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Learning Objectives
• Describe research models that indicate the presence of cognitive learning in animals
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, or the manipulation of information using the mind, the most prominent method of human learning. In fact, that is how you are learning right now by reading this information. As students read, they can make mental images of objects or organisms, imagining changes to them or behaviors by them as they 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 (discussed in the previous concept) 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 along with several boxes 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 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 the presence of 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. 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, figuring 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. They did not begin to catch up to the control group until the day food was given; it then took two days longer to learn the maze.
It may not be immediately obvious that this type of learning is different from 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 limited just 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.” 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; some have 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.
Key Points
• Cognitive learning involves the manipulation of information using the mind; it is a great deal more powerful than either operant or classical conditioning.
• The development of complex language by humans has made cognitive learning the most prominent method of human learning.
• Cognitive learning is not limited to primates; rats have demonstrated the ability to build cognitive maps, as well, which are mental representations used to acquire, code, store, recall, and decode information about the environment.
• Sociobiology argues that all animal and human behavior, including aggressiveness and other social interactions, can be explained almost solely in terms of genetics and natural selection.
• Sociobiology is controversial: some have criticized the approach for ignoring the environmental effects on behavior and for being similar to “biological determinism,” or the belief that all behaviors are hardwired into our genes.
Key Terms
• cognitive map: a mental epresentation which serves an organism to acquire, code, store, recall, and decode information about the relative locations and attributes of phenomena in their everyday environment
• cognitive learning: the process by which one acquires knowledge or skill in cognitive processes, which include reasoning, abstract thinking, and problem solving
• sociobiology: the science that applies the principles of evolutionary biology to the study of social behaviour in both humans and animals | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/45%3A_Population_and_Community_Ecology/45.07%3A_Learned_Animal_Behavior/45.7C%3A_Cognitive_Learning_and_Sociobiology.txt |
Learning Objectives
• Explain ecosystem dynamics
An ecosystem is a community of living organisms (plants, animals, and microbes) existing in conjunction with the nonliving components of their environment (air, water, and mineral soil), interacting as a system. These biotic and abiotic components are linked together through nutrient cycles and energy flows. As ecosystems are defined by the network of interactions among organisms, or between organisms and their environment, they can be of any size, but usually encompass specific, limited spaces.
Internal and External Factors
Ecosystems are dynamic entities controlled both by external and internal factors. External factors, such as climate and the parent material that forms the soil, control the overall structure of an ecosystem and the way things work within it, but are not themselves influenced by the ecosystem. While the resource inputs are generally controlled by external processes, the availability of these resources within the ecosystem is controlled by internal factors such as decomposition, root competition, or shading. Other internal factors include disturbance, succession, and the types of species present. From one year to another, ecosystems experience variation in their biotic and abiotic environments. A drought, an especially cold winter, and a pest outbreak all constitute short-term variability in environmental conditions. Animal populations vary from year to year, building up during resource-rich periods, but crashing as the food supply becomes scarce.
Equilibrium is the steady state of an ecosystem where all organisms are in balance with their environment and with each other. In equilibrium, any small changes to the system will be balanced by negative feedback, allowing the system to return to its original state.
Resistance and Resilience
In ecology, two parameters are used to measure changes in ecosystems: resistance and resilience. Resistance is the ability of an ecosystem to remain at equilibrium despite disturbances. Resilience is the speed at which an ecosystem recovers to equilibrium after being disturbed. Humans may impact the nature of an ecosystem to such a degree that the ecosystem can lose its resilience entirely. In these cases, external human influences can lead to the complete destruction or irreversible altering of the ecosystem equilibrium.
The Sin Nombre Virus: Ecosystem Dynamics in a Human Population
In 1993, a change in ecosystem dynamics caused a disease outbreak in a human population. In May of 1993, an unexplained pulmonary illness struck inhabitants of the southwestern United States in an area shared by Arizona, New Mexico, Colorado and Utah known as “The Four Corners. ” A young, physically fit Navajo man suffering from shortness of breath was rushed to a hospital in New Mexico and died rapidly. After further investigation, state officials located another five young, healthy people who had all died after acute respiratory failure.
When laboratory tests failed to identify the disease causing the deaths, New Mexico state health officials notified the Centers for Disease Control (CDC), the United States government agency responsible for managing potential epidemics. As additional cases of the disease were reported in the following weeks, physicians and scientists worked intensively to narrow down the list of possible causes. Virologists at the CDC linked the pulmonary syndrome with a virus – a previously unknown type of hantavirus. The hantavirus became known as Sin Nombre, the virus “with no name. ”
Although they identified the virus as the cause of the disease, researchers did not understand how it was transmitted. The researchers trapped and examined rodents that lived in and around the homes of the victims, and found that almost 30% of the deer mice were infected with the Sin Nombre hantavirus. The virus had been transmitted to humans via aerosolized mouse droppings, and a dramatic increase in the deer mouse population increased human infection rates.
The Four Corners area had experienced a drought until early 1993, when there were heavy snows and rainfall. The end of the drought caused an increase in vegetation, and particularly pinon nut production. With the sudden increase in food supply, the local deer mice population exploded and reproduced so rapidly that there were ten times more mice in May 1993 than there had been in May of 1992. The higher population of deer mice meant more mouse droppings and more opportunities to transmit hantavirus to humans.
As part of the effort to locate the source of the virus, researchers located and examined stored samples of lung tissue from people who had died of unexplained lung disease. Some of these samples showed evidence of previous infection with Sin Nombre virus, indicating that the earlier cases of the disease had not been recognized. The Navajo Native Americans recognize a similar disease in their medical traditions, and associate its occurrence with mice.
Key Points
• Biotic and abiotic factors interact through nutrient cycles and energy flows.
• External factors control resource inputs and are not influenced by the ecosystem itself.
• Internal factors are processes that exist within the ecosystem, such as decomposition, succession, and the types of species present.
• While in equilibrium, an ecosystem can recover from small changes through negative feedback, returning to its original state.
• Resistance describes an ecosystem’s ability to resist disturbances to the ecosystems dynamics.
• Human disturbances to ecosystems can overwhelm the ecosystem’s resilience, crippling its ability to return to equilibrium.
Key Terms
• resilience: the speed with which an ecosystem returns to its initial state after a disturbance
• equilibrium: the condition of a system in which competing influences are balanced, resulting in no net change
• resistance: the tendency of a system to remain close to its equilibrium state, despite disturbances | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/46%3A_Ecosystems/46.01%3A__Ecology_of_Ecosystems/46.1A%3A_Ecosystem_Dynamics.txt |
Learning Objectives
• Distinguish between food chains and food webs as models of energy flow in ecosystems
In ecology, a food web describes the feeding connections between organisms in a biotic community. Both energy and nutrients flow through a food web, moving through organisms as they are consumed by an organism above them in the food web. A single path of energy through a food web is called a food chain.
Trophic Levels
Each organism within a food web can be classified by trophic level according to their position within the web. Depending on an organism’s location in a food web, it may be grouped into more than one of these categories. Energy and nutrients move up trophic levels in the following order:
1. Primary producers
2. Primary consumers
3. Secondary consumers
4. Tertiary and other high-level consumers
In both food webs and food chains, arrows point from an organism that is consumed to the organism that consumes it. In many ecosystems, the bottom of the food chain consists of photosynthetic organisms, such as plants or phytoplankton, known as primary producers. The organisms that consume the primary producers are herbivores: the primary consumers. Secondary consumers are usually carnivores that eat the primary consumers, while tertiary consumers are carnivores that eat other carnivores. Higher-level consumers feed on the next lower trophic levels, and so on, up to the organisms at the top of the food chain, which are called the apex consumers. Some lines within a food web may point to more than one organism; those organisms may occupy different trophic levels depending on their position in each food chain within the web.
The Loss of Energy in Tropic Levels
It is rare to find food chains that have more than four or five links because the loss of energy limits the length of food chains. At each trophic level, most of the energy is lost through biological processes such as respiration or finding food. Only the energy that is directly assimilated into an animal’s consumable mass will be transferred to the next level when that animal is eaten. Therefore, after a limited number of trophic energy transfers, the amount of energy remaining in the food chain cannot support a higher trophic level. Although energy is lost, nutrients are recycled through waste or decomposition.
A scientist named Howard T. Odum demonstrated the loss of energy in each trophic level in the Silver Springs, Florida, ecosystem in the 1940s. He found that 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. In each successive trophic level, the energy available to the next level decreased significantly.
Types of Food Webs
Two general types of food webs are often shown interacting within a single ecosystem. As an example, a grazing food web 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.
Key Points
• Organisms can be organized into trophic levels: primary producer, primary consumer, secondary consumer, and tertiary or higher-order consumer.
• Energy decreases in each successive trophic level, preventing more than four or five levels in a food chain.
• An ecosystem usually has two different types of food webs: a grazing food web based on photosynthetic plants or algae, along with a detrital food web based on decomposers (such as fungi).
• There are different types of food webs including grazing food webs based on photosynthetic plants (such as algae) or detrital food webs based on decomposers (such as fungi).
Key Terms
• detritivore: an organism that feeds on detritus; a decomposer
• food chain: the feeding relationships between species in a biotic community; a linear path through a food web
• trophic level: a particular position occupied by a group of organisms in a food chain (primary producer, primary consumer, secondary consumer, or tertiary consumer) | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/46%3A_Ecosystems/46.01%3A__Ecology_of_Ecosystems/46.1B%3A_Food_Chains_and_Food_Webs.txt |
Learning Objectives
• Differentiate between conceptual, analytical, and simulation models of ecosystem dynamics, and mesocosm and microcosm research studies
Ecosystem dynamics is the study of the changes in ecosystem structure caused by environmental disturbances or by internal forces. Various research methodologies measure ecosystem dynamics. Some ecologists study ecosystems using controlled experimental systems, while some study entire ecosystems in their natural state; others use both approaches.
Holistic Ecosystem Model
A holistic ecosystem model attempts to quantify the composition, interaction, and dynamics of entire ecosystems. A food web is an example of a holistic ecosystem model, which is the most representative of the ecosystem in its natural state. However, this type of study is limited by time and expense, as well as its limited feasibility to conduct experiments on large natural ecosystems.
Experimental Systems
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, but 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.
Ecosystem Models
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: conceptual models, analytical models, and simulation models.
A conceptual model 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, although its ability to predict the effects of these disturbances is limited.
Analytical and simulation models are mathematical methods of describing ecosystems that are capable of predicting the effects of potential environmental changes without direct experimentation, although with limitations in accuracy. An analytical model is created using simple mathematical formulas to predict the effects of environmental disturbances on ecosystem structure and dynamics.
A simulation model 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. They can serve as a guide to ecosystem managers (such as conservation ecologists or fisheries biologists) in the practical maintenance of ecosystem health.
Key Points
• A holistic ecosystem model quantifies the dynamics of an entire ecosystem.
• Scientists can use experimental systems, such as a microcosms or mesocosms, to study ecosystems under controlled laboratory conditions.
• A conceptual model uses flow charts to show the interactions between living and nonliving components of the ecosystem.
• An analytical model uses simple mathematical formulas to predict the effects of environmental disturbances on an ecosystem’s structure and dynamics.
• A simulation model predicts the effects of environmental disturbances using complex computer algorithms; they are usually fairly-reliable predictors.
Key Terms
• mesocosm: a small portion of the natural environment that is brought under controlled conditions for experimental purposes
• microcosm: an artificial, simplified ecosystem that is used to simulate and predict the behaviour of natural ecosystems under controlled conditions | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/46%3A_Ecosystems/46.01%3A__Ecology_of_Ecosystems/46.1C%3A_Studying_Ecosystem_Dynamics.txt |
Learning Objectives
• Compare and contrast conceptual, analytical, and simulation models of ecosystem dynamics
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. 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.
Human combustion of fossil fuels accelerates this conversion by releasing large amounts of carbon dioxide into the atmosphere, which may be a large contributor to 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, while the number of photosynthetic trees have decreased because of worldwide deforestation. Most scientists agree that high atmospheric carbon dioxide is a major cause of global climate change.
Analytical and simulation models
Conceptual models are limited; they poorly predict the consequences of changes in ecosystem species and/or environment. Ecosystems are dynamic entities that are subject to a variety of abiotic and biotic disturbances. In these cases, scientists often use analytical or simulation models. These models predict how ecosystems recover from disturbances, returning 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 multiple equilibrium states. Since human impact can greatly and rapidly alter the species content and habitat of an ecosystem, it is crucial for scientists to develop models that predict how ecosystems respond to these changes.
Analytical models
Analytical models generally work best when dealing with relatively-simple, linear systems; specifically, those that can be accurately described by a set of mathematical equations whose behavior is well known. They are mathematically complex models that are good at predicting components of ecosystems such as food chains. However, their accuracy is limited by their simplification of complex ecosystems.
Simulation models
Like analytical models, simulation models use complex algorithms to predict ecosystem dynamics. However, sophisticated computer programs have enabled simulation models to predict responses in complex ecosystems. Simulation models use numerical techniques to solve problems for which analytic solutions are impractical or impossible. These kinds of models tend to be more widely used. They are generally considered more ecologically realistic, while analytic models are valued for their mathematical elegance and explanatory power. These simulations are considered to be the most accurate and predictive of ecosystem dynamics.
Key Points
• Conceptual models are often flow charts that demonstrate the relationships between different organisms in a community and their environment, including the transfer of energy and nutrients.
• Analytical models use mathematical equations to predict and describe simple, linear components of ecosystems, such as food chains.
• Simulation models use computer algorithms to predict ecosystem dynamics; they are considered the most ecologically-realistic and accurate.
Key Terms
• conceptual model: a model that is represented by conceptual representations of the relationships between different organisms in a community and their environment
• analytical model: a model that works best when dealing with relatively simple (often linear) systems, specifically those that can be accurately described by a set of mathematical equations whose behavior is well known
• simulation model: a model that utilizes mathematical algorithms to predict complex responses in ecosystem dynamics | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/46%3A_Ecosystems/46.01%3A__Ecology_of_Ecosystems/46.1D%3A_Modeling_Ecosystem_Dynamics.txt |
Learning Objectives
• Distinguish between photoautotrophs and chemoautotrophs and the ways in which they acquire energy
How Organisms Acquire Energy in a Food Web
All living things require energy in one form or another since energy is required by most, complex, metabolic pathways (often in the form of ATP ); 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. 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 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 act as producers and 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. 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.
Heterotrophs function as consumers in the food chain; they obtain energy in the form of organic carbon by eating autotrophs or other heterotrophs. They break down complex organic compounds produced by autotrophs into simpler compounds, releasing energy by oxidizing carbon and hydrogen atoms into carbon dioxide and water, respectively. Unlike autotrophs, heterotrophs are unable to synthesize their own food. If they cannot eat other organisms, they will die.
Key Points
• Food webs illustrate how energy flows through ecosystems, including how efficiently organisms acquire and use it.
• Autotrophs, producers in food webs, can be photosynthetic or chemosynthetic.
• Photoautotrophs use light energy to synthesize their own food, while chemoautotrophs use inorganic molecules.
• Chemoautotrophs are usually bacteria that live in ecosystems where sunlight is unavailable.
• Heterotrophs cannot synthesize their own energy, but must obtain it from autotrophs or other heterotrophs; they act as consumers in food webs.
Key Terms
• photoautotroph: an organism that can synthesize its own food by using light as a source of energy
• chemoautotroph: a simple organism, such as a protozoan, that derives its energy from chemical processes rather than photosynthesis
• heterotroph: an organism that requires an external supply of energy in the form of food, as it cannot synthesize its own
46.2B: Productivity within Trophic Levels
Learning Objectives
• Explain the concept of primary production and distinguish between gross primary production and net primary production
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. Photoautotrophy is the process by which an organism (such as a green plant) synthesizes its own food from inorganic material using light as a source of energy; chemoautotrophy, on the other hand, is the process by which simple organisms (such as bacteria or archaea) derive energy from chemical processes rather than photosynthesis. The rate at which photosynthetic primary producers incorporate energy from the sun is called gross primary productivity. An example of gross primary productivity is the compartment diagram of energy flow within the Silver Springs aquatic ecosystem. In this ecosystem, the total energy accumulated by the primary producers was shown to be 20,810 kcal/m2/yr.
Because all organisms need to use some of this energy for their own functions (such as 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 the 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.
Key Points
• A biomass is the total mass of living and previously-living organisms within a trophic level; ecosystems have characteristic amounts of biomass at each trophic level.
• The productivity of the primary producers ( gross primary productivity ) is important to ecosystems because these organisms bring energy to other living organisms.
• Net primary productivity (energy that remains in the primary producers after accounting for respiration and heat loss) is available to the primary consumers at the next trophic level.
Key Terms
• biomass: the total mass of all living things within a specific area, habitat, etc.
• gross primary productivity: rate at which photosynthetic primary producers incorporate energy from the sun
• net primary productivity: energy that remains in the primary producers after accounting for the organisms’ respiration and heat loss
• trophic level: a particular position occupied by a group of organisms in a food chain (primary producer, primary consumer, secondary consumer, or tertiary consumer) | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/46%3A_Ecosystems/46.02%3A_Energy_Flow_through_Ecosystems/46.2A%3A_Strategies_for_Acquiring_Energy.txt |
Learning Objectives
• Illustrate the transfer of energy between trophic levels
Large amounts of energy are lost from the ecosystem between one trophic level and 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 are consumed by the next level. 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:
TLTE=productionatpresenttrophiclevelproductionatprevioustrophiclevelx100TLTE=productionatpresenttrophiclevelproductionatprevioustrophiclevelx100
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 ecosystem food web, only three energy transfers occurred between the primary producer (green algae) and the tertiary, or 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; sometimes the quantification of energy transfers has to be estimated.
Net production efficiency
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:
NPE=netconsumerproductivityassimilationx100NPE=netconsumerproductivityassimilationx100
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 obtain 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. Because the NPE is low, much of the energy from animal feed is lost. For example, it costs about \$0.01 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.
Key Points
• Energy decreases as it moves up trophic levels because energy is lost as metabolic heat when the organisms from one trophic level are consumed by organisms from the next level.
• Trophic level transfer efficiency (TLTE) measures the amount of energy that is transferred between trophic levels.
• A food chain can usually sustain no more than six energy transfers before all the energy is used up.
• Net production efficiency (NPE) measures how efficiently each trophic level uses and incorporates the energy from its food into biomass to fuel the next trophic level.
• Endotherms have a low NPE and use more energy for heat and respiration than ectotherms, so most endotherms have to eat more often than ectotherms to get the energy they need for survival.
• Since cattle and other livestock have low NPEs, it is more costly to produce energy content in the form of meat and other animal products than in the form of corn, soybeans, and other crops.
Key Terms
• assimilation: the biomass 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
• net consumer productivity: energy content available to the organisms of the next trophic level
• 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/Book%3A_General_Biology_(Boundless)/46%3A_Ecosystems/46.02%3A_Energy_Flow_through_Ecosystems/46.2C%3A_Transfer_of_Energy_between_Trophic_Levels.txt |
Learning Objectives
• Explain the shape and structure of the ecological pyramid
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. Ecological pyramids can also be called trophic pyramids or energy pyramids.
Pyramids of numbers can be either upright or inverted, depending on the ecosystem. A typical grassland during the summer has an upright shape since it has a base of many plants, with the numbers of organisms decreasing 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, 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, the inverted biomass 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, which minimizes their biomass at any particular point in time. However, since phytoplankton reproduce quickly, 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. Pyramids of energy are always upright, since energy is lost at each trophic level; 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.
Key Points
• Pyramids of numbers can be either upright or inverted, depending on the ecosystem.
• Pyramids of biomass measure the amount of energy converted into living tissue at the different trophic levels.
• The English Channel ecosystem exhibits an inverted biomass pyramid since the primary producers make up less biomass than the primary consumers.
• Pyramid ecosystem modeling can also be used to show energy flow through the trophic levels; pyramids of energy are always upright since energy decreases at each trophic level.
• 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.
Key Terms
• ecological pyramid: diagram that shows the relative amounts of energy or matter or numbers of organisms within each trophic level in a food chain or food web | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/46%3A_Ecosystems/46.02%3A_Energy_Flow_through_Ecosystems/46.2D%3A_Ecological_Pyramids.txt |
Learning Objectives
• Describe the consequences of biomagnification between trophic levels
Consequences of Food Webs: Biological Magnification
One of the most important environmental consequences of ecosystem dynamics is biomagnification: 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, which 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. In a study performed by the National Oceanic and Atmospheric Administration (NOAA) in the Saginaw Bay of Lake Huron, PCB concentrations increased from the ecosystem’s primary producers (phytoplankton) through the different trophic levels of fish species. The apex consumer (walleye) had 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, sardines, 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.
Key Points
• Biomagnification increases the concentration of toxic substances in organisms at higher trophic levels.
• DDT is an example of a substance that biomagnifies; birds accumulate sufficient amounts of DDT from eating fish to cause adverse effects on bird populations.
• The presence of polychlorinated biphenyls (PCB) in phytoplankton causes increased PCB concentrations in walleyes and birds.
• Heavy metals, such as mercury and cadmium, found in certain types of seafood can also biomagnify.
Key Terms
• biomagnification: the process, in an ecosystem, in which a higher concentration of a substance in an organism is obtained higher up the food chain
• dichlorodiphenyltrichloroethane: a chlorinated hydrocarbon which is mainly used as an insecticide (DDT)
• apex consumer: consumers with few to no predators of their own, residing at the top of their food chain | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/46%3A_Ecosystems/46.02%3A_Energy_Flow_through_Ecosystems/46.2E%3A_Biological_Magnification.txt |
Learning Objectives
• Summarize the concept of biogeochemical cycles
Biogeochemocal Cycles: Introduction
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 movement 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.
The components of organic molecules are constantly being stored and recycled as part of their biogeochemical cycle. Water, which contains hydrogen and oxygen, is essential to all living processes. The hydrosphere is the area of the earth where water movement and storage occurs. Water can be liquid on the surface and beneath the surface or frozen (rivers, lakes, oceans, groundwater, polar ice caps, and glaciers) or exist as water vapor in the atmosphere. Carbon, found in all organic macromolecules, is an important constituent of fossil fuels. Nitrogen, a major component of our nucleic acids and proteins, 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 all 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.
Key Points
• Carbon, nitrogen, hydrogen, oxygen, phosphorus, and sulfur are conserved and recycled in the atmosphere, on land, in water, or beneath the earth’s surface.
• Materials are recycled via erosion, weathering, water drainage, and the movement of tectonic plates.
• Water is essential to all living processes, while carbon is found in all organic macromolecules.
• Nitrogen and phosphorus are major components of nucleic acids and play major roles in agriculture.
• Sulfur plays a role in the three-dimensional folding of proteins and is released into the atmosphere by the burning of fossil fuels.
Key Terms
• hydrosphere: combined mass of water found on, under, and over the surface of a planet
• biogeochemical cycle: cycling of mineral nutrients through ecosystems and through the non-living world
46.3B: The Water (Hydrologic) Cycle
Learning Objectives
• Explain the path of the hydrologic cycle and its importance
Water is the basis of all living processes. More than half of the human body is made up of water, while 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. 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 as it has a major influence on climate and, thus, on the environments of ecosystems. For example, when water evaporates, it takes up energy from its surroundings, cooling the environment. When it condenses, it releases energy, warming the environment. The evaporation phase of the cycle purifies water, which then replenishes the land with fresh water. The flow of liquid water and ice transports minerals across the globe. It is also involved in reshaping the geological features of the earth through processes including erosion and sedimentation. The water cycle is also essential for the maintenance of most life and ecosystems on the planet. Most of the water on earth is stored for long periods in the oceans, underground, and as ice. 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, which 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, which is eventually followed by precipitation (rain or snow), returning water to the earth’s surface. Rain eventually percolates 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. Rain and surface runoff are major ways in which minerals, including carbon, nitrogen, phosphorus, and sulfur, are cycled from land to water.
Key Points
• Water cycling affects the climate, transports minerals, purifies water, and replenishes the land with fresh water.
• Water with a longer residence time, such as water in oceans and glaciers, is not available for short-term cycling, which occurs via evaporation.
• Surface water evaporates (water to water vapor) or sublimates (ice to water vapor), which deposits large amounts of water vapor into the atmosphere.
• Water vapor in the atmosphere condenses into clouds and is eventually followed by precipitation, which returns water to the earth’s surface.
• Rain percolates into the ground, where it may evaporate or enter bodies of water.
• Surface runoff enters oceans directly or via streams and lakes.
Key Terms
• residence time: the average time a particular molecule of water will remain in a body of water
• condensation: the conversion of a gas to a liquid; the condensate so formed
• surface runoff: overland flow of excess water (with or without accumulated contaminants) that cannot be absorbed by the ground as infiltration
• Evaporation: the process of a liquid converting to the gaseous state
• sublimation: the transition of a substance from the solid phase directly to the vapor state such that it does not pass through the intermediate liquid phase | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/46%3A_Ecosystems/46.03%3A_Biogeochemical_Cycles/46.3A%3A_Biogeochemical_Cycles.txt |
Learning Objectives
• Distinguish between the biological and biogeochemical cycles of carbon
Carbon, the second most abundant element in living organisms, is present in all organic molecules. Its role in the structure of macromolecules is of primary importance to living organisms. Carbon compounds contain especially- high forms of energy, which humans use as fuel. Since the 1800s (the beginning of the Industrial Revolution), the number of countries using massive amounts of fossil fuels increased, which raised the levels of carbon dioxide in the atmosphere. This increase in carbon dioxide has been associated with climate change and other disturbances of the earth’s ecosystems. It is a major environmental concern worldwide.
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 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. 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 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 of the oxygen content in the atmosphere that we observe today.
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 than the biological carbon cycle. 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, a major reservoir of carbon in the form of carbon dioxide, 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; each affects the other reciprocally. Carbon dioxide (CO2) from the atmosphere dissolves in water, combining with water molecules to form carbonic acid. It then ionizes to carbonate and bicarbonate ions.
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 or the 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 is either regenerated very slowly or not at all. Another way for carbon to enter the atmosphere is from land 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 breeding and raising of livestock. 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, 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.
Key Points
• Carbon is present in all organic molecules; carbon compounds contain large amounts of energy, which humans use as fuel.
• The biological carbon cycle is the rapid exchange of carbon among living things; autotrophs use carbon dioxide produced by heterotrophs to produce glucose and oxygen, which are then utilized by heterotrophs.
• The biogeochemical cycle occurs at a much slower rate than the biological cycle since carbon is stored in carbon reservoirs for long periods of time.
• Carbon dioxide from the atmosphere dissolves in water, combining with water molecules to form carbonic acid, which then ionizes to carbonate and bicarbonate ions.
• Most of the carbon in the ocean is in the form of bicarbonate ions, which can combine with seawater calcium to form calcium carbonate (CaCO3), a major component of marine organism shells.
