
4. Endergonic reactions take place slowly and exergonic reactions take place quickly.
8.
Which of the following is the best way to judge the relative activation energies between two given chemical reactions?
1. Compare the ∆G values between the two reactions.
2. Compare their reaction rates.
3. Compare their ideal environmental conditions.
4. Compare the spontaneity between the two reactions.
9.
Which of the following is not an example of an energy transformation?
1. turning on a light switch
2. solar panels at work
3. formation of static electricity
4. none of the above
10.
In each of the three systems, determine the state of entropy (low or high) when comparing the first and second: i. the instant that a perfume bottle is sprayed compared with 30 seconds later, ii. an old 1950s car compared with a brand new car, and iii. a living cell compared with a dead cell.
1. i. low, ii. high, iii. low
2. i. low, ii. high, iii. high
3. i. high, ii. low, iii. high
4. i. high, ii. low, iii. low
11.
The energy released by the hydrolysis of ATP is____
1. primarily stored between the alpha and beta phosphates
2. equal to −57 kcal/mol
3. harnessed as heat energy by the cell to perform work
4. providing energy to coupled reactions
12.
Which of the following molecules is likely to have the most potential energy?
1. sucrose
2. ATP
3. glucose
4. ADP
13.
Which of the following is not true about enzymes:
1. They increase ∆G of reactions.
2. They are usually made of amino acids.
3. They lower the activation energy of chemical reactions.
4. Each one is specific to the particular substrate(s) to which it binds.
14.
An allosteric inhibitor does which of the following?
1. Binds to an enzyme away from the active site and changes the conformation of the active site, increasing its affinity for substrate binding.
2. Binds to the active site and blocks it from binding substrate.
3. Binds to an enzyme away from the active site and changes the conformation of the active site, decreasing its affinity for the substrate.
4. Binds directly to the active site and mimics the substrate.
15.
Which of the following analogies best describes the induced-fit model of enzyme-substrate binding?
1. a hug between two people
2. a key fitting into a lock
3. a square peg fitting through the square hole and a round peg fitting through the round hole of a children’s toy
4. the fitting together of two jigsaw puzzle pieces
2.3.11: Critical Thinking Questions
16.
Does physical exercise involve anabolic and/or catabolic processes? Give evidence for your answer.
17.
Name two different cellular functions that require energy that parallel human energy-requiring functions.
18.
Explain in your own words the difference between a spontaneous reaction and one that occurs instantaneously, and what causes this difference.
19.
Describe the position of the transition state on a vertical energy scale, from low to high, relative to the position of the reactants and products, for both endergonic and exergonic reactions.
20.
Imagine an elaborate ant farm with tunnels and passageways through the sand where ants live in a large community. Now imagine that an earthquake shook the ground and demolished the ant farm. In which of these two scenarios, before or after the earthquake, was the ant farm system in a state of higher or lower entropy?
21.
Energy transfers take place constantly in everyday activities. Think of two scenarios: cooking on a stove and driving. Explain how the second law of thermodynamics applies to these two scenarios.
22.
Do you think that the EA for ATP hydrolysis is relatively low or high? Explain your reasoning.
23.
With regard to enzymes, why are vitamins necessary for good health? Give examples.
24.
Explain in your own words how enzyme feedback inhibition benefits a cell. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.03%3A_Metabolism/2.3.09%3A_Visual_Connection_Questions.txt |
Like a generating plant, plants and animals also must take in energy from the environment and convert it into a form that their cells can use. Energy enters an organism’s body in one form and is converted into another form that can fuel the organism’s life functions. In the process of photosynthesis, plants and other photosynthetic producers take in energy in the form of light (solar energy) and convert it into chemical energy, glucose, which stores this energy in its chemical bonds. Then, a series of metabolic pathways, collectively called cellular respiration, extracts the energy from the bonds in glucose and converts it into a form that all living things can use—both producers, such as plants, and consumers, such as animals.
• 2.4.1: Introduction
Energy enters an organism’s body in one form and is converted into another form that can fuel the organism’s life functions. A series of metabolic pathways, collectively called cellular respiration, extracts the energy from the bonds in glucose and converts it into a form that all living things can use—both producers, such as plants, and consumers, such as animals.
• 2.4.2: Energy in Living Systems
Energy production within a cell involves many coordinated chemical pathways. Most of these pathways are combinations of oxidation and reduction reactions. Oxidation and reduction occur in tandem. An oxidation reaction strips an electron from an atom in a compound, and the addition of this electron to another compound is a reduction reaction. Because oxidation and reduction usually occur together, these pairs of reactions are called oxidation reduction reactions, or redox reactions.
• 2.4.3: Glycolysis
Glycolysis is the first step in the breakdown of glucose to extract energy for cellular metabolism. Nearly all living organisms carry out glycolysis as part of their metabolism. The process does not use oxygen and is therefore anaerobic. Glycolysis takes place in the cytoplasm of both prokaryotic and eukaryotic cells.
• 2.4.4: Oxidation of Pyruvate and the Citric Acid Cycle
If oxygen is available, aerobic respiration will go forward. In eukaryotic cells, the pyruvate molecules produced at the end of glycolysis are transported into mitochondria, which are the sites of cellular respiration. There, pyruvate will be transformed into an acetyl group that will be picked up and activated by a carrier compound called coenzyme A (CoA). The resulting compound is called acetyl CoA. CoA is made from vitamin B5, pantothenic acid.
• 2.4.5: Oxidative Phosphorylation
You have just read about two pathways in glucose catabolism—glycolysis and the citric acid cycle—that generate ATP. Most of the ATP generated during the aerobic catabolism of glucose, however, is not generated directly from these pathways. Rather, it is derived from a process that begins with moving electrons through a series of electron transporters that undergo redox reactions. This causes hydrogen ions to accumulate within the matrix space.
• 2.4.6: Metabolism without Oxygen
In aerobic respiration, the final electron acceptor is an oxygen molecule, O2. If aerobic respiration occurs, then ATP will be produced using the energy of high-energy electrons carried by NADH or FADH2 to the electron transport chain. If aerobic respiration does not occur, NADH must be reoxidized to NAD+ for reuse as an electron carrier for the glycolytic pathway to continue.
• 2.4.7: Connections of Carbohydrate, Protein, and Lipid Metabolic Pathways
All of the catabolic pathways for carbohydrates, proteins, and lipids eventually connect into glycolysis and the citric acid cycle pathways. Metabolic pathways should be thought of as porous—that is, substances enter from other pathways, and intermediates leave for other pathways. These pathways are not closed systems. Many of the substrates, intermediates, and products in a particular pathway are reactants in other pathways.
• 2.4.8: Regulation of Cellular Respiration
Cellular respiration must be regulated in order to provide balanced amounts of energy in the form of ATP. The cell also must generate a number of intermediate compounds that are used in the anabolism and catabolism of macromolecules. Without controls, metabolic reactions would quickly come to a stand still as the forward and backward reactions reached a state of equilibrium. Resources would be used inappropriately.
• 2.4.9: Key Terms
• 2.4.10: Chapter Summary
• 2.4.11: Visual Connection Questions
• 2.4.12: Review Questions
• 2.4.13: Critical Thinking Questions
Thumbnail: The generalized structure of a prokaryotic cell. (CC BY 4.0; OpenStax).
2.04: Cellular Respiration
Figure 7.1 This geothermal energy plant transforms thermal energy from deep in the ground into electrical energy, which can be easily used. (credit: modification of work by the U.S. Department of Defense)
The electrical energy plant in Figure 7.1 converts energy from one form to another form that can be more easily used. This type of generating plant starts with underground thermal energy (heat) and transforms it into electrical energy that will be transported to homes and factories. Like a generating plant, plants and animals also must take in energy from the environment and convert it into a form that their cells can use. Mass and its stored energy enter an organism’s body in one form and are converted into another form that can fuel the organism’s life functions. In the process of photosynthesis, plants and other photosynthetic producers take in energy in the form of light (solar energy) and convert it into chemical energy in the form of glucose, which stores this energy in its chemical bonds. Then, a series of metabolic pathways, collectively called cellular respiration, extracts the energy from the bonds in glucose and converts it into a form that all living things can use. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.04%3A_Cellular_Respiration/2.4.01%3A_Introduction.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Discuss the importance of electrons in the transfer of energy in living systems
• Explain how ATP is used by cells as an energy source
Energy production within a cell involves many coordinated chemical pathways. Most of these pathways are combinations of oxidation and reduction reactions, which occur at the same time. An oxidation reaction strips an electron from an atom in a compound, and the addition of this electron to another compound is a reduction reaction. Because oxidation and reduction usually occur together, these pairs of reactions are called oxidation reduction reactions, or redox reactions.
Figure 7.2 Stages of oxidation/reduction of a single carbon. Electrons are lost from carbon as methane is oxidized to carbon dioxide. The loss of electrons is also accompanied by the loss of energy. Electrons are gained during the reduction of carbon dioxide to methane. The gain of an electron is accompanied by a gain in potential energy and often by the addition of a proton (H+). Credit: Ryan, K., Rao, A.and Fletcher, S. Department of Biology, Texas A&M University.
Electrons and Energy
The removal of an electron from a molecule (oxidizing it), results in a decrease in potential energy in the oxidized compound. However, the electron (sometimes as part of a hydrogen atom) does not remain unbonded in the cytoplasm of a cell. Rather, the electron is shifted to a second compound, reducing the second compound. The shift of an electron from one compound to another removes some potential energy from the first compound (the oxidized compound) and increases the potential energy of the second compound (the reduced compound). The transfer of electrons between molecules is important because most of the energy stored in atoms and used to fuel cell functions is in the form of high-energy electrons. The transfer of energy in the form of high-energy electrons allows the cell to transfer and use energy in an incremental fashion—in small packages rather than in a single, destructive burst. This chapter focuses on the extraction of energy from food; you will see that as you track the path of the transfers, you are tracking the path of electrons moving through metabolic pathways.
Electron Carriers
In living systems, a small class of compounds functions as electron shuttles: they bind and carry high-energy electrons between compounds in biochemical pathways. The principal electron carriers we will consider are derived from the B vitamin group and are derivatives of nucleotides. These compounds can be easily reduced (that is, they accept electrons) or oxidized (they lose electrons). Nicotinamide adenine dinucleotide (NAD) (Figure 7.3) is derived from vitamin B3, niacin. NAD+ is the oxidized form of the molecule; NADH is the reduced form of the molecule after it has accepted two electrons and a proton (which together are the equivalent of a hydrogen atom with an extra electron). Note that if a compound has an “H” on it, it is generally reduced (e.g., NADH is the reduced form of NAD).
NAD+ can accept electrons from an organic molecule according to the general equation:
$RH Reducing agent + NAD + Oxidizing agent → NADH Reduced + R Oxidized RH Reducing agent + NAD + Oxidizing agent → NADH Reduced + R Oxidized$
When electrons are added to a compound, it is reduced. A compound that reduces another is called a reducing agent. In the above equation, RH is a reducing agent, and NAD+ is reduced to NADH. When electrons are removed from a compound, it is oxidized. A compound that oxidizes another is called an oxidizing agent. In the above equation, NAD+ is an oxidizing agent, and RH is oxidized to R.
Similarly, flavin adenine dinucleotide (FAD+) is derived from vitamin B2, also called riboflavin. Its reduced form is FADH2. A second variation of NAD, NADP, contains an extra phosphate group. Both NAD+ and FAD+ are extensively used in energy extraction from sugars, and NADP plays an important role in anabolic reactions and photosynthesis in plants.
Figure 7.3 The oxidized form of the electron carrier (NAD+) is shown on the left, and the reduced form (NADH) is shown on the right. The nitrogenous base in NADH has one more hydrogen ion and two more electrons than in NAD+.
ATP in Living Systems
A living cell cannot store significant amounts of free energy. Excess free energy would result in an increase of heat in the cell, which would result in excessive thermal motion that could damage and then destroy the cell. Rather, a cell must be able to handle that energy in a way that enables the cell to store energy safely and release it for use only as needed. Living cells accomplish this by using the compound adenosine triphosphate (ATP). ATP is often called the “energy currency” of the cell, and, like currency, this versatile compound can be used to fill any energy need of the cell. How? It functions similarly to a rechargeable battery.
When ATP is broken down, usually by the removal of its terminal phosphate group, energy is released. The energy is used to do work by the cell, usually when the released phosphate binds to another molecule, thereby activating it. For example, in the mechanical work of muscle contraction, ATP supplies the energy to move the contractile muscle proteins. Recall the active transport work of the sodium-potassium pump in cell membranes. ATP alters the structure of the integral protein that functions as the pump, changing its affinity for sodium and potassium. In this way, the cell performs work, pumping ions against their electrochemical gradients.
ATP Structure and Function
At the heart of ATP is a molecule of adenosine monophosphate (AMP), which is composed of an adenine molecule bonded to a ribose molecule and to a single phosphate group (Figure 7.4). Ribose is a five-carbon sugar found in RNA, and AMP is one of the nucleotides in RNA. The addition of a second phosphate group to this core molecule results in the formation of adenosine diphosphate (ADP); the addition of a third phosphate group forms adenosine triphosphate (ATP).
Figure 7.4 ATP (adenosine triphosphate) has three phosphate groups that can be removed by hydrolysis (addition of H2O) to form ADP (adenosine diphosphate) or AMP (adenosine monophosphate). The negative charges on the phosphate group naturally repel each other, requiring energy to bond them together and releasing energy when these bonds are broken.
The addition of a phosphate group to a molecule requires energy. Phosphate groups are negatively charged and thus repel one another when they are arranged in series, as they are in ADP and ATP. This repulsion makes the ADP and ATP molecules inherently unstable. The release of one or two phosphate groups from ATP, a process called dephosphorylation, releases energy.
Energy from ATP
Hydrolysis is the process of breaking complex macromolecules apart. During hydrolysis, water is split, or lysed, and the resulting hydrogen atom (H+) and a hydroxyl group (OH-), or hydroxide, are added to the larger molecule. The hydrolysis of ATP produces ADP, together with an inorganic phosphate ion (Pi), and the release of free energy. To carry out life processes, ATP is continuously broken down into ADP, and like a rechargeable battery, ADP is continuously regenerated into ATP by the reattachment of a third phosphate group. Water, which was broken down into its hydrogen atom and hydroxyl group (hydroxide) during ATP hydrolysis, is regenerated when a third phosphate is added to the ADP molecule, reforming ATP.
Obviously, energy must be infused into the system to regenerate ATP. Where does this energy come from? In nearly every living thing on Earth, the energy comes from the metabolism of glucose, fructose, or galactose, all isomers with the chemical formula C6H12O6 but different molecular configurations. In this way, ATP is a direct link between the limited set of exergonic pathways of glucose catabolism and the multitude of endergonic pathways that power living cells.
Phosphorylation
Recall that, in some chemical reactions, enzymes may bind to several substrates that react with each other on the enzyme, forming an intermediate complex. An intermediate complex is a temporary structure, and it allows one of the substrates (such as ATP) and reactants to more readily react with each other; in reactions involving ATP, ATP is one of the substrates and ADP is a product. During an endergonic chemical reaction, ATP forms an intermediate complex with the substrate and enzyme in the reaction. This intermediate complex allows the ATP to transfer its third phosphate group, with its energy, to the substrate, a process called phosphorylation. Phosphorylation refers to the addition of the phosphate (~P). This is illustrated by the following generic reaction, in which A and B represent two different substrates:
$A + enzyme + ATP→ [ A − enzyme − ∼P ] → B + enzyme + ADP + phosphate ion A + enzyme + ATP→ [ A − enzyme − ∼P ] → B + enzyme + ADP + phosphate ion$
When the intermediate complex breaks apart, the energy is used to modify the substrate and convert it into a product of the reaction. The ADP molecule and a free phosphate ion are released into the medium and are available for recycling through cell metabolism.
Substrate Phosphorylation
ATP is generated through two mechanisms during the breakdown of glucose. A few ATP molecules are generated (that is, regenerated from ADP) as a direct result of the chemical reactions that occur in the catabolic pathways. A phosphate group is removed from an intermediate reactant in the pathway, and the free energy of the reaction is used to add the third phosphate to an available ADP molecule, producing ATP (Figure 7.5). This very direct method of phosphorylation is called substrate-level phosphorylation.
Figure 7.5 In phosphorylation reactions, the gamma (third) phosphate of ATP is attached to a protein. In substrate-level phosphorylation, a phosphate group that is covalently attached to another molecule is transferred to ADP to form ATP. Credit: Rao, A., Ryan, K. and Fletcher, S. Department of Biology, Texas A&M University.
Oxidative Phosphorylation
Most of the ATP generated during glucose catabolism, however, is derived from a much more complex process, chemiosmosis, which takes place in mitochondria (Figure 7.6) within a eukaryotic cell or the plasma membrane of a prokaryotic cell. Chemiosmosis, a process of ATP production in cellular metabolism, is used to generate 90 percent of the ATP made during glucose catabolism and is also the method used in the light reactions of photosynthesis to harness the energy of sunlight. The production of ATP using the process of chemiosmosis is called oxidative phosphorylation because of the involvement of oxygen in the process.
Figure 7.6 In eukaryotes, oxidative phosphorylation takes place in mitochondria. In prokaryotes, this process takes place in the plasma membrane. (Credit: modification of work by Mariana Ruiz Villareal)
Career Connection
Career Connections
Mitochondrial Disease PhysicianWhat happens when the critical reactions of cellular respiration do not proceed correctly? This may happen in mitochondrial diseases, which are genetic disorders of metabolism. Mitochondrial disorders can arise from mutations in nuclear or mitochondrial DNA, and they result in the production of less energy than is normal in body cells. In type 2 diabetes, for instance, the oxidation efficiency of NADH is reduced, impacting oxidative phosphorylation but not the other steps of respiration. Symptoms of mitochondrial diseases can include muscle weakness, lack of coordination, stroke-like episodes, and loss of vision and hearing. Most affected people are diagnosed in childhood, although there are some adult-onset diseases. Identifying and treating mitochondrial disorders is a specialized medical field. The educational preparation for this profession requires a college education, followed by medical school with a specialization in medical genetics. Medical geneticists can be board certified by the American Board of Medical Genetics and go on to become associated with professional organizations devoted to the study of mitochondrial diseases, such as the Mitochondrial Medicine Society and the Society for Inherited Metabolic Disorders. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.04%3A_Cellular_Respiration/2.4.02%3A_Energy_in_Living_Systems.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Describe the overall result in terms of molecules produced during the chemical breakdown of glucose by glycolysis
• Compare the output of glycolysis in terms of ATP molecules and NADH molecules produced
As you have read, nearly all of the energy used by living cells comes to them in the bonds of the sugar glucose. Glycolysis is the first step in the breakdown of glucose to extract energy for cellular metabolism. In fact, nearly all living organisms carry out glycolysis as part of their metabolism. The process does not use oxygen directly and therefore is termed anaerobic. Glycolysis takes place in the cytoplasm of both prokaryotic and eukaryotic cells. Glucose enters heterotrophic cells in two ways. One method is through secondary active transport in which the transport takes place against the glucose concentration gradient. The other mechanism uses a group of integral proteins called GLUT proteins, also known as glucose transporter proteins. These transporters assist in the facilitated diffusion of glucose.
Glycolysis begins with the six-carbon ring-shaped structure of a single glucose molecule and ends with two molecules of a three-carbon sugar called pyruvate. Glycolysis consists of two distinct phases. The first part of the glycolysis pathway traps the glucose molecule in the cell and uses energy to modify it so that the six-carbon sugar molecule can be split evenly into the two three-carbon molecules. The second part of glycolysis extracts energy from the molecules and stores it in the form of ATP and NADH—remember: this is the reduced form of NAD.
Figure 7.7 Glycolysis begins with an energy investment phase which requires 2 ATP to phosphorylate the starting glucose molecule. The 6-carbon intermediate is then split into 2, 3-carbon sugar molecules. In the energy recovery phase, each 3-carbon sugar is then oxidized to pyruvate with the energy transferred to form NADH and 2 ATP. Credit: Rao, A. and Ryan, K. Department of Biology, Texas A&M University
First Half of Glycolysis (Energy-Requiring Steps)
Step 1. The first step in glycolysis (Figure 7.8) is catalyzed by hexokinase, an enzyme with broad specificity that catalyzes the phosphorylation of six-carbon sugars. Hexokinase phosphorylates glucose using ATP as the source of the phosphate, producing glucose-6-phosphate, a more reactive form of glucose. This reaction prevents the phosphorylated glucose molecule from continuing to interact with the GLUT proteins, and it can no longer leave the cell because the negatively charged phosphate will not allow it to cross the hydrophobic interior of the plasma membrane.
Step 2. In the second step of glycolysis, an isomerase converts glucose-6-phosphate into one of its isomers, fructose-6-phosphate (this isomer has a phosphate attached at the location of the sixth carbon of the ring). An isomerase is an enzyme that catalyzes the conversion of a molecule into one of its isomers. (This change from phosphoglucose to phosphofructose allows the eventual split of the sugar into two three-carbon molecules.)
Step 3. The third step is the phosphorylation of fructose-6-phosphate, catalyzed by the enzyme phosphofructokinase. A second ATP molecule donates a high-energy phosphate to fructose-6-phosphate, producing fructose-1,6-bisphosphate. In this pathway, phosphofructokinase is a rate-limiting enzyme. It is active when the concentration of ADP is high; it is less active when ADP levels are low and the concentration of ATP is high. Thus, if there is “sufficient” ATP in the system, the pathway slows down. This is a type of end product inhibition, since ATP is the end product of glucose catabolism.
Step 4. The newly added high-energy phosphates further destabilize fructose-1,6-bisphosphate. The fourth step in glycolysis employs an enzyme, aldolase, to cleave fructose-1,6-bisphosphate into two three-carbon isomers: dihydroxyacetone phosphate and glyceraldehyde-3-phosphate.
Step 5. In the fifth step, an isomerase transforms the dihydroxyacetone-phosphate into its isomer, glyceraldehyde-3-phosphate. Thus, the pathway will continue with two molecules of a glyceraldehyde-3-phosphate. At this point in the pathway, there is a net investment of energy from two ATP molecules in the breakdown of one glucose molecule.
Figure 7.8 The first half of glycolysis uses two ATP molecules in the phosphorylation of glucose, which is then split into two three-carbon molecules.
Second Half of Glycolysis (Energy-Releasing Steps)
So far, glycolysis has cost the cell two ATP molecules and produced two small, three-carbon sugar molecules. Both of these molecules will proceed through the second half of the pathway, and sufficient energy will be extracted to pay back the two ATP molecules used as an initial investment and produce a profit for the cell of two additional ATP molecules and two even higher-energy NADH molecules.
Step 6. The sixth step in glycolysis (Figure 7.9) oxidizes the sugar (glyceraldehyde-3-phosphate), extracting high-energy electrons, which are picked up by the electron carrier NAD+, producing NADH. The sugar is then phosphorylated by the addition of a second phosphate group, producing 1,3-bisphosphoglycerate. Note that the second phosphate group does not require another ATP molecule.
Figure 7.9 The second half of glycolysis involves phosphorylation without ATP investment (step 6) and produces two NADH and four ATP molecules per glucose.
Here again is a potential limiting factor for this pathway. The continuation of the reaction depends upon the availability of the oxidized form of the electron carrier, NAD+. Thus, NADH must be continuously oxidized back into NAD+ in order to keep this step going. If NAD+ is not available, the second half of glycolysis slows down or stops. If oxygen is available in the system, the NADH will be oxidized readily, though indirectly, and the high-energy electrons from the hydrogen released in this process will be used to produce ATP. In an environment without oxygen, an alternate pathway (fermentation) can provide the oxidation of NADH to NAD+.
Step 7. In the seventh step, catalyzed by phosphoglycerate kinase (an enzyme named for the reverse reaction), 1,3-bisphosphoglycerate donates a high-energy phosphate to ADP, forming one molecule of ATP. (This is an example of substrate-level phosphorylation.) A carbonyl group on the 1,3-bisphosphoglycerate is oxidized to a carboxyl group, and 3-phosphoglycerate is formed.
Step 8. In the eighth step, the remaining phosphate group in 3-phosphoglycerate moves from the third carbon to the second carbon, producing 2-phosphoglycerate (an isomer of 3-phosphoglycerate). The enzyme catalyzing this step is a mutase (isomerase).
Step 9. Enolase catalyzes the ninth step. This enzyme causes 2-phosphoglycerate to lose water from its structure; this is a dehydration reaction, resulting in the formation of a double bond that increases the potential energy in the remaining phosphate bond and produces phosphoenolpyruvate (PEP).
Step 10. The last step in glycolysis is catalyzed by the enzyme pyruvate kinase (the enzyme in this case is named for the reverse reaction of pyruvate’s conversion into PEP) and results in the production of a second ATP molecule by substrate-level phosphorylation and the compound pyruvic acid (or its salt form, pyruvate). Many enzymes in enzymatic pathways are named for the reverse reactions, since the enzyme can catalyze both forward and reverse reactions (these may have been described initially by the reverse reaction that takes place in vitro, under nonphysiological conditions).
Link to Learning
Link to Learning
Gain a better understanding of the breakdown of glucose by glycolysis by visiting this site to see the process in action.
Outcomes of Glycolysis
Glycolysis begins with glucose and produces two pyruvate molecules, four new ATP molecules, and two molecules of NADH. (Note: two ATP molecules are used in the first half of the pathway to prepare the six-carbon ring for cleavage, so the cell has a net gain of two ATP molecules and two NADH molecules for its use). If the cell cannot catabolize the pyruvate molecules further, it will harvest only two ATP molecules from one molecule of glucose. Mature mammalian red blood cells do not have mitochondria and thus are not capable of aerobic respiration—the process in which organisms convert energy in the presence of oxygen—and glycolysis is their sole source of ATP. If glycolysis is interrupted, these cells lose their ability to maintain their sodium-potassium pumps, and eventually, they die.
The last step in glycolysis will not occur if pyruvate kinase, the enzyme that catalyzes the formation of pyruvate, is not available in sufficient quantities. In this situation, the entire glycolysis pathway will proceed, but only two ATP molecules will be made in the second half. Thus, pyruvate kinase is a rate-limiting enzyme for glycolysis. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.04%3A_Cellular_Respiration/2.4.03%3A_Glycolysis.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Explain how a circular pathway, such as the citric acid cycle, fundamentally differs from a linear biochemical pathway, such as glycolysis
• Describe how pyruvate, the product of glycolysis, is prepared for entry into the citric acid cycle
If oxygen is available, aerobic respiration will go forward. In eukaryotic cells, the pyruvate molecules produced at the end of glycolysis are transported into the mitochondria, which are the sites of cellular respiration. There, pyruvate is transformed into an acetyl group that will be picked up and activated by a carrier compound called coenzyme A (CoA). The resulting compound is called acetyl CoA. CoA is derived from vitamin B5, pantothenic acid. Acetyl CoA can be used in a variety of ways by the cell, but its major function is to deliver the acetyl group derived from pyruvate to the next stage of the pathway in glucose catabolism.
Breakdown of Pyruvate
In order for pyruvate, the product of glycolysis, to enter the next pathway, it must undergo several changes. The conversion is a three-step process (Figure 7.10).
Step 1. A carboxyl group is removed from pyruvate, releasing a molecule of carbon dioxide into the surrounding medium. This reaction creates a two-carbon hydroxyethyl group bound to the enzyme (pyruvate dehydrogenase). We should note that this is the first of the six carbons from the original glucose molecule to be removed. (This step proceeds twice because there are two pyruvate molecules produced at the end of glycolsis for every molecule of glucose metabolized anaerobically; thus, two of the six carbons will have been removed at the end of both steps.)
Step 2. The hydroxyethyl group is oxidized to an acetyl group, and the electrons are picked up by NAD+, forming NADH. The high-energy electrons from NADH will be used later to generate ATP.
Step 3. The enzyme-bound acetyl group is transferred to CoA, producing a molecule of acetyl CoA.
Figure 7.10 Upon entering the mitochondrial matrix, a multienzyme complex converts pyruvate into acetyl CoA. In the process, carbon dioxide is released, and one molecule of NADH is formed. Credit: Rao, A., Ryan, K. and Tag, A. Department of Biology, Texas A&M University.
Note that during the second stage of glucose metabolism, whenever a carbon atom is removed, it is bound to two oxygen atoms, producing carbon dioxide, one of the major end products of cellular respiration.
Acetyl CoA to CO2
In the presence of oxygen, acetyl CoA delivers its acetyl (2C) group to a four-carbon molecule, oxaloacetate, to form citrate, a six-carbon molecule with three carboxyl groups; this pathway will harvest the remainder of the extractable energy from what began as a glucose molecule and release the remaining four CO2 molecules. This single pathway is called by different names: the citric acid cycle (for the first intermediate formed—citric acid, or citrate—when acetate joins to the oxaloacetate), the TCA cycle (because citric acid or citrate and isocitrate are tricarboxylic acids), and the Krebs cycle, after Hans Krebs, who first identified the steps in the pathway in the 1930s in pigeon flight muscles.
Citric Acid Cycle
Like the conversion of pyruvate to acetyl CoA, the citric acid cycle takes place in the matrix of mitochondria. Almost all of the enzymes of the citric acid cycle are soluble, with the single exception of the enzyme succinate dehydrogenase, which is embedded in the inner membrane of the mitochondrion. Unlike glycolysis, the citric acid cycle is a closed loop: the last part of the pathway regenerates the compound used in the first step. The eight steps of the cycle are a series of redox, dehydration, hydration, and decarboxylation reactions that produce two carbon dioxide molecules, one GTP/ATP, and the reduced carriers NADH and FADH2 (Figure 7.11). This is considered an aerobic pathway because the NADH and FADH2 produced must transfer their electrons to the next pathway in the system, which will use oxygen. If this transfer does not occur, the oxidation steps of the citric acid cycle also do not occur. Note that the citric acid cycle produces very little ATP directly and does not directly consume oxygen.
Figure 7.11 In the citric acid cycle, the acetyl group from acetyl CoA is attached to a four-carbon oxaloacetate molecule to form a six-carbon citrate molecule. Through a series of steps, citrate is oxidized, releasing two carbon dioxide molecules for each acetyl group fed into the cycle. In the process, three NAD+ molecules are reduced to NADH, one FAD molecule is reduced to FADH2, and one ATP or GTP (depending on the cell type) is produced (by substrate-level phosphorylation). Because the final product of the citric acid cycle is also the first reactant, the cycle runs continuously in the presence of sufficient reactants. Credit: Rao, A., Ryan, K., Tag, A., and Fletcher, S. Department of Biology, Texas A&M University.
Steps in the Citric Acid Cycle
Step 1. Prior to the first step, a transitional phase occurs during which pyruvic acid is converted to acetyl CoA. Then, the first step of the cycle begins: This condensation step combines the two-carbon acetyl group with a four-carbon oxaloacetate molecule to form a six-carbon molecule of citrate. CoA is bound to a sulfhydryl group (-SH) and diffuses away to eventually combine with another acetyl group. This step is irreversible because it is highly exergonic. The rate of this reaction is controlled by negative feedback and the amount of ATP available. If ATP levels increase, the rate of this reaction decreases. If ATP is in short supply, the rate increases.
Step 2. In step two, citrate loses one water molecule and gains another as citrate is converted into its isomer, isocitrate.
Step 3. In step three, isocitrate is oxidized, producing a five-carbon molecule, α-ketoglutarate, along with a molecule of CO2 and two electrons, which reduce NAD+ to NADH. This step is also regulated by negative feedback from ATP and NADH and a positive effect of ADP.
Step 4. Steps three and four are both oxidation and decarboxylation steps, which as we have seen, release electrons that reduce NAD+ to NADH and release carboxyl groups that form CO2 molecules. Alpha-ketoglutarate is the product of step three, and a succinyl group is the product of step four. CoA binds with the succinyl group to form succinyl CoA. The enzyme that catalyzes step four is regulated by feedback inhibition of ATP, succinyl CoA, and NADH.
Step 5. In step five, a carboxyl group is substituted for coenzyme A, and a high-energy bond is formed. This energy is used in substrate-level phosphorylation (during the conversion of the succinyl group to succinate) to form either guanine triphosphate (GTP) or ATP. There are two forms of the enzyme, called isoenzymes, for this step, depending upon the type of animal tissue in which they are found. One form is found in tissues that use large amounts of ATP, such as heart and skeletal muscle. This form produces ATP. The second form of the enzyme is found in tissues that have a high number of anabolic pathways, such as liver. This form produces GTP. GTP is energetically equivalent to ATP; however, its use is more restricted. In particular, protein synthesis primarily uses GTP.
Step 6. Step six is a dehydration process that converts succinate into fumarate. Two hydrogen atoms are transferred to FAD, reducing it to FADH2. (Note: the energy contained in the electrons of these hydrogens is insufficient to reduce NAD+ but adequate to reduce FAD.) Unlike NADH, this carrier remains attached to the enzyme and transfers the electrons to the electron transport chain directly. This process is made possible by the localization of the enzyme catalyzing this step inside the inner membrane of the mitochondrion.
Step 7. Water is added by hydrolysis to fumarate during step seven, and malate is produced. The last step in the citric acid cycle regenerates oxaloacetate by oxidizing malate. Another molecule of NADH is then produced in the process.
Link to Learning
Link to Learning
View an animation of the citric acid cycle here.
Products of the Citric Acid Cycle
Two carbon atoms come into the citric acid cycle from each acetyl group, representing four out of the six carbons of one glucose molecule. Two carbon dioxide molecules are released on each turn of the cycle; however, these do not necessarily contain the most recently added carbon atoms. The two acetyl carbon atoms will eventually be released on later turns of the cycle; thus, all six carbon atoms from the original glucose molecule are eventually incorporated into carbon dioxide. Each turn of the cycle forms three NADH molecules and one FADH2 molecule. These carriers will connect with the last portion of aerobic respiration, the electron transport chain, to produce ATP molecules. One GTP or ATP is also made in each cycle. Several of the intermediate compounds in the citric acid cycle can be used in synthesizing nonessential amino acids; therefore, the cycle is amphibolic (both catabolic and anabolic). | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.04%3A_Cellular_Respiration/2.4.04%3A_Oxidation_of_Pyruvate_and_the_Citric_Acid_Cycle.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Describe how electrons move through the electron transport chain and explain what happens to their energy levels during this process
• Explain how a proton (H+) gradient is established and maintained by the electron transport chain
You have just read about two pathways in glucose catabolism—glycolysis and the citric acid cycle—that generate ATP. Most of the ATP generated during the aerobic catabolism of glucose, however, is not generated directly from these pathways. Instead, it is derived from a process that begins by moving electrons through a series of electron carriers that undergo redox reactions. This process causes hydrogen ions to accumulate within the intermembranous space. Therefore, a concentration gradient forms in which hydrogen ions diffuse out of the intermembranous space into the mitochondrial matrix by passing through ATP synthase. The current of hydrogen ions powers the catalytic action of ATP synthase, which phosphorylates ADP, producing ATP.
Electron Transport Chain
The electron transport chain (Figure 7.12) is the last component of aerobic respiration and is the only part of glucose metabolism that uses atmospheric oxygen. Oxygen continuously diffuses into plant tissues (typically through stomata), as well as into fungi and bacteria; however, in animals, oxygen enters the body through a variety of respiratory systems. Electron transport is a series of redox reactions that resembles a relay race or bucket brigade in that electrons are passed rapidly from one component to the next, to the endpoint of the chain where the electrons reduce molecular oxygen and, along with associated protons, produces water. There are four complexes composed of proteins, labeled I through IV in Figure 7.12, and the aggregation of these four complexes, together with associated mobile, accessory electron carriers, is called the electron transport chain. The electron transport chain is present with multiple copies in the inner mitochondrial membrane of eukaryotes and within the plasma membrane of prokaryotes.