• Carbon can enter the soil as a result of the decomposition of living organisms, the weathering of rocks, the eruption of volcanoes, and other geothermal systems.
Key Terms
• subduction: movement of one tectonic plate beneath another
• non-renewable resource: resource, such as fossil fuel, that is either regenerated very slowly or not at all
• autotroph: Any organism that can synthesize its food from inorganic substances, using heat or light as a source of energy
• heterotroph: an organism that requires an external supply of energy in the form of food, as it cannot synthesize its own | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/46%3A_Ecosystems/46.03%3A_Biogeochemical_Cycles/46.3C%3A__The_Carbon_Cycle.txt |
Learning Objectives
• Describe 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. Rhizobiumbacteria live symbiotically in the root nodules of legumes (such as peas, beans, and peanuts), providing 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 as many ecosystem processes, such as primary production and decomposition, are limited by the available supply of nitrogen. 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.
Human activity can release nitrogen into the environment by two primary means: the combustion of fossil fuels, which releases different nitrogen oxides, and 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, becoming 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.
Key Points
• Bacteria, such as cyanobacteria, convert nitrogen into nitrogen gas via nitrogen fixation.
• Nitrogen fixation occurs in three steps: ammonification, nitrification, and denitrification.
• Human activity can release nitrogen into the environment by the combustion of fossil fuels and by the use of artificial fertilizers in agriculture.
• Atmospheric nitrogen is responsible for acid rain, the release of greenhouse gasses, and eutrophication.
• Nitrogen fixation can be performed by marine bacteria; nitrogen falls to the ocean floor as sediment and is then moved to land, becoming incorporated into terrestrial rock.
Key Terms
• denitrification: process of converting nitrates into nitrogen gas, especially by the action of bacteria
• nitrification: the conversion of ammonium into nitrites (NO2−) by nitrifying bacteria
• ammonification: the formation of ammonia or its compounds from nitrogenous compounds, especially as a result of bacterial decomposition | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/46%3A_Ecosystems/46.03%3A_Biogeochemical_Cycles/46.3D%3A__The_Nitrogen_Cycle.txt |
Learning Objectives
• Describe the phosphorus cycle and the effects of phosphorus on the environment
Phosphorus is an essential nutrient for living processes. It is a major component of nucleic acid, both DNA and RNA; of phospholipids, the major component of cell membranes; and, as calcium phosphate, makes up the supportive components of our bones. Phosphorus is often the limiting nutrient (necessary for growth) in aquatic ecosystems.
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.
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; 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 8,463 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, which was one of the first ecosystems to have identified dead zones.
Key Points
• Phosphorus, a major component of nucleic acid and phospholipids, also makes up the supportive components of our bones; it is often necessary for growth in aquatic ecosystems.
• Phosphates (PO43) are sent into rivers, lakes, and the ocean by leaching and natural surface runoff.
• Phosphate-containing ocean sediments slowly move to land by the uplifting of areas of the earth’s surface.
• Excess phosphorus and nitrogen in the ecosystem leads to the death of many organisms, causing dead zones.
• Dead zones are caused by by eutrophication, oil spills, dumping of toxic chemicals, and other human activities.
Key Terms
• eutrophication: process whereby excess levels of nitrogen or phosphorus cause excessive growth of microorganisms, depleting dissolved oxygen levels and kill ecosystem fauna
• dead zone: an area within a freshwater or marine ecosystem where large areas are depleted of their normal flora and fauna; caused by excessive nutrient pollution | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/46%3A_Ecosystems/46.03%3A_Biogeochemical_Cycles/46.3E%3A_The_Phosphorus_Cycle.txt |
Learning Objectives
• Describe 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. Sulfur cycles exist between the oceans, land, and atmosphere.
On land, sulfur is deposited in four major ways: precipitation, direct fallout from the atmosphere, rock weathering, and decomposition of organic materials. Atmospheric sulfur is found in the form of sulfur dioxide (SO2). As rain falls through the atmosphere, sulfur is dissolved in the form of weak sulfuric acid (H2SO4), creating acid rain. Sulfur can also fall directly from the atmosphere in a process called fallout. The weathering of sulfur-containing rocks also releases sulfur into the soil. These rocks originate from ocean sediments that are moved to land by the geologic uplift. Terrestrial ecosystems can then make use of these soil sulfates (SO42). Upon the death and decomposition of these organisms, sulfur is released back into the atmosphere as hydrogen sulfide (H2S) gas. Sulfur may also enter the atmosphere through geothermal vents.
Sulfur enters the ocean via runoff from land, fallout, and underwater geothermal vents. Some marine 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 large amounts of hydrogen sulfide gas into the atmosphere, creating acid rain. Acid rain is corrosive rain that causes damage to aquatic ecosystems and the natural environment by lowering the pH of lakes, which kills many of the resident fauna; it also affects the human-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.
Key Points
• Sulfur is an essential element for the macromolecules of living things since it determines the 3-D folding patterns of proteins.
• On land, sulfur enters the atmosphere via acid rain, fallout, the weathering of rocks, decompostion of organic materials, and geothermal vents.
• Sulfur enters the ocean via runoff, fallout, and underwater geothermal vents; some marine ecosystems also rely on chemoautotrophs as a sulfur source.
• The burning of fossil fuels increases the amount of sulfide in the atmosphere and causes acid rain.
• Acid rain is corrosive rain that causes damage to aquatic ecosystems by lowering the pH of lakes, killing many of the resident fauna; it also degrades buildings and human-made structures.
Key Terms
• chemoautotroph: a simple organism, such as a protozoan, that derives its energy from chemical processes rather than photosynthesis
• fallout: direct deposit of solid minerals on land or in the ocean from the atmosphere
• 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 | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/46%3A_Ecosystems/46.03%3A_Biogeochemical_Cycles/46.3E%3A_The_Sulfur_Cycle.txt |
Learning Objectives
• Explain the biodiversity crisis
The Biodiversity Crisis
Traditionally, ecologists have measured biodiversity, a general term for the variety of species 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, yet 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.
Cichlids in Lake Victoria
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 was not a problem until the 1980s when its population began to surge 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. These factors included not only the Nile perch, but also the declining lake water quality due to agriculture and land clearing on the shores of Lake Victoria, and increased fishing pressure. Scientists had not even cataloged all of the species present, so many were lost that they were never named. The diversity is now a shadow of what it once was.
Causes of Biodiversity
The cichlids of Lake Victoria are a thumbnail sketch of contemporary rapid species loss caused by human activity occurring all over earth. Extinction, a natural process of macroevolution, 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. 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 invasive 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. The five previous extinctions on this scale were caused by cataclysmic events that changed the course of the history of life in each instance. Earth is now in one of those times.
Key Points
• Biodiversity is the variety of species present in the biosphere; the main goal of conservationists is to preserve biodiversity.
• An example of biodiversity loss was the extinction of over 200 species of cichlids in Lake Victoria; this was caused by the introduction of the Nile Perch as well as increased agriculture and fishing.
• Unlike the five previous mass extinctions, the current one is a result of detrimental human activities.
• Current human-caused biodiversity loss is the result activities such as habitat destruction, the introduction of exotic invasive species, and the over-harvesting of species.
Key Terms
• biodiversity: the diversity (number and variety of species) of plant and animal life within a region
• adaptive radiation: the diversification of species into separate forms that each adapt to occupy a specific environmental niche
• invasive species: any species that has been introduced to an environment where it is not native and has since become a nuisance through rapid spread and increase in numbers, often to the detriment of native species
• extinction: disappearance of a species from earth; local extinction is the disappearance of a species from a region | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/47%3A_Conservation_Biology_and_Biodiversity/47.01%3A__The_Biodiversity_Crisis/47.1A%3A_Loss_of_Biodiversity.txt |
Learning Objectives
• Differentiate among the types of biodiversity
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 by-products 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; its decline is troubling to biologists and agricultural scientists.
It is also useful to define ecosystem diversity: the number of different ecosystems on the planet or in a given geographic area. 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 co-adaptation, 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. Now, they have mostly disappeared, 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 number of identified eukaryote species, 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 1.5 million 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 knows little about what is being lost.
There are various initiatives to catalog described species in accessible ways; 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.
Naming and counting species may seem an unimportant pursuit given the other needs of humanity, but it is not as simple as counting. 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, which 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.
Key Points
• A genus with a high variety of species will have more genetic diversity; the most genetically-diverse species will have the greatest potential for evolution and preservation.
• The loss of ecosystem diversity results in the loss of interactions between species, unique features of co- adaptation, and biological productivity.
• Human-generated species diversity has decreased due to migration, market forces, and agriculture.
• Humans have only been able to estimate the number of species that inhabit earth; this estimate accounts for about 20 percent of predicted species on the planet.
• Humans have only been able to estimate the number of species that inhabit Earth; this estimate only accounts for 20 percent of predicted species on the planet.
Key Terms
• genetic diversity: variety of genes in a species or other taxonomic group or ecosystem; can refer to allelic diversity or genome-wide diversity
• ecosystem diversity: variety of ecosystems in a biosphere or the variety of species and ecological processes that occur in different physical settings
• chemical diversity: variety of metabolic compounds in an ecosystem | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/47%3A_Conservation_Biology_and_Biodiversity/47.01%3A__The_Biodiversity_Crisis/47.1B%3A_Types_of_Biodiversity.txt |
Learning Objectives
• Describe how biodiversity has changed through geological time as a result of mass extinctions
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.
Paleontologists have identified five strata in the fossil record that appear to show sudden and dramatic losses in biodiversity known as 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.
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.
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 was a period of glaciation followed by warming. These two extinction events, cooling and warming, were separated by about 1 million years; 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. It may account for climate changes observed at the time.
The late Devonian extinction may have occurred over a relatively long period of time. Its causes are poorly-understood and it appears to have have affected only marine species.
The end-Permian extinction was the largest in the history of life. Estimates predict that 96 percent of all marine species and 70 percent of all terrestrial species were lost.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 composition and the course of evolution.
The causes of the Triassic–Jurassic extinction event are not clear. 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. The Cretaceous-Paleogene (K-Pg) 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 credible. Now, an abundance of geological evidence supports the hypothesis. Recovery times for biodiversity after the end-Cretaceous extinction were shorter, in geological time, than for the end-Permian extinction: on the order of 10 million years.
Key Points
• Fossil records have been instrumental in differentiating between five periods that appear to show sudden and dramatic losses in biodiversity.
• Although there have been smaller periods of extinction, the five mass extinction periods demonstrate a continuous series of large extinction events.
• The Ordovician-Silurian extinction event was caused by glaciation followed by warming; it led to the extinction of 85 percent of marine species.
• The late Devonian extinction affected only marine species; the end- Permian extinction, the largest in history, may have been caused by volcanic activity, leading to a global-warming type event.
• The Triassic–Jurassic extinction event may have been caused by climate change, asteroid impact, or volcanic eruptions; however, the main cause is still unclear.
• The end- Cretaceous extinction event, in which the extinction of the dinosaurs occurred, is believed to have been caused by the impact of a large asteroid.
Key Terms
• macroevolution: large-scale patterns or processes in the history of life, including the origins of novel organism designs, evolutionary trends, adaptive radiations and extinctions
• theropod: any large, bipedal dinosaur, of the suborder Theropoda, from the Jurassic and Cretaceous periods
• anoxic: suffering from a reduced supply of oxygen | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/47%3A_Conservation_Biology_and_Biodiversity/47.01%3A__The_Biodiversity_Crisis/47.1C%3A_Biodiversity_Change_through_Geological_Time.txt |
Learning Objectives
• Describe the biodiversity loss associated with the Pleistocene extinction
The Pleistocene Extinction is one of the lesser extinctions and a relatively-recent one. It is well known that the North American, and to some degree Eurasian, megafauna disappeared toward the end of the last glaciation period. The extinction appears to have happened in a relatively-restricted time period between 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), mastodons, giant beavers, giant ground sloths, saber-toothed cats, and the North American camel, to name just 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 probable that over-hunting was a factor in 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, 10,000 to 20,000 years 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 to 12,000 years ago, several thousand years after the first evidence of humans in North America. 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 with the coincidence of 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; the large mammals (prosimians) 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 to over one million 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, human hunting was an additional factor in the extinctions.
Key Points
• The Pleistocene extinction in North America appears to have happened 10,000–12,000 years ago; this is several thousand years after the arrival of humans, who may have contributed to the extinction through hunting.
• Regions that experienced relatively-recent human arrivals show patterns of dramatic extinctions of megafauna hundreds to thousands of years after humans arrived; the same patterns are not observed in Eurasia and Africa as they did not experience a relatively-recent arrival of humans.
• To date, over-hunting by humans is one probable factor for the extinction of large mammals in the Pleistocene period.
Key Terms
• Pleistocene: of a geologic epoch within the Neogene period from about 2.6 million to 11,000 years ago; marked by the evolution of humans and the extinction of the large mammals
• megafauna: the large animals of a given region or time, considered as a group | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/47%3A_Conservation_Biology_and_Biodiversity/47.01%3A__The_Biodiversity_Crisis/47.1D%3A_The_Pleistocene_Extinction.txt |
Learning Objectives
• Describe the biodiversity loss during the Holocene extinction
Present-Time Extinctions
The sixth, or Holocene, mass extinction appears to have begun earlier than previously believed and is mostly due to the activities of Homo sapiens. Since the beginning of the Holocene period, there have been numerous recent extinctions of individual species that are recorded in human writings. Most of these coincide with the expansion of the European colonies in the 1500s.
One of the earlier and popularly-known examples of extinction in this period is the dodo bird. The dodo bird lived in the forests of Mauritius, an island in the Indian Ocean, but became extinct around 1662. It was hunted for its meat by sailors as it 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.
Another example, Steller’s sea cows, became extinct in 1768.The sea cow, first discovered by Europeans in 1741, was hunted for meat and oil. The last of the species was killed in 1768, which amounts to 27 years between the species’ first contact with Europeans and its extinction. In addition, the last living passenger pigeon died in a zoo in Cincinnati, Ohio in 1914. This species was hunted and suffered from habitat loss through the clearing of forests for farmland. Furthermore, in 1918, the last living Carolina parakeet died in captivity. This species, once common in the eastern United States, was a victim of habitat loss and hunting as well. Adding to the extinction list, the Japanese sea lion, which inhabited a broad area around Japan and the coast of Korea, became extinct in the 1950s due to overfishing. The Caribbean monk seal, found in the Caribbean Sea, was driven to extinction through 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 made extinct by over-hunting 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 since there are many organisms that are of less interest to humans 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.
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. Secondly, the number of recently-extinct species is increasing because extinct species now are being described from skeletal remains. Lastly, 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-day 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, suggesting 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.
Key Points
• The dodo was one of the first-known examples of a species that went extinct (in the 1600s) during the Holocene period.
• Steller’s sea cows, passenger pigeons, Carolina parakeets, Japanese sea lions, and Caribbean monk seals are examples of species that went extinct from the 1700s-1900s.
• Major reasons for species extinctions during the Holocene period are due to overhunting, overfishing, and other human-related activities.
• Extinction rates can be estimated by comparing extinction events since the 1500s, but this method may underestimate the actual extinction rate value.
• Extinction rates can be estimated by observing species-area relationships and correlating species loss with habitat loss; however, this method may lead to overestimation.
Key Terms
• 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
• Holocene: of a geologic epoch within the Neogene period from about 11,000 years ago to the present
• extinction rate: number of species becoming extinct over time, sometimes defined as extinctions per million species–years to make numbers manageable (E/MSY) | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/47%3A_Conservation_Biology_and_Biodiversity/47.01%3A__The_Biodiversity_Crisis/47.1E%3A_Present-Time_Extinctions.txt |
Learning Objectives
• Describe the benefits to human health of maintaining biodiversity
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 plants from insects and other animals that eat them, but some of which also work as medicines. For centuries in Europe, older knowledge about the medicinal 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. 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. 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 one-third of pharmaceutical research and development is spent on natural compounds. 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. It is beneficial to humans, therefore, for medicinal purposes and many others, to maintain biodiversity.
Key Points
• 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.
• 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; at least five of these drugs have been FDA approved since 2007.
Key Terms
• atropine: an alkaloid extracted from the plant deadly nightshade (Atropa belladonna); used as a drug in medicine for its paralytic effects (in surgery to relax muscles, in dentistry to dry the mouth, etc.)
• vincristine: a particular drug used in chemotherapy
• antibiotic: any substance that can destroy or inhibit the growth of bacteria and similar microorganisms | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/47%3A_Conservation_Biology_and_Biodiversity/47.02%3A__The_Importance_of_Biodiversity_to_Human_Life/47.2A%3A__Human_Health_and_Biodiversity.txt |
Learning Objectives
• Assess the interactions of biodiversity with 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, while the number of varieties is probably in the thousands. Each variety has been bred to thrive at particular elevations and soil and climate conditions. The diversity is driven by the 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 and microclimates.
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 occurred 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; 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. Sometimes, however, seed banks are lost through accidents; there is no way to replace them. In 2008, the Svalbard Global Seed Vault 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 those stored here. 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.
Key Points
• Agricultural diversity is driven by the demands of the topography, the limited movement of people, and the needs for crop rotation of varieties that do well in different fields.
• Resistance to disease is a chief benefit to maintaining crop biodiversity; lack of diversity in crop species risks an entire crop being wiped out by a disease to which it is susceptible.
• 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 that can be bred with existing varieties.
• Seed companies must continually breed new varieties to keep up with evolving pest organisms.
Key Terms
• blight: any of many plant diseases causing damage to, or the death of, leaves, fruit or other parts | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/47%3A_Conservation_Biology_and_Biodiversity/47.02%3A__The_Importance_of_Biodiversity_to_Human_Life/47.2B%3A_Agricultural_Diversity.txt |
Learning Objectives
• Explain the impact that the collapse of marine fisheries will have on human diet and health
Managing Wild Food Resources
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 dramatically. Despite considerable effort, few fisheries on the planet are managed for sustainability.
Overfishing
Overfishing is the harvest of an aquatic population to a level that is too low for that population to replenish itself. Resource depletion, low biological growth rates, and critically low biomass levels result from overfishing. For example, overfishing of sharks has disrupted entire marine ecosystems.
The ability of a fishery to recover from overfishing depends on the species’ natural ability to replenish itself as well as the ecosystem’s conditions. Dramatic changes in species composition can result in an ecosystem shift, where other equilibrium energy flows involve species compositions different from those that had been present before overfishing occurred. For example, once trout have been overfished, carp might take over in a way that makes it impossible for the trout to re-establish a breeding population.
Sustainable Ecosystem Management
Fishery extinctions rarely lead to complete extinction of the harvested species, but rather to a radical restructuring of the marine ecosystem in which an abundant species is so over-harvested that it becomes a minor player, ecologically. In general, the fish taken from fisheries have shifted to smaller species as larger species are fished to extinction. 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. 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, not only the fishermen who depend directly on the fish stocks but all of the workers who are part of the industry, such as chefs, fish mongers, truck drivers, boat mechanics, and many more. In addition, the loss of an inexpensive protein source to populations that cannot afford to replace it can increase the cost of living and limit societies in other ways. The ultimate outcomes of overfishing and the commercial extinctions of fish stocks could include the loss of aquatic systems as food sources and economic crises for societies that depend on them.
Sustainable seafood is a movement that has gained momentum as more people become aware of overfishing and environmentally-destructive fishing methods. Sustainable seafood is seafood from either fished or farmed sources that can maintain or increase production in the future without jeopardizing the ecosystems from which it was acquired. In general, slow-growing fish that reproduce late in life, such as orange roughy, are vulnerable to overfishing and are considered unsustainable seafood. Seafood species that grow quickly and breed young, such as anchovies and sardines, are much more resistant to overfishing and are therefore labeled “sustainable” and promoted as good alternatives.
Key Points
• Dramatic changes in species composition can result in an ecosystem shift, where species compositions differ from those that had been present before the depletion of the original fish stock.
• In general, the fish taken from fisheries have shifted to smaller species as larger species are fished to extinction; if such trends continue, aquatic ecosystems could become unavailable as food sources.
• Sustainable seafood is seafood from either fished or farmed sources that can maintain or increase production in the future without affecting the ecosystem in which it lives.
Key Terms
• sustainability: configuring society so that each can meet his own needs and greatest potential, while preserving biodiversity and natural ecosystems, and planning for future generations to maintain this potential.
• overfishing: fishing that reduces an aquatic population, or stock, to a level that is inadequate for the stock to replenish itself | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/47%3A_Conservation_Biology_and_Biodiversity/47.02%3A__The_Importance_of_Biodiversity_to_Human_Life/47.2C%3A_Managing_Fisheries.txt |
Learning Objectives
• Describe the effects of habitat loss to biodiversity and concept of sustainability
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 estuary, or a marine environment – will kill the individuals within most 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.
Effects of Habitat Loss on Biodiversity
Habitat loss is a process of environmental change in which a natural habitat is rendered functionally unable to support the species present. This process may be natural or unnatural, and may be caused by habitat fragmentation, geological processes, climate change, or human activities such as the introduction of invasive species or ecosystem nutrient depletion. In the process of habitat destruction, the organisms that previously used the site are displaced or destroyed, reducing biodiversity.
Human destruction of habitats has accelerated greatly in the latter half of the twentieth century. Natural habitats are often destroyed through human activity for the purpose of harvesting natural resources for industry production and urbanization. Clearing habitats for agriculture, for example, is the principal cause of habitat destruction. Other important causes of habitat destruction include mining, logging, and urban sprawl. Habitat destruction is currently ranked as the primary cause of species extinction worldwide.
Consider the exceptional biodiversity of Sumatra. It is home to one sub-species of orangutan, a species of critically endangered elephant, and the Sumatran tiger; however half of Sumatra’s forest is now gone. The neighboring island of Borneo, home to the other sub-species of orangutan, has lost a similar area of forest, and forest loss continues in protected areas. 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 being removed for their timber, and to clear space for plantations of palm oil, an oil used in Europe for many items including food products, cosmetics, and biodiesel.
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 also represent the extinction of species because of high levels of endemism.
Since the Neolithic Revolution, about 47% of the world’s forests have been lost to human use. Present-day forests occupy about a quarter of the world’s ice-free land, with about half of these occurring in the tropics. In temperate and boreal regions, forest area is gradually increasing (with the exception of Siberia), but deforestation in the tropics is of major concern.
Feeding more than seven billion human bodies takes a heavy toll on the earth’s resources. This begins with the appropriation of about 38 percent of the earth’s land surface and about 20 percent of its net primary productivity. Added to this are the resource-hungry activities of industrial agribusiness: everything from crops’ need for irrigation water, synthetic fertilizers, and pesticides, to the resource costs of food packaging, transport (now a major part of global trade), and retail.
Sustainability
Sustainability is a concept that describes how biological systems remain diverse and productive over time. Long-lived and healthy wetlands and forests are examples of sustainable biological systems. For humans, sustainability is the potential for long-term maintenance of well-being, which has ecological, economic, political, and cultural dimensions. Sustainability requires the reconciliation of environmental, social, and economic demands, which are also referred to as the “three pillars” of sustainability.
Healthy ecosystems and environments are necessary for the survival and flourishing of humans and other organisms, and there are a number of ways to reduce humans’ negative impact on the environment. One approach is environmental management, which is based largely on information gained from earth science, environmental science, and conservation biology. A second approach is management of human consumption of resources, which is based largely on information gained from economics. A third, more recent, approach adds cultural and political concerns into the sustainability matrix.
Loss of biodiversity stems largely from the habitat loss and fragmentation produced by human appropriation of land for development, forestry and agriculture as natural capital is progressively converted to human-made capital. At the local human scale, sustainability benefits accrue from the creation of green cities and sustainable parks and gardens. Similarly, environmental problems associated with industrial agriculture and agribusiness are now being addressed through such movements as sustainable agriculture, organic farming, and more-sustainable business practices.
Key Points
• Habitat destruction renders entire habitats functionally unable to support the species present; biodiversity is reduced in this process when existing organisms in the habitat are displaced or destroyed.
• Clearing areas for agricultural purposes is the main cause of habitat destruction; other principal causes include mining, logging, and urban sprawl.
• The primary cause of species extinction worldwide is habitat destruction.
• Sustainability is a term that describes how biological systems remain diverse and productive over time, creating the potential for long-term maintenance of human well-being.
• Reducing negative human impact requires three concepts: environmental management, management of human consumption of resources, and awareness of cultural and political concerns to increase sustainability.
Key Terms
• sustainability: Configuring society so that each person can meet their own needs and greatest potential, while preserving biodiversity and natural ecosystems, and planning for future generations to maintain this potential.
• endemism: The ecological state of a species being unique to a defined geographic location, such as an island, nation, country or other defined zone, or habitat type; organisms that are indigenous to a place are not endemic to it if they are also found elsewhere.
• biodiversity: The diversity (number and variety of species) of plant and animal life within a region. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/47%3A_Conservation_Biology_and_Biodiversity/47.03%3A_Threats_to_Biodiversity/47.3A%3A_Habitat_Loss_and_Sustainability.txt |
Learning Objectives
• Explain why overharvesting is a threat to biodiversity
Overharvesting
Overharvesting, also called overexploitation, refers to harvesting a renewable resource to the point of diminishing returns. Ecologists use the term to describe populations that are harvested at a rate that is unsustainable, given their natural rates of mortality and capacities for reproduction. The term applies to natural resources such as wild medicinal plants, grazing pastures, game animals, fish stocks, forests, and water aquifers. Sustained overharvesting can lead to the destruction of the resource, and is one of the five main activities – along with pollution, introduced species, habitat fragmentation, and habitat destruction – that threaten global biodiversity today.
All living organisms require resources to survive. Overharvesting these resources for extended periods of time can deplete natural resources to the point where they are unable to recover within a short time frame. Humans have always harvested food and other resources they have needed to survive; however, human populations, historically, were small and methods of collection limited to small quantities. Exponential increase in human population, expanding markets, and increasing demand, combined with improved access and techniques for capture, are causing the exploitation of many species beyond sustainable levels.
Effects of overharvesting
As mentioned above, sustained overharvesting is one of the primary threats to biodiversity. Overharvesting can lead to resource destruction, including extinction at the population level and even extinction of whole species. Depleting the numbers or amount of certain resources can also change their quality; for example, the overharvesting of footstool palm (a wild palm tree found in Southeast Asia, the leaves of which are used for thatching and food wrapping) has resulted in its leaf size becoming smaller.
Overharvesting not only threatens the resource being harvested, but can directly impact humans as well – for example by decreasing the biodiversity necessary for medicinal resources. A significant proportion of drugs and medicines are natural products which are derived, directly or indirectly, from biological sources. However, unregulated and inappropriate harvesting could potentially lead to overexploitation, ecosystem degradation, and loss of biodiversity; further, it can negatively impact the rights of the communities and states from which the resources are taken.
Tragedy of the commons
Overharvesting is a serious threat to many species, especially aquatic ones. Common resources – or resources that are shared, such as fisheries – are subject to an economic pressure known as “the tragedy of the commons,” in which essentially no harvester has a motivation to exercise restraint in harvesting from a certain area, because that area is not owned by that harvester. The natural outcome of harvesting common resources is their overexploitation.
For example, most fisheries are managed as a common resource even when the fishing territory lies within a country’s territorial waters; because of this, fishers have very little motivation to limit their harvesting, and in fact 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 (for example, whales) economic forces will always drive toward fishing the population to extinction.
Cascade Effects
Overexploitation of species can also result in cascade effects, particularly if a habitat loses its apex predator. Because of the loss of the top predator, a dramatic increase in their prey species can occur. In turn, the unchecked prey can then overexploit their own food resources until population numbers dwindle, possibly to the point of extinction.
Key Points
• Until recently, human populations harvested resources in limited quantities. Today, new methods of harvest and capture contribute to overharvesting and overexploitation.
• Overharvesting stems from several factors, including an exponential increase in the human population, expanding markets, increasing demand, and improved access and techniques for capture.
• Overharvesting natural resources for extended periods of time depletes these resources until they cannot recover within a short period of time; some may never recover.
• Overharvesting is one of five primary activities threatening global biodiversity; others include pollution, introduced species, habitat fragmentation, and habitat destruction.
• Aquatic species are especially threatened by overharvesting, due to a situation known as the tragedy of the commons.
Key Terms
• overexploitation: Excessive and damaging use of natural resources, including plants and animals.
• trawler: A fishing boat that uses a dragnet, or “trawl net,” to catch fish.
• apex predator: An animal at the top of the food chain, preying on other species but not prey itself. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/47%3A_Conservation_Biology_and_Biodiversity/47.03%3A_Threats_to_Biodiversity/47.3B%3A_Overharvesting.txt |
Learning Objectives
• Describe the impact of exotic and invasive species on native species
Exotic species are those that have been intentionally or unintentionally introduced by humans into an ecosystem in which they did not evolve. Such introductions probably 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 one foot each day. It is now a pest species, covering over seven 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, resetting the ecological conditions in the new environment, while threatening the species that exist there. For this reason, exotic species, also called invasive species, can threaten other species through competition for resources, predation, or disease.
Exotic Species Threaten Native Species
Invasive species can change the functions of ecosystems. For example, invasive plants can alter the fire regimen, nutrient cycling, and hydrology in native ecosystems. Invasive species that are closely related to rare native species have the potential to hybridize with the native species. Harmful effects of hybridization have led to a decline and even extinction of native species. For example, hybridization with introduced cordgrass, Spartina alterniflora, threatens the existence of California cordgrass in San Francisco Bay. Invasive species cause competition for native species. Four hundred of the 958 endangered species under the Endangered Species Act are at risk due to this competition.
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 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. There is evidence that the fungus, native to Africa, 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 Batrachochytriumdendrobatidis and can act as a reservoir for the disease.
Key Points
• Exotic species introduced to new environments often reset the ecological conditions in that new habitat, threatening the species that exist there; this is the reason that they are also termed invasive species.
• Invasive species that are closely related to rare native species have the potential to hybridize with the native species; harmful effects of hybridization have led to a decline and even extinction of native species.
• Biologists studying frogs and toads may be inadvertently responsible for the worldwide spread of a fungus deadly to amphibians.
Key Terms
• invasive species: any species that has been introduced to an environment where it is not native and has since become a nuisance through rapid spread and increase in numbers, often to the detriment of native species | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/47%3A_Conservation_Biology_and_Biodiversity/47.03%3A_Threats_to_Biodiversity/47.3C%3A__Exotic_Species.txt |
Learning Objectives
• Evaluate climate change and its impact on biodiversity
Climate Change
Climate change, specifically, the anthropogenic (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 probable magnitude of the effects, with extinction rate estimates ranging from 15 percent to 40 percent of species 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.
Impact of Climate Change on Biodiversity
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, with their ranges are overlapping, 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 recently been documented.
Range shifts are already being observed. For example, some European bird species’ ranges have moved 91 km northward. The same study suggests 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 glacial melt and the greater volume of warmer water. Shorelines will be inundated, reducing island size, which will have an effect on many species; 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.
Key Points
• This warming trend is persistently shifting colder climates further toward the north and south poles, forcing species to move with their own adapted climate norms, while also facing habitat gaps along the way.
• Climate shifts will move up mountains, resulting in the crowding of species higher in altitude and eliminating the habitat for those species adapted to those high elevations; indeed, some climates will completely disappear.
• Global warming will also raise ocean water levels due to melted water from glaciers and the greater volume of warmer water; shorelines will be flooded, affecting many species; many islands will disappear altogether.
Key Terms
• anthropogenic: having its origin in the influence of human activity on nature
• biodiversity: the diversity (number and variety of species) of plant and animal life within a region | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/47%3A_Conservation_Biology_and_Biodiversity/47.03%3A_Threats_to_Biodiversity/47.3D%3A_Climate_Change_and_Biodiversity.txt |
Learning Objectives
• Explain how DNA barcoding aids in measuring biodiversity
Measuring Biodiversity
The technologies of molecular genetics, data processing, and data storage are maturing to the point where cataloging the planet’s species in an accessible way is close to feasible. DNA barcoding is one molecular genetic method, which takes advantage of the rapid evolution in a mitochondrial gene present in eukaryotes, to identify species using the sequence of portions of the gene. Plants may be barcoded using a combination of chloroplast genes.
DNA Barcoding
DNA barcoding is a taxonomic method that uses a short genetic marker in an organism’s DNA to identify it as belonging to a particular species. It differs from molecular phylogeny in that the main goal is not to determine patterns of relationship, but to identify an unknown sample in terms of a preexisting classification. The most commonly-used barcode region for animals, at least, is a segment of approximately 600 base pairs of the mitochondrial gene cytochrome oxidase I (COI).
Applications include, for example, identifying plant leaves (even when flowers or fruit are not available), identifying insect larvae (which may have fewer diagnostic characters than adults and are frequently less well-known), identifying the diet of an animal (based on its stomach contents or feces), and identifying products in commerce (for example, herbal supplements or wood).
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 (International Union for Conservation of Nature) which maintains the Red List: an online listing of endangered species categorized by taxonomy, type of threat, and other criteria. The Red List is supported by scientific research. In 2011, the list contained 61,000 species, all with supporting documentation.
Key Points
• DNA barcoding is a taxonomic method that uses a short genetic marker in an organism’s DNA to identify it as belonging to a particular species.
• Barcoding allows us to classify organisms that would otherwise be difficult to identify, such as in situations where only part of an organism is available, or is too immature to identify by conventional methods.
• At the present rate of description of new species, it will take close to 500 years before the complete catalog of life is known; however, most species will be extinct before this time.
• Even with barcoding, it is difficult to know which species are threatened and to what degree they are threatened, a task carried out by the non-profit IUCN (International Union for Conservation of Nature).
Key Terms
• barcoding: a taxonomic method that uses a short genetic marker in an organism’s DNA to identify it as belonging to a particular species
• phylogeny: the evolutionary history of an organism
• taxonomy: the science of finding, describing, classifying and naming organisms | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/47%3A_Conservation_Biology_and_Biodiversity/47.04%3A_Preserving_Biodiversity/47.4A%3A_Measuring_Biodiversity.txt |
Learning Objectives
• Detail the benefits and limitations of different human responses to climate change and species loss, such as using preserves to conserve species
Human Responses to Climate Change and Species Loss
Legislation throughout the world has been enacted to protect species and include 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 worth hundreds of millions of dollars. Illegal wildlife trade is monitored by another non-profit, the 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. The U.S. Fish & Wildlife Service is required by law to develop management plans that protect the species listed as at risk in the Act in order to 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 inefficient as it 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).
In relation to global warming, 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, while China did so because of a concern that 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.
Using Preserves to Conserve Species
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 groups mentioned above.
Many nations have laws that protect endangered species: for example, forbidding hunting, restricting land development, or creating preserves. Preserves are purchased land for the explicit purpose of attempting to protect species and ecosystems. They also protect biodiversity in many ways, such as through captive breeding and private farming.
Captive breeding is the process of breeding rare or endangered species in human-controlled environments with restricted settings, such as wildlife preserves and conservation facilities. Captive breeding is meant to prevent species extinction and to stabilize the population of the species so that it will not disappear. This technique has worked for many species for some time, such as for Pere David’s deer. However, captive breeding techniques are usually difficult to implement for such highly-mobile species as some migratory birds (e.g. cranes) and fish (e.g. hilsa). Additionally, if the captive-breeding population is too small, then inbreeding may occur due to a reduced gene pool, which may also reduce immunity.
Key Points
• Legislation throughout the world has been enacted to protect species; the legislation includes international treaties as well as national and state laws.
• The international response to global warming has been mixed; the Kyoto Protocol, an international agreement that came out of the United Nations climate change convention that committed countries to reducing greenhouse gas emissions, was ratified by some countries, but spurned by others.
• Many nations have laws that protect endangered species: for example, forbidding hunting, restricting land development, or creating preserves (purchased land for the explicit purpose of attempting to protect species and ecosystems ).
• Preserves protect biodiversity in many ways, two of which are captive breeding and private farming.
Key Terms
• endangered species: a species which is in danger of becoming extinct | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/47%3A_Conservation_Biology_and_Biodiversity/47.04%3A_Preserving_Biodiversity/47.4B%3A_Changing_Human_Behavior_in_Response_to_Biodiversity_Loss.txt |
Learning Objectives
• Explain the purpose of ecological restoration projects
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 in order to strengthen their viability as long-term solutions.
Due to the way protected lands are allocated (they tend to contain less economically-valuable resources rather than being set aside specifically for at-risk species or ecosystems) 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 (International Union for Conservation of Nature) 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 solely outside preserves; these percentages are much higher when only threatened species and high-quality preserves are considered.
Limitations on Preserves
Some of the limitations on preserves as conservation tools stem from preserve designs. Additionally, political and economic pressures typically make preserves smaller, never larger, so setting aside areas that are large enough is difficult. 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. Some argue 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.
Habitat Restoration
Habitat restoration holds considerable promise as a mechanism for restoring and maintaining biodiversity. Restoration ecology aims to return ecosystems to a more natural, pre-disturbance state. 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, which function to suppress elk and coyote populations, provide more-abundant resources to the guild of carrion (flesh) eaters. Reducing elk populations has allowed re-vegetation of riparian areas, which has increased the diversity of species in that habitat. Decreasing the coyote population 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: it is 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. Similarly, restoring a keystone species can have dramatic effects. 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. 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.
Key Points
• Ecological preserves, while effective in the short term, are not yet viable, long-term solutions.
• Some of the limitations on preserves as conservation tools include preserve designs, political and economic pressures, and climate change.
• Habitat restoration is a promising tool for restoring and maintaining biodiversity; restoration can improve the biodiversity of degraded ecosystems.
Key Terms
• biodiversity: the diversity (number and variety of species) of plant and animal life within a region
• keystone species: a species that exerts a large, stabilizing influence throughout an ecological community, despite its relatively small numerical abundance
• carrion: dead flesh; carcasses | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/47%3A_Conservation_Biology_and_Biodiversity/47.04%3A_Preserving_Biodiversity/47.4C%3A_Ecological_Restoration.txt |
• 1.0: Prelude to The Study of Life
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: 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.E: The Study of Life (Exercises)
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: The Study of Life
Viewed from space, Earth offers no clues about the diversity of life forms that reside there. 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: The Science of Biology
Skills to Develop
• 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
What is 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 (Figure \(1\)). Listening to the daily news, you will quickly realize how many aspects of biology are discussed every day. For example, recent news topics include Escherichia coli (Figure \(2\)) 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.
The Process of Science
Biology is a science, but what exactly is science? What does the study of biology share with other scientific disciplines? Science (from the Latin scientia, meaning “knowledge”) can be defined 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 the application of the 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.
The steps of the scientific method will be examined 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 can be tested. 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 it becomes more difficult to repeat experiments.
These areas of study are still sciences, however. Consider archeology—even though one cannot perform repeatable experiments, hypotheses may still be supported. For instance, an archeologist can hypothesize that an ancient culture existed based on finding a piece of pottery. Further hypotheses could be made about various characteristics of this culture, and these hypotheses may be found to 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. Science may be better defined 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? Or, maybe all of the above? Science includes such diverse fields as astronomy, biology, computer sciences, geology, logic, physics, chemistry, and mathematics (Figure \(3\)). However, those fields of science related to the physical world and its phenomena and processes are considered natural sciences. Thus, a museum of natural sciences might contain any of the items listed above.
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. Natural sciences are sometimes referred to 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 the raw data can be supplemented 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 the analysis of a large amount of data. Brain studies provide an example. In this type of research, many live brains are observed while people are doing a specific activity, such as viewing images of food. The part of the brain that “lights up” during this activity is then predicted to be the part controlling the response to the selected stimulus, in this case, images of food. The “lighting up” of the various areas of the brain is caused by excess absorption of radioactive sugar derivatives by active areas of the brain. The resultant increase in radioactivity is observed by a scanner. 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 reason, 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 forecast specific results. From those general principles, a scientist can extrapolate 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. These predictions have been made and tested, and many such changes have been found, such as the modification of arable areas for agriculture, with change based on temperature averages.
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 can be tested. 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 developed a company 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. This approach is common to other sciences as well and is often referred to as the scientific method. The scientific method was used even in ancient times, but it was first documented by England’s Sir Francis Bacon (1561–1626) (Figure \(4\)), who set up inductive methods for scientific inquiry. The scientific method is not exclusively used by biologists but can be applied to almost all fields of study as a logical, rational problem-solving method.
The scientific process typically starts with an observation (often a problem to be solved) 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 can be tested. To solve a problem, several hypotheses may be proposed. For example, one hypothesis might be, “The classroom is warm because no one turned on the air conditioning.” But there could be other responses to the question, and therefore other hypotheses may be proposed. A second hypothesis might be, “The classroom is warm because there is a power failure, and so the air conditioning doesn’t work.”
Once a hypothesis has been selected, 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 it can be disproven by experimental results. 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 is hypothesized about. Therefore, if the results of the experimental group 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 this hypothesis should be rejected. 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 this hypothesis should be rejected. Each hypothesis should be tested by carrying out appropriate experiments. Be aware that rejecting one hypothesis does not determine whether or not the other hypotheses can be accepted; it simply eliminates one hypothesis that is not valid (Figure \(5\)). Using the scientific method, the hypotheses that are inconsistent with experimental data are rejected.
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, specific results are predicted from a general premise. This type of reasoning is called deductive reasoning: deduction proceeds from the general to the particular. But the reverse of the process is also possible: sometimes, scientists reach a general conclusion from a number of specific observations. This type of reasoning is called inductive reasoning, and it proceeds from the particular to the general. Inductive and deductive reasoning are often used in tandem to advance scientific knowledge (Figure \(6\)).
Art Connection
In the example below, the scientific method is used to solve an everyday problem. Order 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
2. Question
3. Hypothesis (answer)
4. Prediction
5. Experiment
6. Result
1. There is something wrong with the electrical outlet.
2. If something is wrong with the outlet, my coffeemaker also won’t work when plugged into it.
3. My toaster doesn’t toast my bread.
4. I plug my coffee maker into the outlet.
5. My coffeemaker works.
6. Why doesn’t my toaster work?
Art Connection
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, DNA is the genetic material.
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 the scientific method can be applied 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, though 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 \(7\)). In applied science, the problem is usually defined for the researcher.
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?” A careful look at the history of science, however, 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 an application is developed; therefore, applied science relies on the results generated through basic science. Other scientists think that it is time to move on from basic science and instead to find solutions to actual problems. Both approaches are valid. It is true that there are problems that demand immediate attention; however, few solutions would be found without the help of the wide knowledge foundation generated through basic science.
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. Strands of DNA, unique in every human, are found in our cells, where they provide the instructions necessary for life. During DNA replication, DNA makes new copies of itself, shortly before a cell divides. Understanding the mechanisms of DNA replication enabled scientists to develop laboratory techniques that are now used to identify genetic diseases, pinpoint individuals who were at a crime scene, and determine paternity. Without basic science, it is unlikely that applied science would exist.
Another example of the link between basic and applied research is the Human Genome Project, a study in which each human chromosome was analyzed and mapped to determine the precise sequence of DNA subunits and the exact location of each gene. (The gene is the basic unit of heredity; an individual’s complete collection of genes is his or her genome.) Other less complex organisms have also been studied as part of this project in order to gain a better understanding of human chromosomes. The Human Genome Project (Figure \(8\)) relied on basic research carried out 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.
While research efforts in both basic science and applied science are usually carefully planned, it is important to note that some discoveries are made by serendipity, that is, by means of a fortunate accident or a lucky surprise. Penicillin was discovered when biologist Alexander Fleming accidentally left a petri dish of Staphylococcus bacteria open. An unwanted mold grew on the dish, killing the bacteria. The mold turned out to be Penicillium, and a new antibiotic was discovered. 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—are all 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 are reviewed by a scientist’s colleagues, or peers. 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 described 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. The experimental results must be consistent with the findings of other scientists.
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 hypothesis or research question driving the research will be presented. 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 considered plagiarism.
The materials and methods section includes a complete and accurate description of the substances used, and the method and techniques used by the researchers 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 measurements were made and what types of calculations and statistical analyses were 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 the combination of both sections, the results section simply narrates the findings without any further interpretation. The results are presented by means of tables or graphs, but no duplicate information should be presented. In the discussion section, the researcher 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, proper citations are included in this section as well.
Finally, the conclusion section summarizes the importance of the experimental findings. While the scientific paper almost certainly answered one or more scientific questions that were stated, any good research should lead to more questions. Therefore, a well-done scientific paper leaves doors open for the researcher 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.
Summary
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 considered 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.
Two types of logical reasoning are used in science. 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 the use of 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 research done in a particular field over a period of time.
Art Connections
Figure \(5\): In the example below, the scientific method is used to solve an everyday problem. Order 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
2. Question
3. Hypothesis (answer)
4. Prediction
5. Experiment
6. Result
1. There is something wrong with the electrical outlet.
2. If something is wrong with the outlet, my coffeemaker also won’t work when plugged into it.
3. My toaster doesn’t toast my bread.
4. I plug my coffee maker into the outlet.
5. My coffeemaker works.
6. Why doesn’t my toaster work?
Answer
1: C; 2: F; 3: A; 4: B; 5: D; 6: E. The original hypothesis is incorrect, as the coffeemaker works when plugged into the outlet. Alternative hypotheses include that the toaster might be broken or that the toaster wasn't turned on.
Figure \(6\): 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, DNA is the genetic material.
4. Animals as diverse as humans, insects, and wolves all exhibit social behavior. Therefore, social behavior must have an evolutionary advantage.
Answer
1: inductive; 2: deductive; 3: deductive; 4: inductive.
Glossary
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
basic science
science that seeks to expand knowledge and understanding regardless of the short-term application of that knowledge
biology
the study of living organisms and their interactions with one another and their environments
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 forecast 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
falsifiable
able to be disproven by experimental results
hypothesis
suggested explanation for an observation, which can be tested
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
materials and methods
section of a scientific paper that includes a complete description of the substances, methods, and techniques used by the researchers to gather data
natural science
field of science that is related to the physical world and its phenomena and processes
peer-reviewed manuscript
scientific paper that is reviewed by a scientist’s colleagues who are experts in the field of study
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
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
variable
part of an experiment that the experimenter can vary or change | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/1%3A_The_Chemistry_of_Life/1%3A_The_Study_of_Life/1.0%3A_Prelude_to_The_Study_of_Life.txt |
Skills to Develop
• 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 sub disciplines 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. It turns out that 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”? 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.
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 nine characteristics serve to define life.
Order
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 make up molecules; these in turn make up cell organelles and other cellular inclusions. In multicellular organisms (Figure \(1\)), 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
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 \(2\)). Even tiny bacteria can move toward or away from chemicals (a process called chemotaxis) or light (phototaxis). Movement toward a stimulus is considered a positive response, while movement away from a stimulus is considered a negative response.
Link to Learning
Video: 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 germline cells that will form new individuals. When reproduction occurs, genes containing DNA 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.
Growth and Development
Organisms grow and develop following specific instructions coded for by their genes. These genes provide instructions that will direct cellular growth and development, ensuring that a species’ young (Figure \(3\)) will grow up to exhibit many of the same characteristics as its parents.
Regulation
Even the smallest organisms are complex and require multiple regulatory mechanisms to coordinate internal functions, respond to stimuli, and cope with environmental stresses. 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.
Homeostasis
In order to function properly, cells need to have 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 internal conditions within a narrow range almost constantly, despite environmental changes, through homeostasis (literally, “steady state”)—the ability of an organism to maintain constant internal conditions. For example, an organism needs to regulate body temperature through a process known as thermoregulation. Organisms that live in cold climates, such as the polar bear (Figure \(4\)), 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
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 \(5\)).
Levels of Organization of Living Things
Living things are highly organized and structured, following a hierarchy that can be examined on a scale from small to large. The atom is the smallest and most fundamental unit of matter. 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 \(6\)), which contains the instructions for the structure and functioning of all living organisms.
Link to Learning
Video: Watch this video that animates the three-dimensional structure of the DNA molecule shown in Figure \(6\).
Some cells contain aggregates of macromolecules surrounded by membranes; these are called 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 viruses are not considered 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. Cells are classified 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 considered organisms and are typically referred to as microorganisms.
All the individuals of a species living within a specific area are collectively called a population. For example, a forest may include many pine trees. All of these pine trees 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 and also 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, non-living parts of that environment such as nitrogen in the soil or rain water. At the highest level of organization (Figure \(7\)), 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.
Art Connection
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 during which new species arise from older species. Evolutionary biologists study the evolution of living things in everything from the microscopic world to ecosystems.
The evolution of various life forms on Earth can be summarized in a phylogenetic tree (Figure \(8\)). A phylogenetic tree is a diagram showing the evolutionary relationships among biological species based on similarities and differences in genetic or physical traits or both. A phylogenetic tree is composed of nodes and branches. The internal nodes represent ancestors and are points in evolution when, based on scientific evidence, an ancestor is thought to have diverged to form two new species. The length of each branch is proportional to the time elapsed since the split.
Evolution Connection: Carl Woese and the Phylogenetic Tree
In the past, biologists grouped living organisms into five kingdoms: animals, plants, fungi, protists, and bacteria. The organizational scheme was based mainly on physical features, as opposed to physiology, biochemistry, or molecular biology, all of which are used by modern systematics. The pioneering work of American microbiologist Carl Woese 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 together with the four original kingdoms (excluding bacteria). Woese defined Archaea as a new domain, and this resulted in a new taxonomic tree (Figure \(8\)). 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’s tree was constructed from comparative sequencing of the genes that are universally distributed, present in every organism, and conserved (meaning that these genes have remained essentially unchanged throughout evolution). Woese’s approach was revolutionary because comparisons of physical features are insufficient to differentiate between the prokaryotes that appear fairly similar in spite of their tremendous biochemical diversity and genetic variability (Figure \(9\)). The comparison of homologous DNA and RNA sequences provided Woese with a sensitive device that revealed the extensive variability of prokaryotes, and which justified the separation of the prokaryotes into two domains: bacteria and archaea.
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: Forensic Scientist
Forensic 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, the development of molecular techniques and the establishment of 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 \(10\)) 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 be required to take chemistry and biology courses as well as some intensive math courses.
Another field of biological study, neurobiology, studies the biology of the nervous system, and although it is considered a branch of biology, it is also recognized as an interdisciplinary field of study known as neuroscience. Because of its interdisciplinary nature, this subdiscipline studies different functions of the nervous system using molecular, cellular, developmental, medical, and computational approaches.
Paleontology, another branch of biology, uses fossils to study life’s history (Figure \(11\)). 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.
Summary
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. Organisms, in turn, are grouped as populations, communities, ecosystems, and the biosphere. The great diversity of life today evolved from less-diverse ancestral organisms over billions of years. A diagram called a phylogenetic tree can be used 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.
Art Connections
Figure \(7\): 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.
Answer
Communities exist within populations which exist within ecosystems.
Glossary
atom
smallest and most fundamental unit of matter
biochemistry
study of the chemistry of biological organisms
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
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
process of gradual change during which new species arise from older species and some species become extinct
homeostasis
ability of an organism to maintain constant internal conditions
macromolecule
large molecule, typically formed by the joining of smaller molecules
microbiology
study of the structure and function of microorganisms
molecule
chemical structure consisting of at least two atoms held together by one or more chemical bonds
molecular biology
study of biological processes and their regulation at the molecular level, including interactions among molecules such as DNA, RNA, and proteins
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
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
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
tissue
group of similar cells carrying out related functions
zoology
study of animals | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/1%3A_The_Chemistry_of_Life/1%3A_The_Study_of_Life/1.2%3A_Themes_and_Concepts_of_Biology.txt |
1.1: The Science of Biology
Review Questions
The first forms of life on Earth were ________.
1. plants
2. microorganisms
3. birds
4. dinosaurs
Answer
B
A suggested and testable explanation for an event is called a ________.
1. hypothesis
2. variable
3. theory
4. control
Answer
A
Which of the following sciences is not considered a natural science?
1. biology
2. astronomy
3. physics
4. computer science
Answer
D
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
Answer
D
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
Answer
C
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
Answer
A
Free Response
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.
Answer
Answers will vary, but should apply the steps of the scientific method. One possibility could be a car which doesn’t start. The hypothesis could be that the car doesn’t start because the battery is dead. The experiment would be to change the battery or to charge the battery and then check whether the car starts or not. If it starts, the problem was due to the battery, and the hypothesis is accepted.
Give an example of how applied science has had a direct effect on your daily life.
Answer
Answers will vary. One example of how applied science has had a direct effect on daily life is the presence of vaccines. Vaccines to prevent diseases such polio, measles, tetanus, and even influenza affect daily life by contributing to individual and societal health.
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.
Answer
Answers will vary. Topics that fall inside the area of biological study include how diseases affect human bodies, how pollution impacts a species’ habitat, and how plants respond to their environments. Topics that fall outside of biology (the “study of life”) include how metamorphic rock is formed and how planetary orbits function.
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
Answer
Answers will vary. Basic science: What evolutionary purpose might cancer serve? Applied science: What strategies might be found to prevent cancer from reproducing at the cellular level?
1.2: Themes and Concepts of Biology
Review Questions
The smallest unit of biological structure that meets the functional requirements of “living” is the ________.
1. organ
2. organelle
3. cell
4. macromolecule
Answer
C
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
Answer
A
The presence of a membrane-enclosed nucleus is a characteristic of ________.
1. prokaryotic cells
2. eukaryotic cells
3. living organisms
4. bacteria
Answer
B
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
Answer
C
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
Answer
D
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
Answer
D
Free Response
Select two items that biologists agree are necessary in order to consider an organism “alive.” For each, give an example of a non-living object that otherwise fits the definition of “alive.”