Figure 7.12 The electron transport chain is a series of electron transporters embedded in the inner mitochondrial membrane that shuttles electrons from NADH and FADH2 to molecular oxygen. In the process, protons are pumped from the mitochondrial matrix to the intermembrane space, and oxygen is reduced to form water.
Complex I
First, two electrons are carried to the first complex via NADH. This complex, labeled I, is composed of flavin mononucleotide (FMN) and an iron-sulfur (Fe-S)-containing protein. FMN, which is derived from vitamin B2 (also called riboflavin), is one of several prosthetic groups or cofactors in the electron transport chain. A prosthetic group is a nonprotein molecule required for the activity of a protein. Prosthetic groups are organic or inorganic, nonpeptide molecules bound to a protein that facilitate its function. Prosthetic groups include coenzymes, which are the prosthetic groups of enzymes. The enzyme in complex I is NADH dehydrogenase and is composed of 44 separate polypeptide chains. Complex I can pump four hydrogen ions across the membrane from the matrix into the intermembrane space, and it is in this way that the hydrogen ion gradient is established and maintained between the two compartments separated by the inner mitochondrial membrane.
Q and Complex II
Complex II directly receives FADH2—which does not pass through complex I. The compound connecting the first and second complexes to the third is ubiquinone B. The Q molecule is lipid soluble and freely moves through the hydrophobic core of the membrane. Once it is reduced (QH2), ubiquinone delivers its electrons to the next complex in the electron transport chain. Q receives the electrons derived from NADH from complex I, and the electrons derived from FADH2 from complex II. This enzyme and FADH2 form a small complex that delivers electrons directly to the electron transport chain, bypassing the first complex. Since these electrons bypass and thus do not energize the proton pump in the first complex, fewer ATP molecules are made from the FADH2 electrons. The number of ATP molecules ultimately obtained is directly proportional to the number of protons pumped across the inner mitochondrial membrane.
Complex III
The third complex is composed of cytochrome b—another Fe-S protein, a Rieske center (2Fe-2S center), and cytochrome c proteins. This complex is also called cytochrome oxidoreductase. Cytochrome proteins have a prosthetic group of heme. The heme molecule is similar to the heme in hemoglobin, but it carries electrons, not oxygen. As a result, the iron ion at its core is reduced and oxidized as it passes the electrons, fluctuating between different oxidation states: Fe++ (reduced) and Fe+++ (oxidized). The heme molecules in the cytochromes have slightly different characteristics due to the effects of the different proteins binding to them, giving slightly different characteristics to each complex. Complex III pumps protons through the membrane and passes its electrons to cytochrome c for transport to the fourth complex of proteins and enzymes. (Cytochrome c receives electrons from Q; however, whereas Q carries pairs of electrons, cytochrome c can accept only one at a time.)
Complex IV
The fourth complex is composed of cytochrome proteins c, a, and a3. This complex contains two heme groups (one in each of the two cytochromes, a, and a3) and three copper ions (a pair of CuA and one CuB in cytochrome a3). The cytochromes hold an oxygen molecule very tightly between the iron and copper ions until the oxygen is completely reduced by the gain of two electrons. The reduced oxygen then picks up two hydrogen ions from the surrounding medium to make water (H2O). The removal of the hydrogen ions from the system contributes to the ion gradient that forms the foundation for the process of chemiosmosis.
Chemiosmosis
In chemiosmosis, the free energy from the series of redox reactions just described is used to pump hydrogen ions (protons) across the mitochondrial membrane. The uneven distribution of H+ ions across the membrane establishes both concentration and electrical gradients (thus, an electrochemical gradient), owing to the hydrogen ions’ positive charge and their aggregation on one side of the membrane.
If the membrane were continuously open to simple diffusion by the hydrogen ions, the ions would tend to diffuse back across into the matrix, driven by the concentrations producing their electrochemical gradient. Recall that many ions cannot diffuse through the nonpolar regions of phospholipid membranes without the aid of ion channels. Similarly, hydrogen ions in the matrix space can only pass through the inner mitochondrial membrane by an integral membrane protein called ATP synthase (Figure 7.13). This complex protein acts as a tiny generator, turned by the force of the hydrogen ions diffusing through it, down their electrochemical gradient. The turning of parts of this molecular machine facilitates the addition of a phosphate to ADP, forming ATP, using the potential energy of the hydrogen ion gradient.
Visual Connection
Visual Connection
Figure 7.13 ATP synthase is a complex, molecular machine that uses a proton (H+) gradient to form ATP from ADP and inorganic phosphate (Pi). (Credit: modification of work by Klaus Hoffmeier)
Dinitrophenol (DNP) is an “uncoupler” that makes the inner mitochondrial membrane “leaky” to protons. It was used until 1938 as a weight-loss drug. What effect would you expect DNP to have on the change in pH across the inner mitochondrial membrane? Why do you think this might be an effective weight-loss drug?
Chemiosmosis (Figure 7.14) is used to generate 90 percent of the ATP made during aerobic glucose catabolism; it is also the method used in the light reactions of photosynthesis to harness the energy of sunlight in the process of photophosphorylation. Recall that the production of ATP using the process of chemiosmosis in mitochondria is called oxidative phosphorylation. The overall result of these reactions is the production of ATP from the energy of the electrons removed from hydrogen atoms. These atoms were originally part of a glucose molecule. At the end of the pathway, the electrons are used to reduce an oxygen molecule to oxygen ions. The extra electrons on the oxygen attract hydrogen ions (protons) from the surrounding medium, and water is formed. Thus, oxygen is the final electron acceptor in the electron transport chain.
Visual Connection
Visual Connection
Figure 7.14 In oxidative phosphorylation, the pH gradient formed by the electron transport chain is used by ATP synthase to form ATP. Credit: Rao, A., Ryan, K., Fletcher, S. and Tag, A. Department of Biology, Texas A&M University.
Cyanide inhibits cytochrome c oxidase, a component of the electron transport chain. If cyanide poisoning occurs, would you expect the pH of the intermembrane space to increase or decrease? What effect would cyanide have on ATP synthesis?
ATP Yield
The number of ATP molecules generated from the catabolism of glucose varies. For example, the number of hydrogen ions that the electron transport chain complexes can pump through the membrane varies between species. Another source of variance stems from the shuttle of electrons across the membranes of the mitochondria. (The NADH generated from glycolysis cannot easily enter mitochondria.) Thus, electrons are picked up on the inside of mitochondria by either NAD+ or FAD+. As you have learned earlier, these FAD+ molecules can transport fewer ions; consequently, fewer ATP molecules are generated when FAD+ acts as a carrier. NAD+ is used as the electron transporter in the liver and FAD+ acts in the brain.
Another factor that affects the yield of ATP molecules generated from glucose is the fact that intermediate compounds in these pathways are also used for other purposes. Glucose catabolism connects with the pathways that build or break down all other biochemical compounds in cells, and the result is somewhat messier than the ideal situations described thus far. For example, sugars other than glucose are fed into the glycolytic pathway for energy extraction. In addition, the five-carbon sugars that form nucleic acids are made from intermediates in glycolysis. Certain nonessential amino acids can be made from intermediates of both glycolysis and the citric acid cycle. Lipids, such as cholesterol and triglycerides, are also made from intermediates in these pathways, and both amino acids and triglycerides are broken down for energy through these pathways. Overall, in living systems, these pathways of glucose catabolism extract about 34 percent of the energy contained in glucose, with the remainder being released as heat. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.04%3A_Cellular_Respiration/2.4.05%3A_Oxidative_Phosphorylation.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Discuss the fundamental difference between anaerobic cellular respiration and fermentation
• Describe the type of fermentation that readily occurs in animal cells and the conditions that initiate that fermentation
In aerobic respiration, the final electron acceptor is an oxygen molecule, O2. If aerobic respiration occurs, then ATP will be produced using the energy of high-energy electrons carried by NADH or FADH2 to the electron transport chain. If aerobic respiration does not occur, NADH must be reoxidized to NAD+ for reuse as an electron carrier for the glycolytic pathway to continue. How is this done? Some living systems use an organic molecule as the final electron acceptor. Processes that use an organic molecule to regenerate NAD+ from NADH are collectively referred to as fermentation. n contrast, in some living systems the electron transport chain (ETC) uses an inorganic molecule as a final electron acceptor, which is called anaerobic cellular respiration. Both processes allow organisms to convert energy for their use in the absence of oxygen. Both methods are called anaerobic cellular respiration, in which organisms convert energy for their use in the absence of oxygen.
Anaerobic Cellular Respiration
Certain prokaryotes, including some species in the domains Bacteria and Archaea, use anaerobic respiration. For example, a group of archaeans called methanogens reduces carbon dioxide to methane to oxidize NADH. These microorganisms are found in soil and in the digestive tracts of ruminants, such as cows and sheep. Similarly, sulfate-reducing bacteria, most of which are anaerobic (Figure 7.15), reduce sulfate to hydrogen sulfide to regenerate NAD+ from NADH.
Figure 7.15 The green color seen in these coastal waters is from an eruption of hydrogen sulfide–producing bacteria. These anaerobic, sulfate-reducing bacteria release hydrogen sulfide gas as they decompose algae in the water. (credit: modification of work by NASA/Jeff Schmaltz, MODIS Land Rapid Response Team at NASA GSFC, Visible Earth Catalog of NASA images)
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Link to Learning
Visit this site to see anaerobic cellular respiration in action.
Lactic Acid Fermentation
The fermentation method used by animals and certain bacteria, such as those in yogurt, is lactic acid fermentation (Figure 7.16). This type of fermentation is used routinely in mammalian red blood cells, which do not have mitochondria, and in skeletal muscle that has an insufficient oxygen supply to allow aerobic respiration to continue (that is, in muscles used to the point of fatigue). In muscles, lactic acid accumulation must be removed by the blood circulation, and when the lactic acid loses a hydrogen, the resulting lactate is brought to the liver for further metabolism. The chemical reactions of lactic acid fermentation are the following:
$Pyruvic acid + NADH ↔ lactic acid + NAD + Pyruvic acid + NADH ↔ lactic acid + NAD +$
The enzyme used in this reaction is lactate dehydrogenase (LDH). The reaction can proceed in either direction, but the reaction from left to right is inhibited by acidic conditions. Such lactic acid accumulation was once believed to cause muscle stiffness, fatigue, and soreness, although more recent research disputes this hypothesis. Once the lactic acid has been removed from the muscle and circulated to the liver, it can be reconverted into pyruvic acid and further catabolized for energy.
Visual Connection
Visual Connection
Figure 7.16 During glycolysis, glucose is oxidized to pyruvate while NAD+ is reduced to NADH. Two molecules of ATP are also produced by substrate level phosphorylation. In the absence of oxygen in some cell types, fermentation allows the reduction of pyruvate to lactate and the reoxidation of NADH to NAD+. The regeneration of NAD+ allows glycolysis to continue to make ATP by substrate level phosphorylation. Credit: Rao, A., Ryan, K., Tag, A., and Fletcher, S. Department of Biology, Texas A&M University.
Tremetol, a metabolic poison found in the white snakeroot plant, prevents the metabolism of lactate. When cows eat this plant, tremetol is concentrated in the milk they produce. Humans who consume the milk can become seriously ill. Symptoms of this disease, which include vomiting, abdominal pain, and tremors, become worse after exercise. Why do you think this is the case?
Alcohol Fermentation
Another familiar fermentation process is alcohol fermentation (Figure 7.17), which produces ethanol. The first chemical reaction of alcohol fermentation is the following (CO2 does not participate in the second reaction):
$pyruvic acid + H + → CO 2 + acetaldehyde + NADH + H + → ethanol + NAD + pyruvic acid + H + → CO 2 + acetaldehyde + NADH + H + → ethanol + NAD +$
The first reaction is catalyzed by pyruvate decarboxylase, a cytoplasmic enzyme, with a coenzyme of thiamine pyrophosphate (TPP, derived from vitamin B1 and also called thiamine). A carboxyl group is removed from pyruvic acid, releasing carbon dioxide as a gas. The loss of carbon dioxide reduces the size of the molecule by one carbon, producing acetaldehyde. The second reaction is catalyzed by alcohol dehydrogenase to oxidize NADH to NAD+ and reduce acetaldehyde to ethanol. The fermentation of pyruvic acid by yeast produces the ethanol found in alcoholic beverages. Ethanol tolerance of yeast is variable, ranging from about 5 percent to 21 percent, depending on the yeast strain and environmental conditions.
Figure 7.17 Fermentation of grape juice into wine produces CO2 as a byproduct. Fermentation tanks have valves so that the pressure inside the tanks created by the carbon dioxide produced can be released.
Other Types of Fermentation
Other fermentation methods take place in bacteria. We should note that many prokaryotes are facultatively anaerobic. This means that they can switch between aerobic respiration and fermentation, depending on the availability of free oxygen. Certain prokaryotes, such as Clostridia, are obligate anaerobes. Obligate anaerobes live and grow in the absence of molecular oxygen. Oxygen is a poison to these microorganisms and kills them on exposure. We should also note that all forms of fermentation, except lactic acid fermentation, produce gas. The production of particular types of gas is used as an indicator of the fermentation of specific carbohydrates, which plays a role in the laboratory identification of the bacteria. Various methods of fermentation are used by assorted organisms to ensure an adequate supply of NAD+ for the sixth step in glycolysis. Without these pathways, this step would not occur, and ATP could not be harvested from the breakdown of glucose. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.04%3A_Cellular_Respiration/2.4.06%3A_Metabolism_without_Oxygen.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Discuss the ways in which carbohydrate metabolic pathways, glycolysis, and the citric acid cycle interrelate with protein and lipid metabolic pathways
• Explain why metabolic pathways are not considered closed systems
You have learned about the catabolism of glucose, which provides energy to living cells. But living things consume organic compounds other than glucose for food. How does a turkey sandwich end up as ATP in your cells? This happens because all of the catabolic pathways for carbohydrates, proteins, and lipids eventually connect into glycolysis and the citric acid cycle pathways (see Figure 7.19). Metabolic pathways should be thought of as porous and interconnecting—that is, substances enter from other pathways, and intermediates leave for other pathways. These pathways are not closed systems! Many of the substrates, intermediates, and products in a particular pathway are reactants in other pathways.
Connections of Other Sugars to Glucose Metabolism
Glycogen, a polymer of glucose, is an energy storage molecule in animals. When there is adequate ATP present, excess glucose is stored as glycogen in both liver and muscle cells. The glycogen will be hydrolyzed into glucose 1-phosphate monomers (G-1-P) if blood sugar levels drop. The presence of glycogen as a source of glucose allows ATP to be produced for a longer period of time during exercise. Glycogen is broken down into glucose-1-phosphate (G-1-P) and converted into glucose-6-phosphate (G-6-P) in both muscle and liver cells, and this product enters the glycolytic pathway.
Sucrose is a disaccharide with a molecule of glucose and a molecule of fructose bonded together with a glycosidic linkage. Fructose is one of the three “dietary” monosaccharides, along with glucose and galactose (part of the milk sugar disaccharide lactose), which are absorbed directly into the bloodstream during digestion. The catabolism of both fructose and galactose produces the same number of ATP molecules as glucose.
Connections of Proteins to Glucose Metabolism
Proteins are hydrolyzed by a variety of enzymes in cells. Most of the time, the amino acids are recycled into the synthesis of new proteins. If there are excess amino acids, however, or if the body is in a state of starvation, some amino acids will be shunted into the pathways of glucose catabolism (Figure 7.18). It is very important to note that each amino acid must have its amino group removed prior to entry into these pathways. The amino group is converted into ammonia. In mammals, the liver synthesizes urea from two ammonia molecules and a carbon dioxide molecule. Thus, urea is the principal waste product in mammals, produced from the nitrogen originating in amino acids, and it leaves the body in urine. It should be noted that amino acids can be synthesized from the intermediates and reactants in the cellular respiration cycle.
Figure 7.18 The carbon skeletons of certain amino acids (indicated in boxes) derived from proteins can feed into the citric acid cycle. (credit: modification of work by Mikael Häggström)
Connections of Lipid and Glucose Metabolisms
The lipids connected to the glucose pathway include cholesterol and triglycerides. Cholesterol is a lipid that contributes to cell membrane flexibility and is a precursor of steroid hormones. The synthesis of cholesterol starts with acetyl groups and proceeds in only one direction. The process cannot be reversed.
Triglycerides—made from the bonding of glycerol and three fatty acids—are a form of long-term energy storage in animals. Animals can make most of the fatty acids they need. Triglycerides can be both made and broken down through parts of the glucose catabolism pathways. Glycerol can be phosphorylated to glycerol-3-phosphate, which continues through glycolysis. Fatty acids are catabolized in a process called beta-oxidation, which takes place in the matrix of the mitochondria and converts their fatty acid chains into two-carbon units of acetyl groups. The acetyl groups are picked up by CoA to form acetyl CoA that proceeds into the citric acid cycle.
Figure 7.19 Glycogen from the liver and muscles, as well as other carbohydrates, hydrolyzed into glucose-1-phosphate, together with fats and proteins, can feed into the catabolic pathways for carbohydrates.
Evolution Connection
Evolution Connection
Pathways of Photosynthesis and Cellular MetabolismThe processes of photosynthesis and cellular metabolism consist of several very complex pathways. It is generally thought that the first cells arose in an aqueous environment—a “soup” of nutrients—possibly on the surface of some porous clays, perhaps in warm marine environments. If these cells reproduced successfully and their numbers climbed steadily, it follows that the cells would begin to deplete the nutrients from the medium in which they lived as they shifted the nutrients into the components of their own bodies. This hypothetical situation would have resulted in natural selection favoring those organisms that could exist by using the nutrients that remained in their environment and by manipulating these nutrients into materials upon which they could survive. Selection would favor those organisms that could extract maximal value from the nutrients to which they had access.
An early form of photosynthesis developed that harnessed the sun’s energy using water as a source of hydrogen atoms, but this pathway did not produce free oxygen (anoxygenic photosynthesis). (Another type of anoxygenic photosynthesis did not produce free oxygen because it did not use water as the source of hydrogen ions; instead, it used materials such as hydrogen sulfide and consequently produced sulfur). It is thought that glycolysis developed at this time and could take advantage of the simple sugars being produced but that these reactions were unable to fully extract the energy stored in the carbohydrates. The development of glycolysis probably predated the evolution of photosynthesis, as it was well suited to extract energy from materials spontaneously accumulating in the “primeval soup.” A later form of photosynthesis used water as a source of electrons and hydrogen and generated free oxygen. Over time, the atmosphere became oxygenated, but not before the oxygen released oxidized metals in the ocean and created a “rust” layer in the sediment, permitting the dating of the rise of the first oxygenic photosynthesizers. Living things adapted to exploit this new atmosphere that allowed aerobic respiration as we know it to evolve. When the full process of oxygenic photosynthesis developed and the atmosphere became oxygenated, cells were finally able to use the oxygen expelled by photosynthesis to extract considerably more energy from the sugar molecules using the citric acid cycle and oxidative phosphorylation. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.04%3A_Cellular_Respiration/2.4.07%3A_Connections_of_Carbohydrate_Protein_and_Lipid_Metabolic_Pathways.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Describe how feedback inhibition would affect the production of an intermediate or product in a pathway
• Identify the mechanism that controls the rate of the transport of electrons through the electron transport chain
Cellular respiration must be regulated in order to provide balanced amounts of energy in the form of ATP. The cell also must generate a number of intermediate compounds that are used in the anabolism and catabolism of macromolecules. Without controls, metabolic reactions would quickly come to a standstill as the forward and backward reactions reached a state of equilibrium. Resources would be used inappropriately. A cell does not need the maximum amount of ATP that it can make all the time: At times, the cell needs to shunt some of the intermediates to pathways for amino acid, protein, glycogen, lipid, and nucleic acid production. In short, the cell needs to control its metabolism.
Regulatory Mechanisms
A variety of mechanisms is used to control cellular respiration. Some type of control exists at each stage of glucose metabolism. Access of glucose to the cell can be regulated using the GLUT (glucose transporter) proteins that transport glucose (Figure 7.20). Different forms of the GLUT protein control passage of glucose into the cells of specific tissues.
Figure 7.20 GLUT4 is a glucose transporter that is stored in vesicles. A cascade of events that occurs upon insulin binding to a receptor in the plasma membrane causes GLUT4-containing vesicles to fuse with the plasma membrane so that glucose may be transported into the cell.
Some reactions are controlled by having two different enzymes—one each for the two directions of a reversible reaction. Reactions that are catalyzed by only one enzyme can go to equilibrium, stalling the reaction. In contrast, if two different enzymes (each specific for a given direction) are necessary for a reversible reaction, the opportunity to control the rate of the reaction increases, and equilibrium is not reached.
A number of enzymes involved in each of the pathways—in particular, the enzyme catalyzing the first committed reaction of the pathway—are controlled by attachment of a molecule to an allosteric site on the protein. The molecules most commonly used in this capacity are the nucleotides ATP, ADP, AMP, NAD+, and NADH. These regulators—allosteric effectors—may increase or decrease enzyme activity, depending on the prevailing conditions. The allosteric effector alters the steric structure of the enzyme, usually affecting the configuration of the active site. This alteration of the protein’s (the enzyme’s) structure either increases or decreases its affinity for its substrate, with the effect of increasing or decreasing the rate of the reaction. The attachment signals to the enzyme. This binding can increase or decrease the enzyme’s activity, providing a feedback mechanism. This feedback type of control is effective as long as the chemical affecting it is attached to the enzyme. Once the overall concentration of the chemical decreases, it will diffuse away from the protein, and the control is relaxed.
Control of Catabolic Pathways
Enzymes, proteins, electron carriers, and pumps that play roles in glycolysis, the citric acid cycle, and the electron transport chain tend to catalyze nonreversible reactions. In other words, if the initial reaction takes place, the pathway is committed to proceeding with the remaining reactions. Whether a particular enzyme activity is released depends upon the energy needs of the cell (as reflected by the levels of ATP, ADP, and AMP).
Glycolysis
The control of glycolysis begins with the first enzyme in the pathway, hexokinase (Figure 7.21). This enzyme catalyzes the phosphorylation of glucose, which helps to prepare the compound for cleavage in a later step. The presence of the negatively charged phosphate in the molecule also prevents the sugar from leaving the cell. When hexokinase is inhibited, glucose diffuses out of the cell and does not become a substrate for the respiration pathways in that tissue. The product of the hexokinase reaction is glucose-6-phosphate, which accumulates when a later enzyme, phosphofructokinase, is inhibited.
Figure 7.21 The glycolysis pathway is primarily regulated at the three key enzymatic steps (1, 3, and 10) as indicated. Note that the first two steps that are regulated occur early in the pathway and involve hydrolysis of ATP.
Phosphofructokinase is the main enzyme controlled in glycolysis. High levels of ATP or citrate or a lower, more acidic pH decreases the enzyme’s activity. An increase in citrate concentration can occur because of a blockage in the citric acid cycle. Fermentation, with its production of organic acids such as lactic acid, frequently accounts for the increased acidity in a cell; however, the products of fermentation do not typically accumulate in cells.
The last step in glycolysis is catalyzed by pyruvate kinase. The pyruvate produced can proceed to be catabolized or converted into the amino acid alanine. If no more energy is needed and alanine is in adequate supply, the enzyme is inhibited. The enzyme’s activity is increased when fructose-1,6-bisphosphate levels increase. (Recall that fructose-1,6-bisphosphate is an intermediate in the first half of glycolysis.) The regulation of pyruvate kinase involves phosphorylation by a kinase (pyruvate kinase), resulting in a less-active enzyme. Dephosphorylation by a phosphatase reactivates it. Pyruvate kinase is also regulated by ATP (a negative allosteric effect).
If more energy is needed, more pyruvate will be converted into acetyl CoA through the action of pyruvate dehydrogenase. If either acetyl groups or NADH accumulates, there is less need for the reaction, and the rate decreases. Pyruvate dehydrogenase is also regulated by phosphorylation: a kinase phosphorylates it to form an inactive enzyme, and a phosphatase reactivates it. The kinase and the phosphatase are also regulated.
Citric Acid Cycle
The citric acid cycle is controlled through the enzymes that catalyze the reactions that make the first two molecules of NADH (Figure 7.11). These enzymes are isocitrate dehydrogenase and α-ketoglutarate dehydrogenase. When adequate ATP and NADH levels are available, the rates of these reactions decrease. When more ATP is needed, as reflected in rising ADP levels, the rate increases. Alpha-ketoglutarate dehydrogenase will also be affected by the levels of succinyl CoA—a subsequent intermediate in the cycle—causing a decrease in activity. A decrease in the rate of operation of the pathway at this point is not necessarily negative, as the increased levels of the α-ketoglutarate not used by the citric acid cycle can be used by the cell for amino acid (glutamate) synthesis.
Electron Transport Chain
Specific enzymes of the electron transport chain are unaffected by feedback inhibition, but the rate of electron transport through the pathway is affected by the levels of ADP and ATP. Greater ATP consumption by a cell is indicated by a buildup of ADP. As ATP usage decreases, the concentration of ADP decreases, and now, ATP begins to build up in the cell. This change in the relative concentration of ADP to ATP triggers the cell to slow down the electron transport chain.
Link to Learning
Link to Learning
Visit this site to see an animation of the electron transport chain and ATP synthesis.
For a summary of feedback controls in cellular respiration, see Table 7.1.
Summary of Feedback Controls in Cellular Respiration
Pathway Enzyme affected Elevated levels of effector Effect on pathway activity
glycolysis hexokinase glucose-6-phosphate decrease
phosphofructokinase low-energy charge (ATP, AMP), fructose-6-phosphate via fructose-2,6-bisphosphate increase
high-energy charge (ATP, AMP), citrate, acidic pH decrease
pyruvate kinase fructose-1,6-bisphosphate increase
high-energy charge (ATP, AMP), alanine decrease
pyruvate to acetyl CoA conversion pyruvate dehydrogenase ADP, pyruvate increase
acetyl CoA, ATP, NADH decrease
citric acid cycle isocitrate dehydrogenase ADP increase
ATP, NADH decrease
α-ketoglutarate dehydrogenase calcium ions, ADP increase
ATP, NADH, succinyl CoA decrease
electron transport chain ADP increase
ATP decrease
Table 7.1 | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.04%3A_Cellular_Respiration/2.4.08%3A_Regulation_of_Cellular_Respiration.txt |
acetyl CoA
combination of an acetyl group derived from pyruvic acid and coenzyme A, which is made from pantothenic acid (a B-group vitamin)
aerobic respiration
process in which organisms convert energy in the presence of oxygen
anaerobic
process that does not use oxygen
anaerobic cellular respiration
process in which organisms convert energy for their use in the absence of oxygen
ATP synthase
(also F1F0 ATP synthase) membrane-embedded protein complex that adds a phosphate to ADP with energy from protons diffusing through it
chemiosmosis
process in which there is a production of adenosine triphosphate (ATP) in cellular metabolism by the involvement of a proton gradient across a membrane
citric acid cycle
(also Krebs cycle) series of enzyme-catalyzed chemical reactions of central importance in all living cells for extraction of energy from carbohydrates
dephosphorylation
removal of a phosphate group from a molecule
fermentation
process of regenerating NAD+ with either an inorganic or organic compound serving as the final electron acceptor; occurs in the absence of oxygen
GLUT protein
integral membrane protein that transports glucose
glycolysis
process of breaking glucose into two three-carbon molecules with the production of ATP and NADH
isomerase
enzyme that converts a molecule into its isomer
Krebs cycle
(also citric acid cycle) alternate name for the citric acid cycle, named after Hans Krebs, who first identified the steps in the pathway in the 1930s in pigeon flight muscles; see citric acid cycle
oxidative phosphorylation
production of ATP using the process of chemiosmosis in the presence of oxygen
phosphorylation
addition of a high-energy phosphate to a compound, usually a metabolic intermediate, a protein, or ADP
prosthetic group
(also prosthetic cofactor) molecule bound to a protein that facilitates the function of the protein
pyruvate
three-carbon sugar that can be decarboxylated and oxidized to make acetyl CoA, which enters the citric acid cycle under aerobic conditions; the end product of glycolysis
redox reaction
chemical reaction that consists of the coupling of an oxidation reaction and a reduction reaction
substrate-level phosphorylation
production of ATP from ADP using the excess energy from a chemical reaction and a phosphate group from a reactant
TCA cycle
(also citric acid cycle) alternate name for the citric acid cycle, named after the group name for citric acid, tricarboxylic acid (TCA); see citric acid cycle
ubiquinone
soluble electron transporter in the electron transport chain that connects the first or second complex to the third
2.4.10: Chapter Summary
7.1 Energy in Living Systems
ATP functions as the energy currency for cells. It allows the cell to store energy briefly and transport it within the cell to support endergonic chemical reactions. The structure of ATP is that of an RNA nucleotide with three phosphates attached. As ATP is used for energy, a phosphate group or two are detached, and either ADP or AMP is produced. Energy derived from glucose catabolism is used to convert ADP into ATP. When ATP is used in a reaction, the third phosphate is temporarily attached to a substrate in a process called phosphorylation. The two processes of ATP regeneration that are used in conjunction with glucose catabolism are substrate-level phosphorylation and oxidative phosphorylation through the process of chemiosmosis.
7.2 Glycolysis
Glycolysis is the first pathway within the cytoplasm used in the breakdown of glucose to extract energy. It was probably one of the earliest metabolic pathways to evolve and is used by nearly all of the organisms on Earth. Glycolysis consists of two parts: The first part prepares the six-carbon ring of glucose for cleavage into two three-carbon sugars. ATP is invested in the process during this half to energize the separation. The second half of glycolysis extracts ATP and high-energy electrons from hydrogen atoms and attaches them to NAD+. Two ATP molecules are invested in the first half and four ATP molecules are formed by substrate phosphorylation during the second half. This produces a net gain of two ATP and two NADH molecules for the cell.
7.3 Oxidation of Pyruvate and the Citric Acid Cycle
In the presence of oxygen, pyruvate is transformed into an acetyl group attached to a carrier molecule of coenzyme A. The resulting acetyl CoA can enter several pathways, but most often, the acetyl group is delivered to the citric acid cycle for further catabolism. During the conversion of pyruvate into the acetyl group, a molecule of carbon dioxide and two high-energy electrons are removed. The carbon dioxide accounts for two (conversion of two pyruvate molecules) of the six carbons of the original glucose molecule. The electrons are picked up by NAD+, and the NADH carries the electrons to a later pathway for ATP production. At this point, the glucose molecule that originally entered cellular respiration has been completely oxidized. Chemical potential energy stored within the glucose molecule has been transferred to electron carriers or has been used to synthesize a few ATPs.
The citric acid cycle is a series of redox and decarboxylation reactions that removes high-energy electrons and carbon dioxide. The electrons, temporarily stored in molecules of NADH and FADH2, are used to generate ATP in a subsequent pathway. One molecule of either GTP or ATP is produced by substrate-level phosphorylation on each turn of the cycle. There is no comparison of the cyclic pathway with a linear one.
7.4 Oxidative Phosphorylation
The electron transport chain is the portion of aerobic respiration that uses free oxygen as the final electron acceptor of the electrons removed from the intermediate compounds in glucose catabolism. The electron transport chain is composed of four large, multiprotein complexes embedded in the inner mitochondrial membrane and two small diffusible electron carriers shuttling electrons between them. The electrons are passed through a series of redox reactions, with a small amount of free energy used at three points to transport hydrogen ions across a membrane. This process contributes to the gradient used in chemiosmosis. The electrons passing through the electron transport chain gradually lose energy. High-energy electrons donated to the chain by either NADH or FADH2 complete the chain, as low-energy electrons reduce oxygen molecules and form water. The level of free energy of the electrons drops from about 60 kcal/mol in NADH or 45 kcal/mol in FADH2 to about 0 kcal/mol in water. The end products of the electron transport chain are water and ATP. A number of intermediate compounds of the citric acid cycle can be diverted into the anabolism of other biochemical molecules, such as nonessential amino acids, sugars, and lipids. These same molecules can serve as energy sources for the glucose pathways.
7.5 Metabolism without Oxygen
If NADH cannot be oxidized through aerobic respiration, another electron acceptor is used. Most organisms will use some form of fermentation to accomplish the regeneration of NAD+, ensuring the continuation of glycolysis. The regeneration of NAD+ in fermentation is not accompanied by ATP production; therefore, the potential of NADH to produce ATP using an electron transport chain is not utilized.
7.6 Connections of Carbohydrate, Protein, and Lipid Metabolic Pathways
The breakdown and synthesis of carbohydrates, proteins, and lipids connect with the pathways of glucose catabolism. The simple sugars are galactose, fructose, glycogen, and pentose. These are catabolized during glycolysis. The amino acids from proteins connect with glucose catabolism through pyruvate, acetyl CoA, and components of the citric acid cycle. Cholesterol synthesis starts with acetyl groups, and the components of triglycerides come from glycerol-3-phosphate from glycolysis and acetyl groups produced in the mitochondria from pyruvate.
7.7 Regulation of Cellular Respiration
Cellular respiration is controlled by a variety of means. The entry of glucose into a cell is controlled by the transport proteins that aid glucose passage through the cell membrane. Most of the control of the respiration processes is accomplished through the control of specific enzymes in the pathways. This is a type of negative feedback mechanism, turning the enzymes off. The enzymes respond most often to the levels of the available nucleosides ATP, ADP, AMP, NAD+, and FAD. Other intermediates of the pathway also affect certain enzymes in the systems. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.04%3A_Cellular_Respiration/2.4.09%3A_Key_Terms.txt |
1.
Figure 7.13 Dinitrophenol (DNP) is an "uncoupler" that makes the inner mitochondrial membrane "leaky" to protons. It was used until 1938 as a weight-loss drug. What effect would you expect DNP to have on the change in pH across the inner mitochondrial membrane? Why do you think this might be an effective weight-loss drug?
2.
Figure 7.14 Cyanide inhibits cytochrome c oxidase, a component of the electron transport chain. If cyanide poisoning occurs, would you expect the pH of the intermembrane space to increase or decrease? What effect would cyanide have on ATP synthesis?
3.
Figure 7.16 Tremetol, a metabolic poison found in the white snake root plant, prevents the metabolism of lactate. When cows eat this plant, tremetol is concentrated in the milk they produce. Humans who consume the milk can become seriously ill. Symptoms of this disease, which include vomiting, abdominal pain, and tremors, become worse after exercise. Why do you think this is the case?
2.4.12: Review Questions
4.
The energy currency used by cells is ________.
1. ATP
2. ADP
3. AMP
4. adenosine
5.
A reducing chemical reaction ________.
1. reduces the compound to a simpler form
2. adds an electron to the substrate
3. removes a hydrogen atom from the substrate
4. is a catabolic reaction
6.
During the second half of glycolysis, what occurs?
1. ATP is used up.
2. Fructose is split in two.
3. ATP is made.
4. Glucose becomes fructose.
7.
What is removed from pyruvate during its conversion into an acetyl group?
1. oxygen
2. ATP
3. B vitamin
4. carbon dioxide
8.
What do the electrons added to NAD+ do?
1. They become part of a fermentation pathway.
2. They go to another pathway for ATP production.
3. They energize the entry of the acetyl group into the citric acid cycle.
4. They are converted to NADP.
9.
GTP or ATP is produced during the conversion of ________.
1. isocitrate into α-ketoglutarate
2. succinyl CoA into succinate
3. fumarate into malate
4. malate into oxaloacetate
10.
How many NADH molecules are produced on each turn of the citric acid cycle?
1. one
2. two
3. three
4. four
11.
What compound receives electrons from NADH?
1. FMN
2. ubiquinone
3. cytochrome c1
4. oxygen
12.
Chemiosmosis involves ________.
1. the movement of electrons across the cell membrane
2. the movement of hydrogen atoms across a mitochondrial membrane
3. the movement of hydrogen ions across a mitochondrial membrane
4. the movement of glucose through the cell membrane
13.
Which of the following fermentation methods can occur in animal skeletal muscles?
1. lactic acid fermentation
2. alcohol fermentation
3. mixed acid fermentation
4. propionic fermentation
14.
A major connection for sugars in glycolysis is ________.
1. glucose-6-phosphate
2. fructose-1,6-bisphosphate
3. dihydroxyacetone phosphate
4. phosphoenolpyruvate
15.
Beta-oxidation is ________.
1. the breakdown of sugars
2. the assembly of sugars
3. the breakdown of fatty acids
4. the removal of amino groups from amino acids
16.
The effect of high levels of ADP is to ________ in cellular respiration.
1. increase the activity of specific enzymes
2. decrease the activity of specific enzymes
3. have no effect on the activity of specific enzymes
4. slow down the pathway
17.
The control of which enzyme exerts the most control on glycolysis?
1. hexokinase
2. phosphofructokinase
3. glucose-6-phosphatase
4. aldolase
2.4.13: Critical Thinking Questions
18.
Why is it beneficial for cells to use ATP rather than energy directly from the bonds of carbohydrates? What are the greatest drawbacks to harnessing energy directly from the bonds of several different compounds?
19.
Nearly all organisms on Earth carry out some form of glycolysis. How does this fact support or not support the assertion that glycolysis is one of the oldest metabolic pathways?
20.
Because they lose their mitochondria during development, red blood cells cannot perform aerobic respiration; however, they do perform glycolysis in the cytoplasm. Why do all cells need an energy source, and what would happen if glycolysis were blocked in a red blood cell?
21.
What is the primary difference between a circular pathway and a linear pathway?
22.
How do the roles of ubiquinone and cytochrome c differ from the roles of the other components of the electron transport chain?
23.
What accounts for the different number of ATP molecules that are formed through cellular respiration?
24.
What is the primary difference between fermentation and anaerobic respiration?
25.
Would you describe metabolic pathways as inherently wasteful or inherently economical? Why?
26.
How does citrate from the citric acid cycle affect glycolysis?
27.
Why might negative feedback mechanisms be more common than positive feedback mechanisms in living cells? | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.04%3A_Cellular_Respiration/2.4.11%3A_Visual_Connection_Questions.txt |
The processes in all organisms—from bacteria to humans—require energy. To get this energy, many organisms access stored energy by eating, that is, by ingesting other organisms. But where does the stored energy in food originate? All of this energy can be traced back to photosynthesis.
• 2.5.1: Introduction
Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that can later be released to fuel the organisms' activities (energy transformation).
• 2.5.2: Overview of Photosynthesis
Photosynthesis is essential to all life on earth; both plants and animals depend on it. It is the only biological process that can capture energy that originates in outer space (sunlight) and convert it into chemical compounds (carbohydrates) that every organism uses to power its metabolism. In brief, the energy of sunlight is captured and used to energize electrons, which are then stored in the covalent bonds of sugar molecules.
• 2.5.3: The Light-Dependent Reactions of Photosynthesis
Like all other forms of kinetic energy, light can travel, change form, and be harnessed to do work. In the case of photosynthesis, light energy is converted into chemical energy, which photoautotrophs use to build carbohydrate molecules. However, autotrophs only use a few specific components of sunlight.
• 2.5.4: Using Light Energy to Make Organic Molecules
The products of the light-dependent reactions, ATP and NADPH, have lifespans in the range of millionths of seconds, whereas the products of the light-independent reactions (carbohydrates and other forms of reduced carbon) can survive for hundreds of millions of years. The carbohydrate molecules made will have a backbone of carbon atoms. Where does the carbon come from? It comes from carbon dioxide, the gas that is a waste product of respiration in microbes, fungi, plants, and animals.
• 2.5.5: Key Terms
• 2.5.6: Chapter Summary
• 2.5.7: Visual Connection Questions
• 2.5.8: Review Questions
• 2.5.9: Critical Thinking Questions
Thumbnail: Plant cells (bounded by purple walls) filled with chloroplasts (green), which are the site of photosynthesis. (CC BY-SA 3.0; Kristian Peters).
2.05: Photosynthesis
Figure 8.1 This world map shows Earth’s distribution of photosynthetic activity determined by chlorophyll a concentrations. On land, chlorophyll is evident from terrestrial plants, and within oceanic zones, from chlorophyll from phytoplankton. (credit: modification of work by SeaWiFS Project, NASA/Goddard Space Flight Center and ORBIMAGE)
The metabolic processes in all organisms—from bacteria to humans—require energy. To get this energy, many organisms access stored energy by eating, that is, by ingesting other organisms. But where does the stored energy in food originate? All of this energy can be traced back to photosynthesis.
2.5.02: Overview of Photosynthesis
Learning Objectives
By the end of this section, you will be able to do the following:
• Explain the significance of photosynthesis to other living organisms
• Describe the main structures involved in photosynthesis
• Identify the substrates and products of photosynthesis
Photosynthesis is essential to all life on earth; both plants and animals depend on it. It is the only biological process that can capture energy that originates from sunlight and converts it into chemical compounds (carbohydrates) that every organism uses to power its metabolism. It is also a source of oxygen necessary for many living organisms. In brief, the energy of sunlight is “captured” to energize electrons, whose energy is then stored in the covalent bonds of sugar molecules. How long lasting and stable are those covalent bonds? The energy extracted today by the burning of coal and petroleum products represents sunlight energy captured and stored by photosynthesis 350 to 200 million years ago during the Carboniferous Period.
Plants, algae, and a group of bacteria called cyanobacteria are the only organisms capable of performing photosynthesis (Figure 8.2). Because they use light to manufacture their own food, they are called photoautotrophs (literally, “self-feeders using light”). Other organisms, such as animals, fungi, and most other bacteria, are termed heterotrophs (“other feeders”), because they must rely on the sugars produced by photosynthetic organisms for their energy needs. A third very interesting group of bacteria synthesize sugars, not by using sunlight’s energy, but by extracting energy from inorganic chemical compounds. For this reason, they are referred to as chemoautotrophs.
Figure 8.2 Photoautotrophs including (a) plants, (b) algae, and (c) cyanobacteria synthesize their organic compounds via photosynthesis using sunlight as an energy source. Cyanobacteria and planktonic algae can grow over enormous areas in water, at times completely covering the surface. In a (d) deep sea vent, chemoautotrophs, such as these (e) thermophilic bacteria, capture energy from inorganic compounds to produce organic compounds. The ecosystem surrounding the vents has a diverse array of animals, such as tubeworms, crustaceans, and octopuses that derive energy from the bacteria. (credit a: modification of work by Steve Hillebrand, U.S. Fish and Wildlife Service; credit b: modification of work by "eutrophication&hypoxia"/Flickr; credit c: modification of work by NASA; credit d: University of Washington, NOAA; credit e: modification of work by Mark Amend, West Coast and Polar Regions Undersea Research Center, UAF, NOAA)
The importance of photosynthesis is not just that it can capture sunlight’s energy. After all, a lizard sunning itself on a cold day can use the sun’s energy to warm up in a process called behavioral thermoregulation. In contrast, photosynthesis is vital because it evolved as a way to store the energy from solar radiation (the “photo-” part) to energy in the carbon-carbon bonds of carbohydrate molecules (the “-synthesis” part). Those carbohydrates are the energy source that heterotrophs use to power the synthesis of ATP via respiration. Therefore, photosynthesis powers 99 percent of Earth’s ecosystems. When a top predator, such as a wolf, preys on a deer (Figure 8.3), the wolf is at the end of an energy path that went from nuclear reactions on the surface of the sun, to visible light, to photosynthesis, to vegetation, to deer, and finally to the wolf.
Figure 8.3 The energy stored in carbohydrate molecules from photosynthesis passes through the food chain. The predator that eats these deer receives a portion of the energy that originated in the photosynthetic vegetation that the deer consumed. (credit: modification of work by Steve VanRiper, U.S. Fish and Wildlife Service)
Main Structures and Summary of Photosynthesis
Photosynthesis is a multi-step process that requires specific wavelengths of visible sunlight, carbon dioxide (which is low in energy), and water as substrates (Figure 8.4). After the process is complete, it releases oxygen and produces glyceraldehyde-3-phosphate (G3P), as well as simple carbohydrate molecules (high in energy) that can then be converted into glucose, sucrose, or any of dozens of other sugar molecules. These sugar molecules contain energy and the energized carbon that all living things need to survive.
Figure 8.4 Photosynthesis uses solar energy, carbon dioxide, and water to produce energy-storing carbohydrates. Oxygen is generated as a waste product of photosynthesis.
The following is the chemical equation for photosynthesis (Figure 8.5):
Figure 8.5 The basic equation for photosynthesis is deceptively simple. In reality, the process takes place in many steps involving intermediate reactants and products. Glucose, the primary energy source in cells, is made from two three-carbon G3Ps.
Although the equation looks simple, the many steps that take place during photosynthesis are actually quite complex. Before learning the details of how photoautotrophs turn sunlight into food, it is important to become familiar with the structures involved.
Basic Photosynthetic Structures
In plants, photosynthesis generally takes place in leaves, which consist of several layers of cells. The process of photosynthesis occurs in a middle layer called the mesophyll. The gas exchange of carbon dioxide and oxygen occurs through small, regulated openings called stomata (singular: stoma), which also play roles in the regulation of gas exchange and water balance. The stomata are typically located on the underside of the leaf, which helps to minimize water loss due to high temperatures on the upper surface of the leaf. Each stoma is flanked by guard cells that regulate the opening and closing of the stomata by swelling or shrinking in response to osmotic changes.
In all autotrophic eukaryotes, photosynthesis takes place inside an organelle called a chloroplast. For plants, chloroplast-containing cells exist mostly in the mesophyll. Chloroplasts have a double membrane envelope (composed of an outer membrane and an inner membrane), and are ancestrally derived from ancient free-living cyanobacteria. Within the chloroplast are stacked, disc-shaped structures called thylakoids. Embedded in the thylakoid membrane is chlorophyll, a pigment (molecule that absorbs light) responsible for the initial interaction between light and plant material, and numerous proteins that make up the electron transport chain. The thylakoid membrane encloses an internal space called the thylakoid lumen. As shown in Figure 8.6, a stack of thylakoids is called a granum, and the liquid-filled space surrounding the granum is called stroma or “bed” (not to be confused with stoma or “mouth,” an opening on the leaf epidermis).
Visual Connection
Visual Connection
Figure 8.6 Photosynthesis takes place in chloroplasts, which have an outer membrane and an inner membrane. Stacks of thylakoids called grana form a third membrane layer.
On a hot, dry day, the guard cells of plants close their stomata to conserve water. What impact will this have on photosynthesis?
The Two Parts of Photosynthesis
Photosynthesis takes place in two sequential stages: the light-dependent reactions and the light-independent reactions. In the light-dependent reactions, energy from sunlight is absorbed by chlorophyll and that energy is converted into stored chemical energy. In the light-independent reactions, the chemical energy harvested during the light-dependent reactions drives the assembly of sugar molecules from carbon dioxide. Therefore, although the light-independent reactions do not use light as a reactant, they require the products of the light-dependent reactions to function. In addition, however, several enzymes of the light-independent reactions are activated by light. The light-dependent reactions utilize certain molecules to temporarily store the energy: These are referred to as energy carriers. The energy carriers that move energy from light-dependent reactions to light-independent reactions can be thought of as “full” because they are rich in energy. After the energy is released, the “empty” energy carriers return to the light-dependent reaction to obtain more energy. Figure 8.7 illustrates the components inside the chloroplast where the light-dependent and light-independent reactions take place.
Figure 8.7 Photosynthesis takes place in two stages: light-dependent reactions and the Calvin cycle. Light-dependent reactions, which take place in the thylakoid membrane, use light energy to make ATP and NADPH. The Calvin cycle, which takes place in the stroma, uses energy derived from these compounds to make G3P from CO2. Credit: Rao, A., Ryan, K., Fletcher, S., Hawkins, A. and Tag, A. Texas A&M University.
Link to Learning
Link to Learning
Click the link to learn more about photosynthesis.
Everyday Connection
Everyday Connection
Photosynthesis at the Grocery Store
Figure 8.8 Foods that humans consume originate from photosynthesis. (credit: Associação Brasileira de Supermercados)
Major grocery stores in the United States are organized into departments, such as dairy, meats, produce, bread, cereals, and so forth. Each aisle (Figure 8.8) contains hundreds, if not thousands, of different products for customers to buy and consume.
Although there is a large variety, each item ultimately can be linked back to photosynthesis. Meats and dairy link, because the animals were fed plant-based foods. The breads, cereals, and pastas come largely from starchy grains, which are the seeds of photosynthesis-dependent plants. What about desserts and drinks? All of these products contain sugar—sucrose is a plant product, a disaccharide, a carbohydrate molecule, which is built directly from photosynthesis. Moreover, many items are less obviously derived from plants: For instance, paper goods are generally plant products, and many plastics (abundant as products and packaging) are derived from “algae” (unicellular plant-like organisms, and cyanobacteria). Virtually every spice and flavoring in the spice aisle was produced by a plant as a leaf, root, bark, flower, fruit, or stem. Ultimately, photosynthesis connects to every meal and every food a person consumes. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.05%3A_Photosynthesis/2.5.01%3A_Introduction.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Explain how plants absorb energy from sunlight
• Describe short and long wavelengths of light
• Describe how and where photosynthesis takes place within a plant
How can light energy be used to make food? When a person turns on a lamp, electrical energy becomes light energy. Like all other forms of kinetic energy, light can travel, change form, and be harnessed to do work. In the case of photosynthesis, light energy is converted into chemical energy, which photoautotrophs use to build basic carbohydrate molecules (Figure 8.9). However, autotrophs only use a few specific wavelengths of sunlight.
Figure 8.9 Photoautotrophs can capture visible light energy in specific wavelengths from the sun, converting it into the chemical energy used to build food molecules. (credit: Gerry Atwell)
What Is Light Energy?
The sun emits an enormous amount of electromagnetic radiation (solar energy in a spectrum from very short gamma rays to very long radio waves). Humans can see only a tiny fraction of this energy, which we refer to as “visible light.” The manner in which solar energy travels is described as waves. Scientists can determine the amount of energy of a wave by measuring its wavelength (shorter wavelengths are more powerful than longer wavelengths)—the distance between consecutive crest points of a wave. Therefore, a single wave is measured from two consecutive points, such as from crest to crest or from trough to trough (Figure 8.10).
Figure 8.10 The wavelength of a single wave is the distance between two consecutive points of similar position (two crests or two troughs) along the wave.
Visible light constitutes only one of many types of electromagnetic radiation emitted from the sun and other stars. Scientists differentiate the various types of radiant energy from the sun within the electromagnetic spectrum. The electromagnetic spectrum is the range of all possible frequencies of radiation (Figure 8.11). The difference between wavelengths relates to the amount of energy carried by them.
Figure 8.11 The sun emits energy in the form of electromagnetic radiation. This radiation exists at different wavelengths, each of which has its own characteristic energy. All electromagnetic radiation, including visible light, is characterized by its wavelength.
Each type of electromagnetic radiation travels at a particular wavelength. The longer the wavelength, the less energy it carries. Short, tight waves carry the most energy. This may seem illogical, but think of it in terms of a piece of moving heavy rope. It takes little effort by a person to move a rope in long, wide waves. To make a rope move in short, tight waves, a person would need to apply significantly more energy.
The electromagnetic spectrum (Figure 8.11) shows several types of electromagnetic radiation originating from the sun, including X-rays and ultraviolet (UV) rays. The higher-energy waves can penetrate tissues and damage cells and DNA, which explains why both X-rays and UV rays can be harmful to living organisms.
Absorption of Light
Light energy initiates the process of photosynthesis when pigments absorb specific wavelengths of visible light. Organic pigments, whether in the human retina or the chloroplast thylakoid, have a narrow range of energy levels that they can absorb. Energy levels lower than those represented by red light are insufficient to raise an orbital electron to an excited (quantum) state. Energy levels higher than those in blue light will physically tear the molecules apart, in a process called bleaching. Our retinal pigments can only “see” (absorb) wavelengths between 700 nm and 400 nm of light, a spectrum that is therefore called visible light. For the same reasons, plants, pigment molecules absorb only light in the wavelength range of 700 nm to 400 nm; plant physiologists refer to this range for plants as photosynthetically active radiation.
The visible light seen by humans as white light actually exists in a rainbow of colors. Certain objects, such as a prism or a drop of water, disperse white light to reveal the colors to the human eye. The visible light portion of the electromagnetic spectrum shows the rainbow of colors, with violet and blue having shorter wavelengths, and therefore higher energy. At the other end of the spectrum toward red, the wavelengths are longer and have lower energy (Figure 8.13).
Figure 8.12 Light energy can excite electrons. When a photon of light energy interacts with an electron, the electron may absorb the energy and jump from its lowest energy ground state to an excited state. Credit: Rao, A. and Ryan, K. Department of Biology, Texas A&M University.
Figure 8.13 The colors of visible light do not carry the same amount of energy. Violet has the shortest wavelength and therefore carries the most energy, whereas red has the longest wavelength and carries the least amount of energy. (credit: modification of work by NASA)
Understanding Pigments
Different kinds of pigments exist, and each absorbs only specific wavelengths (colors) of visible light. Pigments reflect or transmit the wavelengths they cannot absorb, making them appear a mixture of the reflected or transmitted light colors.
Chlorophylls and carotenoids are the two major classes of photosynthetic pigments found in plants and algae; each class has multiple types of pigment molecules. There are five major chlorophylls: a, b, c and d and a related molecule found in prokaryotes called bacteriochlorophyll. Chlorophyll a and chlorophyll b are found in higher plant chloroplasts and will be the focus of the following discussion.
With dozens of different forms, carotenoids are a much larger group of pigments. The carotenoids found in fruit—such as the red of tomato (lycopene), the yellow of corn seeds (zeaxanthin), or the orange of an orange peel (β-carotene)—are used as advertisements to attract seed dispersers. In photosynthesis, carotenoids function as photosynthetic pigments that are very efficient molecules for the disposal of excess energy. When a leaf is exposed to full sun, the light-dependent reactions are required to process an enormous amount of energy; if that energy is not handled properly, it can do significant damage. Therefore, many carotenoids reside in the thylakoid membrane, absorb excess energy, and safely dissipate that energy as heat.
Each type of pigment can be identified by the specific pattern of wavelengths it absorbs from visible light: This is termed the absorption spectrum. The graph in Figure 8.14 shows the absorption spectra for chlorophyll a, chlorophyll b, and a type of carotenoid pigment called β-carotene (which absorbs blue and green light). Notice how each pigment has a distinct set of peaks and troughs, revealing a highly specific pattern of absorption. Chlorophyll a absorbs wavelengths from either end of the visible spectrum (blue and red), but not green. Because green is reflected or transmitted, chlorophyll appears green. Carotenoids absorb in the short-wavelength blue region, and reflect the longer yellow, red, and orange wavelengths.
Figure 8.14 (a) Chlorophyll a, (b) chlorophyll b, and (c) β-carotene are hydrophobic organic pigments found in the thylakoid membrane. Chlorophyll a and b, which are identical except for the part indicated in the red box, are responsible for the green color of leaves. β-carotene is responsible for the orange color in carrots. Each pigment has (d) a unique absorbance spectrum. Credit: Rao, A., Ryan, K., Tag, A., Fletcher, S. and Hawkins, A. Department of Biology, Texas A&M University.
Many photosynthetic organisms have a mixture of pigments, and by using these pigments, the organism can absorb energy from a wider range of wavelengths. Not all photosynthetic organisms have full access to sunlight. Some organisms grow underwater where light intensity and quality decrease and change with depth. Other organisms grow in competition for light. Plants on the rainforest floor must be able to absorb any bit of light that comes through, because the taller trees absorb most of the sunlight and scatter the remaining solar radiation (Figure 8.15).
Figure 8.15 Plants that commonly grow in the shade have adapted to low levels of light by changing the relative concentrations of their chlorophyll pigments. (credit: Jason Hollinger)
When studying a photosynthetic organism, scientists can determine the types of pigments present by generating absorption spectra. An instrument called a spectrophotometer can differentiate which wavelengths of light a substance can absorb. Spectrophotometers measure transmitted light and compute from it the absorption. By extracting pigments from leaves and placing these samples into a spectrophotometer, scientists can identify which wavelengths of light an organism can absorb. Additional methods for the identification of plant pigments include various types of chromatography that separate the pigments by their relative affinities to solid and mobile phases.
How Light-Dependent Reactions Work
The overall function of light-dependent reactions is to convert solar energy into chemical energy in the form of NADPH and ATP. This chemical energy supports the light-independent reactions and fuels the assembly of sugar molecules. The light-dependent reactions are depicted in Figure 8.16. Protein complexes and pigment molecules work together to produce NADPH and ATP. The numbering of the photosystems is derived from the order in which they were discovered, not in the order of the transfer of electrons.
Figure 8.16 A photosystem consists of 1) a light-harvesting complex and 2) a reaction center. Pigments in the light-harvesting complex pass light energy to two special chlorophyll a molecules in the reaction center. The light excites an electron from the chlorophyll a pair, which passes to the primary electron acceptor. The excited electron must then be replaced. Credit: Rao, A., Ryan, K., Fletcher, S. and Hawkins, A. Department of Biology, Texas A&M University.
The actual step that converts light energy into chemical energy takes place in a multiprotein complex called a photosystem, two types of which are found embedded in the thylakoid membrane: photosystem II (PSII) and photosystem I (PSI) (Figure 8.17). The two complexes differ on the basis of what they oxidize (that is, the source of the low-energy electron supply) and what they reduce (the place to which they deliver their energized electrons).
Both photosystems have the same basic structure; a number of antenna proteins to which the chlorophyll molecules are bound surround the reaction center where the photochemistry takes place. Each photosystem is serviced by the light-harvesting complex, which passes energy from sunlight to the reaction center; it consists of multiple antenna proteins that contain a mixture of 300 to 400 chlorophyll a and b molecules as well as other pigments like carotenoids. The absorption of a single photon or distinct quantity or “packet” of light by any of the chlorophylls pushes that molecule into an excited state. In short, the light energy has now been captured by biological molecules but is not stored in any useful form yet. The energy is transferred from chlorophyll to chlorophyll until eventually (after about a millionth of a second), it is delivered to the reaction center. Up to this point, only energy has been transferred between molecules, not electrons.
Visual Connection
Visual Connection
Figure 8.17 In the photosystem II (PSII) reaction center, energy from sunlight is used to extract electrons from water. The electrons travel through the chloroplast electron transport chain to photosystem I (PSI), which reduces NADP+ to NADPH. The electron transport chain moves protons across the thylakoid membrane into the lumen. At the same time, splitting of water adds protons to the lumen, and reduction of NADPH removes protons from the stroma. The net result is a low pH in the thylakoid lumen, and a high pH in the stroma. ATP synthase uses this electrochemical gradient to make ATP. Credit: Rao, A., Ryan, K., Fletcher, S. Department of Biology, Texas A&M University.
What is the initial source of electrons for the chloroplast electron transport chain?
1. water
2. oxygen
3. carbon dioxide
4. NADPH
The reaction center contains a pair of chlorophyll a molecules with a special property. Those two chlorophylls can undergo oxidation upon excitation; they can actually give up an electron in a process called a photoact. It is at this step in the reaction center during photosynthesis that light energy is converted into an excited electron. All of the subsequent steps involve getting that electron onto the energy carrier NADPH for delivery to the Calvin cycle where the electron is deposited onto carbon for long-term storage in the form of a carbohydrate. PSII and PSI are two major components of the photosynthetic electron transport chain, which also includes the cytochrome complex. The cytochrome complex, an enzyme composed of two protein complexes, transfers the electrons from the carrier molecule plastoquinone (Pq) to the protein plastocyanin (Pc), thus enabling both the transfer of protons across the thylakoid membrane and the transfer of electrons from PSII to PSI.
The reaction center of PSII (called P680) delivers its high-energy electrons, one at the time, to the primary electron acceptor, and through the electron transport chain (Pq to cytochrome complex to plastocyanine) to PSI. P680’s missing electron is replaced by extracting a low-energy electron from water; thus, water is “split” during this stage of photosynthesis, and PSII is re-reduced after every photoact. Splitting one H2O molecule releases two electrons, two hydrogen atoms, and one atom of oxygen. However, splitting two molecules is required to form one molecule of diatomic O2 gas. About 10 percent of the oxygen is used by mitochondria in the leaf to support oxidative phosphorylation. The remainder escapes to the atmosphere where it is used by aerobic organisms to support respiration.
As electrons move through the proteins that reside between PSII and PSI, they lose energy. This energy is used to move hydrogen atoms from the stromal side of the membrane to the thylakoid lumen. Those hydrogen atoms, plus the ones produced by splitting water, accumulate in the thylakoid lumen and will be used synthesize ATP in a later step. Because the electrons have lost energy prior to their arrival at PSI, they must be re-energized by PSI, hence, another photon is absorbed by the PSI antenna. That energy is relayed to the PSI reaction center (called P700). P700 is oxidized and sends a high-energy electron to NADP+ to form NADPH. Thus, PSII captures the energy to create proton gradients to make ATP, and PSI captures the energy to reduce NADP+ into NADPH. The two photosystems work in concert, in part, to guarantee that the production of NADPH will roughly equal the production of ATP. Other mechanisms exist to fine-tune that ratio to exactly match the chloroplast’s constantly changing energy needs.
Generating an Energy Carrier: ATP
As in the intermembrane space of the mitochondria during cellular respiration, the buildup of hydrogen ions inside the thylakoid lumen creates a concentration gradient. The passive diffusion of hydrogen ions from high concentration (in the thylakoid lumen) to low concentration (in the stroma) is harnessed to create ATP, just as in the electron transport chain of cellular respiration. The ions build up energy because of diffusion and because they all have the same electrical charge, repelling each other.
To release this energy, hydrogen ions will rush through any opening, similar to water jetting through a hole in a dam. In the thylakoid, that opening is a passage through a specialized protein channel called the ATP synthase. The energy released by the hydrogen ion stream allows ATP synthase to attach a third phosphate group to ADP, which forms a molecule of ATP (Figure 8.17). The flow of hydrogen ions through ATP synthase is called chemiosmosis because the ions move from an area of high to an area of low concentration through a semi-permeable structure of the thylakoid.
Link to Learning
Link to Learning
Visit this site and click through the animation to view the process of photosynthesis within a leaf. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.05%3A_Photosynthesis/2.5.03%3A_The_Light-Dependent_Reactions_of_Photosynthesis.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Describe the Calvin cycle
• Define carbon fixation
• Explain how photosynthesis works in the energy cycle of all living organisms
After the energy from the sun is converted into chemical energy and temporarily stored in ATP and NADPH molecules, the cell has the fuel needed to build carbohydrate molecules for long-term energy storage. The products of the light-dependent reactions, ATP and NADPH, have lifespans in the range of millionths of seconds, whereas the products of the light-independent reactions (carbohydrates and other forms of reduced carbon) can survive almost indefinitely. The carbohydrate molecules made will have a backbone of carbon atoms. But where does the carbon come from? It comes from carbon dioxide—the gas that is a waste product of respiration in microbes, fungi, plants, and animals.
The Calvin Cycle
In plants, carbon dioxide (CO2) enters the leaves through stomata, where it diffuses over short distances through intercellular spaces until it reaches the mesophyll cells. Once in the mesophyll cells, CO2 diffuses into the stroma of the chloroplast—the site of light-independent reactions of photosynthesis. These reactions actually have several names associated with them. Another term, the Calvin cycle, is named for the man who discovered it, and because these reactions function as a cycle. Others call it the Calvin-Benson cycle to include the name of another scientist involved in its discovery. The most outdated name is “dark reaction,” because light is not directly required (Figure 8.18). However, the term dark reaction can be misleading because it implies incorrectly that the reaction only occurs at night or is independent of light, which is why most scientists and instructors no longer use it.
Figure 8.18 Light reactions harness energy from the sun to produce chemical bonds, ATP, and NADPH. These energy-carrying molecules are made in the stroma where carbon fixation takes place. Credit: Rao, A., Ryan, K., Tag, A., Fletcher, S. and Hawkins, A. Department of Biology, Texas A&M University.
The light-independent reactions of the Calvin cycle can be organized into three basic stages: fixation, reduction, and regeneration.
Stage 1: Fixation
In the stroma, in addition to CO2, two other components are present to initiate the light-independent reactions: an enzyme called ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), and three molecules of ribulose bisphosphate (RuBP), as shown in Figure 8.19. RuBP has five atoms of carbon, flanked by two phosphates.
Visual Connection
Visual Connection
Figure 8.19 The Calvin cycle has three stages. In stage 1, the enzyme RuBisCO incorporates carbon dioxide into an organic molecule, 3-PGA. In stage 2, the organic molecule is reduced using electrons supplied by NADPH. In stage 3, RuBP, the molecule that starts the cycle, is regenerated so that the cycle can continue. Only one carbon dioxide molecule is incorporated at a time, so the cycle must be completed three times to produce a single three-carbon G3P molecule, and six times to produce a six-carbon glucose molecule. Credit: Rao, A., Ryan, K., Tag, A., Fletcher, S. and Hawkins, A. Department of Biology, Texas A&M University.
Which of the following statements is true?
1. In photosynthesis, oxygen, carbon dioxide, ATP, and NADPH are reactants. G3P and water are products.
2. In photosynthesis, chlorophyll, water, and carbon dioxide are reactants. G3P and oxygen are products.
3. In photosynthesis, water, carbon dioxide, ATP, and NADPH are reactants. RuBP and oxygen are products.
4. In photosynthesis, water and carbon dioxide are reactants. G3P and oxygen are products.
RuBisCO catalyzes a reaction between CO2 and RuBP. For each CO2 molecule that reacts with one RuBP, two molecules of another compound 3-phospho glyceric acid (3-PGA) form. PGA has three carbons and one phosphate. Each turn of the cycle involves only one RuBP and one carbon dioxide and forms two molecules of 3-PGA. The number of carbon atoms remains the same, as the atoms move to form new bonds during the reactions (3 C atoms from 3CO2 + 15 C atoms from 3RuBP = 18 C atoms in 6 molecules of 3-PGA). This process is called carbon fixation, because CO2 is “fixed” from an inorganic form into organic molecules.
Stage 2: Reduction
ATP and NADPH are used to convert the six molecules of 3-PGA into six molecules of a chemical called glyceraldehyde 3-phosphate (G3P). That is a reduction reaction because it involves the gain of electrons by 3-PGA. (Recall that a reduction is the gain of an electron by an atom or molecule.) Six molecules of both ATP and NADPH are used. For ATP, energy is released with the loss of the terminal phosphate atom, converting it into ADP; for NADPH, both energy and a hydrogen atom are lost, converting it into NADP+. Both of these molecules return to the nearby light-dependent reactions to be reused and re-energized.
Stage 3: Regeneration
Interestingly, at this point, only one of the G3P molecules leaves the Calvin cycle and is sent to the cytoplasm to contribute to the formation of other compounds needed by the plant. Because the G3P exported from the chloroplast has three carbon atoms, it takes three “turns” of the Calvin cycle to fix enough net carbon to export one G3P. But each turn makes two G3Ps, thus three turns make six G3Ps. One is exported while the remaining five G3P molecules remain in the cycle and are used to regenerate RuBP, which enables the system to prepare for more CO2 to be fixed. Three more molecules of ATP are used in these regeneration reactions.
Link to Learning
Link to Learning
This link leads to an animation of photosynthesis and the Calvin cycle.
Evolution Connection
Evolution Connection
PhotosynthesisDuring the evolution of photosynthesis, a major shift occurred from the bacterial type of photosynthesis that involves only one photosystem and is typically anoxygenic (does not generate oxygen) into modern oxygenic (does generate oxygen) photosynthesis, employing two photosystems. This modern oxygenic photosynthesis is used by many organisms—from giant tropical leaves in the rainforest to tiny cyanobacterial cells—and the process and components of this photosynthesis remain largely the same. Photosystems absorb light and use electron transport chains to convert energy into the chemical energy of ATP and NADH. The subsequent light-independent reactions then assemble carbohydrate molecules with this energy.
In the harsh dry heat of the desert, plants must conserve and use every drop of water to survive. Because stomata must open to allow for the uptake of CO2, water escapes from the leaf during active photosynthesis. Desert plants have evolved processes to conserve water and deal with harsh conditions. Mechanisms to capture and store CO2 allows plants to adapt to living with less water. Some plants such as cacti (Figure 8.20) can prepare materials for photosynthesis during the night by a temporary carbon fixation/storage process, because opening the stomata at this time conserves water due to cooler temperatures. During the day cacti use the captured CO2 for photosynthesis, and keep their stomata closed.
Figure 8.20 The harsh conditions of the desert have led plants like these cacti to evolve variations of the light-independent reactions of photosynthesis. These variations increase the efficiency of water usage, helping to conserve water and energy. (credit: Piotr Wojtkowski)
The Energy Flow
Whether the organism is a bacterium, plant, or animal, all living things access energy by breaking down carbohydrate and other carbon-rich organic molecules. But if plants make carbohydrate molecules, why would they need to break them down, especially when it has been shown that the gas organisms release as a “waste product” (CO2) acts as a substrate for the formation of more food in photosynthesis? Remember, living things need energy to perform life functions. In addition, an organism can either make its own food or eat another organism—either way, the food still needs to be broken down. Finally, in the process of breaking down food, called cellular respiration, heterotrophs release needed energy and produce “waste” in the form of CO2 gas.
However, in nature, there is no such thing as “waste.” Every single atom of matter and energy is conserved, recycled over and over infinitely. Substances change form or move from one type of molecule to another, but their constituent atoms never disappear (Figure 8.22).
In reality, CO2 is no more a form of waste than oxygen is wasteful to photosynthesis. Both are byproducts of reactions that move on to other reactions. Photosynthesis absorbs light energy to build carbohydrates in chloroplasts, and aerobic cellular respiration releases energy by using oxygen to metabolize carbohydrates in the cytoplasm and mitochondria. Both processes use electron transport chains to capture the energy necessary to drive other reactions. These two powerhouse processes, photosynthesis and cellular respiration, function in biological, cyclical harmony to allow organisms to access life-sustaining energy that originates millions of miles away in a burning star humans call the sun.
Figure 8.21 Connection between Photosynthesis and Respiration Photosynthesis in chloroplasts is the process by which light energy is converted to chemical energy and stored in sugars. Initially, the light energy is converted into chemical energy during ATP synthesis in a process that gives off oxygen. The energy in ATP is then used to reduce CO2 to simple sugars. In contrast, cellular respiration is the process in which the chemical energy stored in sugars is converted into ATP, a source of chemical energy that can be used by the rest of the cell. In the process of converting the energy stored in the sugars to ATP, CO2 is released and oxygen is consumed. Credit: Rao, A., Ryan, and Tag, A. Department of Biology, Texas A&M University.