Answer
Answers will vary. Layers of sedimentary rock have order but are not alive. Technology is capable of regulation but is not, of itself, alive.
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.
Answer
Smallest level of organization to largest: hydrogen atom, water molecule, skin cell, liver, elephant, wolf pack, tropical rainforest, planet Earth
You go for a long walk on a hot day. Give an example of a way in which homeostasis keeps your body healthy.
Answer
During your walk, you may begin to perspire, which cools your body and helps your body to maintain a constant internal temperature. You might also become thirsty and pause long enough for a cool drink, which will help to restore the water lost during perspiration.
Using examples, explain how biology can be studied from a microscopic approach to a global approach.
Answer
Researchers can approach biology from the smallest to the largest, and everything in between. For instance, an ecologist may study a population of individuals, the population’s community, the community’s ecosystem, and the ecosystem’s part in the biosphere. When studying an individual organism, a biologist could examine the cell and its organelles, the tissues that the cells make up, the organs and their respective organ systems, and the sum total—the organism itself. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/1%3A_The_Chemistry_of_Life/1%3A_The_Study_of_Life/1.E%3A_The_Study_of_Life_%28Exercises%29.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.
• 2.0: Prelude to The Chemical Foundation of Life
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.
• 2.1: 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.
• 2.2: 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.
• 2.3: 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.
• 2.E: The Chemical Foundation of Life (Exercises)
Thumbnail: Fatty acid molecules with cis and trans configurations. (CC BY 4.0 / modified from original; OpenStax).
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 cells, tissues, organ systems, and entire organisms.
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_1e_(OpenStax)/1%3A_The_Chemistry_of_Life/2%3A_The_Chemical_Foundation_of_Life/2.0%3A_Prelude_to_The_Chemical_Foundation_of_Life.txt |
Skills to Develop
• 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 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.
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 non-living world, elements are found in different proportions, and some elements common to living organisms are relatively rare on the earth as a whole, as shown in Table $1$. 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 non-living world.
Table $1$: Approximate Percentage of Elements in Living Organisms (Humans) Compared to the Non-living 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
The Structure of the Atom
To understand how elements come together, we must first discuss the smallest component or building block of an element, the atom. An atom is the smallest unit of matter that retains all of the chemical properties of an element. For example, one gold atom has all of the properties of gold in that it is a solid metal at room temperature. A gold coin is simply a very large number of gold atoms molded into the shape of a coin and containing small amounts of other elements known as impurities. Gold atoms cannot be broken down into anything smaller while still retaining the properties of gold.
An atom is composed of two regions: the nucleus, which is in the center of the atom and contains protons and neutrons, and the outermost region of the atom which holds its electrons in orbit around the nucleus, as illustrated in Figure $1$. Atoms contain protons, electrons, and neutrons, among other subatomic particles. The only exception is hydrogen (H), which is made of one proton and one electron with no neutrons.
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 shown in Table $2$. 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 positive charge of a proton. 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 volume of an atom—greater than 99 percent—is, in fact, 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.
Table $2$: Protons, Neutrons, and Electrons
Charge Mass (amu) Location
Proton +1 1 nucleus
Neutron 0 1 nucleus
Electron –1 0 orbitals
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 and is used 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 the number of neutrons determine an element’s mass number, as illustrated in Figure $2$. Note that the small contribution of mass from electrons is disregarded in calculating the mass number. This approximation of mass can be used 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).
Art Connection
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 losing neutrons to eventually become carbon-12) describes the energy loss that occurs when an unstable atom’s nucleus releases radiation.
Evolution Connection: Carbon Dating
Carbon is normally present in the atmosphere in the form of gaseous compounds like carbon dioxide and methane. Carbon-14 ($\ce C^{14}$) is a naturally occurring radioisotope that is created in the atmosphere from atmospheric $\ce N^{14}$ (nitrogen) by the addition of a neutron and the loss of a proton because of cosmic rays. This is a continuous process, so more $\ce C^{14}$ is always being created. As a living organism incorporates $\ce C^{14}$ initially as carbon dioxide fixed in the process of photosynthesis, the relative amount of $\ce C^{14}$ in its body is equal to the concentration of $\ce C^{14}$ in the atmosphere. When an organism dies, it is no longer ingesting $\ce C^{14}$, so the ratio between $\ce C^{14}$ and $\ce C^{12}$ will decline as $\ce C^{14}$ decays gradually to $\ce N^{14}$ by a process called beta decay—the emission of electrons or positrons. This decay gives off energy in a slow process.
After approximately 5,730 years, half of the starting concentration of $\ce C^{14}$ will have been converted back to $\ce N^{14}$. The time it takes for half of the original concentration of an isotope to decay back to its more stable form is called its half-life. Because the half-life of $\ce C^{14}$ is long, it is used to date formerly living objects such as old bones or wood. Comparing the ratio of the $\ce C^{14}$ concentration found in an object to the amount of $\ce C^{14}$ detected in the atmosphere, the amount of the isotope that has not yet decayed can be determined. On the basis of this amount, the age of the material, such as the pygmy mammoth shown in Figure $3$, can be calculated with accuracy if it is not much older than about 50,000 years. Other elements have isotopes with different half lives. For example, $\ce K^{40}$ (potassium-40) has a half-life of 1.25 billion years, and $\ce U^{235}$ (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.
Link to Learning
Video: To learn more about atoms, isotopes, and how to tell one isotope from another, visit this site and run the simulation.
The Periodic Table
The different elements are organized and displayed in the periodic table. 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, shown in Figure $4$, 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 12.11.
The periodic table groups elements according to chemical properties. The differences in chemical reactivity between the elements are based 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
It should be stressed 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.
An early model of the atom was developed in 1913 by Danish scientist Niels Bohr (1885–1962). 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 illustrated in Figure $5$. 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.
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 will be filled with one electron in each energy level before a second electron is added. The electrons of the outermost energy level determine the energetic stability of the atom 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. Examples of some neutral atoms and their electron configurations are shown in Figure $6$. Notice that in this figure, 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.
Art Connection
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 organization of the periodic table is based on the total number of protons (and electrons) helps us know how electrons are distributed among the outer shell. The periodic table is arranged in columns and rows based on the number of electrons and where these electrons are located. Take a closer look at the some of the elements in the table’s far right column in Figure $6$. 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. Their non-reactivity has resulted in their being named the inert gases (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 columns of the periodic table 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 of the atom does not accurately reflect how electrons are spatially distributed surrounding the nucleus. They do not circle the nucleus like the earth orbits the sun, but are found 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 known as wave functions can predict within a certain level of probability where an electron might be at any given time. The area where an electron is most likely to be found is called 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 where an electron is located, scientists know that it is most probably located within its orbital path. Subshells are designated by the letter s, p, d, and f. 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 illustrated in Figure $7$. Subshells d and f have more complex shapes and contain five and seven orbitals, respectively. These are not shown 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 found in the energy levels increases. Progressing from one atom to the next in the periodic table, the electron structure can be worked out by fitting an extra electron into the next available orbital.
The closest orbital to the nucleus, called the 1s orbital, can hold up to two electrons. This orbital is equivalent to the innermost electron shell of the Bohr model of the atom. It is called the 1s orbital because it is spherical around the nucleus. The 1s orbital is the closest orbital to the nucleus, and it is always filled first, before any other orbital can be filled. Hydrogen has one electron; therefore, it has only one spot within the 1s orbital occupied. This is designated 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. This is designated as 1s2, referring to the two electrons of helium in the 1s orbital. On the periodic table Figure $4$, 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 shown in Figure $7$. After the 1s orbital is filled, the second electron shell is filled, 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, a second may be added. 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), on the other hand, 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, making up the third electron shell. While the concepts of electron shells and orbitals are closely related, orbitals provide a more accurate depiction of the electron configuration of an atom because the orbital model specifies the different shapes and special orientations of all the places that electrons may occupy.
Link to Learning
Video: 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 illustrated in Figure $8$. Atoms can form molecules by donating, accepting, or sharing electrons to fill their outer shells.
Chemical reactions occur when two or more atoms bond together to form molecules or when bonded atoms are broken apart. The substances used in the beginning of a chemical reaction are called the reactants (usually found on the left side of a chemical equation), and the substances found at the end of the reaction are known as the products (usually found on the right side of a chemical equation). An arrow is typically drawn between the reactants and products to indicate the direction of the chemical reaction; this direction is not always a “one-way street.” For the creation of the water molecule shown above, the chemical equation would be:
$\ce{2H + O \rightarrow H_2O} \nonumber$
An example of a simple chemical reaction is the breaking down of hydrogen peroxide molecules, each of which consists of two hydrogen atoms bonded to two oxygen atoms (H2O2). The reactant hydrogen peroxide is broken 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 the number of atoms of each element 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.
$\ce{2H_2O_2\: (hydrogen\: peroxide) \rightarrow 2H_2O\: (water) + O_2\: (oxygen)} \nonumber$
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, on the other hand, as shown in Figure $9$, consists of two doubly bonded oxygen atoms and is not classified as a compound but as a mononuclear molecule.
Some chemical reactions, such as the one shown above, can proceed in one direction until the reactants are all used up. 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 are turned into products, but when the concentration of product goes beyond a certain threshold (characteristic of the particular reaction), some of these products will be converted back into reactants; at this point, the designations of products and reactants are reversed. This back and forth continues until a certain relative balance between reactants and products occurs—a state called equilibrium. These situations of reversible reactions are often denoted by a chemical equation with a double headed arrow pointing towards both the reactants and products.
For example, in human blood, excess hydrogen ions (H+) bind to bicarbonate ions (HCO3-) forming an equilibrium state with carbonic acid (H2CO3). If carbonic acid were added to this system, some of it would be converted to bicarbonate and hydrogen ions.
$\ce{HCO^{-}_3 + H^+ \leftrightarrow H_2CO_3} \nonumber$
In biological reactions, however, equilibrium is rarely obtained because the concentrations of the reactants or products or both are constantly changing, often with a product of one reaction being a reactant for another. To return to the example of excess hydrogen ions in the blood, the formation of carbonic acid will be the major direction of the reaction. However, the carbonic acid can also leave the body as carbon dioxide gas (via exhalation) instead of being converted back to bicarbonate ion, thus driving the reaction to the right by the chemical law known as law of mass action. These reactions are important for maintaining the homeostasis of our blood.
$\ce{HCO_3^- + H^+ \leftrightarrow H_2CO_3 \leftrightarrow CO_2 + H_2O} \nonumber$
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 are formed by losing electrons. Negative ions are formed by gaining electrons and are called anions. Anions are designated by their elemental name being altered to end in “-ide”: the anion of chlorine is called chloride, and the anion of sulfur is called sulfide, for example.
This movement of electrons from one element to another is referred to as electron transfer. As Figure $10$ 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. It is now referred to 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. It is now referred to 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.
Ionic bonds are formed 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.
Certain salts are referred to in physiology 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 the octet rule can be satisfied is by the sharing of electrons between atoms to form covalent bonds. These bonds are stronger and much more common than ionic bonds in the molecules of living organisms. Covalent bonds are commonly found in carbon-based organic molecules, such as our DNA and proteins. Covalent bonds are also found in inorganic molecules like H2O, CO2, and O2. One, two, or three pairs of electrons may be shared, 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, the sharing of these three pairs of electrons between the two nitrogen atoms allows for the filling of 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.
The formation of water molecules provides an example of covalent bonding. The hydrogen and oxygen atoms that combine to form water molecules are bound together by covalent bonds, as shown in Figure $8$. The electron from the hydrogen splits its time between the incomplete outer shell of the hydrogen atoms and the incomplete outer shell of the oxygen atoms. To completely fill the outer shell of oxygen, which has six electrons in its outer shell but which would be more stable with eight, two electrons (one from each hydrogen atom) are needed: hence the well-known formula H2O. The electrons are shared between the two elements to fill the outer shell of each, making both elements more stable.
Link to Learning
Video: 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, shown in Figure $11$, the electrons are unequally shared by the atoms and are attracted more to one nucleus than the other. Because of the unequal distribution of electrons 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 nucleus of the oxygen atom is more attractive to the electrons of the hydrogen atoms 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 in the vicinity of the oxygen nucleus than they do near the nucleus of the hydrogen atoms, giving the atoms of oxygen and hydrogen 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 the development of partial charges whenever one element is significantly more electronegative than the other, and the charges generated by these polar bonds may then be used for the formation of hydrogen bonds based on the attraction of opposite partial charges. (Hydrogen bonds, which are discussed 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 will be equally distributed between the two oxygen atoms.
Another example of a nonpolar covalent bond is methane (CH4), also shown in Figure $11$. Carbon has four electrons in its outermost shell and needs four more to fill it. It gets 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.
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 δ+of the hydrogen from one molecule and the δ– charge on the more electronegative atoms of another molecule, usually oxygen or nitrogen, or within the same molecule. This interaction is called 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 three-dimensional structure of the proteins in our cells that is necessary for their proper function.
Career Connection: Pharmaceutical Chemist
Pharmaceutical chemists are responsible for the development of 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. Drugs can be found in the natural environment or can be synthesized in the laboratory. In many cases, potential drugs found in nature are changed chemically in the laboratory to make them safer and more effective, and sometimes synthetic versions of drugs substitute for the version found in nature.
After the initial discovery or synthesis of a drug, the chemist then develops the drug, perhaps chemically altering it, testing it to see if the drug is toxic, and then designing methods for efficient large-scale production. Then, the process of getting the drug approved for human use begins. In the United States, drug approval is handled by the Food and Drug Administration (FDA) and involves a series of large-scale experiments using human subjects to make sure the drug is not harmful and effectively treats the condition it aims to treat. 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 any biologically active compounds are found within them. Sometimes, traditional medicine can give modern medicine clues to where an active compound can be found. For example, the use of willow bark to make medicine has been known for thousands of years, dating back to ancient Egypt. It was not until the late 1800s, however, that the aspirin molecule, known as acetylsalicylic acid, was purified and marketed for human use.
Occasionally, drugs developed for one use are found to have unforeseen effects that allow these drugs to be used in other, unrelated ways. For example, the drug minoxidil (Rogaine) was originally developed to treat high blood pressure. When tested on humans, it was noticed that individuals taking the drug would grow new hair. Eventually the drug was marketed to men and women with baldness to restore lost hair.
The career of the pharmaceutical chemist may involve detective work, experimentation, and drug development, all with the goal of making human beings healthier.
Summary
Matter is anything that occupies space and has mass. It is made up of elements. All of the 92 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 be transferred, shared, or cause charge disparities between atoms to create bonds, including ionic, covalent, and hydrogen bonds, as well as van der Waals interactions.
Art Connections
Figure $2$: How many neutrons do carbon-12 and carbon-13 have, respectively?
Answer
Carbon-12 has six neutrons. Carbon-13 has seven neutrons.
Figure $6$: 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?
Answer
Elements in group 1 need to lose one electron to achieve a stable electron configuration. Elements in groups 14 and 17 need to gain four and one electrons, respectively, to achieve a stable configuration.
Glossary
anion
negative ion that is formed by an atom gaining one or more electrons
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
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 the formation of molecules
chemical reaction
process leading to the rearrangement of atoms in molecules
chemical reactivity
the ability to combine and to chemically bond with each other
compound
substance composed of molecules consisting of atoms of at least two different elements
covalent bond
type of strong bond formed between two of the same or different elements; forms when electrons are shared between atoms
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 an electron is most likely to be found
electron transfer
movement of electrons from one element to another; important in creation of 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 be broken down into smaller substances; each element has unique properties and a specified number of protons
equilibrium
steady state of relative reactant and product concentration in reversible chemical reactions in a closed system
hydrogen bond
weak bond between slightly positively charged hydrogen atoms to slightly negatively charged atoms in other molecules
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 uni-directionally to form products
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
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 the nucleus of an atom; 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 electrons
periodic table
organizational chart of elements indicating the atomic number and atomic mass of each element; provides key information about the properties of the elements
polar covalent bond
type of covalent bond that forms as a result of unequal sharing of electrons, resulting in the creation of slightly positive and slightly negative charged regions of the molecule
product
molecule found on the right side of a chemical equation
proton
positively charged particle that resides in the nucleus of an atom; has a mass of one amu and a charge of +1
radioisotope
isotope that emits radiation composed of subatomic particles to form more stable elements
reactant
molecule found on the left side of a chemical equation
reversible chemical reaction
chemical reaction that functions bi-directionally, where products may turn into reactants if their concentration is great enough
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_1e_(OpenStax)/1%3A_The_Chemistry_of_Life/2%3A_The_Chemical_Foundation_of_Life/2.1%3A_Atoms_Isotopes_Ions_and_Molecules_-_The_Building_Blocks.txt |
Skills to Develop
• 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. Approximately 60–70 percent of the human body is made up of water. 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 the generation of 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, the polarity of water creates a slightly positive charge on hydrogen and a slightly negative charge on oxygen, contributing to water’s properties of attraction. Water’s charges are generated because oxygen is more electronegative than hydrogen, making it more likely that a shared electron would be found 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. A polar substance that interacts readily with or dissolves in water is referred to as hydrophilic (hydro- = “water”; -philic = “loving”). In contrast, non-polar molecules such as oils and fats do not interact well with water, as shown in Figure $1$ and separate from it rather than dissolve in it, as we see in salad dressings containing oil and vinegar (an acidic water solution). These nonpolar compounds are called hydrophobic (hydro- = “water”; -phobic = “fearing”).
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 are constantly formed and broken as the water molecules slide past each other. The breaking of these bonds is caused by the motion (kinetic energy) of the water molecules due to the heat contained in the system. When the heat is raised as water is boiled, the higher kinetic energy of the water molecules causes the hydrogen bonds to break completely and allows water molecules to escape into the air as gas (steam or water vapor). On the other hand, when the temperature of water is reduced 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 not seen in the solidification of other liquids.
Water’s lower density in its solid form is due to the way hydrogen bonds are oriented as it freezes: the water molecules are pushed farther apart compared to liquid water. With most other liquids, solidification when the temperature drops includes the lowering of 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, illustrated and pictured in Figure $2$, an anomaly, causes it to float at the surface of liquid water, such as in an iceberg or in the ice cubes in a glass of ice water. In lakes and ponds, ice will form on the surface of the water creating an insulating barrier that protects the animals and plant life in the pond from freezing. Without this layer of insulating ice, plants and animals living in the pond would freeze in the solid block of ice and could not survive. The detrimental effect of freezing on living organisms is caused by the expansion of ice relative to liquid water. The ice crystals that form upon freezing rupture the delicate membranes essential for the function of living cells, irreversibly damaging them. Cells can only survive freezing if the water in them is temporarily replaced by another liquid like glycerol.
Link to Learning
Video: Click here to see a 3-D animation of the structure of an ice lattice. (Image credit: Jane Whitney. Image created using Visual Molecular Dynamics VMD software.2)
Water’s High Heat Capacity
Water’s high heat capacity is a property caused by hydrogen bonding among water molecules. Water has the highest specific heat capacity of any liquids. Specific heat is defined 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 long time to cool. In fact, the specific heat capacity of water 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, water is used by warm blooded animals 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 surface of water. 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: this process is known as evaporation.
The fact that hydrogen bonds need to be broken for water to evaporate means that a substantial amount of energy is used 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 homeostasis of body temperature can be maintained.
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, water is referred to 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. This is referred to as a sphere of hydration, or a hydration shell, as illustrated in Figure $3$ and serves to keep the particles separated or dispersed in the water.
When ionic compounds are added to water, the individual ions react with the polar regions of the water molecules 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 NaCl crystals are added to water, the molecules of NaCl dissociate into Na+ and Cl ions, and spheres of hydration form around the ions, illustrated in Figure $3$. The positively charged sodium ion is surrounded by the partially negative charge of the water molecule’s oxygen. The negatively charged chloride ion is surrounded by the partially positive charge of the hydrogen on the water molecule.
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 the development of surface tension, the capacity of a substance to withstand being ruptured when placed under tension or stress. This is also why water forms droplets when placed on a dry surface rather than being flattened out by gravity. When a small scrap of paper is placed onto the droplet of water, the paper floats on top of the water droplet even though paper is denser (heavier) than the water. Cohesion and surface tension keep the hydrogen bonds of water molecules 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 it is placed gently without breaking the surface tension, as shown in Figure $4$.
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 found on the inside of thin glass tubes known as capillary tubes. Adhesion is observed when water “climbs” up the tube placed in a glass of water: notice that the water appears to be higher on the sides of the tube than in the middle. This is because the water molecules are attracted to the charged glass walls of the capillary more than they are to each other and therefore adhere to it. This type of adhesion is called capillary action, and is illustrated in Figure $5$.
Why are cohesive and adhesive forces important for life? Cohesive and adhesive forces are important for the transport of 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 being evaporated on the surface of the plant 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, shown in Figure $6$, use the surface tension of water to stay afloat on the surface layer of water and even mate there.
pH, Buffers, Acids, and Bases
The pH of a solution indicates its acidity or alkalinity.
$\ce{H_2O(I) \leftrightharpoons H^+ (aq) + O^- (aq)} \nonumber$
litmus or pH paper, filter paper that has been treated with a natural water-soluble dye so it can be used as a pH indicator, to test how much acid (acidity) or base (alkalinity) 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 the concentration of hydrogen ions in a given solution.
Hydrogen ions are spontaneously generated 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, are immediately attracted to un-ionized water molecules, forming hydronium ions (H30+). 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), with one mole being equal to 6.02 x 1023 particles of the substance. Therefore, 1 mole of water is equal to 6.02 x 1023 water molecules. The pH is calculated 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 known as neutral pH. The pH inside of human cells and blood are examples of two areas of the body 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 the concentration of hydrogen ions (H+) 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 considered 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 placed in water, thereby raising the pH. An example of a weak basic solution is seawater, which has a pH near 8.0, close enough to neutral pH that marine organisms adapted to this saline environment are able to thrive in it.
The pH scale is, as previously mentioned, an inverse logarithm and ranges from 0 to 14 (Figure $7$). 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 considered 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. So how do the cells of the stomach 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. New stomach cells are constantly produced to replace dead ones, which are digested by the stomach acids. It is estimated that the lining of the human stomach is completely replaced every seven to ten days.
Link to Learning
Watch this video for a straightforward explanation of pH and its logarithmic scale.
So 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 pH of the body 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, hydrogen ions are removed, moderating pH changes. Similarly, as shown in Figure $8$, excess carbonic acid can be converted to carbon dioxide gas and exhaled 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 is introduced 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.
Other examples of buffers are antacids used 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 that suffer “heartburn” after eating. The unique properties of water 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
To learn more about water. Visit the U.S. Geological Survey Water Science for Schools All About Water! website.
Summary
Water has many properties that are critical to maintaining life. It is a polar molecule, allowing for the formation of 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 a lot of 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 the evaporation of sweat. Water’s cohesive forces allow for the property of surface tension, whereas its adhesive properties are seen 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.
Footnotes
1. 1 W. Humphrey W., A. Dalke, and K. Schulten, “VMD—Visual Molecular Dynamics,” Journal of Molecular Graphics 14 (1996): 33-38.
2. 2 W. Humphrey W., A. Dalke, and K. Schulten, “VMD—Visual Molecular Dynamics,” Journal of Molecular Graphics 14 (1996): 33-38.
Glossary
acid
molecule that donates hydrogen ions and increases the concentration of hydrogen ions in a solution
adhesion
attraction between water molecules and other molecules
base
molecule that donates hydroxide ions or otherwise binds excess hydrogen ions and decreases the concentration of hydrogen ions in a solution
buffer
substance that prevents 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 sides of the tubes
cohesion
intermolecular forces between water molecules caused by the polar nature of water; responsible for surface tension
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-
evaporation
separation of individual molecules from the surface of a body of water, leaves of a plant, or the skin of an organism
heat of vaporization of water
high amount of energy required for liquid water to turn into water vapor
hydrophilic
describes ions or polar molecules that interact well with other polar molecules such as water
hydrophobic
describes uncharged non-polar molecules that do not interact well with polar molecules such as water
litmus paper
(also, pH paper) filter paper that has been treated with a natural water-soluble dye that changes its color as the pH of the environment changes so it can be used as a pH indicator
pH paper
see litmus paper
pH scale
scale ranging from zero to 14 that is inversely proportional to the concentration of hydrogen ions in a solution
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
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 molecules of the liquid | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/1%3A_The_Chemistry_of_Life/2%3A_The_Chemical_Foundation_of_Life/2.2%3A_Water.txt |
Skills to Develop
• Explain why carbon is important for life
• Describe the role of functional groups in biological molecules
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. 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 is released when these molecules are burned (oxidized). Methane, an excellent fuel, is the simplest hydrocarbon molecule, with a central carbon atom bonded to four different hydrogen atoms, as illustrated in Figure \(1\). The geometry of the methane molecule, where the atoms reside in three dimensions, is determined by the shape of its electron orbitals. The carbons and the four hydrogen atoms form a shape known as a tetrahedron, with four triangular faces; for this reason, methane is described as having tetrahedral geometry.
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 geometry of the molecule 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
Hydrocarbon chains are formed by successive bonds between carbon atoms and may be branched or unbranched. Furthermore, the overall geometry of the molecule is altered by the different geometries of single, double, and triple covalent bonds, illustrated in Figure \(2\). The hydrocarbons ethane, ethene, and ethyne serve as examples of how different carbon-to-carbon bonds affect the geometry of the molecule. 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, butane, and butyne for four carbon molecules, and so on. Double and triple bonds change the geometry of the molecule: single bonds allow rotation along the axis of the bond, 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.
Hydrocarbon Rings
So far, the hydrocarbons we have discussed have been aliphatic hydrocarbons, which consist of linear chains of carbon atoms. Another type of hydrocarbon, aromatic hydrocarbons, consists of closed rings of carbon atoms. Ring structures are found in hydrocarbons, sometimes with the presence of double bonds, which can be seen by comparing the structure of cyclohexane to benzene in Figure \(3\). Examples of biological molecules that incorporate the benzene ring include some amino acids and cholesterol and its derivatives, including the hormones estrogen and testosterone. The benzene ring is also found 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.
Isomers
The three-dimensional placement of atoms and chemical bonds within organic molecules is central to understanding their chemistry. Molecules that share the same chemical formula but differ in the placement (structure) of their atoms and/or chemical bonds are known as isomers. Structural isomers (like butane and isobutene shown in Figure \(4\)a differ in the placement of their covalent bonds: both molecules have four carbons and ten hydrogens (C4H10), but the different arrangement of the atoms within the molecules leads to differences in their chemical properties. For example, due to their different chemical properties, butane is suited for use as a fuel for cigarette lighters and torches, whereas isobutene is suited for use as a refrigerant and a propellant in spray cans.
Geometric isomers, on the other hand, 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 illustrated in Figure \(4\)b. 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.
Art Connection
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, illustrated in Figure \(5\). 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 carbon backbone of the chain means that triglyceride molecules cannot pack tightly, so they remain liquid (oil) at room temperature. On the other hand, 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, triglycerides without double bonds between carbon atoms are called saturated fats, meaning that they contain all the hydrogen atoms available. Saturated fats are a solid at room temperature and usually of animal origin.
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 mirror images. As shown in Figure \(6\), an amino acid alanine example, the two structures are non-superimposable. In nature, only the L-forms of amino acids are used to make proteins. Some D forms of amino acids are seen in the cell walls of bacteria, but never in their proteins. Similarly, the D-form of glucose is the main product of photosynthesis and the L-form of the molecule is rarely seen in nature.
Functional Groups
Functional groups are groups of atoms that occur within molecules and confer specific chemical properties to those molecules. They are found along the “carbon backbone” of macromolecules. This carbon backbone is formed by chains and/or rings of carbon atoms with the occasional substitution of an element such as nitrogen or oxygen. 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. Some of the important functional groups in biological molecules are shown in Figure \(7\); they include: hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl. These groups play an important role in the formation of molecules like DNA, proteins, carbohydrates, and lipids. Functional groups are usually classified as hydrophobic or hydrophilic depending on their charge or polarity characteristics. An example of a hydrophobic group is the non-polar methane molecule. Among the hydrophilic functional groups is the carboxyl group found 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 it is found on. 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.
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 illustrated in Figure \(8\).
Summary
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.
Art Connections
Figure \(4\): 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.
Answer
C
Glossary
aliphatic hydrocarbon
hydrocarbon consisting of a linear chain of carbon atoms
aromatic hydrocarbon
hydrocarbon consisting of closed rings of carbon atoms
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
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
hydrocarbon
molecule that consists only of carbon and hydrogen
isomers
molecules that differ from one another even though they share the same chemical formula
organic molecule
any molecule containing carbon (except carbon dioxide)
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 | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/1%3A_The_Chemistry_of_Life/2%3A_The_Chemical_Foundation_of_Life/2.3%3A_Carbon.txt |
2.1: Atoms, Isotopes, Ions, and Molecules - The Building Blocks
Review Questions
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
Answer
A
Atoms that vary in the number of neutrons found in their nuclei are called ________.
1. ions
2. neutrons
3. neutral atoms
4. isotopes
Answer
D
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
Answer
C
Which type of bond represents a weak chemical bond?
1. hydrogen bond
2. atomic bond
3. covalent bond
4. nonpolar covalent bond
Answer
A
Free Response
What makes ionic bonds different from covalent bonds?
Answer
Ionic bonds are created between ions. The electrons are not shared between the atoms, but rather are associated more with one ion than the other. Ionic bonds are strong bonds, but are weaker than covalent bonds, meaning it takes less energy to break an ionic bond compared with a covalent one.
Why are hydrogen bonds and van der Waals interactions necessary for cells?
Answer
Hydrogen bonds and van der Waals interactions form weak associations between different molecules or within different regions of the same molecule. They provide the structure and shape necessary for proteins and DNA within cells so that they function properly.
2.2: Water
Review Questions
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.
Answer
D
When acids are added to a solution, the pH should ________.
1. decrease
2. increase
3. stay the same
4. cannot tell without testing
Answer
A
A molecule that binds up excess hydrogen ions in a solution is called a(n) ________.
1. acid
2. isotope
3. base
4. donator
Answer
C
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+).
Answer
B
Free Response
Discuss how buffers help prevent drastic swings in pH.
Answer
Buffers absorb the free hydrogen ions and hydroxide ions that result from chemical reactions. Because they can bond these ions, they prevent increases or decreases in pH. An example of a buffer system is the bicarbonate system in the human body. This system is able to absorb hydrogen and hydroxide ions to prevent changes in pH and keep cells functioning properly.
Why can some insects walk on water?
Answer
Some insects can walk on water, although they are heavier (denser) than water, because of the surface tension of water. Surface tension results from cohesion, or the attraction between water molecules at the surface of the body of water (the liquid-air/gas interface).
2.3: Carbon
Review Questions
Each carbon molecule can bond with as many as________ other atom(s) or molecule(s).
1. one
2. two
3. six
4. four
Answer
D
Which of the following is not a functional group that can bond with carbon?
1. sodium
2. hydroxyl
3. phosphate
4. carbonyl
Answer
A
Free Response
What property of carbon makes it essential for organic life?
Answer
Carbon is unique and found in all living things because it can form up to four covalent bonds between atoms or molecules. These can be nonpolar or polar covalent bonds, and they allow for the formation of long chains of carbon molecules that combine to form proteins and DNA.
Compare and contrast saturated and unsaturated triglycerides.
Answer
Saturated triglycerides contain no double bonds between carbon atoms; they are usually solid at room temperature. Unsaturated triglycerides contain at least one double bond between carbon atoms and are usually liquid at room temperature. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/1%3A_The_Chemistry_of_Life/2%3A_The_Chemical_Foundation_of_Life/New_Page.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.
• 3.0: Prelude to 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.
• 3.1: 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).
• 3.2: 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.
• 3.3: 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.
• 3.4: 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.
• 3.5: 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.
• 3.E: Biological Macromolecules (Exercises)
Thumbnail: 1K6F_Crystal Structure Of The Collagen Triple Helix Model Pro- Pro-Gly103. (CC-SA-BY-3.0; Nevit Dilmen)
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. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/1%3A_The_Chemistry_of_Life/3%3A_Biological_Macromolecules/3.0%3A_Prelude_to_Biological_Macromolecules.txt |
Skills to Develop
• Understand the synthesis of macromolecules
• 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 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). 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 known as dehydration synthesis, which means “to put together while losing water.”
In a dehydration synthesis reaction (Figure \(1\)), the hydrogen of one monomer combines with the hydroxyl group of another monomer, releasing a molecule of water. 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 types of monomers 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 are broken down into monomers in a process known as hydrolysis, which means “to split water,” a reaction in which a water molecule is used during the breakdown (Figure \(2\)). During these reactions, the polymer is broken into two components: one part gains a hydrogen atom (H+) and the other gains a hydroxyl molecule (OH–) from a split water molecule.
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, in our bodies, food is hydrolyzed, or broken down, into smaller molecules by catalytic enzymes in the digestive system. This allows for easy absorption of nutrients by cells in the intestine. Each macromolecule is broken down by a specific enzyme. For instance, carbohydrates are broken down by amylase, sucrase, lactase, or maltase. Proteins are broken down by the enzymes pepsin and peptidase, and by hydrochloric acid. Lipids are broken down by lipases. Breakdown of these macromolecules provides energy for cellular activities.
Link to Learning
Visit this site to see visual representations of dehydration synthesis and hydrolysis.
Summary
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 made up of single units known as 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 the maintenance of cellular osmotic conditions. A monomer joins with another monomer with the release of a water molecule, leading to the formation of a covalent bond. These types of reactions are known as dehydration or condensation reactions. When polymers are broken down into smaller units (monomers), a molecule of water is used for each bond broken by these reactions; such reactions are known as 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.
Glossary
biological macromolecule
large molecule necessary for life that is built from smaller organic molecules
dehydration synthesis
(also, condensation) reaction that links monomer molecules together, releasing a molecule of water for each bond formed
hydrolysis
reaction causes breakdown of larger molecules into smaller molecules with the utilization of water
monomer
smallest unit of larger molecules called polymers
polymer
chain of monomer residues that is linked by covalent bonds; polymerization is the process of polymer formation from monomers by condensation | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/1%3A_The_Chemistry_of_Life/3%3A_Biological_Macromolecules/3.1%3A_Synthesis_of_Biological_Macromolecules.txt |
Skills to Develop
• Discuss the role of carbohydrates in cells and in the extracellular materials of animals and plants
• Explain the classifications of carbohydrates
• 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 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.
Molecular Structures
Carbohydrates can be represented by the stoichiometric formula (CH2O)n, where n is the number of carbons in the molecule. 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”). Carbohydrates are classified 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 known as an aldose, and if it has a ketone group (the functional group with the structure RC(=O)R'), it is known as a ketose. Depending on the number of carbons in the sugar, they also may be known as trioses (three carbons), pentoses (five carbons), and or hexoses (six carbons). See Figure \(1\) for an illustration of the monosaccharides.
The chemical formula for glucose is C6H12O6. In humans, glucose is an important source of energy. During cellular respiration, energy is released from glucose, and that energy is used to help make adenosine triphosphate (ATP). Plants synthesize glucose using carbon dioxide and water, and glucose in turn is used for energy requirements for the plant. Excess glucose is often stored as starch that is catabolized (the breakdown of larger molecules by cells) by humans and other animals that feed on plants.
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 known as isomers) because of the different arrangement of functional groups around the asymmetric carbon; all of these monosaccharides have more than one asymmetric carbon (Figure\(2\)).
Art Connection
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 found in ring forms (Figure \(3\)). Glucose in a ring form can have two different arrangements of the hydroxyl group (OH) around the anomeric carbon (carbon 1 that becomes asymmetric in the process of ring formation). If the hydroxyl group is below carbon number 1 in the sugar, it is said to be in the alpha (α) position, and if it is above the plane, it is said to be in the beta (β) position.
Disaccharides
Disaccharides (di- = “two”) form when two monosaccharides undergo a dehydration reaction (also known as a condensation reaction or dehydration synthesis). During this process, the hydroxyl group of one monosaccharide combines with the hydrogen of another monosaccharide, releasing a molecule of water and forming a covalent bond. A covalent bond formed between a carbohydrate molecule and another molecule (in this case, between two monosaccharides) is known as a glycosidic bond (Figure \(4\)). Glycosidic bonds (also called glycosidic linkages) can be of the alpha or the beta type.
Common disaccharides include lactose, maltose, and sucrose (Figure \(5\)). Lactose is a disaccharide consisting of the monomers glucose and galactose. It is found 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 composed of the monomers glucose and fructose.
Polysaccharides
A long chain of monosaccharides linked by glycosidic bonds is known as 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 monomers joined. Starch, glycogen, cellulose, and chitin are primary examples of polysaccharides.
Starch is the stored form of sugars in plants and is made up of a mixture of amylose and amylopectin (both polymers of glucose). Plants are able to synthesize glucose, and the excess glucose, beyond the plant’s immediate energy needs, is stored 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 source of food for humans and animals. The starch that is consumed by humans is broken down by enzymes, such as salivary amylases, into smaller molecules, such as maltose and glucose. The cells can then absorb the glucose.
Starch is made up of glucose 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 illustrated in Figure \(6\), amylose is starch formed by unbranched chains of glucose monomers (only α 1-4 linkages), whereas amylopectin is a branched polysaccharide (α 1-6 linkages at the branch points).
Glycogen is the storage form of glucose in humans and other vertebrates and is made up 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 is broken down to release glucose in a process known as glycogenolysis.
Cellulose is the most abundant natural biopolymer. The cell wall of plants is mostly made of cellulose; this provides structural support to the cell. Wood and paper are mostly cellulosic in nature. Cellulose is made up of glucose monomers that are linked by β 1-4 glycosidic bonds (Figure \(7\)).
As shown in Figure \(7\), 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 the β 1-4 linkage cannot be broken down by human digestive enzymes, herbivores such as cows, koalas, buffalos, and horses 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 these animals, certain species of bacteria and protists reside in the rumen (part of the digestive system of herbivores) and secrete the enzyme cellulase. The appendix of grazing animals also contains bacteria that digest cellulose, giving it an important role in the digestive systems of ruminants. Cellulases can break down cellulose into glucose monomers that can be used as an energy source by the animal. 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, called the exoskeleton, which protects their internal body parts (as seen in the bee in Figure \(8\)). This exoskeleton is made of the biological macromolecule chitin, which is a polysaccharide-containing nitrogen. It is made of repeating units of N-acetyl-β-d-glucosamine, 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.
Career Connections: Registered Dietitian
Obesity 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 registered dietitians are increasingly sought after 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? People who wish to lose weight are often told that carbohydrates are bad for them and should be avoided. 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.
Carbohydrates should be supplemented with proteins, vitamins, and fats to be parts of a well-balanced diet. 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 is known as fiber, which is mostly cellulose. Fiber has many uses; it promotes regular bowel movement by adding bulk, and it regulates the rate of consumption of blood glucose. 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, and then cholesterol 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 is broken down during the process of cellular respiration, which produces ATP, the energy currency of the cell. Without the consumption of carbohydrates, the availability of “instant energy” would be reduced. Eliminating carbohydrates from the diet is not the best way to lose weight. A low-calorie diet that is rich in whole grains, fruits, vegetables, and lean meat, together with plenty of exercise and plenty of water, is the more sensible way to lose weight.
Link to Learning
For an additional perspective on carbohydrates, explore “Biomolecules: the Carbohydrates” through this interactive animation.
Summary
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. Carbohydrates are classified as monosaccharides, disaccharides, and polysaccharides depending on the number of monomers in the molecule. Monosaccharides are linked by glycosidic bonds that are formed as a result of dehydration reactions, forming disaccharides and polysaccharides with the elimination of 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. Storage of glucose, 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 excessive water uptake by the cell.
Art Connections
Figure \(2\): What kind of sugars are these, aldose or ketose?
Answer
Glucose and galactose are aldoses. Fructose is a ketose.
Glossary
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 the a cellular exoskeleton of arthropods
cellulose
polysaccharide that makes up the cell wall of plants; provides structural support to the cell
chitin
type of carbohydrate that forms the outer skeleton of all arthropods that include crustaceans and insects; it also forms the cell walls of fungi
disaccharide
two sugar monomers that are linked together by a glycosidic bond
glycogen
storage carbohydrate in animals
glycosidic bond
bond formed by a dehydration reaction between two monosaccharides with the elimination of a water molecule
monosaccharide
single unit or monomer of carbohydrates
polysaccharide
long chain of monosaccharides; may be branched or unbranched
starch
storage carbohydrate in plants | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/1%3A_The_Chemistry_of_Life/3%3A_Biological_Macromolecules/3.2%3A_Carbohydrates.txt |
Skills to Develop
• 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 functions of steroids
• Explain the how cholesterol helps to maintain the fluid nature of the plasma membrane
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 \(1\)). 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.
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; most common are those containing 12–18 carbons. In a fat molecule, the fatty acids are attached to each of the three carbons of the glycerol molecule with an ester bond through an oxygen atom (Figure \(2\)).
During this ester bond formation, three water molecules are released. The three fatty acids in the triacylglycerol may be similar or dissimilar. Fats are also called 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 said to be 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 \(3\))
When the hydrocarbon chain contains a double bond, the fatty acid is said to be unsaturated. Oleic acid is an example of an unsaturated fatty acid (Figure \(4\)).
Most unsaturated fats are liquid at room temperature and are called oils. If there is one double bond in the molecule, then it is known as a monounsaturated fat (e.g., olive oil), and if there is more than one double bond, then it is known as a polyunsaturated fat (e.g., canola oil).
When a fatty acid has no double bonds, it is known as a saturated fatty acid because no more hydrogen may be added to the carbon atoms of the chain. A fat may contain similar or different fatty acids attached to glycerol. Long straight fatty acids with single bonds tend to get packed 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 called adipocytes, where globules of fat occupy most of the cell’s volume. In plants, fat or oil is stored in many seeds and is used 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 referred to as a cis fat; if the hydrogen atoms are on two different planes, it is referred to as 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 \(5\)). 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.
Trans Fats
In the food industry, oils are artificially hydrogenated 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 be converted 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 an increase in 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 the use of trans fats, and food labels are required to display the trans fat content.
Omega Fatty Acids
Essential fatty acids are fatty acids required but not synthesized by the human body. Consequently, they have to be supplemented through ingestion via the diet. Omega-3 fatty acids (like that shown in Figure \(6\)) fall into this category and are one of only two known for humans (the other being omega-6 fatty acid). These are polyunsaturated fatty acids and are called omega-3 because the third carbon from the end of the hydrocarbon chain is connected to its neighboring carbon by a double bond.
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 known as 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, reduce triglycerides in the blood, lower blood pressure, and prevent thrombosis by inhibiting blood clotting. They also reduce inflammation, and may help reduce the risk of some cancers in animals.
Like carbohydrates, fats have received a lot of 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, “healthy” fats in moderate amounts should be consumed on a regular basis.
Waxes
Wax covers the feathers of some aquatic birds and the leaf surfaces of some plants. Because of the hydrophobic nature of waxes, they prevent water from sticking on the surface (Figure \(7\)). Waxes are made up of long fatty acid chains esterified to long-chain alcohols.
Phospholipids
Phospholipids are major constituents of the plasma membrane, the outermost layer of animal cells. Like fats, they are composed of fatty acid chains attached to a glycerol or sphingosine backbone. Instead of three fatty acids attached as in triglycerides, however, there are two fatty acids forming diacylglycerol, and the third carbon of the glycerol backbone is occupied by a modified phosphate group (Figure \(8\)). A phosphate group alone attached to a diaglycerol does not qualify as a phospholipid; it is phosphatidate (diacylglycerol 3-phosphate), the precursor of phospholipids. The phosphate group is modified by an alcohol. Phosphatidylcholine and phosphatidylserine are two important phospholipids that are found in plasma membranes.
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 \(9\)).
The head is the hydrophilic part, and the tail contains the hydrophobic fatty acids. In a membrane, a bilayer of phospholipids forms the matrix of the structure, the fatty acid tails of phospholipids face inside, away from water, whereas the phosphate group faces the outside, aqueous side (Figure \(9\)).
Phospholipids are responsible for the dynamic nature of the plasma membrane. If a drop of phospholipids is placed in water, it spontaneously forms a structure known as a micelle, where the hydrophilic phosphate heads face the outside and the fatty acids face the interior of this structure.
Steroids
Unlike the phospholipids and fats discussed earlier, steroids have a fused ring structure. Although they do not resemble the other lipids, they are grouped with them because they are also hydrophobicand insoluble in water. All steroids have four linked carbon rings and several of them, like cholesterol, have a short tail (Figure \(10\)). Many steroids also have the –OH functional group, which puts them in the alcohol classification (sterols).
Cholesterol is the most common steroid. Cholesterol is mainly synthesized in the liver and is the precursor to many steroid hormones such as testosterone and estradiol, which are secreted by the gonads and endocrine glands. It is also the precursor to Vitamin D. Cholesterol is also the precursor of bile salts, which help in the emulsification of fats and their subsequent absorption by cells. Although cholesterol is often spoken of in negative terms by lay people, it is necessary for proper functioning of the body. It is a component of the plasma membrane of animal cells and is found within the phospholipid bilayer. Being the outermost structure in animal cells, the plasma membrane is responsible for the transport of materials and cellular recognition and it is involved in cell-to-cell communication.
Link to Learning
For an additional perspective on lipids, explore the interactive animation “Biomolecules: The Lipids”.
Summary
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 made up 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 known as saturated fatty acids. Unsaturated fatty acids may have one or more double bonds in the hydrocarbon chain. Phospholipids make up the matrix of membranes. 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 fluid nature of the membrane. It is also the precursor of steroid hormones such as testosterone.
Glossary
lipid
macromolecule that is nonpolar and insoluble in water
omega fat
type of polyunsaturated fat that is required by the body; the numbering of the carbon omega starts from the methyl end or the end that is farthest from the carboxylic end
phospholipid
major constituent of the membranes; composed of two fatty acids and a phosphate-containing group attached to a glycerol backbone
saturated fatty acid
long-chain of hydrocarbon with single covalent bonds in the carbon chain; the number of hydrogen atoms attached to the carbon skeleton is maximized
steroid
type of lipid composed of four fused hydrocarbon rings forming a planar structure
trans fat
fat formed artificially by hydrogenating oils, leading to a different arrangement of double bond(s) than those found in naturally occurring lipids
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 made 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_1e_(OpenStax)/1%3A_The_Chemistry_of_Life/3%3A_Biological_Macromolecules/3.3%3A_Lipids.txt |
Skills to Develop
• 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, polymers of amino acids, arranged in a linear sequence.
Types and Functions of Proteins
Enzymes, which are produced by living cells, 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) it acts on. The enzyme may help in breakdown, rearrangement, or synthesis reactions. Enzymes that break down their substrates are called catabolic enzymes, enzymes that build more complex molecules from their substrates are called anabolic enzymes, and enzymes that affect the rate of reaction are called catalytic enzymes. It should be noted that all enzymes increase the rate of reaction and, therefore, are considered to be 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 to regulate the blood glucose level. The primary types and functions of proteins are listed in Table \(1\).
Table \(1\): Protein Types and Functions
Type Examples Functions
Digestive Enzymes Amylase, lipase, pepsin, trypsin Help in digestion of food by catabolizing nutrients into monomeric units
Transport Hemoglobin, albumin Carry substances in the blood or lymph throughout the body
Structural Actin, tubulin, keratin Construct different structures, like the cytoskeleton
Hormones Insulin, thyroxine Coordinate the activity of different body systems
Defense Immunoglobulins Protect the body from foreign pathogens
Contractile Actin, myosin Effect muscle contraction
Storage Legume storage proteins, egg white (albumin) Provide nourishment in early development of the embryo and the seedling
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, found in our skin, is a fibrous protein. Protein shape is critical to its function, and this shape is maintained by many different types of chemical bonds. Changes in temperature, pH, and exposure to chemicals may lead to permanent changes in the shape of the protein, leading to loss of function, known as denaturation. All proteins are made up of different arrangements of the same 20 types of amino acids.
Amino Acids
Amino acids are the monomers that make up proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, also known as 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 \(1\)).
The name "amino acid" is derived from the fact that they contain both amino group and carboxyl-acid-group in their basic structure. As mentioned, there are 20 amino acids present in proteins. Ten of these are considered essential amino acids in humans because the human body cannot produce them and they are obtained from the diet. For each amino acid, the R group (or side chain) is different (Figure \(2\)).
Art Connection
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?
The chemical nature of the side chain determines the nature of the amino acid (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 known as 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 standard structure of an animo acid since its amino group is not separate from the side chain (Figure \(2\)).
Amino acids are represented by a single upper case letter or a three-letter abbreviation. For example, valine is known by the letter V or the three-letter symbol val. Just as some fatty acids are essential to a diet, some amino acids are necessary as well. They are known as essential amino acids, and in humans they include isoleucine, leucine, and cysteine. Essential amino acids refer to those necessary for construction of proteins in the body, although not produced by the body; 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. Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond, which is formed by a dehydration reaction. The carboxyl group of one amino acid and the amino group of the incoming amino acid combine, releasing a molecule of water. The resulting bond is the peptide bond (Figure \(3\)).
The products formed by such linkages are called peptides. As more amino acids join to this growing chain, the resulting chain is known as a polypeptide. Each polypeptide has a free amino group at one end. This end is called the N terminal, or the amino terminal, and the other end has a free carboxyl group, also known as 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 the addition of other chemical groups. Only after these modifications is the protein completely functional.
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 found in the cellular organelle, the mitochondrion. This protein has a heme prosthetic group, and the central ion of the heme gets alternately reduced and oxidized 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, evolutionary kinship can be assessed 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 has been sequenced to date, 37 of these amino acids appear in the same position in all samples of cytochrome c. This indicates that there may have been a common ancestor. On comparing the human and chimpanzee protein sequences, no sequence difference was found. When human and rhesus monkey sequences were compared, the single difference found was in one amino acid. In another comparison, human to yeast sequencing shows a difference in the 44th position.
Protein Structure
As discussed earlier, the shape of a protein is critical to its function. For example, an enzyme can bind to a specific substrate at a site known as the 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
The unique sequence of amino acids 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 \(4\)). The sequences of amino acids in the A and B chains are unique to insulin.
The unique sequence for every protein is ultimately determined by the gene encoding the protein. A change in nucleotide sequence of the gene’s coding region may lead to a different amino acid being added 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 is shown in Figure \(5\)) has a single amino acid substitution, causing a change in protein structure and function. Specifically, the amino acid glutamic acid is substituted by valine in the β chain. What is most remarkable to consider is that a hemoglobin molecule is made up of two alpha chains 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 those 600 amino acids are encoded by three nucleotides each, and the mutation is caused by a single base change (point mutation), 1 in 1800 bases.
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 assume a crescent or “sickle” shape, which clogs arteries (Figure \(6\)). This can lead to myriad serious health problems such as breathlessness, dizziness, headaches, and abdominal pain for those affected by this disease.
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 \(7\)). Both structures are the α-helix structure—the helix 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.
Every helical turn in an alpha helix has 3.6 amino acid residues. The R groups (the variant groups) of the polypeptide protrude out from the α-helix chain. In the β-pleated sheet, the “pleats” are formed by hydrogen bonding between atoms on the backbone of the polypeptide chain. The R groups are attached to the carbons and extend above and below the folds of the pleat. The pleated segments align parallel or antiparallel to each other, and hydrogen bonds form between the partially positive nitrogen atom in the amino group and the partially negative oxygen atom in the carbonyl group of the peptide backbone. The α-helix and β-pleated sheet structures are found in most globular and fibrous proteins and they play an important structural role.
Tertiary Structure
The unique three-dimensional structure of a polypeptide is its tertiary structure (Figure \(8\)). This structure is in part due to chemical interactions at work on the polypeptide chain. Primarily, the interactions among R groups creates the complex three-dimensional tertiary structure of a protein. The nature of the R groups found in the amino acids involved can counteract the formation of the hydrogen bonds described for standard secondary structures. For example, R groups with like charges are repelled by each other and those with unlike charges are attracted to each other (ionic bonds). When protein folding takes place, the hydrophobic R groups of nonpolar amino acids lay in the interior of the protein, whereas the hydrophilic R groups lay on the outside. The former types of interactions are also known as hydrophobic interactions. Interaction between cysteine side chains forms disulfide linkages in the presence of oxygen, the only covalent bond forming during protein folding.
All of these interactions, weak and strong, determine the final three-dimensional shape of the protein. When a protein loses its three-dimensional shape, it may no longer be functional.
Quaternary Structure
In nature, some proteins are formed from several polypeptides, also known as 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 bonds and disulfide bonds that cause it to be mostly clumped into a ball shape. Insulin starts out as a single polypeptide and loses some internal sequences in the presence of post-translational modification after the formation of 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.
The four levels of protein structure (primary, secondary, tertiary, and quaternary) are illustrated in Figure \(9\).
Denaturation and Protein Folding
Each protein has its own unique sequence and shape that are held together by chemical interactions. 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 is known as denaturation. Denaturation is often reversible because the primary structure of the polypeptide 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 when an egg is fried. The albumin protein in the liquid egg white is denatured when placed in a hot pan. Not all proteins are denatured 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 digestive enzymes of the stomach retain their activity under these conditions.
Protein folding is critical to its function. It was originally thought that the proteins themselves were responsible for the folding process. Only recently was it found that often they receive assistance in the folding process from protein helpers known as chaperones (or chaperonins) that associate with the target protein during the folding process. They act by preventing aggregation of polypeptides that make up the complete protein structure, and they disassociate from the protein once the target protein is folded.