Figure 8.22 Photosynthesis consumes carbon dioxide and produces oxygen. Aerobic respiration consumes oxygen and produces carbon dioxide. These two processes play an important role in the carbon cycle. (credit: modification of work by Stuart Bassil) | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.05%3A_Photosynthesis/2.5.04%3A_Using_Light_Energy_to_Make_Organic_Molecules.txt |
absorption spectrum
range of wavelengths of electromagnetic radiation absorbed by a given substance
antenna protein
pigment molecule that directly absorbs light and transfers the energy absorbed to other pigment molecules
Calvin cycle
light-independent reactions of photosynthesis that convert carbon dioxide from the atmosphere into carbohydrates using the energy and reducing power of ATP and NADPH
carbon fixation
process of converting inorganic CO2 gas into organic compounds
carotenoid
photosynthetic pigment (yellow-orange-red) that functions to dispose of excess energy
chemoautotroph
organism that can build organic molecules using energy derived from inorganic chemicals instead of sunlight
chlorophyll a
form of chlorophyll that absorbs violet-blue and red light and consequently has a bluish-green color; the only pigment molecule that performs the photochemistry by getting excited and losing an electron to the electron transport chain
chlorophyll b
accessory pigment that absorbs blue and red-orange light and consequently has a yellowish-green tint
chloroplast
organelle in which photosynthesis takes place
cytochrome complex
group of reversibly oxidizable and reducible proteins that forms part of the electron transport chain between photosystem II and photosystem I
electromagnetic spectrum
range of all possible frequencies of radiation
electron transport chain
group of proteins between PSII and PSI that pass energized electrons and use the energy released by the electrons to move hydrogen ions against their concentration gradient into the thylakoid lumen
granum
stack of thylakoids located inside a chloroplast
heterotroph
organism that consumes organic substances or other organisms for food
light harvesting complex
complex that passes energy from sunlight to the reaction center in each photosystem; it consists of multiple antenna proteins that contain a mixture of 300 to 400 chlorophyll a and b molecules as well as other pigments like carotenoids
light-dependent reaction
first stage of photosynthesis where certain wavelengths of the visible light are absorbed to form two energy-carrying molecules (ATP and NADPH)
light-independent reaction
second stage of photosynthesis, through which carbon dioxide is used to build carbohydrate molecules using energy from ATP and NADPH
mesophyll
middle layer of chlorophyll-rich cells in a leaf
P680
reaction center of photosystem II
P700
reaction center of photosystem I
photoact
ejection of an electron from a reaction center using the energy of an absorbed photon
photoautotroph
organism capable of producing its own organic compounds from sunlight
photon
distinct quantity or “packet” of light energy
photosystem
group of proteins, chlorophyll, and other pigments that are used in the light-dependent reactions of photosynthesis to absorb light energy and convert it into chemical energy
photosystem I
integral pigment and protein complex in thylakoid membranes that uses light energy to transport electrons from plastocyanin to NADP+ (which becomes reduced to NADPH in the process)
photosystem II
integral protein and pigment complex in thylakoid membranes that transports electrons from water to the electron transport chain; oxygen is a product of PSII
pigment
molecule that is capable of absorbing certain wavelengths of light and reflecting others (which accounts for its color)
primary electron acceptor
pigment or other organic molecule in the reaction center that accepts an energized electron from the reaction center
reaction center
complex of chlorophyll molecules and other organic molecules that is assembled around a special pair of chlorophyll molecules and a primary electron acceptor; capable of undergoing oxidation and reduction
reduction
gain of electron(s) by an atom or molecule
spectrophotometer
instrument that can measure transmitted light and compute the absorption
stoma
opening that regulates gas exchange and water evaporation between leaves and the environment, typically situated on the underside of leaves
stroma
fluid-filled space surrounding the grana inside a chloroplast where the light-independent reactions of photosynthesis take place
thylakoid
disc-shaped, membrane-bound structure inside a chloroplast where the light-dependent reactions of photosynthesis take place; stacks of thylakoids are called grana
thylakoid lumen
aqueous space bound by a thylakoid membrane where protons accumulate during light-driven electron transport
wavelength
distance between consecutive points of equal position (two crests or two troughs) of a wave in a graphic representation; inversely proportional to the energy of the radiation | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.05%3A_Photosynthesis/2.5.05%3A_Key_Terms.txt |
8.1 Overview of Photosynthesis
The process of photosynthesis transformed life on Earth. By harnessing energy from the sun, the evolution of photosynthesis allowed living things access to enormous amounts of energy. Because of photosynthesis, living things gained access to sufficient energy that allowed them to build new structures and achieve the biodiversity evident today.
Only certain organisms (photoautotrophs), can perform photosynthesis; they require the presence of chlorophyll, a specialized pigment that absorbs certain wavelengths of the visible spectrum and can capture energy from sunlight. Photosynthesis uses carbon dioxide and water to assemble carbohydrate molecules and release oxygen as a byproduct into the atmosphere. Eukaryotic autotrophs, such as plants and algae, have organelles called chloroplasts in which photosynthesis takes place, and starch accumulates. In prokaryotes, such as cyanobacteria, the process is less localized and occurs within folded membranes, extensions of the plasma membrane, and in the cytoplasm.
8.2 The Light-Dependent Reactions of Photosynthesis
The pigments of the first part of photosynthesis, the light-dependent reactions, absorb energy from sunlight. A photon strikes the antenna pigments of photosystem II to initiate photosynthesis. The energy travels to the reaction center that contains chlorophyll a and then to the electron transport chain, which pumps hydrogen ions into the thylakoid interior. This action builds up a high concentration of hydrogen ions. The hydrogen ions flow through ATP synthase during chemiosmosis to form molecules of ATP, which are used for the formation of sugar molecules in the second stage of photosynthesis. Photosystem I absorbs a second photon, which results in the formation of an NADPH molecule, another energy and reducing carrier for the light-independent reactions.
8.3 Using Light Energy to Make Organic Molecules
Using the energy carriers formed in the first steps of photosynthesis, the light-independent reactions, or the Calvin cycle, take in CO2 from the atmosphere. An enzyme, RuBisCO, catalyzes a reaction with CO2 and another organic compound, RuBP. After three cycles, a three-carbon molecule of G3P leaves the cycle to become part of a carbohydrate molecule. The remaining G3P molecules stay in the cycle to be regenerated into RuBP, which is then ready to react with more CO2. Photosynthesis forms an energy cycle with the process of cellular respiration. Because plants contain both chloroplasts and mitochondria, they rely upon both photosynthesis and respiration for their ability to function in both the light and dark, and to be able to interconvert essential metabolites.
2.5.07: Visual Connection Questions
1.
Figure 8.6 On a hot, dry day, the guard cells of plants close their stomata to conserve water. What impact will this have on photosynthesis?
2.
Figure 8.17 What is the initial source of electrons for the chloroplast electron transport chain?
1. Water
2. Oxygen
3. Carbon dioxide
4. NADPH
3.
Figure 8.19 Which of the following statements is true?
1. In photosynthesis, oxygen, carbon dioxide, ATP, and NADPH are reactants. G3P and water are products.
2. In photosynthesis, chlorophyll, water, and carbon dioxide are reactants. G3P and oxygen are products.
3. In photosynthesis, water, carbon dioxide, ATP, and NADPH are reactants. RuBP and oxygen are products.
4. In photosynthesis, water and carbon dioxide are reactants. G3P and oxygen are products. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.05%3A_Photosynthesis/2.5.06%3A_Chapter_Summary.txt |
4.
Which of the following components is not used by both plants and cyanobacteria to carry out photosynthesis?
1. chloroplasts
2. chlorophyll
3. carbon dioxide
4. water
5.
What two main products result from photosynthesis?
1. oxygen and carbon dioxide
2. chlorophyll and oxygen
3. sugars/carbohydrates and oxygen
4. sugars/carbohydrates and carbon dioxide
6.
In which compartment of the plant cell do the light-independent reactions of photosynthesis take place?
1. thylakoid
2. stroma
3. outer membrane
4. mesophyll
7.
Which statement about thylakoids in eukaryotes is not correct?
1. Thylakoids are assembled into stacks.
2. Thylakoids exist as a maze of folded membranes.
3. The space surrounding thylakoids is called stroma.
4. Thylakoids contain chlorophyll.
8.
Predict the end result if a chloroplast’s light-independent enzymes developed a mutation that prevented them from activating in response to light.
1. G3P accumulation
2. ATP and NADPH accumulation
3. Water accumulation
4. Carbon dioxide depletion
9.
How are the NADPH and G3P molecules made during photosynthesis similar?
1. They are both end products of photosynthesis.
2. They are both substrates for photosynthesis.
3. They are both produced from carbon dioxide.
4. They both store energy in chemical bonds.
10.
Which of the following structures is not a component of a photosystem?
1. ATP synthase
2. antenna molecule
3. reaction center
4. primary electron acceptor
11.
How many photons does it take to fully reduce one molecule of NADP+ to NADPH?
1. 1
2. 2
3. 4
4. 8
12.
Which complex is not involved in the establishment of conditions for ATP synthesis?
1. photosystem I
2. ATP synthase
3. photosystem II
4. cytochrome complex
13.
From which component of the light-dependent reactions does NADPH form most directly?
1. photosystem II
2. photosystem I
3. cytochrome complex
4. ATP synthase
14.
Three of the same species of plant are each grown under a different colored light for the same amount of time. Plant A is grown under blue light, Plant B is grown under green light, and Plant C is grown under orange light. Assuming the plants use only chlorophyll a and chlorophyll b for photosynthesis, what would be the predicted order of the plants from most growth to least growth?
1. A, C, B
2. A, B, C
3. C, A, B
4. B, A, C
15.
Plants containing only chlorophyll b are exposed to radiation with the following wavelengths: 10nm (x-rays), 450nm (blue light), 670nm (red light), and 800nm (infrared light). Which plants harness the most energy for photosynthesis?
1. X-ray irradiated plants
2. Blue light irradiated plants
3. Red light irradiated plants
4. Infrared irradiated plants
16.
Which molecule must enter the Calvin cycle continually for the light-independent reactions to take place?
1. RuBisCO
2. RuBP
3. 3-PGA
4. CO2
17.
Which order of molecular conversions is correct for the Calvin cycle?
1. $RuBP + G3P → 3-PGA → sugar RuBP + G3P → 3-PGA → sugar$
2. $RuBisCO → CO 2 → RuBP → G3P RuBisCO → CO 2 → RuBP → G3P$
3. $RuBP + CO 2 → [ RuBisCO ] 3-PGA → G3P RuBP + CO 2 → [ RuBisCO ] 3-PGA → G3P$
4. $CO 2 → 3-PGA → RuBP → G3P CO 2 → 3-PGA → RuBP → G3P$
18.
Where in eukaryotic cells does the Calvin cycle take place?
1. thylakoid membrane
2. thylakoid lumen
3. chloroplast stroma
4. granum
19.
Which statement correctly describes carbon fixation?
1. the conversion of CO2 into an organic compound
2. the use of RuBisCO to form 3-PGA
3. the production of carbohydrate molecules from G3P
4. the formation of RuBP from G3P molecules
5. the use of ATP and NADPH to reduce CO2
20.
If four molecules of carbon dioxide enter the Calvin cycle (four “turns” of the cycle), how many G3P molecules are produced and how many are exported?
1. 4 G3P made, 1 G3P exported
2. 4 G3P made, 2 G3P exported
3. 8 G3P made, 1 G3P exported
4. 8 G3P made, 4 G3P exported
2.5.09: Critical Thinking Questions
21.
What is the overall outcome of the light reactions in photosynthesis?
22.
Why are carnivores, such as lions, dependent on photosynthesis to survive?
23.
Why are energy carriers thought of as either “full” or “empty”?
24.
Describe how the grey wolf population would be impacted by a volcanic eruption that spewed a dense ash cloud that blocked sunlight in a section of Yellowstone National Park.
25.
How does the closing of the stomata limit photosynthesis?
26.
Describe the pathway of electron transfer from photosystem II to photosystem I in light-dependent reactions.
27.
What are the roles of ATP and NADPH in photosynthesis?
28.
How and why would the end products of photosynthesis be changed if a plant had a mutation that eliminated its photosystem II complex?
29.
Why is the third stage of the Calvin cycle called the regeneration stage?
30.
Which part of the light-independent reactions would be affected if a cell could not produce the enzyme RuBisCO?
31.
Why does it take three turns of the Calvin cycle to produce G3P, the initial product of photosynthesis?
32.
Imagine a sealed terrarium containing a plant and a beetle. How does each organism provide resources for the other? Could each organism survive if it was the only living thing in the terrarium? Why or why not?
33.
Compare the flow of energy with the flow of nutrients in a closed, sunny ecosystem consisting of a giraffe and a tree. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.05%3A_Photosynthesis/2.5.08%3A_Review_Questions.txt |
While the necessity for cellular communication in larger organisms seems obvious, even single-celled organisms communicate with each other. Yeast cells signal each other to aid mating. Some forms of bacteria coordinate their actions in order to form large complexes called biofilms or to organize the production of toxins to remove competing organisms. The ability of cells to communicate through chemical signals originated in single cells and was essential for the evolution of multicellular organisms. The efficient and error-free function of communication systems is vital for all life as we know it.
• 2.6.1: Introduction
In multicellular organisms, cells send and receive chemical messages constantly to coordinate the actions of distant organs, tissues, and cells. The ability to send messages quickly and efficiently enables cells to coordinate and fine-tune their functions.
• 2.6.2: Signaling Molecules and Cellular Receptors
Chemical signals are released by signaling cells in the form of small, usually volatile or soluble molecules called ligands. A ligand is a molecule that binds another specific molecule, in some cases, delivering a signal in the process. Ligands can thus be thought of as signaling molecules. Ligands interact with proteins in target cells, which are cells that are affected by chemical signals; these proteins are also called receptors.
• 2.6.3: Propagation of the Signal
Once a ligand binds to a receptor, the signal is transmitted through the membrane and into the cytoplasm. Continuation of a signal in this manner is called signal transduction. Signal transduction only occurs with cell-surface receptors because internal receptors are able to interact directly with DNA in the nucleus to initiate protein synthesis. When a ligand binds to its receptor, conformational changes occur that affect the receptor’s intracellular domain.
• 2.6.4: Response to the Signal
Inside the cell, ligands bind to their internal receptors, allowing them to directly affect the cell’s DNA and protein-producing machinery. Using signal transduction pathways, receptors in the plasma membrane produce a variety of effects on the cell. The results of signaling pathways are extremely varied and depend on the type of cell involved as well as the external and internal conditions. A small sampling of responses is described below.
• 2.6.5: Signaling in Single-Celled Organisms
Within-cell signaling allows bacteria to respond to environmental cues, such as nutrient levels, some single-celled organisms also release molecules to signal to each other.
• 2.6.6: Key Terms
• 2.6.7: Chapter Summary
• 2.6.8: Visual Connection Questions
• 2.6.9: Review Questions
• 2.6.10: Critical Thinking Questions
2.06: Cell Communication
Figure 9.1 Have you ever become separated from a friend while in a crowd? If so, you know the challenge of searching for someone when surrounded by thousands of other people. If you and your friend have cell phones, your chances of finding each other are good. Cell phone networks use various methods of encoding to ensure that the signals reach their intended recipients without interference. Similarly, cells must communicate using specific signals and receptors to ensure that messages are clear. (credit: modification of work by Vincent and Bella Productions)
Imagine what life would be like if you and the people around you could not communicate. You would not be able to express your wishes to others, nor could you ask questions about your location. Social organization is dependent on communication between the individuals that comprise that society; without communication, society would fall apart.
As with people, it is vital for individual cells to be able to interact with their environment. This is true for both a one-celled organism growing in a puddle and a large animal living on a savanna. In order to properly respond to external stimuli, cells have developed complex mechanisms of communication that can receive a message, transfer the information across the plasma membrane, and then produce changes within the cell in response to the message.
In multicellular organisms, cells send and receive chemical messages constantly to coordinate the actions of distant organs, tissues, and cells. The ability to send messages quickly and efficiently enables cells to coordinate and fine-tune their functions.
While the necessity for cellular communication in larger organisms seems obvious, even single-celled organisms communicate with each other. Yeast cells signal each other to aid in finding other yeast cells for reproduction. Some forms of bacteria coordinate their actions in order to form large complexes called biofilms or to organize the production of toxins to remove competing organisms. The ability of cells to communicate through chemical signals originated in single cells and was essential for the evolution of multicellular organisms. The efficient and relatively error-free function of communication systems is vital for all life as we know it. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.06%3A_Cell_Communication/2.6.01%3A_Introduction.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Describe four types of signaling mechanisms found in multicellular organisms
• Compare internal receptors with cell-surface receptors
• Recognize the relationship between a ligand’s structure and its mechanism of action
There are two kinds of communication in the world of living cells. Communication between cells is called intercellular signaling, and communication within a cell is called intracellular signaling. An easy way to remember the distinction is by understanding the Latin origin of the prefixes: inter- means "between" (for example, intersecting lines are those that cross each other) and intra- means "inside" (as in intravenous).
Chemical signals are released by signaling cells in the form of small, usually volatile or soluble molecules called ligands. A ligand is a molecule that binds another specific molecule, in some cases, delivering a signal in the process. Ligands can thus be thought of as signaling molecules. Ligands interact with proteins in target cells, which are cells that are affected by chemical signals; these proteins are also called receptors. Ligands and receptors exist in several varieties; however, a specific ligand will have a specific receptor that typically binds only that ligand.
Forms of Signaling
There are four categories of chemical signaling found in multicellular organisms: paracrine signaling, endocrine signaling, autocrine signaling, and direct signaling across gap junctions (Figure 9.2). The main difference between the different categories of signaling is the distance that the signal travels through the organism to reach the target cell. We should note here that not all cells are affected by the same signals.
Figure 9.2 In chemical signaling, a cell may target itself (autocrine signaling), a cell connected by gap junctions, a nearby cell (paracrine signaling), or a distant cell (endocrine signaling). Paracrine signaling acts on nearby cells, endocrine signaling uses the circulatory system to transport ligands, and autocrine signaling acts on the signaling cell. Signaling via gap junctions involves signaling molecules moving directly between adjacent cells.
Paracrine Signaling
Signals that act locally between cells that are close together are called paracrine signals. Paracrine signals move by diffusion through the extracellular matrix. These types of signals usually elicit quick responses that last only a short period of time. In order to keep the response localized, paracrine ligand molecules are normally quickly degraded by enzymes or removed by neighboring cells. Removing the signals will reestablish the concentration gradient for the signal, allowing them to quickly diffuse through the intracellular space if released again.
One example of paracrine signaling is the transfer of signals across synapses between nerve cells. A nerve cell consists of a cell body, several short, branched extensions called dendrites that receive stimuli, and a long extension called an axon, which transmits signals to other nerve cells or muscle cells. The junction between nerve cells where signal transmission occurs is called a synapse. A synaptic signal is a chemical signal that travels between nerve cells. Signals within the nerve cells are propagated by fast-moving electrical impulses. When these impulses reach the end of the axon, the signal continues on to a dendrite of the next cell by the release of chemical ligands called neurotransmitters from the presynaptic cell (the cell emitting the signal). The neurotransmitters are transported across the very small distances (20–40 nanometers) between nerve cells, which are called chemical synapses (Figure 9.3). The small distance between nerve cells allows the signal to travel quickly; this enables an immediate response, such as, "Take your hand off the stove!"
When the neurotransmitter binds the receptor on the surface of the postsynaptic cell, the electrochemical potential of the target cell changes, and the next electrical impulse is launched. The neurotransmitters that are released into the chemical synapse are degraded quickly or get reabsorbed by the presynaptic cell so that the recipient nerve cell can recover quickly and be prepared to respond rapidly to the next synaptic signal.
Figure 9.3 The distance between the presynaptic cell and the postsynaptic cell—called the synaptic gap—is very small and allows for rapid diffusion of the neurotransmitter. Enzymes in the synapatic gap degrade some types of neurotransmitters to terminate the signal.
Endocrine Signaling
Signals from distant cells are called endocrine signals, and they originate from endocrine cells. (In the body, many endocrine cells are located in endocrine glands, such as the thyroid gland, the hypothalamus, and the pituitary gland.) These types of signals usually produce a slower response but have a longer-lasting effect. The ligands released in endocrine signaling are called hormones, signaling molecules that are produced in one part of the body but affect other body regions some distance away.
Hormones travel the large distances between endocrine cells and their target cells via the bloodstream, which is a relatively slow way to move throughout the body. Because of their form of transport, hormones become diluted and are present in low concentrations when they act on their target cells. This is different from paracrine signaling, in which local concentrations of ligands can be very high.
Autocrine Signaling
Autocrine signals are produced by signaling cells that can also bind to the ligand that is released. This means the signaling cell and the target cell can be the same or a similar cell (the prefix auto- means self, a reminder that the signaling cell sends a signal to itself). This type of signaling often occurs during the early development of an organism to ensure that cells develop into the correct tissues and take on the proper function. Autocrine signaling also regulates pain sensation and inflammatory responses. Further, if a cell is infected with a virus, the cell can signal itself to undergo programmed cell death, killing the virus in the process. In some cases, neighboring cells of the same type are also influenced by the released ligand. In embryological development, this process of stimulating a group of neighboring cells may help to direct the differentiation of identical cells into the same cell type, thus ensuring the proper developmental outcome.
Direct Signaling Across Gap Junctions
Gap junctions in animals and plasmodesmata in plants are connections between the plasma membranes of neighboring cells. These fluid-filled channels allow small signaling molecules, called intracellular mediators, to diffuse between the two cells. Small molecules or ions, such as calcium ions (Ca2+), are able to move between cells, but large molecules like proteins and DNA cannot fit through the channels. The specificity of the channels ensures that the cells remain independent but can quickly and easily transmit signals. The transfer of signaling molecules communicates the current state of the cell that is directly next to the target cell; this allows a group of cells to coordinate their response to a signal that only one of them may have received. In plants, plasmodesmata are ubiquitous, making the entire plant into a giant communication network.
Types of Receptors
Receptors are protein molecules in the target cell or on its surface that bind ligand. There are two types of receptors, internal receptors and cell-surface receptors.
Internal receptors
Internal receptors, also known as intracellular or cytoplasmic receptors, are found in the cytoplasm of the cell and respond to hydrophobic ligand molecules that are able to travel across the plasma membrane. Once inside the cell, many of these molecules bind to proteins that act as regulators of mRNA synthesis (transcription) to mediate gene expression. Gene expression is the cellular process of transforming the information in a cell's DNA into a sequence of amino acids, which ultimately forms a protein. When the ligand binds to the internal receptor, a conformational change is triggered that exposes a DNA-binding site on the protein. The ligand-receptor complex moves into the nucleus, then binds to specific regulatory regions of the chromosomal DNA and promotes the initiation of transcription (Figure 9.4). Transcription is the process of copying the information in a cell's DNA into a special form of RNA called messenger RNA (mRNA); the cell uses information in the mRNA (which moves out into the cytoplasm and associates with ribosomes) to link specific amino acids in the correct order, producing a protein. Internal receptors can directly influence gene expression without having to pass the signal on to other receptors or messengers.
Figure 9.4 Hydrophobic signaling molecules typically diffuse across the plasma membrane and interact with intracellular receptors in the cytoplasm. Many intracellular receptors are transcription factors that interact with DNA in the nucleus and regulate gene expression.
Cell-Surface Receptors
Cell-surface receptors, also known as transmembrane receptors, are cell surface, membrane-anchored (integral) proteins that bind to external ligand molecules. This type of receptor spans the plasma membrane and performs signal transduction, through which an extracellular signal is converted into an intracellular signal. Ligands that interact with cell-surface receptors do not have to enter the cell that they affect. Cell-surface receptors are also called cell-specific proteins or markers because they are specific to individual cell types.
Because cell-surface receptor proteins are fundamental to normal cell functioning, it should come as no surprise that a malfunction in any one of these proteins could have severe consequences. Errors in the protein structures of certain receptor molecules have been shown to play a role in hypertension (high blood pressure), asthma, heart disease, and cancer.
Each cell-surface receptor has three main components: an external ligand-binding domain called the extracellular domain, a hydrophobic membrane-spanning region called a transmembrane domain, and an intracellular domain inside the cell. The size and extent of each of these domains vary widely, depending on the type of receptor.
Evolution Connection
Evolution Connection
How Viruses Recognize a HostUnlike living cells, many viruses do not have a plasma membrane or any of the structures necessary to sustain metabolic life. Some viruses are simply composed of an inert protein shell enclosing DNA or RNA. To reproduce, viruses must invade a living cell, which serves as a host, and then take over the hosts cellular apparatus. But how does a virus recognize its host?
Viruses often bind to cell-surface receptors on the host cell. For example, the virus that causes human influenza (flu) binds specifically to receptors on membranes of cells of the respiratory system. Chemical differences in the cell-surface receptors among hosts mean that a virus that infects a specific species (for example, humans) often cannot infect another species (for example, chickens).
However, viruses have very small amounts of DNA or RNA compared to humans, and, as a result, viral reproduction can occur rapidly. Viral reproduction invariably produces errors that can lead to changes in newly produced viruses; these changes mean that the viral proteins that interact with cell-surface receptors may evolve in such a way that they can bind to receptors in a new host. Such changes happen randomly and quite often in the reproductive cycle of a virus, but the changes only matter if a virus with new binding properties comes into contact with a suitable host. In the case of influenza, this situation can occur in settings where animals and people are in close contact, such as poultry and swine farms.1 Once a virus jumps the former "species barrier" to a new host, it can spread quickly. Scientists watch newly appearing viruses (called emerging viruses) closely in the hope that such monitoring can reduce the likelihood of global viral epidemics.
Cell-surface receptors are involved in most of the signaling in multicellular organisms. There are three general categories of cell-surface receptors: ion channel-linked receptors, G-protein-linked receptors, and enzyme-linked receptors.
Ion channel-linked receptors bind a ligand and open a channel through the membrane that allows specific ions to pass through. To form a channel, this type of cell-surface receptor has an extensive membrane-spanning region. In order to interact with the double layer of phospholipid fatty acid tails that form the center of the plasma membrane, many of the amino acids in the membrane-spanning region are hydrophobic in nature. Conversely, the amino acids that line the inside of the channel are hydrophilic to allow for the passage of water or ions. When a ligand binds to the extracellular region of the channel, there is a conformational change in the protein's structure that allows ions such as sodium, calcium, magnesium, and hydrogen to pass through (Figure 9.5).
Figure 9.5 Gated ion channels located in the plasma membrane allow for the controlled flow of ions into and out of the cell. The channel proteins remain closed until a signaling molecule (orange teardrop) binds to the channel protein. Then the channel protein changes conformation and allows ions (yellow circles) to flow into (or out of) the cell. When the signaling molecule is released, the channel protein resumes its closed conformation, preventing ion flow. Credit: Rao, A. and Fletcher, S. Department of Biology, Texas A&M University.
G-protein-linked receptors bind a ligand and activate a membrane protein called a G-protein. The activated G-protein then interacts with either an ion channel or an enzyme in the membrane (Figure 9.6). All G-protein-linked receptors have seven transmembrane domains, but each receptor has its own specific extracellular domain and G-protein-binding site.
Cell signaling using G-protein-linked receptors occurs as a cyclic series of events. Before the ligand binds, the inactive G-protein can bind to a newly revealed site on the receptor specific for its binding. Once the G-protein binds to the receptor, the resulting change in shape activates the G-protein, which releases guanosine diphosphate (GDP) and picks up guanosine 3-phosphate (GTP). The subunits of the G-protein then split into the α subunit and the βγ subunit. One or both of these G-protein fragments may be able to activate other proteins as a result. After awhile, the GTP on the active α subunit of the G-protein is hydrolyzed to GDP and the βγ subunit is deactivated. The subunits reassociate to form the inactive G-protein and the cycle begins anew.
Figure 9.6 Heterotrimeric G-proteins have three subunits: α, β, and γ. When a signaling molecule binds to a G-protein-coupled receptor in the plasma membrane, a GDP molecule associated with the α subunit is exchanged for GTP. The β and γ subunits dissociate from the α subunit, and a cellular response is triggered either by the α subunit or the dissociated βγ pair. Hydrolysis of GTP to GDP terminates the signal.
G-protein-linked receptors have been extensively studied and much has been learned about their roles in maintaining health. Bacteria that are pathogenic to humans can release poisons that interrupt specific G-protein-linked receptor function, leading to illnesses such as pertussis, botulism, and cholera. In cholera (Figure 9.7), for example, the water-borne bacterium Vibrio cholerae produces a toxin, choleragen, that binds to cells lining the small intestine. The toxin then enters these intestinal cells, where it modifies a G-protein that controls the opening of a chloride channel and causes it to remain continuously active, resulting in large losses of fluids from the body and potentially fatal dehydration as a result.
Figure 9.7 Transmitted primarily through contaminated drinking water, cholera is a major cause of death in the developing world and in areas where natural disasters interrupt the availability of clean water. The cholera bacterium, Vibrio cholerae, creates a toxin that modifies G-protein-mediated cell signaling pathways in the intestines. Modern sanitation eliminates the threat of cholera outbreaks, such as the one that swept through New York City in 1866. This poster from that era shows how, at that time, the way that the disease was transmitted was not understood. (credit: New York City Sanitary Commission)
Enzyme-linked receptors are cell-surface receptors with intracellular domains that are associated with an enzyme. In some cases, the intracellular domain of the receptor itself is an enzyme. Other enzyme-linked receptors have a small intracellular domain that interacts directly with an enzyme. The enzyme-linked receptors normally have large extracellular and intracellular domains, but the membrane-spanning region consists of a single alpha-helical region of the peptide strand. When a ligand binds to the extracellular domain, a signal is transferred through the membrane, activating the enzyme. Activation of the enzyme sets off a chain of events within the cell that eventually leads to a response. One example of this type of enzyme-linked receptor is the tyrosine kinase receptor (Figure 9.8). A kinase is an enzyme that transfers phosphate groups from ATP to another protein. The tyrosine kinase receptor transfers phosphate groups to tyrosine molecules (tyrosine residues). First, signaling molecules bind to the extracellular domain of two nearby tyrosine kinase receptors. The two neighboring receptors then bond together, or dimerize. Phosphates are then added to tyrosine residues on the intracellular domain of the receptors (phosphorylation). The phosphorylated residues can then transmit the signal to the next messenger within the cytoplasm.
Visual Connection
Visual Connection
Figure 9.8 A receptor tyrosine kinase is an enzyme-linked receptor with a single helical transmembrane region, and extracellular and intracellular domains. 2) Binding of a signaling molecule to the extracellular domain causes the receptor to dimerize. 3) Tyrosine residues on the intracellular domain are then autophosphorylated, 4) triggering a downstream cellular response. The signal is terminated by a phosphatase that removes the phosphates from the phosphotyrosine residues. Credit: Rao, A., Ryan, K., Tag, A., Fletcher, S. and Hawkins, A. Department of Biology, Texas A&M University.
HER2 is a receptor tyrosine kinase. In 30 percent of human breast cancers, HER2 is permanently activated, resulting in unregulated cell division. Lapatinib, a drug used to treat breast cancer, inhibits HER2 receptor tyrosine kinase autophosphorylation (the process by which the receptor adds phosphates onto itself), thus reducing tumor growth by 50 percent. Besides autophosphorylation, which of the following steps would be inhibited by Lapatinib?
1. Signaling molecule binding, dimerization, and the downstream cellular response
2. Dimerization, and the downstream cellular response
3. The downstream cellular response
4. Phosphatase activity, dimerization, and the downsteam cellular response
Signaling Molecules
Produced by signaling cells and the subsequent binding to receptors in target cells, ligands act as chemical signals that travel to the target cells to coordinate responses. The types of molecules that serve as ligands are incredibly varied and range from small proteins to small ions like calcium (Ca2+).
Small Hydrophobic Ligands
Small hydrophobic ligands can directly diffuse through the plasma membrane and interact with internal receptors. Important members of this class of ligands are the steroid hormones. Steroids are lipids that have a hydrocarbon skeleton with four fused rings; different steroids have different functional groups attached to the carbon skeleton. Steroid hormones include the female sex hormone, estradiol, which is a type of estrogen; the male sex hormone, testosterone; and cholesterol, which is an important structural component of biological membranes and a precursor of steroid hormones (Figure 9.9). Other hydrophobic hormones include thyroid hormones and vitamin D. In order to be soluble in blood, hydrophobic ligands must bind to carrier proteins while they are being transported through the bloodstream.
Figure 9.9 Steroid hormones have similar chemical structures to their precursor, cholesterol. Because these molecules are small and hydrophobic, they can diffuse directly across the plasma membrane into the cell, where they interact with internal receptors.
Water-Soluble Ligands
Water-soluble ligands are polar and, therefore, cannot pass through the plasma membrane unaided; sometimes, they are too large to pass through the membrane at all. Instead, most water-soluble ligands bind to the extracellular domain of cell-surface receptors. This group of ligands is quite diverse and includes small molecules, peptides, and proteins.
Other Ligands
Nitric oxide (NO) is a gas that also acts as a ligand. It is able to diffuse directly across the plasma membrane, and one of its roles is to interact with receptors in smooth muscle and induce relaxation of the tissue. NO has a very short half-life and, therefore, only functions over short distances. Nitroglycerin, a treatment for heart disease, acts by triggering the release of NO, which causes blood vessels to dilate (expand), thus restoring blood flow to the heart. NO has become better known recently because the pathway that it affects is targeted by prescription medications for erectile dysfunction, such as Viagra (erection involves dilated blood vessels).
Footnotes
• 1A. B. Sigalov, The School of Nature. IV. Learning from Viruses, Self/Nonself 1, no. 4 (2010): 282-298. Y. Cao, X. Koh, L. Dong, X. Du, A. Wu, X. Ding, H. Deng, Y. Shu, J. Chen, T. Jiang, Rapid Estimation of Binding Activity of Influenza Virus Hemagglutinin to Human and Avian Receptors, PLoS One 6, no. 4 (2011): e18664. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.06%3A_Cell_Communication/2.6.02%3A_Signaling_Molecules_and_Cellular_Receptors.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Explain how the binding of a ligand initiates signal transduction throughout a cell
• Recognize the role of phosphorylation in the transmission of intracellular signals
• Evaluate the role of second messengers in signal transmission
Once a ligand binds to a receptor, the signal is transmitted through the membrane and into the cytoplasm. Continuation of a signal in this manner is called signal transduction. Signal transduction only occurs with cell-surface receptors, which cannot interact with most components of the cell such as DNA. Only internal receptors are able to interact directly with DNA in the nucleus to initiate protein synthesis.
When a ligand binds to its receptor, conformational changes occur that affect the receptor’s intracellular domain. Conformational changes of the extracellular domain upon ligand binding can propagate through the membrane region of the receptor and lead to activation of the intracellular domain or its associated proteins. In some cases, binding of the ligand causes dimerization of the receptor, which means that two receptors bind to each other to form a stable complex called a dimer. A dimer is a chemical compound formed when two molecules (often identical) join together. The binding of the receptors in this manner enables their intracellular domains to come into close contact and activate each other.
Binding Initiates a Signaling Pathway
After the ligand binds to the cell-surface receptor, the activation of the receptor’s intracellular components sets off a chain of events that is called a signaling pathway, sometimes called a signaling cascade. In a signaling pathway, second messengers–enzymes–and activated proteins interact with specific proteins, which are in turn activated in a chain reaction that eventually leads to a change in the cell’s environment (Figure 9.10), such as an increase in metabolism or specific gene expression. The events in the cascade occur in a series, much like a current flows in a river. Interactions that occur before a certain point are defined as upstream events, and events after that point are called downstream events.