Summary
Proteins are a class of macromolecules that perform a diverse range of functions for the cell. They help in metabolism by providing structural support and by acting as enzymes, carriers, or hormones. The building blocks of proteins (monomers) are amino acids. Each amino acid has a central carbon that is linked 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. Each amino acid is linked to its neighbors by a peptide bond. A long chain of amino acids is known as a polypeptide.
Proteins are organized at four levels: primary, secondary, tertiary, and (optional) quaternary. The primary structure is the unique sequence of amino acids. The local folding of the polypeptide 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 known as the quaternary structure of a protein. 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.
Art Connections
Figure \(2\): 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?
Answer
Polar and charged amino acid residues (the remainder after peptide bond formation) are more likely to be found on the surface of soluble proteins where they can interact with water, and nonpolar (e.g., amino acid side chains) are more likely to be found in the interior where they are sequestered from water. In membrane proteins, nonpolar and hydrophobic amino acid side chains associate with the hydrophobic tails of phospholipids, while polar and charged amino acid side chains interact with the polar head groups or with the aqueous solution. However, there are exceptions. Sometimes, positively and negatively charged amino acid side chains interact with one another in the interior of a protein, and polar or charged amino acid side chains that interact with a ligand can be found in the ligand binding pocket.
Glossary
alpha-helix structure (α-helix)
type of secondary structure of proteins formed by folding of the polypeptide into a helix shape with hydrogen bonds stabilizing the structure
amino acid
monomer of a protein; 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 amino acids
beta-pleated sheet (β-pleated)
secondary structure found in proteins in which “pleats” are formed by hydrogen bonding between atoms on the backbone of the polypeptide chain
chaperone
(also, chaperonin) protein that helps nascent protein in the folding process
denaturation
loss of shape in a protein as a result of changes in temperature, pH, or exposure to chemicals
enzyme
catalyst in a biochemical reaction that is usually a complex or conjugated protein
hormone
chemical signaling molecule, usually protein or steroid, secreted by endocrine cells that act to control or regulate specific physiological processes
peptide bond
bond formed between two amino acids by a dehydration reaction
polypeptide
long chain of amino acids linked by peptide bonds
primary structure
linear sequence of amino acids in a protein
protein
biological macromolecule composed of one or more chains of amino acids
quaternary structure
association of discrete polypeptide subunits in a protein
secondary structure
regular structure formed by proteins 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
tertiary structure
three-dimensional conformation of a protein, including interactions between secondary structural elements; formed from interactions between amino acid side chains | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/1%3A_The_Chemistry_of_Life/3%3A_Biological_Macromolecules/3.4%3A_Proteins.txt |
Skills to Develop
• Describe the structure of nucleic acids and define the two types of nucleic acids
• Explain the structure and role of DNA
• Explain the structure and roles of RNA
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.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material found in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is found in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the DNA is not enclosed in a membranous envelope.
The entire genetic content of a cell is known as 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 made up of monomers known as nucleotides. The nucleotides combine with each other to form a polynucleotide, DNA or RNA. Each nucleotide is made up of three components: a nitrogenous base, a pentose (five-carbon) sugar, and a phosphate group (Figure \(1\)). Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to one or more phosphate groups.
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, decreases 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).
Adenine and guanine are classified as purines. The primary structure of a purine is two carbon-nitrogen rings. Cytosine, thymine, and uracil are classified as pyrimidines which have a single carbon-nitrogen ring as their primary structure (Figure \(1\)). Each of these basic carbon-nitrogen rings has different functional groups attached to it. In molecular biology shorthand, the nitrogenous bases are simply known 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 \(1\)). The difference between the sugars is the presence of the hydroxyl group on the second carbon of the ribose and hydrogen on the second carbon of the deoxyribose. 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 is attached 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. The phosphodiester linkage is not formed by simple dehydration reaction like the other linkages connecting monomers in macromolecules: its formation involves the removal of two phosphate groups. A polynucleotide may have thousands of such phosphodiester linkages.
DNA Double-Helix Structure
DNA has a double-helix structure (Figure \(2\)). The sugar and phosphate lie on the outside of the helix, forming the backbone of the DNA. The nitrogenous bases are stacked in the interior, like the steps of a staircase, in pairs; the pairs are bound to each other by hydrogen bonds. Every base pair in the double helivx is separated from the next base pair by 0.34 nm. The two strands of the helix run in opposite directions, meaning that the 5′ carbon end of one strand will face the 3′ carbon end of its matching strand. (This is referred to as antiparallel orientation and is important to DNA replication and in many nucleic acid interactions.)
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 shown in Figure \(3\). This is known as 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 is copied, resulting in a daughter DNA double helix containing one parental DNA strand and a newly synthesized strand.
Art Connection
A mutation occurs, and cytosine is replaced with adenine. 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 made 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 a certain protein to be synthesized, the gene for this product is turned “on” and the messenger RNA is synthesized in the nucleus. The RNA base sequence is complementary to the coding sequence of the DNA 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 \(4\)).
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 rRNA of the ribosome also has an enzymatic activity (peptidyl transferase) and catalyzes the formation of the peptide bonds 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 site of protein synthesis. It is the base pairing between the tRNA and mRNA that allows for the correct amino acid to be inserted in the polypeptide chain. microRNAs are the smallest RNA molecules and their role involves the regulation of gene expression by interfering with the expression of certain mRNA messages. Table \(1\) below summarizes features of DNA and RNA.
Table \(1\): Features of DNA and RNA.
DNA RNA
Function Carries genetic information Involved in protein synthesis
Location Remains in the nucleus Leaves the nucleus
Structure Double helix Usually single-stranded
Sugar Deoxyribose Ribose
Pyrimidines Cytosine, thymine Cytosine, uracil
Purines Adenine, guanine Adenine, guanine
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 known as transcription, and RNA dictates the structure of protein in a process known as translation. This is known as 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
To learn more about DNA, explore the Howard Hughes Medical Institute BioInteractive animations on the topic of DNA.
Summary
Nucleic acids are molecules made up of nucleotides that direct cellular activities such as cell division and protein synthesis. Each nucleotide is made up of a pentose sugar, a nitrogenous base, and a phosphate group. There are two types of nucleic acids: DNA and RNA. DNA carries the genetic blueprint of the cell and is passed 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 single-stranded and is made of a pentose sugar (ribose), a nitrogenous base, and a phosphate group. RNA is involved in protein synthesis and its regulation. Messenger RNA (mRNA) is copied from the DNA, is exported from the nucleus to the cytoplasm, and contains information for the construction of 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. microRNA regulates the use of mRNA for protein synthesis.
Art Connections
Figure \(3\): A mutation occurs, and cytosine is replaced with adenine. What impact do you think this will have on the DNA structure?
Answer
Adenine is larger than cytosine and will not be able to base pair properly with the guanine on the opposing strand. This will cause the DNA to bulge. DNA repair enzymes may recognize the bulge and replace the incorrect nucleotide.
Glossary
deoxyribonucleic acid (DNA)
double-helical molecule that carries the hereditary information of the cell
messenger RNA (mRNA)
RNA that carries information from DNA to ribosomes during protein synthesis
nucleic acid
biological macromolecule that carries the genetic blueprint of a cell and carries instructions for the functioning of the cell
nucleotide
monomer of nucleic acids; contains a pentose sugar, one or more phosphate groups, and a nitrogenous base
phosphodiester
linkage covalent chemical bond that holds together the polynucleotide chains with a phosphate group linking two pentose sugars of neighboring nucleotides
polynucleotide
long chain of nucleotides
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
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 the formation of the peptide linkage
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 formation of protein | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/1%3A_The_Chemistry_of_Life/3%3A_Biological_Macromolecules/3.5%3A_Nucleic_Acids.txt |
3.1: Synthesis of Biological Macromolecules
Review Questions
Dehydration synthesis leads to formation of
1. monomers
2. polymers
3. water and polymers
4. none of the above
Answer
C
During the breakdown of polymers, which of the following reactions takes place?
1. hydrolysis
2. dehydration
3. condensation
4. covalent bond
Answer
A
Free Response
Why are biological macromolecules considered organic?
Answer
Biological macromolecules are organic because they contain carbon.
What role do electrons play in dehydration synthesis and hydrolysis?
Answer
In a dehydration synthesis reaction, the hydrogen of one monomer combines with the hydroxyl group of another monomer, releasing a molecule of water. This creates an opening in the outer shells of atoms in the monomers, which can share electrons and form covalent bonds.
3.2: Carbohydrates
Review Questions
An example of a monosaccharide is ________.
1. fructose
2. glucose
3. galactose
4. all of the above
Answer
D
Cellulose and starch are examples of:
1. monosaccharides
2. disaccharides
3. lipids
4. polysaccharides
Answer
D
Plant cell walls contain which of the following in abundance?
1. starch
2. cellulose
3. glycogen
4. lactose
Answer
B
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
Answer
B
Free Response
Describe the similarities and differences between glycogen and starch.
Answer
Glycogen and starch are polysaccharides. They are the storage form of glucose. Glycogen is stored in animals in the liver and in muscle cells, whereas starch is stored in the roots, seeds, and leaves of plants. Starch has two different forms, one unbranched (amylose) and one branched (amylopectin), whereas glycogen is a single type of a highly branched molecule.
Why is it impossible for humans to digest food that contains cellulose?
Answer
The β 1-4 glycosidic linkage in cellulose cannot be broken down by human digestive enzymes. Herbivores such as cows, buffalos, and horses are able to digest grass that is rich in cellulose and use it as a food source because bacteria and protists in their digestive systems, especially in the rumen, secrete the enzyme cellulase. Cellulases can break down cellulose into glucose monomers that can be used as an energy source by the animal.
3.3: Lipids
Review Questions
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
Answer
D
Phospholipids are important components of ________.
1. the plasma membrane of animal cells
2. the ring structure of steroids
3. the waxy covering on leaves
4. the double bond in hydrocarbon chains
Answer
A
Free Response
Explain at least three functions that lipids serve in plants and/or animals.
Answer
Fat serves as a valuable way for animals to store energy. It can also provide insulation. Waxes can protect plant leaves and mammalian fur from getting wet. Phospholipids and steroids are important components of animal cell membranes, as well as plant, fungal, and bacterial membranes.
Why have trans fats been banned from some restaurants? How are they created?
Answer
Trans fats are created artificially when hydrogen gas is bubbled through oils to solidify them. The double bonds of the cis conformation in the hydrocarbon chain may be converted to double bonds in the trans configuration. Some restaurants are banning trans fats because they cause higher levels of LDL, or “bad” cholesterol.
3.4: Proteins
Review Questions
The monomers that make up proteins are called ________.
1. nucleotides
2. disaccharides
3. amino acids
4. chaperones
Answer
C
The α helix and the β-pleated sheet are part of which protein structure?
1. primary
2. secondary
3. tertiary
4. quaternary
Answer
B
Free Response
Explain what happens if even one amino acid is substituted for another in a polypeptide chain. Provide a specific example.
Answer
A change in gene sequence can lead to a different amino acid being added to a polypeptide chain instead of the normal one. This causes a change in protein structure and function. For example, in sickle cell anemia, the hemoglobin β chain has a single amino acid substitution—the amino acid glutamic acid in position six is substituted by valine. Because of this change, hemoglobin molecules form aggregates, and the disc-shaped red blood cells assume a crescent shape, which results in serious health problems.
Describe the differences in the four protein structures.
Answer
The sequence and number of amino acids in a polypeptide chain is its primary structure. The local folding of the polypeptide in some regions is the secondary structure of the protein. The three-dimensional structure of a polypeptide is known as its tertiary structure, created in part by chemical interactions such as hydrogen bonds between polar side chains, van der Waals interactions, disulfide linkages, and hydrophobic interactions. Some proteins are formed from multiple polypeptides, also known as subunits, and the interaction of these subunits forms the quaternary structure.
3.5: Nucleic Acids
Review Questions
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
Answer
C
The building blocks of nucleic acids are ________.
1. sugars
2. nitrogenous bases
3. peptides
4. nucleotides
Answer
D
Free Response
What are the structural differences between RNA and DNA?
Answer
DNA has a double-helix structure. The sugar and the phosphate are on the outside of the helix and the nitrogenous bases are in the interior. The monomers of DNA are nucleotides containing deoxyribose, one of the four nitrogenous bases (A, T, G and C), and a phosphate group. RNA is usually single-stranded and is made of ribonucleotides that are linked by phosphodiester linkages. A ribonucleotide contains ribose (the pentose sugar), one of the four nitrogenous bases (A,U, G, and C), and the phosphate group.
What are the four types of RNA and how do they function?
Answer
The four types of RNA are messenger RNA, ribosomal RNA, transfer RNA, and microRNA. Messenger RNA carries the information from the DNA that controls all cellular activities. The mRNA binds to the ribosomes that are constructed of proteins and rRNA, and tRNA transfers the correct amino acid to the site of protein synthesis. microRNA regulates the availability of mRNA for translation. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/1%3A_The_Chemistry_of_Life/3%3A_Biological_Macromolecules/New_Page.txt |
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.
• 4.0: Prelude to 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. 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
• 4.1: 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.
• 4.2: 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.
• 4.3: 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.”
• 4.4: 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.
• 4.5: 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.
• 4.6: 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.
• 4.E: Cell Structure (Exercises)
Thumbnail: The generalized structure of a prokaryotic cell. (CC BY 4.0; OpenStax).
04: Cell Structure
Close your eyes and picture a brick wall. What is the basic building block of that wall? A single brick, of course. Like a brick wall, your body is composed of basic building blocks, and the building blocks of your body are cells.
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. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/04%3A_Cell_Structure/4.0%3A_Prelude_to_Cell_Structure.txt |
Skills to Develop
• 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. 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.
Several cells of one kind that interconnect with each other and perform a shared function form tissues, several tissues combine to form an organ (your stomach, heart, or brain), and several organs make up 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, 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. Before discussing the criteria for determining whether a cell is prokaryotic or eukaryotic, let’s first examine how biologists study cells.
Microscopy
Cells vary in size. With few exceptions, individual cells cannot be seen 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. Most photographs of cells are taken with a microscope, and these images can also be called micrographs.
The optics of a microscope’s lenses change the orientation of the image 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 viewed through a microscope, and vice versa. Similarly, if the slide is moved left while looking through the microscope, it will appear to move right, and if moved 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 system of two lenses 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; the head of a pin of is about two thousandths of a meter (two mm) in diameter. That means about 250 red blood cells could fit on the head of a pin.
Most student microscopes are classified as light microscopes (Figure \(1\)a). Visible light passes and is bent 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 commonly used in the undergraduate college 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 ability of a microscope to distinguish two adjacent structures as separate: the higher the resolution, the better the clarity and detail of the image. When oil immersion lenses are used for the study of small objects, magnification is usually increased to 1,000 times. In order to gain a better understanding of cellular structure and function, scientists typically use electron microscopes.
Electron Microscopes
In contrast to light microscopes, electron microscopes (Figure \(1\)b) use a beam of electrons instead of a beam of light. Not only does this allow for higher magnification and, thus, more detail (Figure \(2\)), it also provides higher resolving power. The method used 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 living cells cannot be viewed 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.
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 used in the 1600s by Antony van Leeuwenhoek, a Dutch shopkeeper who had great skill in crafting lenses. Despite the limitations of his now-ancient lenses, van Leeuwenhoek observed the movements of protista (a type of single-celled organism) and sperm, which he collectively termed “animalcules.”
In a 1665 publication called 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 all living things are composed of one or more cells, 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: Cytotechnologist
Have you ever heard of a medical test called a Pap smear (Figure \(3\))? In this test, a doctor takes a small sample of cells from the uterine cervix of a patient 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, who is a medical doctor who can make a clinical diagnosis.
Cytotechnologists play a vital role in saving people’s lives. When abnormalities are discovered early, a patient’s treatment can begin sooner, which usually increases the chances of a successful outcome.
Summary
A cell is the smallest unit of life. Most cells are so tiny that they cannot be seen 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 all organisms are composed of one or more cells, the cell is the basic unit of life, and new cells arise from existing cells.
Glossary
cell theory
see unified cell theory
electron microscope
an instrument that magnifies an object using a beam of electrons passed and bent through a lens system to visualize a specimen
light microscope
an instrument that magnifies an object using a beam visible light passed and bent through a lens system to visualize a specimen
microscope
an instrument that magnifies an object
unified cell theory
a biological concept that states that all organisms are composed of one or more cells; the cell is the basic unit of life; and new cells arise from existing cells | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/04%3A_Cell_Structure/4.1%3A_Studying_Cells.txt |
Skills to Develop
• Name examples of prokaryotic and eukaryotic organisms
• Compare and contrast prokaryotic cells and eukaryotic cells
• Describe the relative sizes of different kinds of cells
• Explain why cells must be small
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.
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 other cellular components are found; 3) DNA, the genetic material of the cell; 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 found in a central part of the cell: the nucleoid (Figure $1$).
Most prokaryotes have a peptidoglycan cell wall and many have a polysaccharide capsule (Figure $1$). 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 are used to exchange genetic material during a type of reproduction called conjugation. Fimbriae are used by bacteria to attach to a host cell.
Career Connection: Microbiologist
The most effective action anyone can take to prevent the spread of contagious illnesses is to wash his or her 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 sources of antibiotics that could be used to treat bacterial infections.
Environmental microbiologists may look for new ways to use specially selected or genetically engineered microbes for the removal of pollutants from soil or groundwater, as well as hazardous elements from contaminated sites. These uses of microbes are called bioremediation technologies. Microbiologists can also work in the field of bioinformatics, providing specialized knowledge and insight for the design, development, 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 $2$). The small size of prokaryotes 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 out. This is not the case in eukaryotic cells, which have developed different structural adaptations to enhance intracellular transport.
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 $4\pi r^2$, while the formula for its volume is $4\pi r^2/3$. 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 the shape of a cube (Figure $3$). 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; another way is to develop organelles that perform specific tasks. These adaptations lead to the development of more sophisticated cells called eukaryotic cells.
Art Connection
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?
Summary
Prokaryotes are predominantly 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.
Art Connections
Figure $3$: 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?
Answer
Substances can diffuse more quickly through small cells. Small cells have no need for organelles and therefore do not need to expend energy getting substances across organelle membranes. Large cells have organelles that can separate cellular processes, enabling them to build molecules that are more complex.
Glossary
nucleoid
central part of a prokaryotic cell in which the chromosome is found
prokaryote
unicellular organism that lacks a nucleus or any other membrane-bound organelle | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/04%3A_Cell_Structure/4.2%3A_Prokaryotic_Cells.txt |
Skills to Develop
• 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 practiced in many industries. 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 be built with several elevator banks; a hospital should be built so that its emergency room is 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 \(1\)). 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 often said to have a “true nucleus.” The word “organelle” means “little organ,” and, as already mentioned, organelles have specialized cellular functions, just as the organs of your body 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.
Exercise \(1\)
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 \(2\)), 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.
The plasma membranes of cells that specialize in absorption are folded into fingerlike projections called microvilli (singular = microvillus); (Figure \(3\)). Such cells are typically found lining 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 found 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.
The Cytoplasm
The cytoplasm is the entire region of a cell between the plasma membrane and the nuclear envelope (a structure to be discussed shortly). It is made up of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals (Figure \(1\)). 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 found in the cytoplasm. Glucose and other simple sugars, polysaccharides, amino acids, nucleic acids, fatty acids, and derivatives of glycerol are found there, too. Ions of sodium, potassium, calcium, and many other elements are also dissolved 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 \(1\)). 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 \(4\)).
The Nuclear Envelope
The nuclear envelope is a double-membrane structure that constitutes the outermost portion of the nucleus (Figure \(4\)). Both the inner and outer membranes of the nuclear envelope 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 consider chromosomes. Chromosomes are 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 nuclei of its body’s cells. 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 are attached to chromosomes, and they resemble an unwound, jumbled bunch of threads. These unwound protein-chromosome complexes are called chromatin (Figure \(5\)); chromatin describes the material that makes up the chromosomes both when condensed and decondensed.
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 viewed 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 cytoplasmic side of the plasma membrane or the cytoplasmic side of the endoplasmic reticulum and the outer membrane of the nuclear envelope (Figure \(1\)). Electron microscopy has shown us that ribosomes, which are large complexes of protein and RNA, consist of two subunits, aptly called large and small (Figure \(6\)). Ribosomes receive their “orders” for protein synthesis from the nucleus where the DNA is transcribed 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.
Because proteins synthesis is an essential function of all cells (including enzymes, hormones, antibodies, pigments, structural components, and surface receptors), ribosomes are found 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
Mitochondria (singular = mitochondrion) are often called the “powerhouses” or “energy factories” of a cell because they are responsible for making adenosine triphosphate (ATP), the cell’s main energy-carrying molecule. ATP represents the short-term stored energy of the cell. Cellular respiration is the process of making ATP using the chemical energy found 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 a lot of energy to keep your body moving. When your cells don’t get enough oxygen, they do not make a lot of ATP. Instead, the small amount of ATP they make in the absence of oxygen is accompanied by the production of lactic acid.
Mitochondria are oval-shaped, double membrane organelles (Figure \(7\)) that have their own ribosomes and DNA. Each membrane is a phospholipid bilayer embedded with proteins. The inner layer has folds called cristae. The area surrounded by the folds is called the mitochondrial matrix. The cristae and the matrix have different roles in cellular respiration.
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, alcohol is detoxified by peroxisomes in liver cells. Glyoxysomes, which are specialized peroxisomes in plants, are responsible for converting stored fats into sugars.
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: The membranes of vesicles 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 membrane of a vacuole 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 called the centrosome. Animal cells each have a centrosome and lysosomes, whereas 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 \(8\)). Each centriole is a cylinder of nine triplets of microtubules.
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 exact function of the centrioles 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 not found in plant cells: lysosomes. The lysosomes are the cell’s “garbage disposal.” In plant cells, the digestive processes take place in vacuoles. Enzymes within the lysosomes aid the breakdown of proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles. These enzymes are active at a much lower pH than that of the cytoplasm. Therefore, the pH within lysosomes is more acidic than the pH of the cytoplasm. 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 \(1\)b, the diagram of a plant cell, you will see a structure external to the plasma membrane called the cell wall. The cell wall is a rigid covering that protects the cell, provides structural support, and gives shape to the cell. Fungal and protistan cells also have cell walls. While the chief component of prokaryotic cell walls is peptidoglycan, the major organic molecule in the plant cell wall is cellulose (Figure \(9\)), a polysaccharide made up 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 rigid cell walls of the celery cells with your teeth.
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, while 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 called thylakoids (Figure \(10\)). Each stack of thylakoids is called a granum (plural = grana). The fluid enclosed by the inner membrane that surrounds the grana is called the stroma.
The chloroplasts contain a green pigment called 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: Endosymbiosis
We 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 as mitochondria and chloroplasts do. 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 \(1\)b, you will see that plant cells each have a large central vacuole that occupies most of the area of the cell. 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 cell walls of plant cells results in the wilted appearance of the plant.
The central vacuole also supports the expansion of the cell. When the central vacuole holds more water, the cell gets larger without having to invest a lot of energy in synthesizing new cytoplasm.
Summary
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 its DNA is surrounded by a membrane), and has other membrane-bound organelles that allow for compartmentalization of functions. The plasma membrane is a phospholipid bilayer embedded with proteins. The nucleus’s nucleolus is the site of ribosome assembly. Ribosomes are either found 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 shape to the cell. Photosynthesis takes place in chloroplasts. The central vacuole can expand without having to produce more cytoplasm.
Art Connections
Figure \(1\): If the nucleolus were not able to carry out its function, what other cellular organelles would be affected?
Answer
Free ribosomes and rough endoplasmic reticulum (which contains ribosomes) would not be able to form.
Glossary
cell wall
rigid cell covering made of cellulose 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
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 building material of chromosomes
chromosome
structure within the nucleus that is made up of chromatin that contains DNA, the hereditary material
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
cytosol
gel-like material of the cytoplasm in which cell structures are suspended
eukaryotic cell
cell that has a membrane-bound nucleus and several other membrane-bound compartments or sacs
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
mitochondria
(singular = mitochondrion) cellular organelles responsible for carrying out cellular respiration, resulting in the production of ATP, the cell’s main energy-carrying molecule
nuclear envelope
double-membrane structure that constitutes the outermost portion of the nucleus
nucleolus
darkly staining body within the nucleus that is responsible for assembling the subunits of the ribosomes
nucleoplasm
semi-solid fluid inside the nucleus that contains the chromatin and nucleolus
nucleus
cell organelle that houses the cell’s DNA and directs the synthesis of ribosomes and proteins
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 internal content of the cell from its surrounding environment
ribosome
cellular structure that carries out protein synthesis
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_1e_(OpenStax)/2%3A_The_Cell/04%3A_Cell_Structure/4.3%3A_Eukaryotic_Cells.txt |
Skills to Develop
• 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 \(1\)) 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, 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 the membranes of either mitochondria or chloroplasts.
Art Connection
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 \(1\)) is a series of interconnected membranous sacs and tubules that collectively modifies proteins and synthesizes lipids. However, these two functions are performed in separate areas of the ER: the rough ER and the smooth ER, respectively.
The hollow portion of the ER tubules is called the lumen or cisternal space. The membrane of the ER, which is a phospholipid bilayer embedded with proteins, is continuous with the nuclear envelope.
Rough ER
The rough endoplasmic reticulum (RER) is so named because the ribosomes attached to its cytoplasmic surface give it a studded appearance when viewed through an electron microscope (Figure \(2\)).
Ribosomes transfer their newly synthesized proteins into the lumen of the RER where they undergo structural modifications, such as folding or the acquisition of side chains. These modified proteins will be incorporated into cellular membranes—the membrane of the ER or those of other organelles—or secreted 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 \(1\)).
Since the RER is engaged in modifying proteins (such as enzymes, for example) that will be secreted from the cell, you would be correct in assuming that the RER is abundant in cells that secrete proteins. This is the case with cells of the liver, 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 \(1\)). Functions of the SER include synthesis of carbohydrates, lipids, and steroid hormones; detoxification of medications and poisons; and storage of calcium ions.
In muscle cells, a specialized SER called the sarcoplasmic reticulum is responsible for storage of the calcium ions that are needed to trigger the coordinated contractions of the muscle cells.
Link to Learning
Video \(1\): You can watch an excellent animation of the endomembrane system here.
Career Connection: Cardiologist
Heart 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 failure of other organs.
The wall of the heart is composed of cardiac muscle tissue. Heart failure occurs when the endoplasmic reticula of cardiac muscle cells 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 make a diagnosis of heart failure via physical examination, results from an electrocardiogram (ECG, a test that measures the electrical activity of the heart), a chest X-ray to see whether the heart is enlarged, and other tests. If heart failure is diagnosed, the cardiologist will typically prescribe appropriate medications and recommend a reduction in 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 to be sorted, packaged, and tagged so that they wind up in the right place. Sorting, tagging, packaging, and distribution of lipids and proteins takes place in the Golgi apparatus (also called the Golgi body), a series of flattened membranes (Figure \(3\)).
The receiving side of the Golgi apparatus is called the cis face. The opposite side is called 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 lumen of the Golgi apparatus. As the proteins and lipids travel through the Golgi, they undergo further modifications that allow them to be sorted. The most frequent modification is the addition of short chains of sugar molecules. These newly modified proteins and lipids are then tagged with phosphate groups or other small molecules so that they can be routed to their proper destinations.
Finally, the modified and tagged proteins are packaged into secretory vesicles that bud from the trans face of the Golgi. While some of these vesicles deposit their contents into other parts of the cell 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 cells of the salivary glands that secrete digestive enzymes or cells of the immune system 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 are used in other parts of the cell.
Career Connection: Geneticist
Many diseases arise from genetic mutations that prevent the synthesis of critical proteins. One such disease is Lowe disease (also called 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 impaired mental abilities.
Lowe disease is a genetic disease caused by a mutation on the X chromosome. The X chromosome is one of the two human sex chromosome, 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. Therefore, females who carry the Lowe disease gene on one of their X chromosomes have a 50/50 chance of having 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. The location of the mutated gene, as well as the locations of many other mutations that cause genetic diseases, has now been identified. Through prenatal testing, a woman can find out if the fetus she is carrying may be afflicted with one of several genetic diseases.
Geneticists analyze the results of prenatal genetic tests and may counsel pregnant women on available options. They may also conduct genetic research that leads to new drugs or foods, or perform DNA analyses that are used in forensic investigations.
Lysosomes
In addition to their role as the digestive component and organelle-recycling facility of animal cells, lysosomes are considered to be parts 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 a group of white blood cells called macrophages, which are part of your body’s immune system. In a process known as phagocytosis or endocytosis, a section of the plasma membrane of the macrophage 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 \(4\)).
Summary
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 used 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 distribution of lipids and proteins take place in the Golgi apparatus. Lysosomes are created by the budding of the membranes of the RER and Golgi. Lysosomes digest macromolecules, recycle worn-out organelles, and destroy pathogens.
Art Connections
Figure \(1\): 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?
Answer
It would end up on the outside. After the vesicle passes through the Golgi apparatus and fuses with the plasma membrane, it turns inside out.
Glossary
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
Golgi apparatus
eukaryotic organelle made up of a series of stacked membranes that sorts, tags, and packages lipids and proteins for distribution
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 | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/04%3A_Cell_Structure/4.4%3A_The_Endomembrane_System_and_Proteins.txt |
Skills to Develop
• 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 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 (Figure \(1\)). Here, we will examine each.
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 made of two intertwined strands of a globular protein called actin (Figure \(2\)). For this reason, microfilaments are also known as actin filaments.
Actin is powered by ATP to assemble its filamentous form, which serves as a track for the movement of a motor protein called myosin. This enables actin to engage in cellular events requiring motion, such as cell division in animal cells and cytoplasmic streaming, which is the circular movement of the cell cytoplasm 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 the site of an infection and phagocytize the pathogen.
Link to Learning
Video \(1\): 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
Intermediate filaments are made of several strands of fibrous proteins that are wound together (Figure \(3\)). These elements of the cytoskeleton get their name from the fact that their diameter, 8 to 10 nm, is between those of microfilaments and microtubules.
Intermediate filaments have no role in cell movement. Their function is purely structural. They bear tension, thus maintaining the shape of the cell, and anchor the nucleus and other organelles in place. Figure \(1\) shows how intermediate filaments create a supportive scaffolding inside the cell.
The intermediate filaments are the most diverse group of cytoskeletal elements. Several types of fibrous proteins are found in the intermediate filaments. You are probably most familiar with keratin, the fibrous protein that strengthens your hair, nails, and the epidermis of the skin.
Microtubules
As their name implies, microtubules are small hollow tubes. The walls of the microtubule are made of polymerized dimers of α-tubulin and β-tubulin, two globular proteins (Figure \(4\)). With a diameter of about 25 nm, microtubules are the widest components of the cytoskeleton. 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 dissolve and reform quickly.
Microtubules are also the structural elements of flagella, cilia, and centrioles (the latter are the two perpendicular bodies of the centrosome). In fact, 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 discussed below.
Flagella and Cilia
To refresh your memory, flagella (singular = flagellum) are long, hair-like structures that extend from the plasma membrane and are used to move an entire cell (for example, sperm, Euglena). When present, the cell has just one flagellum or a few flagella. When cilia (singular = cilium) are present, however, many of them extend along the entire surface of the plasma membrane. They are short, hair-like structures that are used to move entire cells (such as paramecia) or substances along the outer surface of the cell (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 \(5\)).
You have now completed a broad survey of the components of prokaryotic and eukaryotic cells. For a summary of cellular components in prokaryotic and eukaryotic cells, see Table \(1\).
Table \(1\): Cellular components in 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 Oxidizes and thus breaks down fatty acids and amino acids, and detoxifies 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; source of microtubules in animal cells No Yes No
Lysosomes Digestion of macromolecules; recycling of worn-out organelles No Yes No
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 extracellular surface of plasma membrane, and filtration Some Some No
Summary
The cytoskeleton has three different types of protein elements. From narrowest to widest, they are the microfilaments (actin filaments), intermediate filaments, and microtubules. Microfilaments are often associated 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.
Glossary
cilium
(plural = cilia) short, hair-like structure that extends from the plasma membrane in large numbers and is used to move an entire cell or move substances along the outer surface of the cell
cytoskeleton
network of protein fibers that collectively maintain the shape of the cell, secure some organelles in specific positions, allow cytoplasm and vesicles to move within the cell, and enable unicellular organisms to move independently
flagellum
(plural = flagella) long, hair-like structure that extends from the plasma membrane and is used to move the cell
intermediate filament
cytoskeletal component, composed of several intertwined strands of fibrous protein, that bears tension, supports cell-cell junctions, and anchors cells to extracellular structures
microfilament
narrowest element of the cytoskeleton system; it provides rigidity and shape to the cell and enables cellular movements
microtubule
widest element of the cytoskeleton system; 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 | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/04%3A_Cell_Structure/4.5%3A_The_Cytoskeleton.txt |
Skills to Develop
• 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 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.
Extracellular Matrix of Animal Cells
Most animal cells release materials into the extracellular space. The primary components of these materials are proteins, and the most abundant protein is collagen. Collagen fibers are interwoven with carbohydrate-containing protein molecules called proteoglycans. Collectively, these materials are called the extracellular matrix (Figure \(1\)). 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?
Cells have protein receptors on the extracellular surfaces of their plasma membranes. When a molecule within the matrix binds to the receptor, it changes the molecular structure of the receptor. The receptor, in turn, changes the conformation of the microfilaments 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 sections of DNA, which affects the production of associated proteins, thus changing the activities within the cell.
Blood clotting provides an example of the role of the extracellular matrix in cell communication. When the cells lining a blood vessel are damaged, they display a protein receptor called tissue factor. When tissue factor binds with another factor in the extracellular matrix, it causes platelets to adhere to the wall of the damaged blood vessel, 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, referred to as intercellular junctions. There are some differences in the ways that plant and animal cells do this. 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 they are separated by the cell wall that surrounds each cell. 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 called plasmodesmata (singular = plasmodesma), numerous channels that pass between cell walls of adjacent plant cells, connect their cytoplasm, and enable materials to be transported from cell to cell, and thus throughout the plant (Figure \(2\)).
Tight Junctions
A tight junction is a watertight seal between two adjacent animal cells (Figure \(3\)). The cells are held tightly against each other by proteins (predominantly two proteins called claudins and occludins).
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 found only in animal cells are desmosomes, which act like spot welds between adjacent epithelial cells (Figure \(4\)). Short proteins called cadherins in the plasma membrane connect to intermediate filaments to create desmosomes. The cadherins join two adjacent cells together and maintain the cells in a sheet-like formation in organs and tissues that stretch, like the skin, heart, and muscles.
Gap Junctions
Gap junctions in animal cells are like plasmodesmata in plant cells in that they are channels between adjacent cells that allow for the transport of ions, nutrients, and other substances that enable cells to communicate (Figure \(5\)). Structurally, however, gap junctions and plasmodesmata differ.
Gap junctions develop when a set of six proteins (called connexins) in the plasma membrane arrange themselves in an elongated donut-like configuration called a connexon. When the pores (“doughnut holes”) of connexons 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 is passed efficiently through gap junctions, allowing the heart muscle cells to contract in tandem.
Summary
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 surface of the plasma membrane 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.
Glossary
desmosome
linkages between adjacent epithelial cells that form when cadherins in the plasma membrane attach to intermediate filaments
extracellular matrix
material (primarily collagen, glycoproteins, and proteoglycans) secreted from animal cells that provides mechanical protection and anchoring for the cells in the tissue
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
plasmodesma
(plural = plasmodesmata) channel that passes between the cell walls of adjacent plant cells, connects their cytoplasm, and allows materials to be transported from cell to cell
tight junction
firm seal between two adjacent animal cells created by protein adherence | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/04%3A_Cell_Structure/4.6%3A__Connections_between_Cells_and_Cellular_Activities.txt |
4.1: 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.
Review Questions
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
Answer
C
The ________ is the basic unit of life.
1. organism
2. cell
3. tissue
4. organ
Answer
B
Free Response
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?
Answer
A light microscope would be ideal when viewing a small living organism, especially when the cell has been stained to reveal details.
In what situation(s) would the use of a scanning electron microscope be ideal, and why?
Answer
A scanning electron microscope would be ideal when you want to view the minute details of a cell’s surface, because its beam of electrons moves back and forth over the surface to convey the image.
In what situation(s) would a transmission electron microscope be ideal, and why?
Answer
A transmission electron microscope would be ideal for viewing the cell’s internal structures, because many of the internal structures have membranes that are not visible by the light microscope.
What are the advantages and disadvantages of each of these types of microscopes?
Answer
The advantages of light microscopes are that they are easily obtained, and the light beam does not kill the cells. However, typical light microscopes are somewhat limited in the amount of detail they can reveal. Electron microscopes are ideal because you can view intricate details, but they are bulky and costly, and preparation for the microscopic examination kills the specimen.
4.2: 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 (ceu- = “true”) and are made up of eukaryotic cells.
Review Questions
Prokaryotes depend on ________ to obtain some materials and to get rid of wastes.
1. ribosomes
2. flagella
3. cell division
4. diffusion
Answer
D
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
Answer
A
Free Response
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?
Answer
The cell wall would be targeted by antibiotics as well as the bacteria’s ability to replicate. This would inhibit the bacteria’s ability to reproduce, and it would compromise its defense mechanisms.
Explain why not all microbes are harmful.
Answer
Some microbes are beneficial. For instance, E. coli bacteria populate the human gut and help break down fiber in the diet. Some foods such as yogurt are formed by bacteria.
4.3: 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.”
Review Questions
Which of the following is surrounded by two phospholipid bilayers?
1. the ribosomes
2. the vesicles
3. the cytoplasm
4. the nucleoplasm
Answer
D
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
Answer
B
In plant cells, the function of the lysosomes is carried out by __________.
1. vacuoles
2. peroxisomes
3. ribosomes
4. nuclei
Answer
A
Which of the following is found both in eukaryotic and prokaryotic cells?
1. nucleus
2. mitochondrion
3. vacuole
4. ribosomes
Answer
D
Free Response
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?
Answer
Ribosomes are abundant in muscle cells as well because muscle cells are constructed of the proteins made by the ribosomes.
What are the structural and functional similarities and differences between mitochondria and chloroplasts?
Answer
Both are similar in that they are enveloped in a double membrane, both have an intermembrane space, and both make ATP. Both mitochondria and chloroplasts have DNA, and mitochondria have inner folds called cristae and a matrix, while chloroplasts have chlorophyll and accessory pigments in the thylakoids that form stacks (grana) and a stroma.
4.4: 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.
Review Questions
Which of the following is not a component of the endomembrane system?
1. mitochondrion
2. Golgi apparatus
3. endoplasmic reticulum
4. lysosome
Answer
A
The process by which a cell engulfs a foreign particle is known as:
1. endosymbiosis
2. phagocytosis
3. hydrolysis
4. membrane synthesis
Answer
B
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
Answer
C
Which of the following sequences correctly lists in order the steps involved in the incorporation of a proteinaceous molecule within a cell?
1. 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
Answer
C
Free Response
In the context of cell biology, what do we mean by form follows function? What are at least two examples of this concept?
Answer
“Form follows function” refers to the idea that the function of a body part dictates the form of that body part. As an example, compare your arm to a bat’s wing. While the bones of the two correspond, the parts serve different functions in each organism and their forms have adapted to follow that function.
In your opinion, is the nuclear membrane part of the endomembrane system? Why or why not? Defend your answer.
Answer
Since the external surface of the nuclear membrane is continuous with the rough endoplasmic reticulum, which is part of the endomembrane system, then it is correct to say that it is part of the system.
4.5: 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.
Review Questions
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
Answer
B
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
Answer
D
Free Response
What are the similarities and differences between the structures of centrioles and flagella?
Answer
Centrioles and flagella are alike in that they are made up of microtubules. In centrioles, two rings of nine microtubule “triplets” are arranged at right angles to one another. This arrangement does not occur in flagella.
How do cilia and flagella differ?
Answer
Cilia and flagella are alike in that they are made up of microtubules. Cilia are short, hair-like structures that exist in large numbers and usually cover the entire surface of the plasma membrane. Flagella, in contrast, are long, hair-like structures; when flagella are present, a cell has just one or two.
4.6: 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.
Review Questions
Which of the following are found only in plant cells?
1. gap junctions
2. desmosomes
3. plasmodesmata
4. tight junctions
Answer
C
The key components of desmosomes are cadherins and __________.
1. actin
2. microfilaments
3. intermediate filaments
4. microtubules
Answer
C
Free Response
How does the structure of a plasmodesma differ from that of a gap junction?
Answer
They differ because plant cell walls are rigid. Plasmodesmata, which a plant cell needs for transportation and communication, are able to allow movement of really large molecules. Gap junctions are necessary in animal cells for transportation and communication.
Explain how the extracellular matrix functions.
Answer
The extracellular matrix functions in support and attachment for animal tissues. It also functions in the healing and growth of the tissue. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/04%3A_Cell_Structure/4.E%3A_Cell_Structure_%28Exercises%29.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.
• 6.0: Prelude to Metabolism
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.
• 6.1: 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.
• 6.2: 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.
• 6.3: 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.
• 6.4: 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.
• 6.5: 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.
• 6.E: Metabolism (Exercises)
Thumbnail: diagram showing the induced fit model in enzymes (Public Domain; LadyofHats).
06: Metabolism
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. For example, the large proteins that make up muscles are actively built from smaller molecules. Complex carbohydrates are broken 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 for both the synthesis and breakdown of molecules. Additionally, signaling molecules such as hormones and neurotransmitters are transported between cells. Pathogenic bacteria and viruses are ingested and broken down by cells. 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 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 are performed with great efficiency. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/06%3A_Metabolism/6.0%3A_Prelude_to_Metabolism.txt |
Skills to Develop
• Explain what metabolic pathways are and describe the two major types of metabolic pathways
• Discuss how chemical reactions play a role in energy transfer
Scientists use the term bioenergetics to discuss the concept of energy flow (Figure $1$) through living systems, such as cells. 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. All of the chemical reactions that take place inside cells, including those that use energy and those that release energy, are the cell’s metabolism.
Metabolism of Carbohydrates
The metabolism of sugar (a simple carbohydrate) 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 a great deal of energy stored within their bonds. The breakdown of glucose, a simple sugar, is described by the equation:
$\ce{C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O + (energy)} \nonumber$
Carbohydrates that are consumed have their origins in photosynthesizing organisms like plants (Figure 6.1.2). 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 input of energy to proceed. The synthesis of glucose is described by this equation (notice that it is the reverse of the previous equation):
$\ce{6CO_2 + 6H_2O + (energy) \rightarrow C_6H_{12}O_6 + 6O_2} \nonumber$
During the chemical reactions of photosynthesis, energy is provided in the form of a very high-energy molecule called ATP, or adenosine triphosphate, which is the primary energy currency of all cells. Just as the dollar is used as currency to buy goods, cells use molecules of ATP as energy currency to perform immediate work. The sugar (glucose) is stored as starch or glycogen. Energy-storing polymers like these are broken down into glucose to supply molecules of ATP.
Solar energy is required to synthesize a molecule of glucose during the reactions of photosynthesis. In photosynthesis, light energy from the sun is initially transformed into chemical energy that is temporally stored in the energy carrier molecules ATP and NADPH (nicotinamide adenine dinucleotide phosphate). The stored energy in ATP and NADPH is then used later in photosynthesis to build one molecule of glucose from six molecules of CO2. This process is analogous to eating breakfast in the morning to acquire energy for your body that can be used later in the day. Under ideal conditions, energy from 18 molecules of ATP is required to synthesize one molecule of glucose during the reactions of photosynthesis. Glucose molecules can also be combined with and converted into other types of sugars. When sugars are consumed, molecules of glucose eventually make their way into each living cell of the organism. Inside the cell, each sugar molecule is broken 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 is used to make high-energy ATP molecules, which can be used to perform work, powering many chemical reactions in the cell. The amount of energy needed to make one molecule of glucose from six molecules of carbon dioxide is 18 molecules of ATP and 12 molecules of NADPH (each one of which is energetically equivalent to three molecules of ATP), or a total of 54 molecule equivalents required for the synthesis of one molecule of glucose. This process is a fundamental and efficient way for cells to generate the molecular energy that they require.
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. These two opposite processes—the first requiring energy and the second producing energy—are referred to as anabolic (building) and catabolic (breaking down) pathways, respectively. Consequently, metabolism is composed of building (anabolism) and degradation (catabolism).
Evolution Connection: Evolution of Metabolic Pathways
There 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 (the majority of global synthesis is done by planktonic algae) harvest the sun’s energy and convert it into carbohydrates. The by-product of photosynthesis is oxygen, required by some cells to carry out cellular respiration. During cellular respiration, oxygen aids in the catabolic breakdown of carbon compounds, like carbohydrates. Among the products of this catabolism 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 $3$). 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 the synthesis of large proteins from amino acid building blocks, and the synthesis of new DNA strands from nucleic acid building blocks. These biosynthetic processes are critical to the life of the cell, take place constantly, and demand energy provided by ATP and other high-energy molecules like NADH (nicotinamide adenine dinucleotide) and NADPH (Figure $4$).
ATP is an important molecule for cells to have in sufficient supply at all times. The breakdown of sugars illustrates how a single molecule of glucose can store enough energy to make a great deal of ATP, 36 to 38 molecules. This is a catabolic pathway. Catabolic pathways involve the degradation (or breakdown) of complex molecules into simpler ones. Molecular energy stored in the bonds of complex molecules is released in catabolic pathways and harvested in such a way that it can be used to produce ATP. Other energy-storing molecules, such as fats, are also broken down through similar catabolic reactions to release energy and make ATP (Figure $4$).
It is important to know that the chemical reactions of metabolic pathways don’t take place spontaneously. Each reaction step is facilitated, or catalyzed, by a protein called an enzyme. Enzymes are important for catalyzing all types of biological reactions—those that require energy as well as those that release energy.
Summary
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 the breaking down of complex chemicals into simpler ones, such as the breakdown of large macromolecules. This process is referred to as catabolism, and such reactions are associated with a release of energy. On the other end of the spectrum, anabolism refers to metabolic processes that build complex molecules out of simpler ones, such as the synthesis of macromolecules. Anabolic processes require energy. Glucose synthesis and glucose breakdown are examples of anabolic and catabolic pathways, respectively.
Glossary
anabolic
(also, anabolism) pathways that require an input of energy to synthesize complex molecules from simpler ones
bioenergetics
study of energy flowing through living systems
catabolic
(also, catabolism) pathways in which complex molecules are broken down into simpler ones
metabolism
all the chemical reactions that take place inside cells, including anabolism and catabolism | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/06%3A_Metabolism/6.1%3A_Energy_and_Metabolism.txt |
Skills to Develop
• Define “energy”
• Explain the difference between kinetic and potential energy
• Discuss the concepts of free energy and activation energy
• Describe endergonic and exergonic reactions
Energy is defined 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 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. This energy is associated with something as simple as an object held 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 types of energy that exist in the physical world.
Types of Energy
When an object is in motion, there is energy associated with that object. In the example of an airplane in flight, there is a great deal of energy associated with the motion of the airplane. 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 a great deal of damage to other objects. However, a wrecking ball that is not in motion is incapable of performing work. Energy associated with objects in motion is called kinetic energy. A speeding bullet, a walking person, the rapid movement of molecules in the air (which produces heat), and electromagnetic radiation like light all have kinetic energy.
Now what if that same motionless wrecking ball is lifted two stories above a car with a crane? If the suspended wrecking ball is unmoving, is there energy associated with it? The answer is yes. The suspended wrecking ball has energy associated with it that is fundamentally different from the kinetic energy of objects in motion. This form of energy results from the fact that there is the potential for the wrecking ball to do work. If it is released, indeed it would do work. Because this type of energy refers to the potential to do work, it is called 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 is released, its kinetic energy begins to increase because it builds speed due to gravity. At the same time, 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 the energy of water held behind a dam (Figure $1$), or a person about to skydive out of an airplane.
Potential energy is not only associated with the location of matter (such as a child sitting on a tree branch), but also with the structure of matter. A spring on the ground has potential energy if it is compressed; so does a rubber band that is pulled taut. The very existence of living cells relies heavily on structural potential energy. On a chemical level, the bonds that hold the atoms of molecules 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 are broken down. The fact that energy can be released by the breakdown of certain chemical bonds 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 is eventually harnessed for use. This is because these bonds can release energy when broken. The type of potential energy that exists within chemical bonds, and is released when those bonds are broken, is called chemical energy (Figure $2$). Chemical energy is responsible for providing living cells with energy from food. The release of energy is brought about by breaking the molecular bonds within fuel molecules.
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 are broken, an important next question is how is the energy associated with chemical reactions quantified and expressed? How can the energy released from one reaction be compared to that of another reaction? A measurement of free energy is used to quantitate these energy transfers. Free energy is called Gibbs free energy (abbreviated with the letter G) after Josiah Willard Gibbs, the scientist who developed the measurement. Recall that according to the second law of thermodynamics, all energy transfers involve the loss of some amount of energy in an unusable form such as heat, resulting in entropy. Gibbs free energy specifically refers to the energy associated with a chemical reaction that is available after entropy is accounted for. 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). The change in free energy can be calculated 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 total energy change of the system. This total energy change in the system is called enthalpy and is denoted as ∆H . The formula for calculating ∆G is as follows, where the symbol T refers to absolute temperature in Kelvin (degrees Celsius + 273):
$\mathrm{\Delta G = \Delta H - T\Delta S} \nonumber$
The standard free energy change of a chemical reaction is expressed 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. Standard pH, temperature, and pressure conditions are generally calculated at pH 7.0 in biological systems, 25 degrees Celsius, and 100 kilopascals (1 atm pressure), respectively. It is important to 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 is released 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 products of the reaction have less free energy than the reactants, because they gave off some free energy during the reaction. Reactions that have a negative ∆G and consequently release free energy are called exergonic reactions. Think: exergonic means energy is exiting the system. These reactions are also referred to as spontaneous reactions, because they can occur without the addition of 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. An important distinction must be drawn 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. The rusting of iron is an example of a spontaneous reaction that occurs slowly, little by little, over time.
If a chemical reaction requires an input of energy 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, the products of these reactions can be thought of as energy-storing molecules. These chemical reactions are called endergonic reactions, and they are non-spontaneous. An endergonic reaction will not take place on its own without the addition of free energy.
Let’s revisit the example of the synthesis and breakdown of the food molecule, glucose. Remember that the building of 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. On the other hand, the catabolic process of breaking sugar down into simpler molecules releases energy in a series of exergonic reactions. Like the example of rust above, the breakdown of sugar involves spontaneous reactions, but these reactions don’t occur instantaneously. Figure $3$ 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.
Art Connection
Look at each of the processes shown, 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 the study of 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 $4$). 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 a state of equilibrium is reached. This state of equilibrium is one of the lowest possible free energy and a state of maximal entropy. Energy must be put into the system to push the reactants and products away from a state of equilibrium. 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 work needed 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 chemical equilibrium is never reached. In this way, living organisms are in a constant energy-requiring, uphill battle against equilibrium and entropy. This constant supply of energy ultimately comes from sunlight, which is used to produce nutrients in the process of photosynthesis.
Activation Energy
There is another important concept that must be considered regarding endergonic and exergonic reactions. Even exergonic reactions require a small amount of energy input to get going before they can proceed with their energy-releasing steps. These reactions have a net release of energy, but still require some energy in the beginning. This small amount of energy input necessary for all chemical reactions to occur is called the activation energy (or free energy of activation) and is abbreviated EA (Figure $5$).
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 are broken and new ones are formed. For example, when a glucose molecule is broken down, bonds between the carbon atoms of the molecule are broken. 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 called the transition state, and it is a high-energy, unstable state. For this reason, reactant molecules don’t last long in their transition state, but very quickly proceed to the next steps of the chemical reaction. 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
Watch an animation of the move from free energy to transition state at this site.
Where does the activation energy required by chemical reactants come from? The source of the activation energy needed 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 motion of molecules, 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 up 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 will be. The example of iron rusting illustrates an inherently slow reaction. This reaction occurs slowly over time because of its high EA. Additionally, the burning of many fuels, which is strongly exergonic, will take place at a negligible rate unless their activation energy is overcome by sufficient heat from a spark. Once they begin to burn, however, 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 $1$$5$); this is referred to 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 essential components of a cell would disintegrate.
Art Connection
If no activation energy were required to break down sucrose (table sugar), would you be able to store it in a sugar bowl?
Summary
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 the breaking of molecular bonds has the potential to release energy. Living cells depend on the harvesting of potential energy from molecular bonds to perform work. Free energy is a measure of energy that is available to do work. The free energy of a system changes during energy transfers such as chemical reactions, and this change is referred to as ∆G.
The ∆G of a reaction 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 called an exergonic reaction. One with a positive ∆G that requires energy input is called an endergonic reaction. Exergonic reactions are said to be spontaneous, because their products have less energy than their reactants. The products of endergonic reactions have a higher energy state than the reactants, and so these are nonspontaneous reactions. However, all reactions (including spontaneous -∆G reactions) require an initial input of energy in order to reach the transition state, at which they’ll proceed. This initial input of energy is called the activation energy.
Art Connections
Figure $3$: Look at each of the processes shown, and decide if it is endergonic or exergonic. In each case, does enthalpy increase or decrease, and does entropy increase or decrease?