Visual Connection
Visual Connection
Figure 9.10 The epidermal growth factor (EGF) receptor (EGFR) is a receptor tyrosine kinase involved in the regulation of cell growth, wound healing, and tissue repair. When EGF binds to the EGFR, a cascade of downstream events causes the cell to grow and divide. If EGFR is activated at inappropriate times, uncontrolled cell growth (cancer) may occur.
In certain cancers, the GTPase activity of the RAS G-protein is inhibited. This means that the RAS protein can no longer hydrolyze GTP into GDP. What effect would this have on downstream cellular events?
You can see that signaling pathways can get very complicated very quickly because most cellular proteins can affect different downstream events, depending on the conditions within the cell. A single pathway can branch off toward different endpoints based on the interplay between two or more signaling pathways, and the same ligands are often used to initiate different signals in different cell types. This variation in response is due to differences in protein expression in different cell types. Another complicating element is signal integration of the pathways, in which signals from two or more different cell-surface receptors merge to activate the same response in the cell. This process can ensure that multiple external requirements are met before a cell commits to a specific response.
The effects of extracellular signals can also be amplified by enzymatic cascades. At the initiation of the signal, a single ligand binds to a single receptor. However, activation of a receptor-linked enzyme can activate many copies of a component of the signaling cascade, which amplifies the signal.
Link to Learning
Link to Learning
Observe an animation of cell signaling at this site.
Methods of Intracellular Signaling
The induction of a signaling pathway depends on the modification of a cellular component by an enzyme. There are numerous enzymatic modifications that can occur, and they are recognized in turn by the next component downstream. The following are some of the more common events in intracellular signaling.
Phosphorylation
One of the most common chemical modifications that occurs in signaling pathways is the addition of a phosphate group (PO4–3) to a molecule such as a protein in a process called phosphorylation. The phosphate can be added to a nucleotide such as GMP to form GDP or GTP. Phosphates are also often added to serine, threonine, and tyrosine residues of proteins, where they replace the hydroxyl group of the amino acid (Figure 9.11). The transfer of the phosphate is catalyzed by an enzyme called a kinase. Various kinases are named for the substrate they phosphorylate. Phosphorylation of serine and threonine residues often activates enzymes. Phosphorylation of tyrosine residues can either affect the activity of an enzyme or create a binding site that interacts with downstream components in the signaling cascade. Phosphorylation may activate or inactivate enzymes, and the reversal of phosphorylation, dephosphorylation by a phosphatase, will reverse the effect.
Figure 9.11 In protein phosphorylation, a phosphate group (PO4 -3) is added to residues of the amino acids serine, threonine, and tyrosine.
Second Messengers
Second messengers are small molecules that propagate a signal after it has been initiated by the binding of the signaling molecule to the receptor. These molecules help to spread a signal through the cytoplasm by altering the behavior of certain cellular proteins.
Calcium ion is a widely used second messenger. The free concentration of calcium ions (Ca2+) within a cell is very low because ion pumps in the plasma membrane continuously remove it by using adenosine-5'-triphosphate (ATP). For signaling purposes, Ca2+ is stored in cytoplasmic vesicles, such as the endoplasmic reticulum, or accessed from outside the cell. When signaling occurs, ligand-gated calcium ion channels allow the higher levels of Ca2+ that are present outside the cell (or in intracellular storage compartments) to flow into the cytoplasm, which raises the concentration of cytoplasmic Ca2+. The response to the increase in Ca2+ varies and depends on the cell type involved. For example, in the β-cells of the pancreas, Ca2+ signaling leads to the release of insulin, and in muscle cells, an increase in Ca2+ leads to muscle contractions.
Another second messenger utilized in many different cell types is cyclic AMP (cAMP). Cyclic AMP is synthesized by the enzyme adenylyl cyclase from ATP (Figure 9.12). The main role of cAMP in cells is to bind to and activate an enzyme called cAMP-dependent kinase (A-kinase). A-kinase regulates many vital metabolic pathways: It phosphorylates serine and threonine residues of its target proteins, activating them in the process. A-kinase is found in many different types of cells, and the target proteins in each kind of cell are different. Differences give rise to the variation of the responses to cAMP in different cells.
Figure 9.12 This diagram shows the mechanism for the formation of cyclic AMP (cAMP). cAMP serves as a second messenger to activate or inactivate proteins within the cell. Termination of the signal occurs when an enzyme called phosphodiesterase converts cAMP into AMP.
Present in small concentrations in the plasma membrane, inositol phospholipids are lipids that can also be converted into second messengers. Because these molecules are membrane components, they are located near membrane-bound receptors and can easily interact with them. Phosphatidylinositol (PI) is the main phospholipid that plays a role in cellular signaling. Enzymes known as kinases phosphorylate PI to form PI-phosphate (PIP) and PI-bisphosphate (PIP2).
The enzyme phospholipase C cleaves PIP2 to form diacylglycerol (DAG) and inositol triphosphate (IP3) (Figure 9.13). These products of the cleavage of PIP2 serve as second messengers. Diacylglycerol (DAG) remains in the plasma membrane and activates protein kinase C (PKC), which then phosphorylates serine and threonine residues in its target proteins. IP3 diffuses into the cytoplasm and binds to ligand-gated calcium channels in the endoplasmic reticulum to release Ca2+ that continues the signal cascade.
Figure 9.13 The enzyme phospholipase C breaks down PIP2 into IP3 and DAG, both of which serve as second messengers. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.06%3A_Cell_Communication/2.6.03%3A_Propagation_of_the_Signal.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Describe how signaling pathways direct protein expression, cellular metabolism, and cell growth
• Identify the function of PKC in signal transduction pathways
• Recognize the role of apoptosis in the development and maintenance of a healthy organism
Inside the cell, ligands bind to their internal receptors, allowing them to directly affect the cell’s DNA and protein-producing machinery. Using signal transduction pathways, receptors in the plasma membrane produce a variety of effects on the cell. The results of signaling pathways are extremely varied and depend on the type of cell involved as well as the external and internal conditions. A small sampling of responses is described below.
Gene Expression
Some signal transduction pathways regulate the transcription of RNA. Others regulate the translation of proteins from mRNA. An example of a protein that regulates translation in the nucleus is the MAP kinase ERK. The MAPK/ERK pathway (also known as the Ras-Raf-MEK-ERK pathway) is a chain of proteins in the cell that communicates a signal from a receptor on the surface of the cell to the nuclear DNA. ERK is activated in a phosphorylation cascade when epidermal growth factor (EGF) binds the EGF receptor (see Figure 9.10). Upon phosphorylation, ERK enters the nucleus and activates a protein kinase that, in turn, regulates protein translation (Figure 9.14).
Figure 9.14 ERK is a MAP kinase that activates translation when it is phosphorylated. ERK phosphorylates MNK1, which in turn phosphorylates eIF-4E, an elongation initiation factor that, with other initiation factors, is associated with mRNA. When eIF-4E becomes phosphorylated, the mRNA unfolds, allowing protein synthesis in the nucleus to begin. (See Figure 9.10 for the phosphorylation pathway that activates ERK.)
Another mechanism of gene regulation involves PKC, which is a protein that acts as an inhibitor. An inhibitor is a molecule that binds to a protein and prevents it from functioning or reduces its function. In this case, the inhibitor is a protein called Iκ-B, which binds to the regulatory protein NF-κB. (The symbol κ represents the Greek letter kappa.) When Iκ-B is bound to NF-κB, the complex cannot enter the nucleus of the cell, but when Iκ-B is phosphorylated by PKC, it can no longer bind NF-κB, and NF-κB (a transcription factor) can enter the nucleus and initiate RNA transcription. In this case, the effect of phosphorylation is to inactivate an inhibitor and thereby activate the process of transcription.
Increase in Cellular Metabolism
The result of another signaling pathway affects muscle cells. The activation of β-adrenergic receptors in muscle cells by adrenaline leads to an increase in cyclic AMP (cAMP) inside the cell. Also known as epinephrine, adrenaline is a hormone (produced by the adrenal gland located on top of the kidney) that readies the body for short-term emergencies. Cyclic AMP activates PKA (protein kinase A), which in turn phosphorylates two enzymes. The first enzyme promotes the degradation of glycogen by activating intermediate glycogen phosphorylase kinase (GPK) that in turn activates glycogen phosphorylase (GP) that catabolizes glycogen into its constituent glucose monomers. (Recall that your body converts excess glucose to glycogen for short-term storage. When energy is needed, glycogen is quickly reconverted to glucose.) Phosphorylation of the second enzyme, glycogen synthase (GS), inhibits its ability to form glycogen from glucose. In this manner, a muscle cell obtains a ready pool of glucose by activating its formation via glycogen degradation and by inhibiting the use of glucose to form glycogen, thus preventing a futile cycle of glycogen degradation and synthesis. The glucose is then available for use by the muscle cell in response to a sudden surge of adrenaline—the “fight or flight” reflex.
Cell Growth
Cell signaling pathways also play a major role in cell division. Cells do not normally divide unless they are stimulated by signals from other cells. The ligands that promote cell growth are called growth factors. Most growth factors bind to cell-surface receptors that are linked to tyrosine kinases. These cell-surface receptors are called receptor tyrosine kinases (RTKs). Activation of RTKs initiates a signaling pathway that includes a G-protein called RAS, which activates the MAP kinase pathway described earlier. The enzyme MAP kinase then stimulates the expression of proteins that interact with other cellular components to initiate cell division.
Career Connection
Career Connection
Cancer BiologistCancer biologists study the molecular origins of cancer with the goal of developing new prevention methods and treatment strategies that will inhibit the growth of tumors without harming the normal cells of the body. As mentioned earlier, signaling pathways control cell growth. These signaling pathways are controlled by signaling proteins, which are, in turn, expressed by genes. Mutations in these genes can result in malfunctioning signaling proteins. This prevents the cell from regulating its cell cycle, triggering unrestricted cell division and perhaps cancer. The genes that regulate the signaling proteins are one type of oncogene, which is a gene that has the potential to cause cancer. The gene encoding RAS is an oncogene that was originally discovered when mutations in the RAS protein were linked to cancer. Further studies have indicated that 30 percent of cancer cells have a mutation in the RAS gene that leads to uncontrolled growth. If left unchecked, uncontrolled cell division can lead to tumor formation and metastasis, the growth of cancer cells in new locations in the body.
Cancer biologists have been able to identify many other oncogenes that contribute to the development of cancer. For example, HER2 is a cell-surface receptor that is present in excessive amounts in 20 percent of human breast cancers. Cancer biologists realized that gene duplication led to HER2 overexpression in 25 percent of breast cancer patients and developed a drug called Herceptin (trastuzumab). Herceptin is a monoclonal antibody that targets HER2 for removal by the immune system. Herceptin therapy helps to control signaling through HER2. The use of Herceptin in combination with chemotherapy has helped to increase the overall survival rate of patients with metastatic breast cancer.
More information on cancer biology research can be found at the National Cancer Institute website (https://www.cancer.gov/research/areas/biology).
Cell Death
When a cell is damaged, superfluous, or potentially dangerous to an organism, a cell can initiate a mechanism to trigger programmed cell death, or apoptosis. Apoptosis allows a cell to die in a controlled manner that prevents the release of potentially damaging molecules from inside the cell. There are many internal checkpoints that monitor a cell’s health; if abnormalities are observed, a cell can spontaneously initiate the process of apoptosis. However, in some cases, such as a viral infection or uncontrolled cell division due to cancer, the cell’s normal checks and balances fail. External signaling can also initiate apoptosis. For example, most normal animal cells have receptors that interact with the extracellular matrix, a network of glycoproteins that provides structural support for cells in an organism. The binding of cellular receptors to the extracellular matrix initiates a signaling cascade within the cell. However, if the cell moves away from the extracellular matrix, the signaling ceases, and the cell undergoes apoptosis. This system keeps cells from traveling through the body and proliferating out of control, as happens with tumor cells that metastasize.
Another example of external signaling that leads to apoptosis occurs in T-cell development. T-cells are immune cells that bind to foreign macromolecules and particles, and target them for destruction by the immune system. Normally, T-cells do not target “self” proteins (those of their own organism), a process that can lead to autoimmune diseases. In order to develop the ability to discriminate between self and non-self, immature T-cells undergo screening to determine whether they bind to so-called self proteins. If the T-cell receptor binds to self proteins, the cell initiates apoptosis to remove the potentially dangerous cell.
Apoptosis is also essential for normal embryological development. In vertebrates, for example, early stages of development include the formation of web-like tissue between individual fingers and toes (Figure 9.15). During the course of normal development, these unneeded cells must be eliminated, enabling fully separated fingers and toes to form. A cell signaling mechanism triggers apoptosis, which destroys the cells between the developing digits.
Figure 9.15 The histological section of a foot of a 15-day-old mouse embryo, visualized using light microscopy, reveals areas of tissue between the toes, which apoptosis will eliminate before the mouse reaches its full gestational age at 27 days. (credit: modification of work by Michal Mañas)
Termination of the Signal Cascade
The aberrant signaling often seen in tumor cells is proof that the termination of a signal at the appropriate time can be just as important as the initiation of a signal. One method of stopping a specific signal is to degrade the ligand or remove it so that it can no longer access its receptor. One reason that hydrophobic hormones like estrogen and testosterone trigger long-lasting events is because they bind carrier proteins. These proteins allow the insoluble molecules to be soluble in blood, but they also protect the hormones from degradation by circulating enzymes.
Inside the cell, many different enzymes reverse the cellular modifications that result from signaling cascades. For example, phosphatases are enzymes that remove the phosphate group attached to proteins by kinases in a process called dephosphorylation. Cyclic AMP (cAMP) is degraded into AMP by phosphodiesterase, and the release of calcium stores is reversed by the Ca2+ pumps that are located in the external and internal membranes of the cell. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.06%3A_Cell_Communication/2.6.04%3A_Response_to_the_Signal.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Describe how single-celled yeasts use cell signaling to communicate with one another
• Relate the role of quorum sensing to the ability of some bacteria to form biofilms
Within-cell signaling allows bacteria to respond to environmental cues, such as nutrient levels. Some single-celled organisms also release molecules to signal to each other.
Signaling in Yeast
Yeasts are eukaryotes (fungi), and the components and processes found in yeast signals are similar to those of cell-surface receptor signals in multicellular organisms. Budding yeasts (Figure 9.16) are able to participate in a process that is similar to sexual reproduction that entails two haploid cells (cells with one-half the normal number of chromosomes) combining to form a diploid cell (a cell with two sets of each chromosome, which is what normal body cells contain). In order to find another haploid yeast cell that is prepared to mate, budding yeasts secrete a signaling molecule called mating factor. When mating factor binds to cell-surface receptors in other yeast cells that are nearby, they stop their normal growth cycles and initiate a cell signaling cascade that includes protein kinases and GTP-binding proteins that are similar to G-proteins.
Figure 9.16 Budding Saccharomyces cerevisiae yeast cells can communicate by releasing a signaling molecule called mating factor. In this micrograph, they are visualized using differential interference contrast microscopy, a light microscopy technique that enhances the contrast of the sample.
Signaling in Bacteria
Signaling in bacteria enables bacteria to monitor extracellular conditions, ensure that there are sufficient amounts of nutrients, and ensure that hazardous situations are avoided. There are circumstances, however, when bacteria communicate with each other.
The first evidence of bacterial communication was observed in a bacterium that has a symbiotic relationship with Hawaiian bobtail squid. When the population density of the bacteria reaches a certain level, specific gene expression is initiated, and the bacteria produce bioluminescent proteins that emit light. Because the number of cells present in the environment (cell density) is the determining factor for signaling, bacterial signaling was named quorum sensing. In politics and business, a quorum is the minimum number of members required to be present to vote on an issue.
Quorum sensing uses autoinducers as signaling molecules. Autoinducers are signaling molecules secreted by bacteria to communicate with other bacteria of the same kind. The secreted autoinducers can be small, hydrophobic molecules, such as acyl-homoserine lactone (AHL), or larger peptide-based molecules; each type of molecule has a different mode of action. When AHL enters target bacteria, it binds to transcription factors, which then switch gene expression on or off. When the number of bacteria increases so does the concentration of the autoinducer, triggering increased expression of certain genes including autoinducers, which results in a self-amplifying cycle, also known as a positive feedback loop (Figure 9.17). The peptide autoinducers stimulate more complicated signaling pathways that include bacterial kinases. The changes in bacteria following exposure to autoinducers can be quite extensive. The pathogenic bacterium Pseudomonas aeruginosa has 616 different genes that respond to autoinducers.
Some species of bacteria that use quorum sensing form biofilms, complex colonies of bacteria (often containing several species) that exchange chemical signals to coordinate the release of toxins that will attack the host. Bacterial biofilms (Figure 9.18) can sometimes be found on medical equipment; when biofilms invade implants such as hip or knee replacements or heart pacemakers, they can cause life-threatening infections.
Visual Connection
Visual Connection
Figure 9.17 Autoinducers are small molecules or proteins produced by bacteria that regulate gene expression.
Which of the following statements about quorum sensing is false?
1. Autoinducer must bind to receptor to turn on transcription of genes responsible for the production of more autoinducer.
2. The receptor stays in the bacterial cell, but the autoinducer diffuses out.
3. Autoinducer can only act on a different cell: it cannot act on the cell in which it is made.
4. Autoinducer turns on genes that enable the bacteria to form a biofilm.
Visual Connection
Visual Connection
Figure 9.18 Cell-cell communication enables these (a) Staphylococcus aureus bacteria to work together to form a biofilm inside a hospital patient’s catheter, seen here via scanning electron microscopy. S. aureus is the main cause of hospital-acquired infections. (b) Hawaiian bobtail squid have a symbiotic relationship with the bioluminescent bacteria Vibrio fischeri. The luminescence makes it difficult to see the squid from below because it effectively eliminates its shadow. In return for camouflage, the squid provides food for the bacteria. Free-living V. fischeri do not produce luciferase, the enzyme responsible for luminescence, but V. fischeri living in a symbiotic relationship with the squid do. Quorum sensing determines whether the bacteria should produce the luciferase enzyme. (credit a: modifications of work by CDC/Janice Carr; credit b: modifications of work by Cliff1066/Flickr)
What advantage might biofilm production confer on the S. aureus inside the catheter?
Research on the details of quorum sensing has led to advances in growing bacteria for industrial purposes. Recent discoveries suggest that it may be possible to exploit bacterial signaling pathways to control bacterial growth; this process could replace or supplement antibiotics that are no longer effective in certain situations.
Link to Learning
Link to Learning
Watch geneticist Bonnie Bassler discuss her discovery of quorum sensing in biofilm bacteria in squid.
Evolution Connection
Evolution Connection
Cellular Communication in YeastsThe first cellular form of life on our planet likely consisted of single-celled prokaryotic organisms that had limited interaction with each other. While some external signaling occurs between different species of single-celled organisms, the majority of signaling within bacteria and yeasts concerns only other members of the same species. The evolution of cellular communication is an absolute necessity for the development of multicellular organisms, and this innovation is thought to have required approximately 2 billion years to appear in early life forms.
Yeasts are single-celled eukaryotes and, therefore, have a nucleus and organelles characteristic of more complex life forms. Comparisons of the genomes of yeasts, nematode worms, fruit flies, and humans illustrate the evolution of increasingly complex signaling systems that allow for the efficient inner workings that keep humans and other complex life forms functioning correctly.
Kinases are a major component of cellular communication, and studies of these enzymes illustrate the evolutionary connectivity of different species. Yeasts have 130 types of kinases. More complex organisms such as nematode worms and fruit flies have 454 and 239 kinases, respectively. Of the 130 kinase types in yeast, 97 belong to the 55 subfamilies of kinases that are found in other eukaryotic organisms. The only obvious deficiency seen in yeasts is the complete absence of tyrosine kinases. It is hypothesized that phosphorylation of tyrosine residues is needed to control the more sophisticated functions of development, differentiation, and cellular communication used in multicellular organisms.
Because yeasts contain many of the same classes of signaling proteins as humans, these organisms are ideal for studying signaling cascades. Yeasts multiply quickly and are much simpler organisms than humans or other multicellular animals. Therefore, the signaling cascades are also simpler and easier to study, although they contain similar counterparts to human signaling.2
Link to Learning
Link to Learning
Watch this collection of interview clips with biofilm researchers in “What Are Bacterial Biofilms?”
Footnotes
• 2G. Manning, G.D. Plowman, T. Hunter, S. Sudarsanam, “Evolution of Protein Kinase Signaling from Yeast to Man,” Trends in Biochemical Sciences 27, no. 10 (2002): 514–520. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.06%3A_Cell_Communication/2.6.05%3A_Signaling_in_Single-Celled_Organisms.txt |
apoptosis
programmed cell death
autocrine signal
signal that is sent and received by the same or similar nearby cells
autoinducer
signaling molecule secreted by bacteria to communicate with other bacteria of its kind
cell-surface receptor
cell-surface protein that transmits a signal from the exterior of the cell to the interior, even though the ligand does not enter the cell
chemical synapse
small space between axon terminals and dendrites of nerve cells where neurotransmitters function
cyclic AMP (cAMP)
second messenger that is derived from ATP
cyclic AMP-dependent kinase
(also, protein kinase A, or PKA) kinase that is activated by binding to cAMP
diacylglycerol (DAG)
cleavage product of PIP2 that is used for signaling within the plasma membrane
dimer
chemical compound formed when two molecules join together
dimerization
(of receptor proteins) interaction of two receptor proteins to form a functional complex called a dimer
endocrine cell
cell that releases ligands involved in endocrine signaling (hormones)
endocrine signal
long-distance signal that is delivered by ligands (hormones) traveling through an organism's circulatory system from the signaling cell to the target cell
enzyme-linked receptor
cell-surface receptor with intracellular domains that are associated with membrane-bound enzymes
extracellular domain
region of a cell-surface receptor that is located on the cell surface
G-protein-linked receptor
cell-surface receptor that activates membrane-bound G-proteins to transmit a signal from the receptor to nearby membrane components
growth factor
ligand that binds to cell-surface receptors and stimulates cell growth
inhibitor
molecule that binds to a protein (usually an enzyme) and keeps it from functioning
inositol phospholipid
lipid present at small concentrations in the plasma membrane that is converted into a second messenger; it has inositol (a carbohydrate) as its hydrophilic head group
inositol triphosphate (IP3)
cleavage product of PIP2 that is used for signaling within the cell
intercellular signaling
communication between a cell
internal receptor
(also, intracellular receptor) receptor protein that is located in the cytosol of a cell and binds to ligands that pass through the plasma membrane
intracellular mediator
(also, second messenger) small molecule that transmits signals within a cell
intracellular signaling
communication within cells
ion channel-linked receptor
cell-surface receptor that forms a plasma membrane channel, which opens when a ligand binds to the extracellular domain (ligand-gated channels)
kinase
enzyme that catalyzes the transfer of a phosphate group from ATP to another molecule
ligand
molecule produced by a signaling cell that binds with a specific receptor, delivering a signal in the process
mating factor
signaling molecule secreted by yeast cells to communicate to nearby yeast cells that they are available to mate
neurotransmitter
chemical ligand that carries a signal from one nerve cell to the next
paracrine signal
signal between nearby cells that is delivered by ligands traveling in the liquid medium in the space between the cells
phosphatase
enzyme that removes the phosphate group from a molecule that has been previously phosphorylated
phosphodiesterase
enzyme that degrades cAMP, producing AMP, to terminate signaling
quorum sensing
method of cellular communication used by bacteria that informs them of the abundance of similar (or different) bacteria in the environment
receptor
protein in or on a target cell that bind to ligands
second messenger
small, non-protein molecule that propagates a signal within the cell after activation of a receptor causes its release
signal integration
interaction of signals from two or more different cell-surface receptors that merge to activate the same response in the cell
signal transduction
propagation of the signal through the cytoplasm (and sometimes also the nucleus) of the cell
signaling cell
cell that releases signal molecules that allow communication with another cell
signaling pathway
(also signaling cascade) chain of events that occurs in the cytoplasm of the cell to propagate the signal from the plasma membrane to produce a response
synaptic signal
chemical signal (neurotransmitter) that travels between nerve cells
target cell
cell that has a receptor for a signal or ligand from a signaling cell | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.06%3A_Cell_Communication/2.6.06%3A_Key_Terms.txt |
9.1 Signaling Molecules and Cellular Receptors
Cells communicate by both inter- and intracellular signaling. Signaling cells secrete ligands that bind to target cells and initiate a chain of events within the target cell. The four categories of signaling in multicellular organisms are paracrine signaling, endocrine signaling, autocrine signaling, and direct signaling across gap junctions. Paracrine signaling takes place over short distances. Endocrine signals are carried long distances through the bloodstream by hormones, and autocrine signals are received by the same cell that sent the signal or other nearby cells of the same kind. Gap junctions allow small molecules, including signaling molecules, to flow between neighboring cells.
Internal receptors are found in the cell cytoplasm. Here, they bind ligand molecules that cross the plasma membrane; these receptor-ligand complexes move to the nucleus and interact directly with cellular DNA. Cell-surface receptors transmit a signal from outside the cell to the cytoplasm. Ion channel-linked receptors, when bound to their ligands, form a pore through the plasma membrane through which certain ions can pass. G-protein-linked receptors interact with a G-protein on the cytoplasmic side of the plasma membrane, promoting the exchange of bound GDP for GTP and interacting with other enzymes or ion channels to transmit a signal. Enzyme-linked receptors transmit a signal from outside the cell to an intracellular domain of a membrane-bound enzyme. Ligand binding causes activation of the enzyme. Small hydrophobic ligands (like steroids) are able to penetrate the plasma membrane and bind to internal receptors. Water-soluble hydrophilic ligands are unable to pass through the membrane; instead, they bind to cell-surface receptors, which transmit the signal to the inside of the cell.
9.2 Propagation of the Signal
Ligand binding to the receptor allows for signal transduction through the cell. The chain of events that conveys the signal through the cell is called a signaling pathway or cascade. Signaling pathways are often very complex because of the interplay between different proteins. A major component of cell signaling cascades is the phosphorylation of molecules by enzymes known as kinases. Phosphorylation adds a phosphate group to serine, threonine, and tyrosine residues in a protein, changing their shapes, and activating or inactivating the protein. Small molecules like nucleotides can also be phosphorylated. Second messengers are small, non-protein molecules that are used to transmit a signal within a cell. Some examples of second messengers are calcium ions (Ca2+), cyclic AMP (cAMP), diacylglycerol (DAG), and inositol triphosphate (IP3).
9.3 Response to the Signal
The initiation of a signaling pathway is a response to external stimuli. This response can take many different forms, including protein synthesis, a change in the cell’s metabolism, cell growth, or even cell death. Many pathways influence the cell by initiating gene expression, and the methods utilized are quite numerous. Some pathways activate enzymes that interact with DNA transcription factors. Others modify proteins and induce them to change their location in the cell. Depending on the status of the organism, cells can respond by storing energy as glycogen or fat, or making it available in the form of glucose. A signal transduction pathway allows muscle cells to respond to immediate requirements for energy in the form of glucose. Cell growth is almost always stimulated by external signals called growth factors. Uncontrolled cell growth leads to cancer, and mutations in the genes encoding protein components of signaling pathways are often found in tumor cells. Programmed cell death, or apoptosis, is important for removing damaged or unnecessary cells. The use of cellular signaling to organize the dismantling of a cell ensures that harmful molecules from the cytoplasm are not released into the spaces between cells, as they are in uncontrolled death, necrosis. Apoptosis also ensures the efficient recycling of the components of the dead cell. Termination of the cellular signaling cascade is very important so that the response to a signal is appropriate in both timing and intensity. Degradation of signaling molecules and dephosphorylation of phosphorylated intermediates of the pathway by phosphatases are two ways to terminate signals within the cell.
9.4 Signaling in Single-Celled Organisms
Yeasts and multicellular organisms have similar signaling mechanisms. Yeasts use cell-surface receptors and signaling cascades to communicate information on mating with other yeast cells. The signaling molecule secreted by yeasts is called mating factor.
Bacterial signaling is called quorum sensing. Bacteria secrete signaling molecules called autoinducers that are either small, hydrophobic molecules or peptide-based signals. The hydrophobic autoinducers, such as AHL, bind transcription factors and directly affect gene expression. The peptide-based molecules bind kinases and initiate signaling cascades in the cells.
2.6.08: Visual Connection Questions
1.
Figure 9.8 HER2 is a receptor tyrosine kinase. In 30 percent of human breast cancers, HER2 is permanently activated, resulting in unregulated cell division. Lapatinib, a drug used to treat breast cancer, inhibits HER2 receptor tyrosine kinase autophosphorylation (the process by which the receptor adds phosphates onto itself), thus reducing tumor growth by 50 percent. Besides autophosphorylation, which of the following steps would be inhibited by Lapatinib?
1. Signaling molecule binding, dimerization, and the downstream cellular response.
2. Dimerization, and the downstream cellular response.
3. The downstream cellular response.
4. Phosphatase activity, dimerization, and the downsteam cellular response.
2.
Figure 9.10 In certain cancers, the GTPase activity of the RAS G-protein is inhibited. This means that the RAS protein can no longer hydrolyze GTP into GDP. What effect would this have on downstream cellular events?
3.
Figure 9.17 Which of the following statements about quorum sensing is false?
1. Autoinducer must bind to receptor to turn on transcription of genes responsible for the production of more autoinducer.
2. The receptor stays in the bacterial cell, but the autoinducer diffuses out.
3. Autoinducer can only act on a different cell: it cannot act on the cell in which it is made.
4. Autoinducer turns on genes that enable the bacteria to form a biofilm.
4.
Figure 9.18 What advantage might biofilm production confer on the S. aureus inside the catheter? | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.06%3A_Cell_Communication/2.6.07%3A_Chapter_Summary.txt |
5.
What property prevents the ligands of cell-surface receptors from entering the cell?
1. The molecules bind to the extracellular domain.
2. The molecules are hydrophilic and cannot penetrate the hydrophobic interior of the plasma membrane.
3. The molecules are attached to transport proteins that deliver them through the bloodstream to target cells.
4. The ligands are able to penetrate the membrane and directly influence gene expression upon receptor binding.
6.
The secretion of hormones by the pituitary gland is an example of _______________.
1. autocrine signaling
2. paracrine signaling
3. endocrine signaling
4. direct signaling across gap junctions
7.
Why are ion channels necessary to transport ions into or out of a cell?
1. Ions are too large to diffuse through the membrane.
2. Ions are charged particles and cannot diffuse through the hydrophobic interior of the membrane.
3. Ions do not need ion channels to move through the membrane.
4. Ions bind to carrier proteins in the bloodstream, which must be removed before transport into the cell.
8.
Endocrine signals are transmitted more slowly than paracrine signals because ___________.
1. the ligands are transported through the bloodstream and travel greater distances
2. the target and signaling cells are close together
3. the ligands are degraded rapidly
4. the ligands don't bind to carrier proteins during transport
9.
A scientist notices that when she adds a small, water-soluble molecule to a dish of cells, the cells turn off transcription of a gene. She hypothesizes that the ligand she added binds to a(n) ______ receptor.
1. Intracellular
2. Hormone
3. Enzyme-linked
4. Gated ion channel-linked
10.
Where do DAG and IP3 originate?
1. They are formed by phosphorylation of cAMP.
2. They are ligands expressed by signaling cells.
3. They are hormones that diffuse through the plasma membrane to stimulate protein production.
4. They are the cleavage products of the inositol phospholipid, PIP2.
11.
What property enables the residues of the amino acids serine, threonine, and tyrosine to be phosphorylated?
1. They are polar.
2. They are non-polar.
3. They contain a hydroxyl group.
4. They occur more frequently in the amino acid sequence of signaling proteins.
12.
Histamine binds to the H1 G-protein-linked receptor to initiate the itchiness and airway constriction associated with an allergic response. If a mutation in the associated G-protein’s alpha subunit prevented the hydrolysis of GTP how would the allergic response change?
1. More severe allergic response compared to normal G-protein signaling.
2. Less severe allergic response compared to normal G-protein signaling.
3. No allergic response.
4. No change compared to normal G-protein signaling.
13.
A scientist observes a mutation in the transmembrane region of EGFR that eliminates its ability to be stabilized by binding interactions during dimerization after ligand binding. Which hypothesis regarding the effect of this mutation on EGF signaling is most likely to be correct?
1. EGF signaling cascades would be active for longer in the cell.
2. EGF signaling cascades would be active for a shorter period of time in the cell.
3. EGF signaling cascades would not occur.
4. EGF signaling would be unaffected.
14.
What is the function of a phosphatase?
1. A phosphatase removes phosphorylated amino acids from proteins.
2. A phosphatase removes the phosphate group from phosphorylated amino acid residues in a protein.
3. A phosphatase phosphorylates serine, threonine, and tyrosine residues.
4. A phosphatase degrades second messengers in the cell.
15.
How does NF-κB induce gene expression?
1. A small, hydrophobic ligand binds to NF-κB, activating it.
2. Phosphorylation of the inhibitor Iκ-B dissociates the complex between it and NF-κB, and allows NF-κB to enter the nucleus and stimulate transcription.
3. NF-κB is phosphorylated and is then free to enter the nucleus and bind DNA.
4. NF-κB is a kinase that phosphorylates a transcription factor that binds DNA and promotes protein production.
16.
Apoptosis can occur in a cell when the cell is ________________.
1. damaged
2. no longer needed
3. infected by a virus
4. all of the above
17.
What is the effect of an inhibitor binding an enzyme?
1. The enzyme is degraded.
2. The enzyme is activated.
3. The enzyme is inactivated.
4. The complex is transported out of the cell.
18.
How does PKC’s signaling role change in response to growth factor signaling versus an immune response?
1. PKC interacts directly with signaling molecules in both cascades, but only exhibits kinase activity during growth factor signaling.
2. PKC interacts directly with signaling molecules in growth factor cascades, but interacts with signaling inhibitors during immune signaling.
3. PKC amplifies growth factor cascades, but turns off immune cascades.
4. PKC is activated during growth factor cascades, but is inactivated during immune response cascades.
19.
A scientist notices that a cancer cell line fails to die when they add an inducer of apoptosis to his culture of cells. Which hypothesis could explain why the cells fail to die?
1. The cells have a mutation that prevents the initiation of apoptosis signaling.
2. The cells have lost expression of the receptor for the apoptosis-inducing ligand.
3. The cells overexpress a growth factor pathway that inhibits apoptosis.
4. All of the above.
20.
Which type of molecule acts as a signaling molecule in yeasts?
1. steroid
2. autoinducer
3. mating factor
4. second messenger
21.
Quorum sensing is triggered to begin when ___________.
1. treatment with antibiotics occurs
2. bacteria release growth hormones
3. bacterial protein expression is switched on
4. a sufficient number of bacteria are present
22.
A doctor is researching new ways to treat biofilms on artificial joints. Which approach would best help prevent bacterial colonization of the medical implants?
1. Increase antibiotic dosing
2. Create implants with rougher surfaces
3. Vaccinate patients against all pathogenic bacteria
4. Inhibit quorum sensing
2.6.10: Critical Thinking Questions
23.
What is the difference between intracellular signaling and intercellular signaling?
24.
How are the effects of paracrine signaling limited to an area near the signaling cells?
25.
What are the differences between internal receptors and cell-surface receptors?
26.
Cells grown in the laboratory are mixed with a dye molecule that is unable to pass through the plasma membrane. If a ligand is added to the cells, observations show that the dye enters the cells. What type of receptor did the ligand bind to on the cell surface?
27.
Insulin is a hormone that regulates blood sugar by binding to its receptor, insulin receptor tyrosine kinase. How does insulin’s behavior differ from steroid hormone signaling, and what can you infer about its structure?
28.
The same second messengers are used in many different cells, but the response to second messengers is different in each cell. How is this possible?
29.
What would happen if the intracellular domain of a cell-surface receptor was switched with the domain from another receptor?
30.
If a cell developed a mutation in its MAP2K1 gene (encodes the MEK protein) that prevented MEK from being recognized by phosphatases, how would the EGFR signaling cascade and the cell’s behavior change?
31.
What is a possible result of a mutation in a kinase that controls a pathway that stimulates cell growth?
32.
How does the extracellular matrix control the growth of cells?
33.
A scientist notices that a cancer cell line shows high levels of phosphorylated ERK in the absence of EGF. What are two possible explanations for the increase in phosphorylated ERK? Be specific in which proteins are involved.
34.
What characteristics make yeasts a good model for learning about signaling in humans?
35.
Why is signaling in multicellular organisms more complicated than signaling in single-celled organisms?
36.
Pseudomonas infections are very common in hospital settings. Why would it be important for doctors to determine the bacterial load before treating an infected patient? | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.06%3A_Cell_Communication/2.6.09%3A_Review_Questions.txt |
• 2.7.1: Introduction
A human, as well as every sexually reproducing organism, begins life as a fertilized egg (embryo) or zygote. Trillions of cell divisions subsequently occur in a controlled manner to produce a complex, multicellular human. In other words, that original single cell is the ancestor of every other cell in the body. Once a being is fully grown, cell reproduction is still necessary to repair or regenerate tissues.
• 2.7.2: Cell Division
The continuity of life from one cell to another has its foundation in the reproduction of cells by way of the cell cycle. The cell cycle is an orderly sequence of events that describes the stages of a cell’s life from the division of a single parent cell to the production of two new daughter cells. The mechanisms involved in the cell cycle are highly regulated.
• 2.7.3: The Cell Cycle
The cell cycle is an ordered series of events involving cell growth and cell division that produces two new daughter cells. Cells on the path to cell division proceed through a series of precisely timed and carefully regulated stages of growth, DNA replication, and division that produces two identical (clone) cells. The cell cycle has two major phases: interphase and the mitotic phase.
• 2.7.4: Control of the Cell Cycle
The length of the cell cycle is highly variable, even within the cells of a single organism. In humans, the frequency of cell turnover ranges from a few hours in early embryonic development, to an average of two to five days for epithelial cells, and to an entire human lifetime spent in G0 by specialized cells, such as cortical neurons or cardiac muscle cells. There is also variation in the time that a cell spends in each phase of the cell cycle.
• 2.7.5: Cancer and the Cell Cycle
Cancer is the result of unchecked cell division caused by a breakdown of the mechanisms that regulate the cell cycle. The loss of control begins with a change in the DNA sequence of a gene that codes for one of the regulatory molecules. Faulty instructions lead to a protein that does not function as it should. Any disruption of the monitoring system can allow other mistakes to be passed on to the daughter cells. Each successive cell division will give rise to daughter cells with even more damage
• 2.7.6: Prokaryotic Cell Division
In both prokaryotic and eukaryotic cell division, the genomic DNA is replicated and then each copy is allocated into a daughter cell. In addition, the cytoplasmic contents are divided evenly and distributed to the new cells. However, there are many differences between prokaryotic and eukaryotic cell division. Bacteria have a single, circular DNA chromosome but no nucleus. Therefore, mitosis is not necessary in bacterial cell division.
• 2.7.7: Key Terms
• 2.7.8: Chapter Summary
• 2.7.9: Visual Connection Questions
• 2.7.10: Review Questions
• 2.7.11: Critical Thinking Questions
Thumbnail: Life cycle of the cell. (CC BY-SA 4.0; BruceBlaus).
• Connie Rye (East Mississippi Community College), Robert Wise (University of Wisconsin, Oshkosh), Vladimir Jurukovski (Suffolk County Community College), Jean DeSaix (University of North Carolina at Chapel Hill), Jung Choi (Georgia Institute of Technology), Yael Avissar (Rhode Island College) among other contributing authors. Original content by OpenStax (CC BY 4.0; Download for free at http://cnx.org/contents/[email protected]).
2.07: Cell Reproduction
Figure 10.1 A sea urchin begins life as a single diploid cell (zygote) that (a) divides through cell division to form two genetically identical daughter cells, visible here through scanning electron microscopy (SEM). After four rounds of cell division, (b) there are 16 cells, as seen in this SEM image. After many rounds of cell division, the individual develops into a complex, multicellular organism, as seen in this (c) mature sea urchin. (credit a: modification of work by Evelyn Spiegel, Louisa Howard; credit b: modification of work by Evelyn Spiegel, Louisa Howard; credit c: modification of work by Marco Busdraghi; scale-bar data from Matt Russell)
A human, like every sexually reproducing organism, begins life as a fertilized egg (embryo) or zygote. In our species, billions of cell divisions subsequently must occur in a controlled manner in order to produce a complex, multicellular human comprising trillions of cells. Thus, the original single-celled zygote is literally the ancestor of all cells in the body. However, once a human is fully grown, cell reproduction is still necessary to repair and regenerate tissues, and sometimes to increase our size! In fact, all multicellular organisms use cell division for growth and the maintenance and repair of cells and tissues. Cell division is closely regulated, and the occasional failure of this regulation can have life-threatening consequences. Single-celled organisms may also use cell division as their method of reproduction. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.07%3A_Cell_Reproduction/2.7.01%3A_Introduction.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Describe the structure of prokaryotic and eukaryotic genomes
• Distinguish between chromosomes, genes, and traits
• Describe the mechanisms of chromosome compaction
The continuity of life from one cell to another has its foundation in the reproduction of cells by way of the cell cycle. The cell cycle is an orderly sequence of events that describes the stages of a cell’s life from the division of a single parent cell to the production of two new genetically identical daughter cells.
Genomic DNA
Before discussing the steps a cell must undertake to replicate and divide its DNA, a deeper understanding of the structure and function of a cell’s genetic information is necessary. A cell’s DNA, packaged as a double-stranded DNA molecule, is called its genome. In prokaryotes, the genome is composed of a single, double-stranded DNA molecule in the form of a loop or circle (Figure 10.2). The region in the cell containing this genetic material is called a nucleoid. Some prokaryotes also have smaller loops of DNA called plasmids that are not essential for normal growth. Bacteria can exchange these plasmids with other bacteria, sometimes receiving beneficial new genes that the recipient can add to their chromosomal DNA. Antibiotic resistance is one trait that often spreads through a bacterial colony through plasmid exchange from resistant donors to recipient cells.
Figure 10.2 Prokaryotes, including both Bacteria and Archaea, have a single, circular chromosome located in a central region called the nucleoid.
In eukaryotes, the genome consists of several double-stranded linear DNA molecules (Figure 10.3). Each species of eukaryotes has a characteristic number of chromosomes in the nuclei of its cells. Human body (somatic) cells have 46 chromosomes, while human gametes (sperm or eggs) have 23 chromosomes each. A typical body cell contains two matched or homologous sets of chromosomes (one set from each biological parent)—a configuration known as diploid. (Note: The letter n is used to represent a single set of chromosomes; therefore, a diploid organism is designated 2n.) Human cells that contain one set of chromosomes are called gametes, or sex cells; these are eggs and sperm, and are designated 1n, or haploid.
Upon fertilization, each gamete contributes one set of chromosomes, creating a diploid cell containing matched pairs of chromosomes called homologous (“same knowledge”) chromosomes. Homologous chromosomes are the same length and have specific nucleotide segments called genes in exactly the same location, or locus. Genes, the functional units of chromosomes, determine specific characteristics by coding for specific proteins. Traits are the variations of those characteristics. For example, hair color is a characteristic with traits that are blonde, brown, or black, and many colors in between.
Figure 10.3 There are 23 pairs of homologous chromosomes in a female human somatic cell. The condensed chromosomes are viewed within the nucleus (top), removed from a cell during mitosis (also called karyokinesis or nuclear division) and spread out on a slide (right), and artificially arranged according to length (left); an arrangement like this is called a karyotype. In this image, the chromosomes were exposed to fluorescent stains for differentiation of the different chromosomes. A method of staining called “chromosome painting” employs fluorescent dyes that highlight chromosomes in different colors. (credit: National Human Genome Project/NIH)
Each copy of a homologous pair of chromosomes originates from a different parent; therefore, the different genes (alleles) themselves are not identical, although they code for the same traits such as “hair color.” The variation of individuals within a species is due to the specific combination of the genes inherited from both parents. Even a slightly altered sequence of nucleotides within a gene can result in an alternative trait. For example, there are three possible gene sequences on the human chromosome that code for blood type: sequence A, sequence B, and sequence O. Because all diploid human cells have two copies of the chromosome that determines blood type, the blood type (the trait) is determined by the two alleles of the marker gene that are inherited. It is possible to have two copies of the same gene sequence on both homologous chromosomes, with one on each (for example, AA, BB, or OO), or two different sequences, such as AB, AO, or BO.
Apparently minor variations of traits, such as blood type, eye color, and handedness, contribute to the natural variation found within a species, but even though they seem minor, these traits may be connected with the expression of other traits as of yet unknown. However, if the entire DNA sequence from any pair of human homologous chromosomes is compared, the difference is much less than one percent. The sex chromosomes, X and Y, are the single exception to the rule of homologous chromosome uniformity: Other than a small amount of homology that is necessary to accurately produce gametes, the genes found on the X and Y chromosomes are different.
Eukaryotic Chromosomal Structure and Compaction
If the DNA from all 46 chromosomes in a human cell nucleus were laid out end-to-end, it would measure approximately two meters; however, its diameter would be only 2 nm! Considering that the size of a typical human cell is about 10 µm (100,000 cells lined up to equal one meter), DNA must be tightly packaged to fit in the cell’s nucleus. At the same time, it must also be readily accessible for the genes to be expressed. For this reason, the long strands of DNA are condensed into compact chromosomes during certain stages of the cell cycle. There are a number of ways that chromosomes are compacted.
In the first level of compaction, short stretches of the DNA double helix wrap around a core of eight histone proteins at regular intervals along the entire length of the chromosome (Figure 10.4). The DNA-histone complex is called chromatin. The beadlike, histone DNA complex is called a nucleosome, and DNA connecting the nucleosomes is called linker DNA. A DNA molecule in this form is about seven times shorter than the double helix without the histones, and the beads are about 10 nm in diameter, in contrast with the 2-nm diameter of a DNA double helix.
The second level of compaction occurs as the nucleosomes and the linker DNA between them coil into a 30-nm chromatin fiber. This coiling further condenses the chromosome so that it is now about 50 times shorter than the extended form.
In the third level of compaction, a variety of fibrous proteins is used to “pack the chromatin.” These fibrous proteins also ensure that each chromosome in a non-dividing cell occupies a particular area of the nucleus that does not overlap with that of any other chromosome (see the top image in Figure 10.3).
Figure 10.4 Each linear chromosome in a eukaryotic cell is packaged into chromatin, a combination of DNA and proteins. The double-stranded DNA helix associates with the core histones to form nucleosomes. These nucleosomes are further organized into a 30 nm fiber by the linker histone, H1. The fiber then associates with additional proteins to form loops and higher-order heterochromatin packing. DNA packing reaches its most condensed state during metaphase in mitosis in preparation for chromosome separation. Chromatin packing is dynamic and undergoes reversible changes in response to changes in gene expression and the cell cycle. Credit: Rao, A., Ryan, K. Fletcher, S. Hawkins, A. and Tag, A. Department of Biology, Texas A&M University.
DNA replicates in the S phase of interphase, which technically is not a part of mitosis, but must always precede it. After replication, the chromosomes are composed of two linked sister chromatids. When fully compact, the pairs of identically packed chromosomes are bound to each other by cohesin proteins. The connection between the sister chromatids is closest in a region called the centromere. The conjoined sister chromatids, with a diameter of about 1 µm, are visible under a light microscope. The centromeric region is highly condensed and thus will appear as a constricted area.
Link to Learning
Link to Learning
This animation illustrates the different levels of chromosome packing. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.07%3A_Cell_Reproduction/2.7.02%3A_Cell_Division.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Describe the three stages of interphase
• Discuss the behavior of chromosomes during karyokinesis/mitosis
• Explain how the cytoplasmic content is divided during cytokinesis
• Define the quiescent G0 phase
The cell cycle is an ordered series of events involving cell growth and cell division that produces two new daughter cells. Cells on the path to cell division proceed through a series of precisely timed and carefully regulated stages of growth, DNA replication, and nuclear and cytoplasmic division that ultimately produces two identical (clone) cells. The cell cycle has two major phases: interphase and the mitotic phase (Figure 10.5). During interphase, the cell grows and DNA is replicated. During the mitotic phase, the replicated DNA and cytoplasmic contents are separated, and the cell cytoplasm is typically partitioned by a third process of the cell cycle called cytokinesis. We should note, however, that interphase and mitosis (karyokinesis) may take place without cytokinesis, in which case cells with multiple nuclei (multinucleate cells) are produced.
Figure 10.5 The cell cycle in multicellular organisms consists of interphase and the mitotic phase. During interphase, the cell grows and the nuclear DNA is duplicated. Interphase is followed by the mitotic phase. During the mitotic phase, the duplicated chromosomes are segregated and distributed into daughter nuclei. Following mitosis, the cytoplasm is usually divided as well by cytokinesis, resulting in two genetically identical daughter cells.
Interphase
During interphase, the cell undergoes normal growth processes while also preparing for cell division. In order for a cell to move from interphase into the mitotic phase, many internal and external conditions must be met. The three stages of interphase are called G1, S, and G2.
G1 Phase (First Gap)
The first stage of interphase is called the G1 phase (first gap) because, from a microscopic point of view, little change is visible. However, during the G1 stage, the cell is quite active at the biochemical level. The cell is accumulating the building blocks of chromosomal DNA and the associated proteins as well as accumulating sufficient energy reserves to complete the task of replicating each chromosome in the nucleus.
S Phase (Synthesis of DNA)
Throughout interphase, nuclear DNA remains in a semi-condensed chromatin configuration. In the S phase, DNA replication can proceed through the mechanisms that result in the formation of identical pairs of DNA molecules—sister chromatids—that are firmly attached at the centromeric region. The centrosome is also duplicated during the S phase. The two centrosomes will give rise to the mitotic spindle, the apparatus that orchestrates the movement of chromosomes during mitosis. For example, roughly at the center of each animal cell, the centrosomes are associated with a pair of rod-like objects, the centrioles, which are positioned at right angles to each other. Centrioles help organize cell division. We should note, however, that centrioles are not present in the centrosomes of other eukaryotic organisms, such as plants and most fungi.
G2 Phase (Second Gap)
In the G2 phase, the cell replenishes its energy stores and synthesizes proteins necessary for chromosome manipulation and movement. Some cell organelles are duplicated, and the cytoskeleton is dismantled to provide resources for the mitotic phase. There may be additional cell growth during G2. The final preparations for the mitotic phase must be completed before the cell is able to enter the first stage of mitosis.
The Mitotic Phase
The mitotic phase is a multistep process during which the duplicated chromosomes are aligned, separated, and move into two new, identical daughter cells. The first portion of the mitotic phase is called karyokinesis, or nuclear division. As we have just seen, the second portion of the mitotic phase (and often viewed as a process separate from and following mitosis) is called cytokinesis—the physical separation of the cytoplasmic components into the two daughter cells.
Link to Learning
Link to Learning
Revisit the stages of mitosis at this site.
Karyokinesis (Mitosis)
Karyokinesis, also known as mitosis, is divided into a series of phases—prophase, prometaphase, metaphase, anaphase, and telophase—that result in the division of the cell nucleus (Figure 10.6).
Visual Connection
Visual Connection
Figure 10.6 G2 of Interphase – The last stage of interphase is the second gap period, G2. During this stage, cells grow, replenish energy and synthesize needed macromolecules, such as proteins and lipids.
Mitosis - When G2 is complete, the cell will enter mitosis. Although there are 5 phases in mitosis, with the exception of the metaphase to anaphase transition, these phases are not discrete and happen as a continuous process. Prophase is the first stage in mitosis. The nuclear envelope begins to break down and chromosomes condense and are now visible. Spindle fibers start to appear and centrosomes begin to move towards opposite poles.
Prometaphase - Chromosomes continue to condense and are more visible. Kinetochores appear at the centromere and kinetochore microtubules attach. Centrosomes continue to move towards opposite poles.
Metaphase – The mitotic spindle is fully developed and centrosomes are at opposite poles. Chromosomes are aligned at the “equatorial plate”, and each sister chromatid rests on one side of the plate, with spindle fibers attached to them.
Anaphase - Sister chromatids are pulled apart by spindle fibers and are separated from each other. Each chromatid is now a chromosome.
Telophase and Cytokinesis - Chromosomes arrive at opposite poles and start to decondense and become less visible. The nuclear envelope reassembles and begins to surround each new set of chromosomes. The mitotic spindle assembly breaks down and the division of the cytoplasm begins via cytokinesis. This physical separation into two cells are remarkably different processes in plant and animal cells.
Credit: Rao, A., Hawkins, A.and Fletcher, S. Department of Biology, Texas A&M University.
Which of the following is the correct order of events in mitosis?
1. Sister chromatids line up at the metaphase plate. The kinetochore becomes attached to the mitotic spindle. The nucleus reforms and the cell divides. Cohesin proteins break down and the sister chromatids separate.
2. The kinetochore becomes attached to the mitotic spindle. Cohesin proteins break down and the sister chromatids separate. Sister chromatids line up at the metaphase plate. The nucleus reforms and the cell divides.
3. The kinetochore becomes attached to the cohesin proteins. Sister chromatids line up at the metaphase plate. The kinetochore breaks down and the sister chromatids separate. The nucleus reforms and the cell divides.
4. The kinetochore becomes attached to the mitotic spindle. Sister chromatids line up at the metaphase plate. Cohesin proteins break down and the sister chromatids separate. The nucleus reforms and the cell divides.
Prophase (the “first phase”): the nuclear envelope starts to dissociate into small vesicles, and the membranous organelles (such as the Golgi complex [Golgi apparatus] and the endoplasmic reticulum), fragment and disperse toward the periphery of the cell. The nucleolus disappears (disperses) as well, and the centrosomes begin to move to opposite poles of the cell. Microtubules that will form the mitotic spindle extend between the centrosomes, pushing them farther apart as the microtubule fibers lengthen. The sister chromatids begin to coil more tightly with the aid of condensin proteins and now become visible under a light microscope.
Prometaphase (the “first change phase”): Many processes that began in prophase continue to advance. The remnants of the nuclear envelope fragment further, and the mitotic spindle continues to develop as more microtubules assemble and stretch across the length of the former nuclear area. Chromosomes become even more condensed and discrete. Each sister chromatid develops a protein structure called a kinetochore in its centromeric region (Figure 10.7). The proteins of the kinetochore attract and bind to the mitotic spindle microtubules. As the spindle microtubules extend from the centrosomes, some of these microtubules come into contact with and firmly bind to the kinetochores. Once a mitotic fiber attaches to a chromosome, the chromosome will be oriented until the kinetochores of sister chromatids face the opposite poles. Eventually, all the sister chromatids will be attached via their kinetochores to microtubules from opposing poles. Spindle microtubules that do not engage the chromosomes are called polar microtubules. These microtubules overlap each other midway between the two poles and contribute to cell elongation. Astral microtubules are located near the poles, aid in spindle orientation, and are required for the regulation of mitosis.
Figure 10.7 During prometaphase, mitotic spindle microtubules from opposite poles attach to each sister chromatid at the kinetochore. In anaphase, the connection between the sister chromatids breaks down, and the microtubules pull the chromosomes toward opposite poles.
Metaphase (the “change phase”): All the chromosomes are aligned in a plane called the metaphase plate, or the equatorial plane, roughly midway between the two poles of the cell. The sister chromatids are still tightly attached to each other by cohesin proteins. At this time, the chromosomes are maximally condensed.
Anaphase (“upward phase”): The cohesin proteins degrade, and the sister chromatids separate at the centromere. Each chromatid, now called a single chromosome, is pulled rapidly toward the centrosome to which its microtubule is attached. The cell becomes visibly elongated (oval shaped) as the polar microtubules slide against each other at the metaphase plate where they overlap.
Telophase (the “distance phase”): the chromosomes reach the opposite poles and begin to decondense (unravel), relaxing once again into a stretched-out chromatin configuration. The mitotic spindles are depolymerized into tubulin monomers that will be used to assemble cytoskeletal components for each daughter cell. Nuclear envelopes form around the chromosomes, and nucleosomes appear within the nuclear area.
Cytokinesis
Figure 10.8 Mitotic Cell at Metaphase. The microtubule spindle has completed the alignment of chromosomes at the metaphase plate in preparation for the separation of sister chromatids during anaphase. Credit: Fletcher, S., Ryan, K. and Rao, A., Department of Biology, Texas A&M University.
Cytokinesis, or “cell motion,” is sometimes viewed as the second main stage of the mitotic phase, during which cell division is completed via the physical separation of the cytoplasmic components into two daughter cells However, as we have seen earlier, cytokinesis can also be viewed as a separate phase, which may or may not take place following mitosis. If cytokinesis does take place, cell division is not complete until the cell components have been apportioned and completely separated into the two daughter cells. Although the stages of mitosis are similar for most eukaryotes, the process of cytokinesis is quite different for eukaryotes that have cell walls, such as plant cells.
In animal cells, cytokinesis typically starts during late anaphase. A contractile ring composed of actin filaments forms just inside the plasma membrane at the former metaphase plate. The actin filaments pull the equator of the cell inward, forming a fissure. This fissure is called the cleavage furrow. The furrow deepens as the actin ring contracts, and eventually the membrane is cleaved in two (Figure 10.9).
In plant cells, a new cell wall must form between the daughter cells. During interphase, the Golgi apparatus accumulates enzymes, structural proteins, and glucose molecules prior to breaking into vesicles and dispersing throughout the dividing cell. During telophase, these Golgi vesicles are transported on microtubules to form a phragmoplast (a vesicular structure) at the metaphase plate. There, the vesicles fuse and coalesce from the center toward the cell walls; this structure is called a cell plate. As more vesicles fuse, the cell plate enlarges until it merges with the cell walls at the periphery of the cell. Enzymes use the glucose that has accumulated between the membrane layers to build a new cell wall. The Golgi membranes become parts of the plasma membrane on either side of the new cell wall (Figure 10.9).
Figure 10.9 Animal cell cleavage - Contraction of actin filaments by myosin pull the “equator” of the cell causing an invagination of the cell (a fissure called a cleavage furrow). The cleavage furrow gets continuously deeper until it eventually divides the cell into two new, independent daughter cells.
Plant cell wall formation - A mixture of enzymes, proteins, and glucose molecules are transported via vesicles to the center of the cell. These vesicles continuously build upon each other until a completely new cell wall has emerged and two new cells are formed, independent of one another.
Credit: Rao, A., Ryan, K., Hawkins, A.and Fletcher, S. Department of Biology, Texas A&M University.
G0 Phase
Not all cells adhere to the classic cell-cycle pattern in which a newly formed daughter cell immediately enters the preparatory phases of interphase, closely followed by the mitotic phase, and cytokinesis. Cells in G0 phase are not actively preparing to divide. The cell is in a quiescent (inactive) stage that occurs when cells exit the cell cycle. Some cells enter G0 temporarily due to environmental conditions such as availability of nutrients, or stimulation by growth factors. The cell will remain in this phase until conditions improve or until an external signal triggers the onset of G1. Other cells that never or rarely divide, such as mature cardiac muscle and nerve cells, remain in G0 permanently.
Scientific Method Connection
Scientific Method Connection
Determine the Time Spent in Cell-Cycle Stages
Problem: How long does a cell spend in interphase compared to each stage of mitosis?
Background: A prepared microscope slide of whitefish blastula cross-sections will show cells arrested in various stages of the cell cycle. (Note: It is not visually possible to separate the stages of interphase from each other, but the mitotic stages are readily identifiable.) If 100 cells are examined, the number of cells in each identifiable cell-cycle stage will give an estimate of the time it takes for the cell to complete that stage.
Problem Statement: Given the events included in all of interphase and those that take place in each stage of mitosis, estimate the length of each stage based on a 24-hour cell cycle. Before proceeding, state your hypothesis.
Test your hypothesis: Test your hypothesis by doing the following:
1. Place a fixed and stained microscope slide of whitefish blastula cross-sections under the scanning objective of a light microscope.
2. Locate and focus on one of the sections using the low-power objective of your microscope. Notice that the section is a circle composed of dozens of closely packed individual cells.
3. Switch to the medium-power objective and refocus. With this objective, individual cells are clearly visible, but the chromosomes will still be very small.
4. Switch to the high-power objective and slowly move the slide left to right, and up and down to view all the cells in the section (Figure 10.10). As you scan, you will notice that most of the cells are not undergoing mitosis but are in the interphase period of the cell cycle.
Figure 10.10 Slowly scan whitefish blastula cells with the high-power objective as illustrated in image (a) to identify their mitotic stage. (b) A microscopic image of the scanned cells is shown. (credit “micrograph”: modification of work by Linda Flora; scale-bar data from Matt Russell)
• Practice identifying the various stages of the cell cycle, using the drawings of the stages as a guide (Figure 10.6).
• Once you are confident about your identification, begin to record the stage of each cell you encounter as you scan left to right, and top to bottom across the blastula section.
• Keep a tally of your observations and stop when you reach 100 cells identified.
• The larger the sample size (total number of cells counted), the more accurate the results. If possible, gather and record group data prior to calculating percentages and making estimates.
• Record your observations: Make a table similar to Table 10.1 within which to record your observations.
Results of Cell Stage Identification
Phase or StageIndividual TotalsGroup TotalsPercent
Interphase
Prophase
Metaphase
Anaphase
Telophase
Cytokinesis
Totals100100100 percent
Table 10.1
Analyze your data/report your results: To find the length of time whitefish blastula cells spend in each stage, multiply the percent (recorded as a decimal) by 24 hours. Make a table similar to Table 10.2 to illustrate your data.
Estimate of Cell Stage Length
Phase or StagePercentTime in Hours
Interphase
Prophase
Metaphase
Anaphase
Telophase
Cytokinesis
Table 10.2
Draw a conclusion: Did your results support your estimated times? Were any of the outcomes unexpected? If so, discuss those events in that stage that may have contributed to the calculated time. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.07%3A_Cell_Reproduction/2.7.03%3A_The_Cell_Cycle.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Understand how the cell cycle is controlled by mechanisms that are both internal and external to the cell
• Explain how the three internal “control checkpoints” occur at the end of G1, at the G2/M transition, and during metaphase
• Describe the molecules that control the cell cycle through positive and negative regulation
The length of the cell cycle is highly variable, even within the cells of a single organism. In humans, the frequency of cell turnover ranges from a few hours in early embryonic development, to an average of two to five days for epithelial cells, and to an entire human lifetime spent in G0 by specialized cells, such as cortical neurons or cardiac muscle cells.
There is also variation in the time that a cell spends in each phase of the cell cycle. When rapidly dividing mammalian cells are grown in a culture (outside the body under optimal growing conditions), the length of the cell cycle is about 24 hours. In rapidly dividing human cells with a 24-hour cell cycle, the G1 phase lasts approximately nine hours, the S phase lasts 10 hours, the G2 phase lasts about four and one-half hours, and the M phase lasts approximately one-half hour. By comparison, in fertilized eggs (and early embryos) of fruit flies, the cell cycle is completed in about eight minutes. This is because the nucleus of the fertilized egg divides many times by mitosis but does not go through cytokinesis until a multinucleate “zygote” has been produced, with many nuclei located along the periphery of the cell membrane, thereby shortening the time of the cell division cycle. The timing of events in the cell cycle of both “invertebrates” and “vertebrates” is controlled by mechanisms that are both internal and external to the cell.
Regulation of the Cell Cycle by External Events
Both the initiation and inhibition of cell division are triggered by events external to the cell when it is about to begin the replication process. An event may be as simple as the death of nearby cells or as sweeping as the release of growth-promoting hormones, such as human growth hormone (HGH or hGH). A lack of HGH can inhibit cell division, resulting in dwarfism, whereas too much HGH can result in gigantism. Crowding of cells can also inhibit cell division. In contrast, a factor that can initiate cell division is the size of the cell: As a cell grows, it becomes physiologically inefficient due to its decreasing surface-to-volume ratio. The solution to this problem is to divide.
Whatever the source of the message, the cell receives the signal, and a series of events within the cell allows it to proceed into interphase. Moving forward from this initiation point, every parameter required during each cell cycle phase must be met or the cycle cannot progress.
Regulation at Internal Checkpoints
It is essential that the daughter cells produced be exact duplicates of the parent cell. Mistakes in the duplication or distribution of the chromosomes lead to mutations that may be passed forward to every new cell produced from an abnormal cell. To prevent a compromised cell from continuing to divide, there are internal control mechanisms that operate at three main cell-cycle checkpoints: A checkpoint is one of several points in the eukaryotic cell cycle at which the progression of a cell to the next stage in the cycle can be halted until conditions are favorable. These checkpoints occur near the end of G1, at the G2/M transition, and during metaphase (Figure 10.11).
Figure 10.11 The cell cycle is controlled at three checkpoints. The integrity of the DNA is assessed at the G1 checkpoint. Proper chromosome duplication is assessed at the G2 checkpoint. Attachment of each kinetochore to a spindle fiber is assessed at the M checkpoint.
The G1 Checkpoint
The G1 checkpoint determines whether all conditions are favorable for cell division to proceed. The G1 checkpoint, also called the restriction point (in yeast), is a point at which the cell irreversibly commits to the cell division process. External influences, such as growth factors, play a large role in carrying the cell past the G1 checkpoint. In addition to adequate reserves and cell size, there is a check for genomic DNA damage at the G1 checkpoint. A cell that does not meet all the requirements will not be allowed to progress into the S phase. The cell can halt the cycle and attempt to remedy the problematic condition, or the cell can advance into G0 and await further signals when conditions improve.
The G2 Checkpoint
The G2 checkpoint bars entry into the mitotic phase if certain conditions are not met. As at the G1 checkpoint, cell size and protein reserves are assessed. However, the most important role of the G2 checkpoint is to ensure that all of the chromosomes have been replicated and that the replicated DNA is not damaged. If the checkpoint mechanisms detect problems with the DNA, the cell cycle is halted, and the cell attempts to either complete DNA replication or repair the damaged DNA.
The M Checkpoint
The M checkpoint occurs near the end of the metaphase stage of karyokinesis. The M checkpoint is also known as the spindle checkpoint, because it determines whether all the sister chromatids are correctly attached to the spindle microtubules. Because the separation of the sister chromatids during anaphase is an irreversible step, the cycle will not proceed until the kinetochores of each pair of sister chromatids are firmly anchored to at least two spindle fibers arising from opposite poles of the cell.
Link to Learning
Link to Learning
Watch what occurs at the G1, G2, and M checkpoints by visiting this website to see an animation of the cell cycle.
Regulator Molecules of the Cell Cycle
In addition to the internally controlled checkpoints, there are two groups of intracellular molecules that regulate the cell cycle. These regulatory molecules either promote progress of the cell to the next phase (positive regulation) or halt the cycle (negative regulation). Regulator molecules may act individually, or they can influence the activity or production of other regulatory proteins. Therefore, the failure of a single regulator may have almost no effect on the cell cycle, especially if more than one mechanism controls the same event. However, the effect of a deficient or non-functioning regulator can be wide-ranging and possibly fatal to the cell if multiple processes are affected.
Positive Regulation of the Cell Cycle
Two groups of proteins, called cyclins and cyclin-dependent kinases (Cdks), are termed positive regulators. They are responsible for the progress of the cell through the various checkpoints. The levels of the four cyclin proteins fluctuate throughout the cell cycle in a predictable pattern (Figure 10.12). Increases in the concentration of cyclin proteins are triggered by both external and internal signals. After the cell moves to the next stage of the cell cycle, the cyclins that were active in the previous stage are degraded by cytoplasmic enzymes, as shown in Figure 10.12 below.
Figure 10.12 The concentrations of cyclin proteins change throughout the cell cycle. There is a direct correlation between cyclin accumulation and the three major cell-cycle checkpoints. Also note the sharp decline of cyclin levels following each checkpoint (the transition between phases of the cell cycle), as cyclin is degraded by cytoplasmic enzymes. (credit: modification of work by "WikiMiMa"/Wikimedia Commons)
Cyclins regulate the cell cycle only when they are tightly bound to Cdks. To be fully active, the Cdk/cyclin complex must also be phosphorylated in specific locations to activate the complex. Like all kinases, Cdks are enzymes (kinases) that in turn phosphorylate other proteins. Phosphorylation activates the protein by changing its shape. The proteins phosphorylated by Cdks are involved in advancing the cell to the next phase. (Figure 10.13). The levels of Cdk proteins are relatively stable throughout the cell cycle; however, the concentrations of cyclin fluctuate and determine when Cdk/cyclin complexes form. The different cyclins and Cdks bind at specific points in the cell cycle and thus regulate different checkpoints.
Figure 10.13 Cyclin-dependent kinases (Cdks) are protein kinases that, when fully activated, can phosphorylate and thus activate other proteins that advance the cell cycle past a checkpoint. To become fully activated, a Cdk must bind to a cyclin protein and then be phosphorylated by another kinase.
Because the cyclic fluctuations of cyclin levels are largely based on the timing of the cell cycle and not on specific events, regulation of the cell cycle usually occurs by either the Cdk molecules alone or the Cdk/cyclin complexes. Without a specific concentration of fully activated cyclin/Cdk complexes, the cell cycle cannot proceed through the checkpoints.
Although the cyclins are the main regulatory molecules that determine the forward momentum of the cell cycle, there are several other mechanisms that fine-tune the progress of the cycle with negative, rather than positive, effects. These mechanisms essentially block the progression of the cell cycle until problematic conditions are resolved. Molecules that prevent the full activation of Cdks are called Cdk inhibitors. Many of these inhibitor molecules directly or indirectly monitor a particular cell-cycle event. The block placed on Cdks by inhibitor molecules will not be removed until the specific event that the inhibitor monitors is completed.
Negative Regulation of the Cell Cycle
The second group of cell-cycle regulatory molecules are negative regulators, which stop the cell cycle. Remember that in positive regulation, active molecules cause the cycle to progress.
The best understood negative regulatory molecules are retinoblastoma protein (Rb), p53, and p21. Retinoblastoma proteins are a group of tumor-suppressor proteins common in many cells. We should note here that the 53 and 21 designations refer to the functional molecular masses of the proteins (p) in kilodaltons (a dalton is equal to an atomic mass unit, which is equal to one proton or one neutron or 1 g/mol). Much of what is known about cell-cycle regulation comes from research conducted with cells that have lost regulatory control. All three of these regulatory proteins were discovered to be damaged or non-functional in cells that had begun to replicate uncontrollably (i.e., became cancerous). In each case, the main cause of the unchecked progress through the cell cycle was a faulty copy of the regulatory protein.
Rb, p53, and p21 act primarily at the G1 checkpoint. p53 is a multi-functional protein that has a major impact on the commitment of a cell to division because it acts when there is damaged DNA in cells that are undergoing the preparatory processes during G1. If damaged DNA is detected, p53 halts the cell cycle and then recruits specific enzymes to repair the DNA. If the DNA cannot be repaired, p53 can trigger apoptosis, or cell suicide, to prevent the duplication of damaged chromosomes. As p53 levels rise, the production of p21 is triggered. p21 enforces the halt in the cycle dictated by p53 by binding to and inhibiting the activity of the Cdk/cyclin complexes. As a cell is exposed to more stress, higher levels of p53 and p21 accumulate, making it less likely that the cell will move into the S phase.
Rb, which largely monitors cell size, exerts its regulatory influence on other positive regulator proteins. In the active, dephosphorylated state, Rb binds to proteins called transcription factors, most commonly, E2F (Figure 10.14). Transcription factors “turn on” specific genes, allowing the production of proteins encoded by that gene. When Rb is bound to E2F, production of proteins necessary for the G1/S transition is blocked. As the cell increases in size, Rb is slowly phosphorylated until it becomes inactivated. Rb releases E2F, which can now turn on the gene that produces the transition protein, and this particular block is removed. For the cell to move past each of the checkpoints, all positive regulators must be “turned on,” and all negative regulators must be “turned off.”
Visual Connection
Visual Connection
Figure 10.14 Rb halts the cell cycle and releases its hold in response to cell growth.
Rb and other proteins that negatively regulate the cell cycle are sometimes called tumor suppressors. Why do you think the name tumor suppressor might be appropriate for these proteins? | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.07%3A_Cell_Reproduction/2.7.04%3A_Control_of_the_Cell_Cycle.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Describe how cancer is caused by uncontrolled cell growth
• Understand how proto-oncogenes are normal cell genes that, when mutated, become oncogenes
• Describe how tumor suppressors function
• Explain how mutant tumor suppressors cause cancer
Cancer comprises many different diseases caused by a common mechanism: uncontrolled cell growth. Despite the redundancy and overlapping levels of cell-cycle control, errors do occur. One of the critical processes monitored by the cell-cycle checkpoint surveillance mechanism is the proper replication of DNA during the S phase. Even when all of the cell-cycle controls are fully functional, a small percentage of replication errors (mutations) will be passed on to the daughter cells. If changes to the DNA nucleotide sequence occur within a coding portion of a gene and are not corrected, a gene mutation results. All cancers start when a gene mutation gives rise to a faulty protein that plays a key role in cell reproduction.
The change in the cell that results from the malformed protein may be minor: perhaps a slight delay in the binding of Cdk to cyclin or an Rb protein that detaches from its target DNA while still phosphorylated. Even minor mistakes, however, may allow subsequent mistakes to occur more readily. Over and over, small uncorrected errors are passed from the parent cell to the daughter cells and amplified as each generation produces more non-functional proteins from uncorrected DNA damage. Eventually, the pace of the cell cycle speeds up as the effectiveness of the control and repair mechanisms decreases. Uncontrolled growth of the mutated cells outpaces the growth of normal cells in the area, and a tumor (“-oma”) can result.
Figure 10.15 Cell Division and Apoptosis. In an adult organism, normal cell division is balanced by apoptosis (programmed cell death) to maintain a constant cell number in homeostasis. Either an increase in cell division or a decrease in apo ptosis leads an increase in the number of cells and tumor formation. Credit: Rao, A. and Ryan, K. Department of Biology, Texas A&M University.
Proto-oncogenes
The genes that code for the positive cell-cycle regulators are called proto-oncogenes. Proto-oncogenes are normal genes that, when mutated in certain ways, become oncogenes—genes that cause a cell to become cancerous. Consider what might happen to the cell cycle in a cell with a recently acquired oncogene. In most instances, the alteration of the DNA sequence will result in a less functional (or non-functional) protein. The result is detrimental to the cell and will likely prevent the cell from completing the cell cycle; however, the organism is not harmed because the mutation will not be carried forward. If a cell cannot reproduce, the mutation is not propagated and the damage is minimal. Occasionally, however, a gene mutation causes a change that increases the activity of a positive regulator. For example, a mutation that allows Cdk to be activated without being partnered with cyclin could push the cell cycle past a checkpoint before all of the required conditions are met. If the resulting daughter cells are too damaged to undergo further cell divisions, the mutation would not be propagated and no harm would come to the organism. However, if the atypical daughter cells are able to undergo further cell divisions, subsequent generations of cells may accumulate even more mutations, some possibly in additional genes that regulate the cell cycle.
The Cdk gene in the above example is only one of many genes that are considered proto-oncogenes. In addition to the cell-cycle regulatory proteins, any protein that influences the cycle can be altered in such a way as to override cell-cycle checkpoints. An oncogene is any gene that, when altered, leads to an increase in the rate of cell-cycle progression.
Tumor Suppressor Genes
Like proto-oncogenes, many of the negative cell-cycle regulatory proteins were discovered in cells that had become cancerous. Tumor suppressor genes are segments of DNA that code for negative regulator proteins, the type of regulators that, when activated, can prevent the cell from undergoing uncontrolled division. The collective function of the best-understood tumor suppressor gene proteins, Rb, p53, and p21, is to put up a roadblock to cell-cycle progression until certain events are completed. A cell that carries a mutated form of a negative regulator might not be able to halt the cell cycle if there is a problem. Tumor suppressors are similar to brakes in a vehicle: Malfunctioning brakes can contribute to a car crash!
Mutated p53 genes have been identified in more than 50 percent of all human tumor cells. This discovery is not surprising in light of the multiple roles that the p53 protein plays at the G1 checkpoint. A cell with a faulty p53 may fail to detect errors present in the genomic DNA (Figure 10.16). Even if a partially functional p53 does identify the mutations, it may no longer be able to signal the necessary DNA repair enzymes. Either way, damaged DNA will remain uncorrected. At this point, a functional p53 will deem the cell unsalvageable and trigger programmed cell death (apoptosis). The damaged version of p53 found in cancer cells, however, cannot trigger apoptosis.
Visual Connection
Visual Connection
Figure 10.16 The role of normal p53 is to monitor DNA and the supply of oxygen (hypoxia is a condition of reduced oxygen supply). If damage is detected, p53 triggers repair mechanisms. If repairs are unsuccessful, p53 signals apoptosis. A cell with an abnormal p53 protein cannot repair damaged DNA and thus cannot signal apoptosis. Cells with abnormal p53 can become cancerous. (credit: modification of work by Thierry Soussi)
Human papillomavirus can cause cervical cancer. The virus encodes E6, a protein that binds p53. Based on this fact and what you know about p53, what effect do you think E6 binding has on p53 activity?
1. E6 activates p53
2. E6 inactivates p53
3. E6 mutates p53
4. E6 binding marks p53 for degradation
The loss of p53 function has other repercussions for the cell cycle. Mutated p53 might lose its ability to trigger p21 production. Without adequate levels of p21, there is no effective block on Cdk activation. Essentially, without a fully functional p53, the G1 checkpoint is severely compromised and the cell proceeds directly from G1 to S regardless of internal and external conditions. At the completion of this shortened cell cycle, two daughter cells are produced that have inherited the mutated p53 gene. Given the non-optimal conditions under which the parent cell reproduced, it is likely that the daughter cells will have acquired other mutations in addition to the faulty tumor-suppressor gene. Cells such as these daughter cells quickly accumulate both oncogenes and non-functional tumor-suppressor genes. Again, the result is tumor growth.
Link to Learning
Link to Learning
Watch an animation of how cancer results from errors in the cell cycle. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.07%3A_Cell_Reproduction/2.7.05%3A_Cancer_and_the_Cell_Cycle.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Describe the process of binary fission in prokaryotes
• Explain how FtsZ and tubulin proteins are examples of homology
Prokaryotes, such as bacteria, produce daughter cells by binary fission. For unicellular organisms, cell division is the only method to produce new individuals. In both prokaryotic and eukaryotic cells, the outcome of cell reproduction is a pair of daughter cells that are genetically identical to the parent cell. In unicellular organisms, daughter cells are individuals.
To achieve the outcome of cloned offspring, certain steps are essential. The genomic DNA must be replicated and then allocated into the daughter cells; the cytoplasmic contents must also be divided to give both new cells the cellular machinery to sustain life. As we’ve seen with bacterial cells, the genome consists of a single, circular DNA chromosome; therefore, the process of cell division is simplified. Karyokinesis is unnecessary because there is no true nucleus and thus no need to direct one copy of the multiple chromosomes into each daughter cell. This type of cell division is called binary (prokaryotic) fission.
Binary Fission
Due to the relative simplicity of the prokaryotes, the cell division process is a less complicated and much more rapid process than cell division in eukaryotes. As a review of the general information on cell division we discussed at the beginning of this chapter, recall that the single, circular DNA chromosome of bacteria occupies a specific location, the nucleoid region, within the cell (Figure 10.2). Although the DNA of the nucleoid is associated with proteins that aid in packaging the molecule into a compact size, there are no histone proteins and thus no nucleosomes in prokaryotes. The packing proteins of bacteria are, however, related to the cohesin and condensin proteins involved in the chromosome compaction of eukaryotes.
The bacterial chromosome is attached to the plasma membrane at about the midpoint of the cell. The starting point of replication, the origin, is close to the binding site of the chromosome to the plasma membrane (Figure 10.17). Replication of the DNA is bidirectional, moving away from the origin on both strands of the loop simultaneously. As the new double strands are formed, each origin point moves away from the cell wall attachment toward the opposite ends of the cell. As the cell elongates, the growing membrane aids in the transport of the chromosomes. After the chromosomes have cleared the midpoint of the elongated cell, cytoplasmic separation begins. The formation of a ring composed of repeating units of a protein called FtsZ (short for “filamenting temperature-sensitive mutant Z”) directs the partition between the nucleoids. Formation of the FtsZ ring triggers the accumulation of other proteins that work together to recruit new membrane and cell wall materials to the site. A septum is formed between the daughter nucleoids, extending gradually from the periphery toward the center of the cell. When the new cell walls are in place, the daughter cells separate.
Figure 10.17 These images show the steps of binary fission in prokaryotes. (credit: modification of work by “Mcstrother”/Wikimedia Commons)
Evolution Connection
Evolution Connection
Mitotic Spindle Apparatus The precise timing and formation of the mitotic spindle is critical to the success of eukaryotic cell division. Prokaryotic cells, on the other hand, do not undergo karyokinesis and therefore have no need for a mitotic spindle. However, the FtsZ protein that plays such a vital role in prokaryotic cytokinesis is structurally and functionally very similar to tubulin, the building block of the microtubules which make up the mitotic spindle fibers that are necessary for eukaryotic nuclear division. FtsZ proteins can form filaments, rings, and other three-dimensional structures that resemble the way tubulin forms microtubules, centrioles, and various cytoskeletal components. In addition, both FtsZ and tubulin employ the same energy source, GTP (guanosine triphosphate), to rapidly assemble and disassemble complex structures.
FtsZ and tubulin are considered to be homologous structures derived from common evolutionary origins. In this example, FtsZ is the ancestor protein to tubulin (an evolutionarily derived protein). While both proteins are found in extant organisms, tubulin function has evolved and diversified tremendously since evolving from its FtsZ prokaryotic origin. A survey of mitotic assembly components found in present-day unicellular eukaryotes reveals crucial intermediary steps to the complex membrane-enclosed genomes of multicellular eukaryotes (Table 10.3).
Cell Division Apparatus among Various Organisms
Structure of genetic materialDivision of nuclear materialSeparation of daughter cells
ProkaryotesThere is no nucleus. The single, circular chromosome exists in a region of cytoplasm called the nucleoid.Occurs through binary fission. As the chromosome is replicated, the two copies move to opposite ends of the cell by an unknown mechanism.FtsZ proteins assemble into a ring that pinches the cell in two.
Some protistsLinear chromosomes exist in the nucleus.Chromosomes attach to the nuclear envelope, which remains intact. The mitotic spindle passes through the envelope and elongates the cell. No centrioles exist.Microfilaments form a cleavage furrow that pinches the cell in two.
Other protistsLinear chromosomes wrapped around histones exist in the nucleus.A mitotic spindle forms from the centrioles and passes through the nuclear membrane, which remains intact. Chromosomes attach to the mitotic spindle, which separates the chromosomes and elongates the cell.Microfilaments form a cleavage furrow that pinches the cell in two.
Animal cellsLinear chromosomes exist in the nucleus.A mitotic spindle forms from the centrosomes. The nuclear envelope dissolves. Chromosomes attach to the mitotic spindle, which separates the chromosomes and elongates the cell.Microfilaments form a cleavage furrow that pinches the cell in two.
Table 10.3 | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.07%3A_Cell_Reproduction/2.7.06%3A_Prokaryotic_Cell_Division.txt |
anaphase
stage of mitosis during which sister chromatids are separated from each other
binary fission
prokaryotic cell division process
cell cycle
ordered series of events involving cell growth and cell division that produces two new daughter cells
cell plate
structure formed during plant cell cytokinesis by Golgi vesicles, forming a temporary structure (phragmoplast) and fusing at the metaphase plate; ultimately leads to the formation of cell walls that separate the two daughter cells
cell-cycle checkpoint
mechanism that monitors the preparedness of a eukaryotic cell to advance through the various cell-cycle stages
centriole
rod-like structure constructed of microtubules at the center of each animal cell centrosome
centromere
region at which sister chromatids are bound together; a constricted area in condensed chromosomes
chromatid
single DNA molecule of two strands of duplicated DNA and associated proteins held together at the centromere
cleavage furrow
constriction formed by an actin ring during cytokinesis in animal cells that leads to cytoplasmic division
condensin
proteins that help sister chromatids coil during prophase
cyclin
one of a group of proteins that act in conjunction with cyclin-dependent kinases to help regulate the cell cycle by phosphorylating key proteins; the concentrations of cyclins fluctuate throughout the cell cycle
cyclin-dependent kinase (Cdk)
one of a group of protein kinases that helps to regulate the cell cycle when bound to cyclin; it functions to phosphorylate other proteins that are either activated or inactivated by phosphorylation
cytokinesis
division of the cytoplasm following mitosis that forms two daughter cells.
diploid
cell, nucleus, or organism containing two sets of chromosomes (2n)
FtsZ
tubulin-like protein component of the prokaryotic cytoskeleton that is important in prokaryotic cytokinesis (name origin: Filamenting temperature-sensitive mutant Z)
G0 phase
distinct from the G1 phase of interphase; a cell in G0 is not preparing to divide
G1 phase
(also, first gap) first phase of interphase centered on cell growth during mitosis
G2 phase
(also, second gap) third phase of interphase during which the cell undergoes final preparations for mitosis
gamete
haploid reproductive cell or sex cell (sperm, pollen grain, or egg)
gene
physical and functional unit of heredity, a sequence of DNA that codes for a protein.
genome
total genetic information of a cell or organism
haploid
cell, nucleus, or organism containing one set of chromosomes (n)
histone
one of several similar, highly conserved, low molecular weight, basic proteins found in the chromatin of all eukaryotic cells; associates with DNA to form nucleosomes
homologous chromosomes
chromosomes of the same morphology with genes in the same location; diploid organisms have pairs of homologous chromosomes (homologs), with each homolog derived from a different parent
interphase
period of the cell cycle leading up to mitosis; includes G1, S, and G2 phases (the interim period between two consecutive cell divisions)
karyokinesis
mitotic nuclear division
kinetochore
protein structure associated with the centromere of each sister chromatid that attracts and binds spindle microtubules during prometaphase
locus
position of a gene on a chromosome
metaphase
stage of mitosis during which chromosomes are aligned at the metaphase plate
metaphase plate
equatorial plane midway between the two poles of a cell where the chromosomes align during metaphase
mitosis
(also, karyokinesis) period of the cell cycle during which the duplicated chromosomes are separated into identical nuclei; includes prophase, prometaphase, metaphase, anaphase, and telophase
mitotic phase
period of the cell cycle during which duplicated chromosomes are distributed into two nuclei and cytoplasmic contents are divided; includes karyokinesis (mitosis) and cytokinesis
mitotic spindle
apparatus composed of microtubules that orchestrates the movement of chromosomes during mitosis
nucleosome
subunit of chromatin composed of a short length of DNA wrapped around a core of histone proteins
oncogene
mutated version of a normal gene involved in the positive regulation of the cell cycle
origin
(also, ORI) region of the prokaryotic chromosome where replication begins (origin of replication)
p21
cell-cycle regulatory protein that inhibits the cell cycle; its levels are controlled by p53
p53
cell-cycle regulatory protein that regulates cell growth and monitors DNA damage; it halts the progression of the cell cycle in cases of DNA damage and may induce apoptosis
prometaphase
stage of mitosis during which the nuclear membrane breaks down and mitotic spindle fibers attach to kinetochores
prophase
stage of mitosis during which chromosomes condense and the mitotic spindle begins to form
proto-oncogene
normal gene that when mutated becomes an oncogene
quiescent
refers to a cell that is performing normal cell functions and has not initiated preparations for cell division
retinoblastoma protein (Rb)
regulatory molecule that exhibits negative effects on the cell cycle by interacting with a transcription factor (E2F)
S phase
second, or synthesis, stage of interphase during which DNA replication occurs
septum
structure formed in a bacterial cell as a precursor to the separation of the cell into two daughter cells
telophase
stage of mitosis during which chromosomes arrive at opposite poles, decondense, and are surrounded by a new nuclear envelope
tumor suppressor gene
segment of DNA that codes for regulator proteins that prevent the cell from undergoing uncontrolled division | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.07%3A_Cell_Reproduction/2.7.07%3A_Key_Terms.txt |
10.1 Cell Division
Prokaryotes have a single circular chromosome composed of double-stranded DNA, whereas eukaryotes have multiple, linear chromosomes composed of chromatin wrapped around histones, all of which are surrounded by a nuclear membrane. The 46 chromosomes of human somatic cells are composed of 22 pairs of autosomes (matched pairs) and a pair of sex chromosomes, which may or may not be matched. This is the 2n or diploid state. Human gametes have 23 chromosomes, or one complete set of chromosomes; a set of chromosomes is complete with either one of the sex chromosomes, X or Y. This is the n or haploid state. Genes are segments of DNA that code for a specific functional molecule (a protein or RNA). An organism’s traits are determined by the genes inherited from each parent. Duplicated chromosomes are composed of two sister chromatids. Chromosomes are compacted using a variety of mechanisms during certain stages of the cell cycle. Several classes of protein are involved in the organization and packing of the chromosomal DNA into a highly condensed structure. The condensing complex compacts chromosomes, and the resulting condensed structure is necessary for chromosomal segregation during mitosis.
10.2 The Cell Cycle
The cell cycle is an orderly sequence of events. Cells on the path to cell division proceed through a series of precisely timed and carefully regulated stages. In eukaryotes, the cell cycle consists of a long preparatory period, called interphase, during which chromosomes are replicated. Interphase is divided into G1, S, and G2 phases. The mitotic phase begins with karyokinesis (mitosis), which consists of five stages: prophase, prometaphase, metaphase, anaphase, and telophase. The final stage of the cell division process, and sometimes viewed as the final stage of the mitotic phase, is cytokinesis, during which the cytoplasmic components of the daughter cells are separated either by an actin ring (animal cells) or by cell plate formation (plant cells).
10.3 Control of the Cell Cycle
Each step of the cell cycle is monitored by internal controls called checkpoints. There are three major checkpoints in the cell cycle: one near the end of G1, a second at the G2/M transition, and the third during metaphase. Positive regulator molecules allow the cell cycle to advance to the next stage of cell division. Negative regulator molecules monitor cellular conditions and can halt the cycle until specific requirements are met.
10.4 Cancer and the Cell Cycle
Cancer is the result of unchecked cell division caused by a breakdown of the mechanisms that regulate the cell cycle. The loss of control begins with a change in the DNA sequence of a gene that codes for one of the regulatory molecules. Faulty instructions lead to a protein that does not function as it should. Any disruption of the monitoring system can allow other mistakes to be passed on to the daughter cells. Each successive cell division will give rise to daughter cells with even more accumulated damage. Eventually, all checkpoints become nonfunctional, and rapidly reproducing cells crowd out normal cells, resulting in a tumor or leukemia (blood cancer).
10.5 Prokaryotic Cell Division
In both prokaryotic and eukaryotic cell division, the genomic DNA is replicated and then each copy is allocated into a daughter cell. In addition, the cytoplasmic contents are divided evenly and distributed to the new cells. However, there are many differences between prokaryotic and eukaryotic cell division. Bacteria have a single, circular DNA chromosome but no nucleus. Therefore, mitosis (karyokinesis) is not necessary in bacterial cell division. Bacterial cytokinesis is directed by a ring composed of a protein called FtsZ. Ingrowth of membrane and cell wall material from the periphery of the cells results in the formation of a septum that eventually constructs the separate cell walls of the daughter cells.
2.7.09: Visual Connection Questions
1.
Figure 10.14 Rb and other proteins that negatively regulate the cell cycle are sometimes called tumor suppressors. Why do you think the name tumor suppressor might be appropriate for these proteins?
2.
Figure 10.16 Human papillomavirus can cause cervical cancer. The virus encodes E6, a protein that binds p53. Based on this fact and what you know about p53, what effect do you think E6 binding has on p53 activity?
1. E6 activates p53
2. E6 inactivates p53
3. E6 mutates p53
4. E6 binding marks p53 for degradation | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.07%3A_Cell_Reproduction/2.7.08%3A_Chapter_Summary.txt |
3.
A diploid cell has_______ the number of chromosomes as a haploid cell.
1. one-fourth
2. half
3. twice
4. four times
4.
An organism’s traits are determined by the specific combination of inherited _____.
1. cells.
2. genes.
3. proteins.
4. chromatids.
5.
The first level of DNA organization in a eukaryotic cell is maintained by which molecule?
1. cohesin
2. condensin
3. chromatin
4. histone
6.
Identical copies of chromatin held together by cohesin at the centromere are called _____.
1. histones.
2. nucleosomes.
3. chromatin.
4. sister chromatids.
7.
Chromosomes are duplicated during what stage of the cell cycle?
1. G1 phase
2. S phase
3. prophase
4. prometaphase
8.
Which of the following events does not occur during some stages of interphase?
1. DNA duplication
2. organelle duplication
3. increase in cell size
4. separation of sister chromatids
9.
The mitotic spindles arise from which cell structure?
1. centromere
2. centrosome
3. kinetochore
4. cleavage furrow
10.
Attachment of the mitotic spindle fibers to the kinetochores is a characteristic of which stage of mitosis?
1. prophase
2. prometaphase
3. metaphase
4. anaphase
11.
Unpacking of chromosomes and the formation of a new nuclear envelope is a characteristic of which stage of mitosis?
1. prometaphase
2. metaphase
3. anaphase
4. telophase
12.
Separation of the sister chromatids is a characteristic of which stage of mitosis?
1. prometaphase
2. metaphase
3. anaphase
4. telophase
13.
The chromosomes become visible under a light microscope during which stage of mitosis?
1. prophase
2. prometaphase
3. metaphase
4. anaphase
14.
The fusing of Golgi vesicles at the metaphase plate of dividing plant cells forms what structure?
1. cell plate
2. actin ring
3. cleavage furrow
4. mitotic spindle
15.
Figure 10.6 Which of the following is the correct order of events in mitosis?
1. Sister chromatids line up at the metaphase plate. The kinetochore becomes attached to the mitotic spindle. The nucleus reforms and the cell divides. Cohesin proteins break down and the sister chromatids separate.
2. The kinetochore becomes attached to the mitotic spindle. Cohesin proteins break down and the sister chromatids separate. Sister chromatids line up at the metaphase plate. The nucleus reforms and the cell divides.
3. The kinetochore becomes attached to the cohesin proteins. Sister chromatids line up at the metaphase plate. The kinetochore breaks down and the sister chromatids separate. The nucleus reforms and the cell divides.
4. The kinetochore becomes attached to the mitotic spindle. Sister chromatids line up at the metaphase plate. Cohesin proteins break down and the sister chromatids separate. The nucleus reforms and the cell divides.
16.
At which of the cell-cycle checkpoints do external forces have the greatest influence?
1. G1 checkpoint
2. G2 checkpoint
3. M checkpoint
4. G0 checkpoint
17.
What is the main prerequisite for clearance at the G2 checkpoint?
1. cell has reached a sufficient size
2. an adequate stockpile of nucleotides
3. accurate and complete DNA replication
4. proper attachment of mitotic spindle fibers to kinetochores
18.
If the M checkpoint is not cleared, what stage of mitosis will be blocked?
1. prophase
2. prometaphase
3. metaphase
4. anaphase
19.
Which protein is a positive regulator that phosphorylates other proteins when activated?
1. p53
2. retinoblastoma protein (Rb)
3. cyclin
4. cyclin-dependent kinase (Cdk)
20.
Many of the negative regulator proteins of the cell cycle were discovered in what type of cells?
1. gametes
2. cells in G0
3. cancer cells
4. stem cells
21.
Which negative regulatory molecule can trigger cell suicide (apoptosis) if vital cell cycle events do not occur?
1. p53
2. p21
3. retinoblastoma protein (Rb)
4. cyclin-dependent kinase (Cdk)
22.
___________ are changes to the order of nucleotides in a segment of DNA that codes for a protein.
1. Proto-oncogenes
2. Tumor suppressor genes
3. Gene mutations
4. Negative regulators
23.
A gene that codes for a positive cell-cycle regulator is called a(n) _____.
1. kinase inhibitor.
2. tumor suppressor gene.
3. proto-oncogene.
4. oncogene.
24.
A mutated gene that codes for an altered version of Cdk that is active in the absence of cyclin is a(n) _____.
1. kinase inhibitor.
2. tumor suppressor gene.
3. proto-oncogene.
4. oncogene.
25.
Which molecule is a Cdk inhibitor that is controlled by p53?
1. cyclin
2. anti-kinase
3. Rb
4. p21
26.
Which eukaryotic cell-cycle event is missing in binary fission?
1. cell growth
2. DNA duplication
3. karyokinesis
4. cytokinesis
27.
FtsZ proteins direct the formation of a _______ that will eventually form the new cell walls of the daughter cells.
1. contractile ring
2. cell plate
3. cytoskeleton
4. septum
2.7.11: Critical Thinking Questions
28.
Compare and contrast a human somatic cell to a human gamete.
29.
What is the relationship between a genome, chromosomes, and genes?
30.
Eukaryotic chromosomes are thousands of times longer than a typical cell. Explain how chromosomes can fit inside a eukaryotic nucleus.
31.
Briefly describe the events that occur in each phase of interphase.
32.
Chemotherapy drugs such as vincristine (derived from Madagascar periwinkle plants) and colchicine (derived from autumn crocus plants) disrupt mitosis by binding to tubulin (the subunit of microtubules) and interfering with microtubule assembly and disassembly. Exactly what mitotic structure is targeted by these drugs and what effect would that have on cell division?
33.
Describe the similarities and differences between the cytokinesis mechanisms found in animal cells versus those in plant cells.
34.
List some reasons why a cell that has just completed cytokinesis might enter the G0 phase instead of the G1 phase.
35.
What cell-cycle events will be affected in a cell that produces mutated (non-functional) cohesin protein?
36.
Describe the general conditions that must be met at each of the three main cell-cycle checkpoints.
37.
Compare and contrast the roles of the positive cell-cycle regulators negative regulators.
38.
What steps are necessary for Cdk to become fully active?
39.
Rb is a negative regulator that blocks the cell cycle at the G1 checkpoint until the cell achieves a requisite size. What molecular mechanism does Rb employ to halt the cell cycle?
40.
Outline the steps that lead to a cell becoming cancerous.
41.
Explain the difference between a proto-oncogene and a tumor-suppressor gene.
42.
List the regulatory mechanisms that might be lost in a cell producing faulty p53.
43.
p53 can trigger apoptosis if certain cell-cycle events fail. How does this regulatory outcome benefit a multicellular organism?
44.
Name the common components of eukaryotic cell division and binary fission.
45.
Describe how the duplicated bacterial chromosomes are distributed into new daughter cells without the direction of the mitotic spindle. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/02%3A_Unit_II-_The_Cell/2.07%3A_Cell_Reproduction/2.7.10%3A_Review_Questions.txt |
Genetics is the study of genes, heredity, and genetic variation in living organisms. Our comprehensive genetics unit takes learners from the earliest experiments that revealed the basis of genetics through the intricacies of DNA to current applications in the emerging studies of biotechnology and genomics.
• 3.1: Meiosis and Sexual Reproduction
• 3.2: Mendel's Experiments and Heredity
Gregor Johann Mendel was a German-speaking Moravian scientist and Augustinian friar who gained posthumous fame as the founder of the modern science of genetics. Though farmers had known for centuries that crossbreeding of animals and plants could favor certain desirable traits, Mendel's experiments established many of the rules of heredity, now referred to as the laws of Mendelian inheritance.
• 3.3: Modern Understandings of Inheritance
The gene is the physical unit of inheritance, and genes are arranged in a linear order on chromosomes. The behaviors and interactions of chromosomes during meiosis explain, at a cellular level, the patterns of inheritance that we observe in populations. Genetic disorders involving alterations in chromosome number or structure may have dramatic effects and can prevent a fertilized egg from developing altogether.
• 3.4: DNA Structure and Function
On each chromosome, there are thousands of genes that are responsible for determining the genotype and phenotype of the individual. A gene is defined as a sequence of DNA that codes for a functional product. The human haploid genome contains 3 billion base pairs and has between 20,000 and 25,000 functional genes.
• 3.5: Genes and Proteins
Since the rediscovery of Mendel’s work in 1900, the definition of the gene has progressed from an abstract unit of heredity to a tangible molecular entity capable of replication, expression, and mutation. Genes are composed of DNA and are linearly arranged on chromosomes. Genes specify the sequences of amino acids, which are the building blocks of proteins. In turn, proteins are responsible for orchestrating nearly every function of the cell.
• 3.6: Gene Expression
Whereas each cell shares the same genome and DNA sequence, each cell does not turn on, or express, the same set of genes. Each cell type needs a different set of proteins to perform its function. Therefore, only a small subset of proteins is expressed in a cell. In a given cell type, not all genes encoded in the DNA are transcribed into RNA or translated into protein because specific cells in our body have specific functions.
• 3.7: Biotechnology and Genomics
Thumbnail: DNA double helix. (public domain; NIH - Genome Research Institute).
Contributors
Connie Rye (East Mississippi Community College), Robert Wise (University of Wisconsin, Oshkosh), Vladimir Jurukovski (Suffolk County Community College), Jean DeSaix (University of North Carolina at Chapel Hill), Jung Choi (Georgia Institute of Technology), Yael Avissar (Rhode Island College) among other contributing authors. Original content by OpenStax (CC BY 4.0; Download for free at http://cnx.org/contents/[email protected]).
03: Unit III- Genetics
• 3.1.1: Introduction
The ability to reproduce in kind is a basic characteristic of all living things. In kind means that the offspring of any organism closely resemble their parent or parents. Hippopotamuses give birth to hippopotamus calves, Joshua trees produce seeds from which Joshua tree seedlings emerge, and adult flamingos lay eggs that hatch into flamingo chicks. In kind does not generally mean exactly the same.
• 3.1.2: The Process of Meiosis
Sexual reproduction requires fertilization, the union of two cells from two individual organisms. If those two cells each contain one set of chromosomes, then the resulting cell contains two sets of chromosomes. Haploid cells contain one set of chromosomes. Cells containing two sets of chromosomes are called diploid. The number of sets of chromosomes in a cell is called its ploidy level.
• 3.1.3: Sexual Reproduction
Sexual reproduction was an early evolutionary innovation after the appearance of eukaryotic cells. It appears to have been very successful because most eukaryotes are able to reproduce sexually, and in many animals, it is the only mode of reproduction. And yet, scientists recognize some real disadvantages to sexual reproduction. On the surface, creating offspring that are genetic clones of the parent appears to be a better system.
• 3.1.4: Key Terms
• 3.1.5: Chapter Summary
• 3.1.6: Visual Connection Questions
• 3.1.7: Review Questions
• 3.1.8: Critical Thinking Questions
Thumbnail: Example of a Punnett square. (CC BY-SA 3.0; Pbroks13 via Wikimedia Commons).
3.01: Meiosis and Sexual Reproduction
Figure 11.1 Each of us, like the organisms shown above, begins life as a fertilized egg (zygote). After trillions of cell divisions, each of us develops into a complex, multicellular organism. (credit a: modification of work by Frank Wouters; credit b: modification of work by Ken Cole, USGS; credit c: modification of work by Martin Pettitt)
Chapter Outline
The ability to reproduce is a basic characteristic of all organisms: Hippopotamuses give birth to hippopotamus calves; Joshua trees produce seeds from which Joshua tree seedlings emerge; and adult flamingos lay eggs that hatch into flamingo chicks. However, unlike the organisms shown above, offspring may or may not resemble their parents. For example, in the case of most insects such as butterflies (with a complete metamorphosis), the larval forms rarely resemble the adult forms.
Although many unicellular organisms and a few multicellular organisms can produce genetically identical clones of themselves through asexual reproduction, many single-celled organisms and most multicellular organisms reproduce regularly using another method—sexual reproduction. This highly evolved method involves the production by parents of two haploid cells and the fusion of two haploid cells to form a single, genetically recombined diploid cell—a genetically unique organism. In almost all sexually reproducing species, these two haploid cells differ in size, with the smaller cell called “male” and the larger one called “female." These haploid cells are produced by a type of cell division called meiosis. Sexual reproduction, involving both meiosis and fertilization, introduces variation into offspring that may account for the evolutionary success of sexual reproduction. The vast majority of eukaryotic organisms, both multicellular and unicellular, can or must employ some form of meiosis and fertilization to reproduce.
In most plants and animals the zygote formed by fertilization, through thousands of rounds of mitotic cell division, will develop into an adult organism. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/03%3A_Unit_III-_Genetics/3.01%3A_Meiosis_and_Sexual_Reproduction/3.1.01%3A_Introduction.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Describe the behavior of chromosomes during meiosis, and the differences between the first and second meiotic divisions
• Describe the cellular events that take place during meiosis
• Explain the differences between meiosis and mitosis
• Explain the mechanisms within the meiotic process that produce genetic variation among the haploid gametes
Sexual reproduction requires the union of two specialized cells, called gametes, each of which contains one set of chromosomes. When gametes unite, they form a zygote, or fertilized egg that contains two sets of chromosomes. (Note: Cells that contain one set of chromosomes are called haploid; cells containing two sets of chromosomes are called diploid.) If the reproductive cycle is to continue for any sexually reproducing species, then the diploid cell must somehow reduce its number of chromosome sets to produce haploid gametes; otherwise, the number of chromosome sets will double with every future round of fertilization. Therefore, sexual reproduction requires a nuclear division that reduces the number of chromosome sets by half.
Most animals and plants and many unicellular organisms are diploid and therefore have two sets of chromosomes. In each somatic cell of the organism (all cells of a multicellular organism except the gametes or reproductive cells), the nucleus contains two copies of each chromosome, called homologous chromosomes. Homologous chromosomes are matched pairs containing the same genes in identical locations along their lengths. Diploid organisms inherit one copy of each homologous chromosome from each genetic contributor.
Meiosis is the nuclear division that forms haploid cells from diploid cells, and it employs many of the same cellular mechanisms as mitosis. However, as you have learned, mitosis produces daughter cells whose nuclei are genetically identical to the original parent nucleus. In mitosis, both the parent and the daughter nuclei are at the same “ploidy level”—diploid in the case of most multicellular animals. Plants use mitosis to grow as sporophytes, and to grow and produce eggs and sperm as gametophytes; so they use mitosis for both haploid and diploid cells (as well as for all other ploidies). In meiosis, the starting nucleus is always diploid and the daughter nuclei that result are haploid. To achieve this reduction in chromosome number, meiosis consists of one round of chromosome replication followed by two rounds of nuclear division. Because many events that occur during each of the division stages are analogous to the events of mitosis, the same stage names are assigned. However, because there are two rounds of division, the major process and the stages are designated with a “I” or a “II.” Thus, meiosis I is the first round of meiotic division and consists of prophase I, prometaphase I, and so on. Likewise, Meiosis II (during which the second round of meiotic division takes place) includes prophase II, prometaphase II, and so on.
Figure 11.2 Overview of Meiosis. The production of gametes is a crucial process for sexually reproducing organisms. Meiosis is the mechanism used to reduce diploid cells to haploid gametes while introducing genetic diversity. Prior to meiosis, chromosomes are replicated in S-phase to ensure proper number of chromosomes in the resulting gametes. During meiosis, two successive rounds of division reduces the number of chromosomes (ploidy) of the cell by half. going from diploid cells to haploid gametes. Credit: Rao, A., Tag, A, Fletcher, S., and Ryan, K. Department of Biology, Texas A&M University.
Meiosis I
Meiosis is preceded by an interphase consisting of G1, S, and G2 phases, which are nearly identical to the phases preceding mitosis. The G1 phase (the “first gap phase”) is focused on cell growth. During the S phase—the second phase of interphase—the cell copies or replicates the DNA of the chromosomes. Finally, in the G2 phase (the “second gap phase”) the cell undergoes the final preparations for meiosis.
During DNA duplication in the S phase, each chromosome is replicated to produce two identical copies—sister chromatids that are held together at the centromere by cohesin proteins, which hold the chromatids together until anaphase II. (Note: these chromosome copies are called sister chromatids regardless of whether they are in a female gamete or a male gamete.)
Prophase I
Early in prophase I, before the chromosomes can be seen clearly with a microscope, the homologous chromosomes are attached at their tips to the nuclear envelope by proteins. As the nuclear envelope begins to break down, the proteins associated with homologous chromosomes bring the pair closer together. Recall that in mitosis, homologous chromosomes do not pair together. The synaptonemal complex, a lattice of proteins between the homologous chromosomes, first forms at specific locations and then spreads outward to cover the entire length of the chromosomes. The tight pairing of the homologous chromosomes is called synapsis. In synapsis, the genes on the chromatids of the homologous chromosomes are aligned precisely with each other. The synaptonemal complex supports the exchange of chromosomal segments between homologous nonsister chromatids—a process called crossing over. Crossing over can be observed visually after the exchange as chiasmata (singular = chiasma) (Figure 11.3).
In humans, even though the X and Y sex chromosomes are not completely homologous (that is, most of their genes differ), there is a small region of homology that allows the X and Y chromosomes to pair up during prophase I. A partial synaptonemal complex develops only between the regions of homology.
Figure 11.3 Early in prophase I, homologous chromosomes come together to form a synapse. The chromosomes are bound tightly together and in perfect alignment by a protein lattice called a synaptonemal complex and by cohesin proteins at the centromere.
Located at intervals along the synaptonemal complex are large protein assemblies called recombination nodules. These assemblies mark the points of later chiasmata and mediate the multistep process of crossover—or genetic recombination—between the nonsister chromatids. Near the recombination nodule, the double-stranded DNA of each chromatid is cleaved, the cut ends are modified, and a new connection is made between the nonsister chromatids. As prophase I progresses, the synaptonemal complex begins to break down and the chromosomes begin to condense. When the synaptonemal complex is gone, the homologous chromosomes remain attached to each other at the centromere and at chiasmata. The chiasmata remain until anaphase I. The number of chiasmata varies according to the species and the length of the chromosome. There must be at least one chiasma per chromosome for proper separation of homologous chromosomes during meiosis I, but there may be as many as 25. Following crossover, the synaptonemal complex breaks down and the cohesin connection between homologous pairs is removed. At the end of prophase I, the pairs are held together only at the chiasmata (Figure 11.4). These pairs are called tetrads because a total of four sister chromatids of each pair of homologous chromosomes are now visible.
The crossover events are the first source of genetic variation in the nuclei produced by meiosis. A single crossover event between homologous nonsister chromatids leads to a reciprocal exchange of equivalent DNA between an egg-derived chromosome and a sperm-derived chromosome. When a recombinant sister chromatid is moved into a gamete cell it will carry a combination of maternal and paternal genes that did not exist before the crossover. Crossover events can occur almost anywhere along the length of the synapsed chromosomes. Different cells undergoing meiosis will therefore produce different recombinant chromatids, with varying combinations of maternal and parental genes. Multiple crossovers in an arm of the chromosome have the same effect, exchanging segments of DNA to produce genetically recombined chromosomes.
Figure 11.4 Crossover occurs between nonsister chromatids of homologous chromosomes. The result is an exchange of genetic material between homologous chromosomes.
Prometaphase I
The key event in prometaphase I is the attachment of the spindle fiber microtubules to the kinetochore proteins at the centromeres. Kinetochore proteins are multiprotein complexes that bind the centromeres of a chromosome to the microtubules of the mitotic spindle. Microtubules grow from microtubule-organizing centers (MTOCs). In animal cells, MTOCs are centrosomes located at opposite poles of the cell. The microtubules from each pole move toward the middle of the cell and attach to one of the kinetochores of the two fused homologous chromosomes. Each member of the homologous pair attaches to a microtubule extending from opposite poles of the cell so that in the next phase, the microtubules can pull the homologous pair apart. A spindle fiber that has attached to a kinetochore is called a kinetochore microtubule. At the end of prometaphase I, each tetrad is attached to microtubules from both poles, with one homologous chromosome facing each pole. The homologous chromosomes are still held together at the chiasmata. In addition, the nuclear membrane has broken down entirely.
Metaphase I
During metaphase I, the homologous chromosomes are arranged at the metaphase plate—roughly in the midline of the cell, with the kinetochores facing opposite poles. Each homologous pair is oriented randomly at the equator. For example, if the two homologous members of chromosome 1 are labeled a and b, then the chromosomes could line up a-b or b-a. This is important in determining the genes carried by a gamete, as each will only receive one of the two homologous chromosomes. (Recall that homologous chromosomes are not identical. They contain different versions of the same genes, and after recombination during crossing over, each gamete will have a unique genetic makeup that has never existed before.)
The randomness in the alignment of recombined chromosomes at the metaphase plate, coupled with the crossing over events between nonsister chromatids, are responsible for much of the genetic variation in the offspring. To clarify this further, remember that the homologous chromosomes of a sexually reproducing organism are originally inherited as two separate sets, one from each parent. Using humans as an example, one set of 23 chromosomes is present in the egg cell, often called maternal chromosomes because the genetic contributor is often the mother. The other set of 23 chromosomes is contained in the sperm, and the genetic contributor is called a father who provides the paternal chromosomes. Every cell of the multicellular offspring has copies of the original two sets of homologous chromosomes. When the offspring human creates their own gametes through meiosis, the two sets of chromosomes will be rearranged. In prophase I of meiosis, the homologous chromosomes form the tetrads. In metaphase I, these pairs line up at the midway point between the two poles of the cell to form the metaphase plate. Because there is an equal chance that a microtubule fiber will encounter a maternally or paternally inherited chromosome, the arrangement of the tetrads at the metaphase plate is random. Thus, any maternally inherited chromosome may face either pole. Likewise, any paternally inherited chromosome may also face either pole. The orientation of each tetrad is independent of the orientation of the other 22 tetrads.
This event—the random (or independent) assortment of homologous chromosomes at the metaphase plate—is the second mechanism that introduces variation into the gametes or spores. In each cell that undergoes meiosis, the arrangement of the tetrads is different. The number of variations is dependent on the number of chromosomes making up a set. There are two possibilities for orientation at the metaphase plate; the possible number of alignments therefore equals 2n in a diploid cell, where n is the number of chromosomes per haploid set. Humans have 23 chromosome pairs, which results in over eight million (223) possible genetically-distinct gametes just from the random alignment of chromosomes at the metaphase plate. This number does not include the variability that was previously produced by crossing over between the nonsister chromatids. Given these two mechanisms, it is highly unlikely that any two haploid cells resulting from meiosis will have the same genetic composition (Figure 11.5).
To summarize, meiosis I creates genetically diverse gametes in two ways. First, during prophase I, crossover events between the nonsister chromatids of each homologous pair of chromosomes generate recombinant chromatids with new combinations of maternal and paternal genes. Second, the random assortment of tetrads on the metaphase plate produces unique combinations of maternal and paternal chromosomes that will make their way into the gametes.
Figure 11.5 Random, independent assortment during metaphase I is demonstrated by considering a cell with a set of two chromosomes (n = 2). There are two possible homologous chromosome arrangements at the equatorial plane in metaphase I, that are then separated during anaphase I. The total possible number of different gametes is 2n, where n equals the number of chromosomes in a set. In this example, there are four possible genetic combinations for the gametes. With n = 23 in human cells, there are over eight million possible combinations of paternal and maternal chromosomes. Credit: Rao, A.and Fletcher, S. Department of Biology, Texas A&M University.
Anaphase I
In anaphase I, the microtubules pull the linked chromosomes apart. The sister chromatids remain tightly bound together at the centromere. The chiasmata are broken in anaphase I as the microtubules attached to the fused kinetochores pull the homologous chromosomes apart (Figure 11.6).
Telophase I and Cytokinesis
In telophase, the separated chromosomes arrive at opposite poles. The remainder of the typical telophase events may or may not occur, depending on the species. In some organisms, the chromosomes “decondense” and nuclear envelopes form around the separated sets of chromatids produced during telophase I. In other organisms, cytokinesis—the physical separation of the cytoplasmic components into two daughter cells—occurs without reformation of the nuclei. In nearly all species of animals and some fungi, cytokinesis separates the cell contents via a cleavage furrow (constriction of the actin ring that leads to cytoplasmic division). In plants, a cell plate is formed during cell cytokinesis by Golgi vesicles fusing at the metaphase plate. This cell plate will ultimately lead to the formation of cell walls that separate the two daughter cells.
Two haploid cells are the result of the first meiotic division of a diploid cell. The cells are haploid because at each pole, there is just one of each pair of the homologous chromosomes. Therefore, only one full set of the chromosomes is present. This is why the cells are considered haploid—there is only one chromosome set, even though each chromosome still consists of two sister chromatids. Recall that sister chromatids are merely duplicates of one of the two homologous chromosomes (except for changes that occurred during crossing over). In meiosis II, these two sister chromatids will separate, creating four haploid daughter cells.
Link to Learning
Link to Learning
Review the process of meiosis, observing how chromosomes align and migrate, at Meiosis: An Interactive Animation.
Meiosis II
In some species, cells enter a brief interphase, or interkinesis, before entering meiosis II. Interkinesis lacks an S phase, so chromosomes are not duplicated. The two cells produced in meiosis I go through the events of meiosis II in synchrony. During meiosis II, the sister chromatids within the two daughter cells separate, forming four new haploid gametes. The mechanics of meiosis II are similar to mitosis, except that each dividing cell has only one set of homologous chromosomes, each with two chromatids. Therefore, each cell has half the number of sister chromatids to separate out as a diploid cell undergoing mitosis. In terms of chromosomal content, cells at the start of meiosis II are similar to haploid cells in G2, preparing to undergo mitosis.
Prophase II
If the chromosomes decondensed in telophase I, they condense again. If nuclear envelopes were formed, they fragment into vesicles. The MTOCs that were duplicated during interkinesis move away from each other toward opposite poles, and new spindles are formed.
Prometaphase II
The nuclear envelopes are completely broken down, and the spindle is fully formed. Each sister chromatid forms an individual kinetochore that attaches to microtubules from opposite poles.
Metaphase II
The sister chromatids are maximally condensed and aligned at the equator of the cell.
Anaphase II
The sister chromatids are pulled apart by the kinetochore microtubules and move toward opposite poles. Nonkinetochore microtubules elongate the cell.
Figure 11.6 The process of chromosome alignment differs between meiosis I and meiosis II. In prophase I, pairs of homologous chromosomes form chiasmata which allow for crossing over events (genetic diversity). These pairs of homologous chromosomes arrange at the metaphase plate in metaphase I. In anaphase I, homologous chromosomes separate. Telophase I and cytokinesis result in haploid cells with 2 sister chromatids of each chromosome. In prophase II, spindle microtubules form and elongate and any nuclear envelope disappears. Sister chromatids arrange at the midpoint of the cells in metaphase II. In anaphase II, the sister chromatids separate. Telophase II and cytokinesis result in haploid cells with a single copy of each chromosome. Credit: Rao, A., Ryan, K., Fletcher, S. and Tag, A. Department of Biology, Texas A&M University.
Telophase II and Cytokinesis
The chromosomes arrive at opposite poles and begin to decondense. Nuclear envelopes form around the chromosomes. If the parent cell was diploid, as is most commonly the case, then cytokinesis now separates the two cells into four unique haploid cells. The cells produced are genetically unique because of the random assortment of paternal and maternal homologs and because of the recombination of maternal and paternal segments of chromosomes (with their sets of genes) that occurs during crossover. The entire process of meiosis is outlined in Figure 11.7.
Figure 11.7 An animal cell with a diploid number of four (2n = 4) proceeds through the stages of meiosis to form four haploid daughter cells.
Comparing Meiosis and Mitosis
Mitosis and meiosis are both forms of division of the nucleus in eukaryotic cells. They share some similarities, but also exhibit a number of distinct processes that lead to very different outcomes (Figure 11.8). Mitosis is a single nuclear division that results in two nuclei that are usually partitioned into two new cells. The nuclei resulting from a mitotic division are genetically identical to the original nucleus. They have the same number of sets of chromosomes: one set in the case of haploid cells and two sets in the case of diploid cells. In contrast, meiosis consists of two nuclear divisions resulting in four nuclei that are usually partitioned into four new, genetically distinct cells. The four nuclei produced during meiosis are not genetically identical, and they contain one chromosome set only. This is half the number of chromosome sets of the original cell, which is diploid.
The main differences between mitosis and meiosis occur in meiosis I, which is a very different nuclear division than mitosis. In meiosis I, the homologous chromosome pairs physically meet and are bound together with the synaptonemal complex. Following this, the chromosomes develop chiasmata and undergo crossover between nonsister chromatids. In the end, the chromosomes line up along the metaphase plate as tetrads—with kinetochore fibers from opposite spindle poles attached to each kinetochore of a homolog to form a tetrad. All of these events occur only in meiosis I.
When the chiasmata resolve and the tetrad is broken up with the homologous chromosomes moving to one pole or another, the ploidy level—the number of sets of chromosomes in each future nucleus—has been reduced from two to one. For this reason, meiosis I is referred to as a reductional division. There is no such reduction in ploidy level during mitosis.
Meiosis II is analogous to a mitotic division. In this case, the duplicated chromosomes (only one set of them) line up on the metaphase plate with divided kinetochores attached to kinetochore fibers from opposite poles. During anaphase II, as in mitotic anaphase, the kinetochores divide and one sister chromatid—now referred to as a chromosome—is pulled to one pole while the other sister chromatid is pulled to the other pole. If it were not for the fact that there had been crossover, the two products of each individual meiosis II division would be identical (as in mitosis). Instead, they are different because there has always been at least one crossover per chromosome. Meiosis II is not a reduction division because although there are fewer copies of the genome in the resulting cells, there is still one set of chromosomes, as there was at the end of meiosis I.
Figure 11.8 Meiosis and mitosis are both preceded by one cycle of DNA replication; however, meiosis includes two nuclear divisions. The four daughter cells resulting from meiosis are haploid and genetically distinct. The daughter cells resulting from mitosis are diploid and identical to the parent cell.
Evolution Connection
Evolution Connection
The Mystery of the Evolution of MeiosisSome characteristics of organisms are so widespread and fundamental that it is sometimes difficult to remember that they evolved like other simple traits. Meiosis is such an extraordinarily complex series of cellular events that biologists have had trouble testing hypotheses concerning how it may have evolved. Although meiosis is inextricably entwined with sexual reproduction and its advantages and disadvantages, it is important to separate the questions of the evolution of meiosis and the evolution of sex, because early meiosis may have been advantageous for different reasons than it is now. Thinking outside the box and imagining what the early benefits from meiosis might have been is one approach to uncovering how it may have evolved.
Meiosis and mitosis share obvious cellular processes, and it makes sense that meiosis evolved from mitosis. The difficulty lies in the clear differences between meiosis I and mitosis. Adam Wilkins and Robin Holliday1 summarized the unique events that needed to occur for the evolution of meiosis from mitosis. These steps are homologous chromosome pairing and synapsis, crossover exchanges, sister chromatids remaining attached during anaphase, and suppression of DNA replication in interphase. They argue that the first step is the hardest and most important and that understanding how it evolved would make the evolutionary process clearer. They suggest genetic experiments that might shed light on the evolution of synapsis.
There are other approaches to understanding the evolution of meiosis in progress. Different forms of meiosis exist in single-celled protists. Some appear to be simpler or more “primitive” forms of meiosis. Comparing the meiotic divisions of different protists may shed light on the evolution of meiosis. Marilee Ramesh and colleagues2 compared the genes involved in meiosis in protists to understand when and where meiosis might have evolved. Although research is still ongoing, recent scholarship into meiosis in protists suggests that some aspects of meiosis may have evolved later than others. This kind of genetic comparison can tell us what aspects of meiosis are the oldest and what cellular processes they may have borrowed from in earlier cells.
Link to Learning
Link to Learning
Click through the steps of this interactive animation to compare the meiotic process of cell division to that of mitosis at How Cells Divide.
Footnotes
• 1Adam S. Wilkins and Robin Holliday, “The Evolution of Meiosis from Mitosis,” Genetics 181 (2009): 3–12.
• 2Marilee A. Ramesh, Shehre-Banoo Malik and John M. Logsdon, Jr, “A Phylogenetic Inventory of Meiotic Genes: Evidence for Sex in Giardia and an Early Eukaryotic Origin of Meiosis,” Current Biology 15 (2005):185–91. | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/03%3A_Unit_III-_Genetics/3.01%3A_Meiosis_and_Sexual_Reproduction/3.1.02%3A_The_Process_of_Meiosis.txt |
Learning Objectives
By the end of this section, you will be able to do the following:
• Explain that meiosis and sexual reproduction are highly evolved traits
• Identify variation among offspring as a potential evolutionary advantage of sexual reproduction
• Describe the three different life-cycle types among sexually reproducing multicellular organisms.
Sexual reproduction was likely an early evolutionary innovation after the appearance of eukaryotic cells. It appears to have been very successful because most eukaryotes are able to reproduce sexually and, in many animals, it is the only mode of reproduction. And yet, scientists also recognize some real disadvantages to sexual reproduction. On the surface, creating offspring that are genetic clones of the parent appears to be a better system. If the parent organism is successfully occupying a habitat, offspring with the same traits should be similarly successful. There is also the obvious benefit to an organism that can produce offspring whenever circumstances are favorable by asexual budding, fragmentation, or by producing eggs asexually. These methods of reproduction do not require a partner with which to reproduce. Indeed, some organisms that lead a solitary lifestyle have retained the ability to reproduce asexually. In addition, in asexual populations, every individual is capable of reproduction. In sexual populations, the males are not producing the offspring themselves, so hypothetically an asexual population could grow twice as fast.
However, multicellular organisms that exclusively depend on asexual reproduction are exceedingly rare. Why are meiosis and sexual reproductive strategies so common? These are important (and as yet unanswered) questions in biology, even though they have been the focus of much research beginning in the latter half of the 20th century. There are several possible explanations, one of which is that the variation that sexual reproduction creates among offspring is very important to the survival and reproduction of the population. Thus, on average, a sexually reproducing population will leave more descendants than an otherwise similar asexually reproducing population. The only source of variation in asexual organisms is mutation. Mutations that take place during the formation of germ cell lines are also a source of variation in sexually reproducing organisms. However, in contrast to mutation during asexual reproduction, the mutations during sexual reproduction can be continually reshuffled from one generation to the next when different parents combine their unique genomes and the genes are mixed into different combinations by crossovers during prophase I and random assortment at metaphase I.
Evolution Connection
Evolution Connection
The Red Queen HypothesisGenetic variation is the outcome of sexual reproduction, but why are ongoing variations necessary, even under seemingly stable environmental conditions? Enter the Red Queen hypothesis, first proposed by Leigh Van Valen in 1973.3 The concept was named in reference to the Red Queen's race in Lewis Carroll's book, Through the Looking-Glass.
All species coevolve (evolve together) with other organisms. For example, predators evolve with their prey, and parasites evolve with their hosts. Each tiny advantage gained by favorable variation gives a species a reproductive edge over close competitors, predators, parasites, or even prey. However, survival of any given genotype or phenotype in a population is dependent on the reproductive fitness of other genotypes or phenotypes within a given species. The only method that will allow a coevolving species to maintain its own share of the resources is to also continually improve its fitness (the capacity of the members to produce more reproductively viable offspring relative to others within a species). As one species gains an advantage, this increases selection on the other species; they must also develop an advantage or they will be outcompeted. No single species progresses too far ahead because genetic variation among the progeny of sexual reproduction provides all species with a mechanism to improve rapidly. Species that cannot keep up become extinct. The Red Queen’s catchphrase was, “It takes all the running you can do to stay in the same place.” This is an apt description of coevolution between competing species.
Life Cycles of Sexually Reproducing Organisms
Fertilization and meiosis alternate in sexual life cycles. What happens between these two events depends on the organism’s “reproductive strategy.” The process of meiosis reduces the chromosome number by half. Fertilization, the joining of two haploid gametes, restores the diploid condition. Some organisms have a multicellular diploid stage that is most obvious and only produce haploid reproductive cells. Animals, including humans, have this type of life cycle. Other organisms, such as fungi, have a multicellular haploid stage that is most obvious. Plants and some algae have alternation of generations, in which they have multicellular diploid and haploid life stages that are apparent to different degrees depending on the group.
Nearly all animals employ a diploid-dominant life-cycle strategy in which the only haploid cells produced by the organism are the gametes. Early in the development of the embryo, specialized diploid cells, called germ cells, are produced within the gonads (such as the testes and ovaries). Germ cells are capable of mitosis to perpetuate the germ cell line and meiosis to produce haploid gametes. Once the haploid gametes are formed, they lose the ability to divide again. There is no multicellular haploid life stage. Fertilization occurs with the fusion of two gametes, usually from different individuals, restoring the diploid state (Figure 11.9).
Figure 11.9 In animals, sexually reproducing adults form haploid gametes, called egg and sperm, from diploid germ cells. Fusion of the two gametes gives rise to a fertilized egg cell, or zygote. The zygote will undergo multiple rounds of mitosis to produce a multicellular offspring. The germ cells are generated early in the development of the zygote.
Most fungi and algae employ a life-cycle type in which the “body” of the organism—the ecologically important part of the life cycle—is haploid. The haploid cells that make up the tissues of the dominant multicellular stage are formed by mitosis. During sexual reproduction, specialized haploid cells from two individuals—designated the (+) and (−) mating types—join to form a diploid zygote. The zygote immediately undergoes meiosis to form four haploid cells called spores. Although these spores are haploid like the “parents,” they contain a new genetic combination from two parents. The spores can remain dormant for various time periods. Eventually, when conditions are favorable, the spores form multicellular haploid structures through many rounds of mitosis (Figure 11.10).
Visual Connection
Visual Connection
Figure 11.10 Fungi, such as black bread mold (Rhizopus nigricans), have a haploid multicellular stage that produces specialized haploid cells by mitosis that fuse to form a diploid zygote. The zygote undergoes meiosis to produce haploid spores. Each spore gives rise to a multicellular haploid organism by mitosis. Above, different mating hyphae types (denoted as + and –) join to form a zygospore through nuclear fusion. (credit “zygomycota” micrograph: modification of work by “Fanaberka”/Wikimedia Commons)
If a mutation occurs so that a fungus is no longer able to produce a minus mating type, will it still be able to reproduce?
The third life-cycle type, employed by some algae and all plants, is a blend of the haploid-dominant and diploid-dominant extremes. Species with alternation of generations have both haploid and diploid multicellular organisms as part of their life cycle. The haploid multicellular plants are called gametophytes, because they produce gametes from specialized cells. Meiosis is not directly involved in the production of gametes in this case, because the organism that produces the gametes is already haploid. Fertilization between the gametes forms a diploid zygote. The zygote will undergo many rounds of mitosis and give rise to a diploid multicellular plant called a sporophyte. Specialized cells of the sporophyte will undergo meiosis and produce haploid spores. The spores will subsequently develop into the gametophytes (Figure 11.11).
Figure 11.11 Plants have a life cycle that alternates between a multicellular haploid organism and a multicellular diploid organism. In some plants, such as ferns, both the haploid and diploid plant stages are free-living. The diploid plant is called a sporophyte because it produces haploid spores by meiosis. The spores develop into multicellular, haploid plants that are called gametophytes because they produce gametes. The gametes of two individuals will fuse to form a diploid zygote that becomes the sporophyte. (credit “fern”: modification of work by Cory Zanker; credit “sporangia”: modification of work by "Obsidian Soul"/Wikimedia Commons; credit “gametophyte and sporophyte”: modification of work by “Vlmastra”/Wikimedia Commons)
Although all plants utilize some version of the alternation of generations, the relative size of the sporophyte and the gametophyte and the relationship between them vary greatly. In plants such as moss, the gametophyte organism is the free-living plant and the sporophyte is physically dependent on the gametophyte. In other plants, such as ferns, both the gametophyte and sporophyte plants are free-living; however, the sporophyte is much larger. In seed plants, such as magnolia trees and daisies, the gametophyte is composed of only a few cells and, in the case of the female gametophyte, is completely retained within the sporophyte.
Sexual reproduction takes many forms in multicellular organisms. The fact that nearly every multicellular organism on Earth employs sexual reproduction is strong evidence for the benefits of producing offspring with unique gene combinations, though there are other possible benefits as well.
Footnotes
• 3Leigh Van Valen, “A New Evolutionary Law,” Evolutionary Theory 1 (1973): 1–30 | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/03%3A_Unit_III-_Genetics/3.01%3A_Meiosis_and_Sexual_Reproduction/3.1.03%3A_Sexual_Reproduction.txt |
alternation of generations
life-cycle type in which the diploid and haploid stages alternate
chiasmata
(singular, chiasma) the structure that forms at the crossover points after genetic material is exchanged
cohesin
proteins that form a complex that seals sister chromatids together at their centromeres until anaphase II of meiosis
crossover
exchange of genetic material between nonsister chromatids resulting in chromosomes that incorporate genes from both parents of the organism
fertilization
union of two haploid cells from two individual organisms
gametophyte
a multicellular haploid life-cycle stage that produces gametes
germ cells
specialized cell line that produces gametes, such as eggs or sperm
interkinesis
(also, interphase II) brief period of rest between meiosis I and meiosis II
life cycle
the sequence of events in the development of an organism and the production of cells that produce offspring
meiosis
a nuclear division process that results in four haploid cells
meiosis I
first round of meiotic cell division; referred to as reduction division because the ploidy level is reduced from diploid to haploid
meiosis II
second round of meiotic cell division following meiosis I; sister chromatids are separated into individual chromosomes, and the result is four unique haploid cells
recombination nodules
protein assemblies formed on the synaptonemal complex that mark the points of crossover events and mediate the multistep process of genetic recombination between nonsister chromatids of a homologous pair
reduction division
nuclear division that produces daughter nuclei each having one-half as many chromosome sets as the parental nucleus; meiosis I is a reduction division
somatic cell
all the cells of a multicellular organism except the gametes or reproductive cells
spore
haploid cell that can produce a haploid multicellular organism or can fuse with another spore to form a diploid cell
sporophyte
a multicellular diploid life-cycle stage that produces haploid spores by meiosis
synapsis
formation of a close association between homologous chromosomes during prophase I
synaptonemal complex
protein lattice that forms between homologous chromosomes during prophase I, supporting crossover
tetrad
two duplicated homologous chromosomes (four chromatids) bound together by chiasmata during prophase I
3.1.05: Chapter Summary
11.1 The Process of Meiosis
Sexual reproduction requires that organisms produce cells that can fuse during fertilization to produce offspring. In most organisms, fertilization occurs between two haploid cells, the larger being called “female” or “egg” and the smaller being called “male” or “sperm." In most animals, meiosis is used to produce haploid eggs and sperm from diploid parent cells so that the fusion of an egg and sperm produces a diploid zygote. As with mitosis, DNA replication occurs prior to meiosis during the S-phase of the cell cycle so that each chromosome becomes a pair of sister chromatids. In meiosis, there are two rounds of nuclear division resulting in four nuclei and usually four daughter cells, each with half the number of chromosomes as the parent cell. The first division separates homologous chromosomes, and the second—like mitosis—separates chromatids into individual chromosomes. Meiosis generates variation in the daughter nuclei during crossover in prophase I as well as during the random alignment of tetrads at metaphase I. The cells that are produced by meiosis are genetically unique.
Meiosis and mitosis share similar processes, but have distinct outcomes. Mitotic divisions are single nuclear divisions that produce genetically identical daughter nuclei (i.e., each daughter nucleus has the same number of chromosome sets as the original cell). In contrast, meiotic divisions include two nuclear divisions that ultimately produce four genetically different daughter nuclei that have only one chromosome set (instead of the two sets of chromosomes in the parent cell). The main differences between the two nuclear division processes take place during the first division of meiosis: homologous chromosomes pair, crossover, and exchange homologous nonsister chromatid segments. The homologous chromosomes separate into different nuclei during meiosis I, causing a reduction of ploidy level in the first division. The second division of meiosis is similar to a mitotic division, except that the daughter cells do not contain identical genomes because of crossover and chromosome recombination in prophase I.
11.2 Sexual Reproduction
Nearly all eukaryotes undergo sexual reproduction. The variation introduced into the reproductive cells by meiosis provides an important advantage that has made sexual reproduction evolutionarily successful. Meiosis and fertilization alternate in sexual life cycles. The process of meiosis produces unique reproductive cells called gametes, which have half the number of chromosomes as the parent cell. When two haploid gametes fuse, this restores the diploid condition in the new zygote. Thus, most sexually reproducing organisms alternate between haploid and diploid stages. However, the ways in which reproductive cells are produced and the timing between meiosis and fertilization vary greatly.
3.1.06: Visual Connection Questions
1.
Figure 11.10 If a mutation occurs so that a fungus is no longer able to produce a minus mating type, will it still be able to reproduce? | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/03%3A_Unit_III-_Genetics/3.01%3A_Meiosis_and_Sexual_Reproduction/3.1.04%3A_Key_Terms.txt |
2.
Meiosis usually produces ________ daughter cells.
1. two haploid
2. two diploid
3. four haploid
4. four diploid
3.
What structure is most important in forming the tetrads?
1. centromere
2. synaptonemal complex
3. chiasma
4. kinetochore
4.
At which stage of meiosis are sister chromatids separated from each other?
1. prophase I
2. prophase II
3. anaphase I
4. anaphase II
5.
At metaphase I, homologous chromosomes are connected only at what structures?
1. chiasmata
2. recombination nodules
3. microtubules
4. kinetochores
6.
Which of the following is not true in regard to crossover?
1. Spindle microtubules guide the transfer of DNA across the synaptonemal complex.
2. Nonsister chromatids exchange genetic material.
3. Chiasmata are formed.
4. Recombination nodules mark the crossover point.
7.
What phase of mitotic interphase is missing from meiotic interkinesis?
1. G0 phase
2. G1 phase
3. S phase
4. G2 phase
8.
The part of meiosis that is similar to mitosis is ________.
1. meiosis I
2. anaphase I
3. meiosis II
4. interkinesis
9.
If a muscle cell of a typical organism has 32 chromosomes, how many chromosomes will be in a gamete of that same organism?
1. 8
2. 16
3. 32
4. 64
10.
Which statement best describes the genetic content of the two daughter cells in prophase II of meiosis?
1. haploid with one copy of each gene
2. haploid with two copies of each gene
3. diploid with two copies of each gene
4. diploid with four copies of each gene
11.
The pea plants used in Mendel’s genetic inheritance studies were diploid, with 14 chromosomes in somatic cells. Assuming no crossing over events occur, how many unique gametes could one pea plant produce?
1. 28
2. 128
3. 196
4. 16,384
12.
How do telophase I and telophase II differ during meiosis in animal cells?
1. Cells remain diploid at the end of telophase I, but are haploid at the end of telophase II.
2. Daughter cells form a cell plate to divide during telophase I, but divide by cytokinesis during telophase II.
3. Cells enter interphase after telophase I, but not after telophase II.
4. Chromosomes can remain condensed at the end of telophase I, but decondense after telophase II.
13.
What is a likely evolutionary advantage of sexual reproduction over asexual reproduction?
1. Sexual reproduction involves fewer steps.
2. There is a lower chance of using up the resources in a given environment.
3. Sexual reproduction results in variation in the offspring.
4. Sexual reproduction is more cost-effective.
14.
Which type of life cycle has both a haploid and diploid multicellular stage?
1. asexual life cycles
2. most animal life cycles
3. most fungal life cycles
4. alternation of generations
15.
What is the ploidy of the most conspicuous form of most fungi?
1. diploid
2. haploid
3. alternation of generations
4. asexual
16.
A diploid, multicellular life-cycle stage that gives rise to haploid cells by meiosis is called a ________.
1. sporophyte
2. gametophyte
3. spore
4. gamete
17.
Hydras and jellyfish both live in a freshwater lake that is slowly being acidified by the runoff from a chemical plant built upstream. Which population is predicted to be better able to cope with the changing environment?
1. jellyfish
2. hydra
3. The populations will be equally able to cope.
4. Both populations will die.
18.
Many farmers are worried about the decreasing genetic diversity of plants associated with generations of artificial selection and inbreeding. Why is limiting random sexual reproduction of food crops concerning?
1. Mutations during asexual reproduction decrease plant fitness.
2. Consumers do not trust identical-appearing produce.
3. Larger portions of the plant populations are susceptible to the same diseases.
4. Spores are not viable in an agricultural setting.
3.1.08: Critical Thinking Questions
19.
Describe the process that results in the formation of a tetrad.
20.
Explain how the random alignment of homologous chromosomes during metaphase I contributes to the variation in gametes produced by meiosis.
21.
What is the function of the fused kinetochore found on sister chromatids in prometaphase I?
22.
In a comparison of the stages of meiosis to the stages of mitosis, which stages are unique to meiosis and which stages have the same events in both meiosis and mitosis?
23.
Why would an individual with a mutation that prevented the formation of recombination nodules be considered less fit than other members of its species?
24.
Does crossing over occur during prophase II? From an evolutionary perspective, why is this advantageous?
25.
List and briefly describe the three processes that lead to variation in offspring with the same parents.
26.
Animals and plants both have diploid and haploid cells. How does the animal life cycle differ from the alternation of generations exhibited by plants?
27.
Explain why sexual reproduction is beneficial to a population but can be detrimental to an individual offspring.
28.
How does the role of meiosis in gamete production differ between organisms with a diploid-dominant life cycle and organisms with an alternation of generations life cycle?
29.
How do organisms with haploid-dominant life cycles ensure continued genetic diversification in offspring without using a meiotic process to make gametes? | textbooks/bio/Introductory_and_General_Biology/General_Biology_2e_(OpenStax)/03%3A_Unit_III-_Genetics/3.01%3A_Meiosis_and_Sexual_Reproduction/3.1.07%3A_Review_Questions.txt |
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