Answer
A compost pile decomposing is an exergonic process; enthalpy increases (energy is released) and entropy increases (large molecules are broken down into smaller ones). A baby developing from a fertilized egg is an endergonic process; enthalpy decreases (energy is absorbed) and entropy decreases. Sand art being destroyed is an exergonic process; there is no change in enthalpy, but entropy increases. A ball rolling downhill is an exergonic process; enthalpy decreases (energy is released), but there is no change in enthalpy.
Figure $5$: If no activation energy were required to break down sucrose (table sugar), would you be able to store it in a sugar bowl?
Answer
No. We can store chemical energy because of the need to overcome the barrier to its breakdown.
Glossary
activation energy
energy necessary for reactions to occur
chemical energy
potential energy in chemical bonds that is released when those bonds are broken
endergonic
describes chemical reactions that require energy input
enthalpy
total energy of a system
exergonic
describes chemical reactions that release free energy
free energy
Gibbs free energy is the usable energy, or energy that is available to do work.
heat energy
total bond energy of reactants or products in a chemical reaction
kinetic energy
type of energy associated with objects or particles in motion
potential energy
type of energy that has the potential to do work; stored energy
transition state
high-energy, unstable state (an intermediate form between the substrate and the product) occurring during a chemical reaction | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/06%3A_Metabolism/6.2%3A_Potential_Kinetic_Free_and_Activation_Energy.txt |
Skills to Develop
• 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 of that system is called the surroundings. For instance, when heating a pot of water on the stove, the system includes the stove, the pot, and the water. Energy is transferred 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 can be transferred between the system and its surroundings. The stovetop system is open because heat can be lost into the air. A closed system is one that cannot transfer energy to its surroundings.
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.
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 be transferred from place to place or transformed 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 the energy of sunlight into the chemical energy stored within organic molecules (Figure 2.3.b.1). Some examples of energy transformations are shown in Figure \(1\).
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 is transformed through a series of cellular chemical reactions into energy within molecules of ATP. 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.
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 we’ve 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, heat energy is defined as the energy transferred from one system to another that is not doing work. For example, when an airplane flies through the air, some of the energy of the flying plane is lost as heat energy due to friction with the surrounding air. This friction actually heats the air by temporarily increasing the speed of air molecules. 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 (also known as randomness). The more energy that is lost by a system to its surroundings, the less ordered and more random the system is. Scientists refer to the measure of randomness or disorder within a system as entropy. High entropy means high disorder and low energy (Figure \(2\)). 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, the entropy of the house or car 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 Connection: Transfer of Energy and the Resulting Entropy
Set up a simple experiment to understand how energy is transferred 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 temperature of the ice is 0°C. As a result, the entropy of the system 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 entropy of the system higher or lower? Why?
3. Heat the water to its boiling point. What happens to the entropy of the system when the water is heated?
All physical systems can be thought of in this way: Living things are highly ordered, requiring constant energy input to be maintained 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 aren’t useful energy sources. This process increases the entropy of the system’s surroundings. Since all energy transfers result in the loss of some usable energy, the second law of thermodynamics states that every energy transfer or transformation increases the entropy of the universe. Even though living things are highly ordered and maintain a state of low entropy, the entropy of the universe in total is constantly increasing due to the loss of usable energy with each energy transfer that occurs. Essentially, living things are in a continuous uphill battle against this constant increase in universal entropy.
Summary
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 called the surroundings. Single cells are biological systems. Systems can be thought of as having a certain amount of order. It takes energy to make a system more ordered. The more ordered a system is, the lower its entropy. Entropy is a measure of the disorder of a system. As a system becomes more disordered, the lower its energy and the higher its entropy become.
A series of laws, called the laws of thermodynamics, 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 can’t 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 tends toward disorder.
Glossary
entropy (S)
measure of randomness or disorder within a system
heat
energy energy transferred from one system to another that is not work (energy of the motion of molecules or particles)
thermodynamics
study of energy and energy transfer involving physical matter | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/06%3A_Metabolism/6.3%3A_The_Laws_of_Thermodynamics.txt |
Skills to Develop
• Explain the role of ATP as the cellular energy currency
• Describe how energy is released through hydrolysis of ATP
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. ATP is a small, relatively simple molecule (Figure $1$), but within some of its bonds, it contains the potential for a quick burst of energy that can be harnessed to perform cellular work. This molecule can be thought of as the primary energy currency of cells in much the same way that money is the currency that people exchange for things they need. ATP is used to power the majority of energy-requiring cellular reactions.
As its name suggests, adenosine triphosphate is comprised of adenosine bound to three phosphate groups (Figure $1$). 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 labeled 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. The reason that these bonds are considered “high-energy” is 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 with the use of a water molecule, it is considered a hydrolysis reaction. In other words, ATP is hydrolyzed into ADP in the following reaction:
$\ce{ATP + H_2O \rightarrow ADP + P_{i} + free\: energy} \nonumber$
Like most chemical reactions, the hydrolysis of ATP to ADP is reversible. The reverse reaction regenerates ATP from ADP + Pi. Indeed, cells rely on the regeneration of ATP just as people rely on the regeneration of spent money through some sort of income. Since ATP hydrolysis releases energy, ATP regeneration must require an input of free energy. The formation of ATP is expressed in this equation:
$\ce{ADP + P_{i} + free\: energy \rightarrow ATP + H_2O} \nonumber$
Two prominent questions remain with regard to the use of ATP as an energy source. Exactly how much free energy is released with the hydrolysis of ATP, and how is that free energy used to do cellular work? The calculated ∆G for the hydrolysis of one mole of ATP into ADP and Pi is −7.3 kcal/mole (−30.5 kJ/mol). Since this calculation is true under standard conditions, it would be expected that a different value exists under cellular conditions. In fact, the ∆G for the hydrolysis of one mole of ATP 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 posed above, that is, how the energy released by ATP hydrolysis is used to perform work inside the cell, depends on a strategy called energy coupling. Cells couple the exergonic reaction of ATP hydrolysis with endergonic reactions, 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 $2$). A large percentage of a cell’s ATP is spent powering this pump, because cellular processes bring a great deal of sodium into the cell and potassium out of the cell. 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 molecule of ATP must be hydrolyzed. When ATP is hydrolyzed, its gamma phosphate doesn’t simply float away, but is actually transferred onto the pump protein. This process of a phosphate group binding to a molecule is called phosphorylation. As with most cases of ATP hydrolysis, a phosphate from ATP is transferred 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 outside of the cell. It then binds extracellular K+, which, through another conformational change, causes the phosphate to detach from the pump. This release of phosphate triggers the K+ to be released to the inside of the cell. Essentially, the energy released from the hydrolysis of ATP is coupled 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.
Art Connection
The hydrolysis of one ATP molecule 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 be moved by the hydrolysis of one ATP molecule?
Often during cellular metabolic reactions, such as the synthesis and breakdown of nutrients, certain molecules must be altered 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 molecule of the sugar glucose is broken down in the process of glycolysis. In the first step of this process, ATP is required for the phosphorylation of glucose, creating a high-energy but unstable intermediate. This phosphorylation reaction powers a conformational change that allows the phosphorylated glucose molecule to be converted to the phosphorylated sugar fructose. Fructose is a necessary intermediate for glycolysis to move forward. Here, the exergonic reaction of ATP hydrolysis is coupled 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 the phosphorylation of another molecule, creating an unstable intermediate and powering an important conformational change.
Link to Learning
See an interactive animation of the ATP-producing glycolysis process at this site.
Summary
ATP is the primary energy-supplying molecule for living cells. ATP is made up 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 the hydrolysis of ATP into ADP + Pi is used to perform cellular work. Cells use ATP to perform work by coupling the exergonic reaction of ATP hydrolysis with endergonic reactions. ATP donates its phosphate group to another molecule via a process known as phosphorylation. The phosphorylated molecule is at a higher-energy state and is less stable than its unphosphorylated form, and this added energy from the addition of the phosphate allows the molecule to undergo its endergonic reaction.
Art Connections
Figure $2$: The hydrolysis of one ATP molecule 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 be moved by the hydrolysis of one ATP molecule?
Answer
Three sodium ions could be moved by the hydrolysis of one ATP molecule. The ∆G of the coupled reaction must be negative. Movement of three sodium ions across the membrane will take 6.3 kcal of energy (2.1 kcal × 3 Na+ ions = 6.3 kcal). Hydrolysis of ATP provides 7.3 kcal of energy, more than enough to power this reaction. Movement of four sodium ions across the membrane, however, would require 8.4 kcal of energy, more than one ATP molecule can provide.
Glossary
ATP
adenosine triphosphate, the cell’s energy currency
phosphoanhydride bond
bond that connects phosphates in an ATP molecule | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/06%3A_Metabolism/6.4%3A_ATP%3A_Adenosine_Triphosphate.txt |
Skills to Develop
• 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 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. It is important to remember that enzymes don’t change the ∆G of a reaction. In other words, they don’t change whether a reaction is exergonic (spontaneous) or endergonic. This is because they don’t change the free energy of the reactants or products. They only reduce the activation energy required to reach the transition state (Figure \(1\)).
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 is broken 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 called the enzyme’s active site. The active site is where the “action” happens, so to speak. Since enzymes are proteins, there is a unique combination of amino acid residues (also called side chains, or R groups) within the active site. Each residue is characterized by different properties. Residues 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 influences by the local environment. 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 natural properties of a substance. Likewise, the pH of the local environment 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 pH values (acidic or basic) of the environment 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 called induced fit (Figure \(2\)). The induced-fit 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 transition state of the substrate. This ideal binding maximizes the enzyme’s ability to catalyze its reaction.
When an enzyme binds its substrate, an enzyme-substrate complex is formed. This complex lowers the activation energy of the reaction 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 appropriate region of the other molecule with which it must react. Another way in which enzymes promote the reaction of their substrates 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’ve 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 completion of the reaction. One of the hallmark properties of enzymes is that they remain ultimately unchanged by the reactions they catalyze. After an enzyme is done catalyzing a reaction, it releases its product(s).
Control of Metabolism Through Enzyme Regulation
It would seem ideal to have a scenario in which all of the enzymes encoded 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, enzyme activity is partly controlled by environmental factors, like pH and temperature. There are other mechanisms through which cells control the activity of enzymes and determine the rates at which various biochemical reactions will occur.
Regulation of Enzymes by Molecules
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. In some cases of enzyme inhibition, for example, 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 \(3\)). On the other hand, in noncompetitive inhibition, an inhibitor molecule binds to the enzyme in a location other than an allosteric site and still manages to block 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 affinity of the enzyme for its substrate. This type of inhibition is called allosteric inhibition (Figure \(4\)). Most allosterically regulated enzymes are made up of more than one polypeptide, meaning that they have more than one protein subunit. When an allosteric inhibitor binds to an enzyme, all active sites on the protein subunits are changed 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).
Everyday Connection: Drug Discovery by Looking for Inhibitors of Key Enzymes in Specific Pathways
Enzymes are key components of metabolic pathways. Understanding how enzymes work and how they can be regulated is a key principle behind the development of many of the pharmaceutical drugs (Figure \(5\)) on the market today. Biologists working in this field collaborate with other scientists, usually chemists, to design drugs.
Consider statins for example—which is the name given to the 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 levels of cholesterol synthesized in the body can be reduced. 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), its mechanism of action is still not completely understood.
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. Drug targets are identified 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 the target and the pathway are identified, then the actual process of drug design 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 get 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 bound zinc ion (Zn++) to function. Coenzymes are organic helper molecules, with a basic atomic structure made up of carbon and hydrogen, which are required for enzyme action. The most common sources of coenzymes are dietary vitamins (Figure \(6\)). 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 the breakdown of glucose to yield energy is catalysis by a multi-enzyme complex called 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 are supplied primarily by the diets of most organisms.
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 can be 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 the digestion of cellular debris and foreign materials, located within lysosomes.
Feedback Inhibition in Metabolic Pathways
Molecules can regulate enzyme function in many ways. A major question remains, however: What are these molecules and where do they come from? Some are cofactors and coenzymes, ions, and organic molecules, as you’ve 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 of these molecules 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 the products of the cellular metabolic reactions themselves. In a most efficient and elegant way, cells have evolved to use the products of their own reactions for feedback inhibition of enzyme activity. Feedback inhibition involves the use of a reaction product to regulate its own further production (Figure \(7\)). 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 described above.
The production of both amino acids and nucleotides is controlled through feedback inhibition. Additionally, ATP is an allosteric regulator of some of the enzymes involved in the catabolic breakdown of sugar, 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. If too much ATP were present in a cell, much of it would go to waste. On the other hand, ADP serves as a positive allosteric regulator (an allosteric activator) for some of the same enzymes that are inhibited by ATP. Thus, when relative levels of ADP are high compared to ATP, the cell is triggered to produce more ATP through the catabolism of sugar.
Summary
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, made up of certain amino acid R groups (residues). This unique environment is perfectly suited to convert particular chemical reactants for that enzyme, called substrates, into unstable intermediates called transition states. Enzymes and substrates are thought to 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 be more easily broken, 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 are being catalyzed 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 being compartmentalized so that they can only catalyze reactions under certain circumstances. Inhibition and activation of enzymes 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 the function of enzymes allosterically. The most common method by which cells regulate the enzymes in metabolic pathways is through feedback inhibition. During feedback inhibition, the products of a metabolic pathway 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.
Glossary
active site
specific region of the enzyme 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 affinity of the enzyme for its substrate
coenzyme
small organic molecule, such as a vitamin or its derivative, which is required to enhance the activity of an enzyme
cofactor
inorganic ion, such as iron and magnesium ions, required for optimal regulation of enzyme activity
competitive inhibition
type of inhibition in which the inhibitor competes with the substrate molecule by binding to the active site of the enzyme
denature
process that changes the natural properties of a substance
feedback inhibition
effect of a product of a reaction sequence to decrease its further production by inhibiting the activity of the first enzyme in the pathway that produces it
induced fit
dynamic fit between the enzyme and its substrate, in which both components modify their structures to allow for ideal binding
substrate
molecule on which the enzyme acts | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/06%3A_Metabolism/6.5%3A_Enzymes.txt |
6.1: Energy and Metabolism
Multiple Choice
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
Answer
C
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
Answer
A
Free Response
Does physical exercise involve anabolic and/or catabolic processes? Give evidence for your answer.
Answer
Physical exercise involves both anabolic and catabolic processes. Body cells break down sugars to provide ATP to do the work necessary for exercise, such as muscle contractions. This is catabolism. Muscle cells also must repair muscle tissue damaged by exercise by building new muscle. This is anabolism.
Name two different cellular functions that require energy that parallel human energy-requiring functions.
Answer
Energy is required for cellular motion, through beating of cilia or flagella, as well as human motion, produced by muscle contraction. Cells also need energy to perform digestion, as humans require energy to digest food.
6.2: Potential, Kinetic, Free, and Activation Energy
Review Questions
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, 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
Answer
C
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
Answer
D
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
Answer
B
Free Response
Explain in your own words the difference between a spontaneous reaction and one that occurs instantaneously, and what causes this difference.
Answer
A spontaneous reaction is one that has a negative ∆G and thus releases energy. However, a spontaneous reaction need not occur quickly or suddenly like an instantaneous reaction. It may occur over long periods due to a large energy of activation, which prevents the reaction from occurring quickly.
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.
Answer
The transition state is always higher in energy than the reactants and the products of a reaction (therefore, above), regardless of whether the reaction is endergonic or exergonic.
6.3: The Laws of Thermodynamics
Review Questions
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
Answer
A
Label each of the following systems as high or low entropy: 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
Answer
A
Free Response
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?
Answer
The ant farm had lower entropy before the earthquake because it was a highly ordered system. After the earthquake, the system became much more disordered and had higher entropy.
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.
Answer
While cooking, food is heating up on the stove, but not all of the heat goes to cooking the food, some of it is lost as heat energy to the surrounding air, increasing entropy. While driving, cars burn gasoline to run the engine and move the car. This reaction is not completely efficient, as some energy during this process is lost as heat energy, which is why the hood and the components underneath it heat up while the engine is turned on. The tires also heat up because of friction with the pavement, which is additional energy loss. This energy transfer, like all others, also increases entropy.
6.4: ATP: Adenosine Triphosphate
Review Questions
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
Answer
D
Which of the following molecules is likely to have the most potential energy?
1. sucrose
2. ATP
3. glucose
4. ADP
Answer
A
Free Response
Do you think that the EA for ATP hydrolysis is relatively low or high? Explain your reasoning.
Answer
The activation energy for hydrolysis is very low. Not only is ATP hydrolysis an exergonic process with a large −∆G, but ATP is also a very unstable molecule that rapidly breaks down into ADP + Pi if not utilized quickly. This suggests a very low EA since it hydrolyzes so quickly.
6.5: Enzymes
Review Questions
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
Answer
A
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
Answer
C
Which of the following analogies best describe 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.
Answer
A
Free Response
With regard to enzymes, why are vitamins necessary for good health? Give examples.
Answer
Most vitamins and minerals act as coenzymes and cofactors for enzyme action. Many enzymes require the binding of certain cofactors or coenzymes to be able to catalyze their reactions. Since enzymes catalyze many important reactions, it is critical to obtain sufficient vitamins and minerals from the diet and from supplements. Vitamin C (ascorbic acid) is a coenzyme necessary for the action of enzymes that build collagen, an important protein component of connective tissue throughout the body. Magnesium ion (Mg++) is an important cofactor that is necessary for the enzyme pyruvate dehydrogenase to catalyze part of the pathway that breaks down sugar to produce energy. Vitamins cannot be produced in the human body and therefore must be obtained in the diet.
Explain in your own words how enzyme feedback inhibition benefits a cell.
Answer
Feedback inhibition allows cells to control the amounts of metabolic products produced. If there is too much of a particular product relative to what the cell’s needs, feedback inhibition effectively causes the cell to decrease production of that particular product. In general, this reduces the production of superfluous products and conserves energy, maximizing energy efficiency. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/06%3A_Metabolism/New_Page.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.
• 7.0: Prelude to Cellular Respiration
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.
• 7.1: 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.
• 7.2: 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.
• 7.3: 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.
• 7.4: 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.
• 7.5: 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.
• 7.6: 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.
• 7.7: 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.
• 7.E: Cellular Respiration (Exercises)
Thumbnail: The generalized structure of a prokaryotic cell. (CC BY 4.0; OpenStax).
07: Cellular Respiration
The electrical energy plant in Figure \(1\) 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. 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. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/07%3A_Cellular_Respiration/7.0%3A_Prelude_to_Cellular_Respiration.txt |
Skills to Develop
• Discuss the importance of electrons in the transfer of energy in living systems
• Explain how ATP is used by the cell 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. 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.
Electrons and Energy
The removal of an electron from a molecule, oxidizing it, results in a decrease in potential energy in the oxidized compound. The electron (sometimes as part of a hydrogen atom), does not remain unbonded, however, 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 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 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 $1$) is derived from vitamin $B_3$, 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).
NAD+ can accept electrons from an organic molecule according to the general equation:
$\underset{\text{reducing agent}}{\ce{RH}} + \underset{\text{oxidizing agent}}{\ce{NAD^+}} \rightarrow \underset{\text{reduced}}{\ce{NADH}} + \underset{\text{oxidized}}{\ce{R^+}} \nonumber$
When electrons are added to a compound, they are 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 compound, it 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 $B_2$, 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.
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 by the released phosphate binding to another molecule, 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 $2$). 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).
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-) 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 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. 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:
$\text{A} + \text{enzyme} + \text{ATP} \rightarrow \text{[A − enzyme − ∼P]} \rightarrow \text{B} + \text{enzyme} + \text{ADP} + \text{phosphate ion} \nonumber$
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 $3$). This very direct method of phosphorylation is called substrate-level phosphorylation.
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 $4$) 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.
Career Connections: Mitochondrial Disease Physician
What happens when the critical reactions of cellular respiration do not proceed correctly? Mitochondrial diseases 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 Disease.
Summary
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.
Glossary
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
dephosphorylation
removal of a phosphate group from a molecule
oxidative phosphorylation
production of ATP using the process of chemiosmosis and oxygen
phosphorylation
addition of a high-energy phosphate to a compound, usually a metabolic intermediate, a protein, or ADP
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 | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/07%3A_Cellular_Respiration/7.1%3A_Energy_in_Living_Systems.txt |
Skills to Develop
• Describe the overall result in terms of molecules produced in the breakdown of glucose by glycolysis
• Compare the output of glycolysis in terms of ATP molecules and NADH molecules produced
You have read that 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. 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. 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, the reduced form of NAD.
First Half of Glycolysis (Energy-Requiring Steps)
Step 1. The first step in glycolysis (Figure \(1\)) 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. 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 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 single isomer. At this point in the pathway, there is a net investment of energy from two ATP molecules in the breakdown of one glucose molecule.
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 \(2\)) 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.
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 non-physiological conditions).
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 starts with glucose and ends with two pyruvate molecules, a total of four ATP molecules and two molecules of NADH. Two ATP molecules were 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 2 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 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.
Summary
Glycolysis is the first pathway 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.
Glossary
aerobic respiration
process in which organisms convert energy in the presence of oxygen
anaerobic
process that does not use oxygen
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
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 | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/07%3A_Cellular_Respiration/7.2%3A_Glycolysis.txt |
Skills to Develop
• Explain how a circular pathway, such as the citric acid cycle, fundamentally differs from a linear 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 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. 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 \(1\)).
Step 1. A carboxyl group is removed from pyruvate, releasing a molecule of carbon dioxide into the surrounding medium. The result of this step is a two-carbon hydroxyethyl group bound to the enzyme (pyruvate dehydrogenase). This is the first of the six carbons from the original glucose molecule to be removed. This step proceeds twice (remember: there are two pyruvate molecules produced at the end of glycolsis) for every molecule of glucose metabolized; 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.
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 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. 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 (since 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 reduced forms of NADH and FADH2 (Figure \(2\)). 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.
Steps in the Citric Acid Cycle
Step 1. Prior to the start of 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 is a condensation step, combining 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, together 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.
Steps 3 and 4. Steps three and four are both oxidation and decarboxylation steps, which release electrons that reduce NAD+ to NADH and release carboxyl groups that form CO2 molecules. α-Ketoglutarate is the product of step three, and a succinyl group is the product of step four. CoA binds 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 phosphate 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, producing FADH2. The energy contained in the electrons of these atoms 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 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 produced in the process.
Link to Learning
Click through each step 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 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 non-essential amino acids; therefore, the cycle is amphibolic (both catabolic and anabolic).
Summary
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 remove 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.
Glossary
acetyl CoA
combination of an acetyl group derived from pyruvic acid and coenzyme A, which is made from pantothenic acid (a B-group vitamin)
citric acid cycle
(also, Krebs cycle) series of enzyme-catalyzed chemical reactions of central importance in all living cells
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
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 | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/07%3A_Cellular_Respiration/7.3%3A_Oxidation_of_Pyruvate_and_the_Citric_Acid_Cycle.txt |
Skills to Develop
• Describe how electrons move through the electron transport chain and what happens to their energy levels
• 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. 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. Therefore, a concentration gradient forms in which hydrogen ions diffuse out of the matrix space 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 \(1\)) is the last component of aerobic respiration and is the only part of glucose metabolism that uses atmospheric oxygen. Oxygen continuously diffuses into plants; in animals, it enters the body through the respiratory system. Electron transport is a series of redox reactions that resemble 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, producing water. There are four complexes composed of proteins, labeled I through IV in Figure \(1\), 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 in multiple copies in the inner mitochondrial membrane of eukaryotes and the plasma membrane of prokaryotes.
Complex I
To start, two electrons are carried to the first complex aboard 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 co-factors in the electron transport chain. A prosthetic group is a non-protein molecule required for the activity of a protein. Prosthetic groups are organic or inorganic, non-peptide molecules bound to a protein that facilitate its function; prosthetic groups include co-enzymes, which are the prosthetic groups of enzymes. The enzyme in complex I is NADH dehydrogenase and is a very large protein, containing 45 amino acid 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 (Q). 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, including succinate dehydrogenase. 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, 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 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 is the acceptor of 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. 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 used in 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 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 open to diffusion by the hydrogen ions, the ions would tend to diffuse back across into the matrix, driven by 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 through an integral membrane protein called ATP synthase (Figure \(2\)). 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.
Art Connection
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 \(3\)) 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.
Art Connection
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 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. Moreover, 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.
Summary
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.
Art Connections
Figure \(2\): 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?
Answer
After DNP poisoning, the electron transport chain can no longer form a proton gradient, and ATP synthase can no longer make ATP. DNP is an effective diet drug because it uncouples ATP synthesis; in other words, after taking it, a person obtains less energy out of the food he or she eats. Interestingly, one of the worst side effects of this drug is hyperthermia, or overheating of the body. Since ATP cannot be formed, the energy from electron transport is lost as heat.
Figure \(3\): 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?
Answer
After cyanide poisoning, the electron transport chain can no longer pump electrons into the intermembrane space. The pH of the intermembrane space would increase, the pH gradient would decrease, and ATP synthesis would stop.
Glossary
ATP synthase
(also, F1F0 ATP synthase) membrane-embedded protein complex that adds a phosphate to ADP with energy from protons diffusing through it
prosthetic group
(also, prosthetic cofactor) molecule bound to a protein that facilitates the function of the protein
ubiquinone
soluble electron transporter in the electron transport chain that connects the first or second complex to the third | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/07%3A_Cellular_Respiration/7.4%3A_Oxidative_Phosphorylation.txt |
Skills to Develop
• 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. In contrast, some living systems use an inorganic molecule as a final electron acceptor. 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 of bacteria and Archaea, use anaerobic respiration. For example, the group of Archaea 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 and Archaea, most of which are anaerobic (Figure $1$), reduce sulfate to hydrogen sulfide to regenerate NAD+ from NADH.
Link to Learning
Video $1$: Watch this video to see anaerobic cellular respiration in action.
Lactic Acid Fermentation
The fermentation method used by animals and certain bacteria, like those in yogurt, is lactic acid fermentation (Figure $2$). This type of fermentation is used routinely in mammalian red blood cells 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 the lactate brought to the liver for further metabolism. The chemical reactions of lactic acid fermentation are the following:
$\text{Pyruvic} \enspace \text{acid} + \text{NADH} \leftrightarrow \text{lactic} \enspace \text{acid} + \text{NAD}^+ \nonumber$
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.
Exercise $1$
Tremetol, a metabolic poison found in the white snake root plant, prevents the metabolism of lactate. When cows eat this plant, it is concentrated in the milk they produce. Humans who consume the milk become ill. Symptoms of this disease, which include vomiting, abdominal pain, and tremors, become worse after exercise. Why do you think this is the case?
Answer
The illness is caused by lactate accumulation. Lactate levels rise after exercise, making the symptoms worse. Milk sickness is rare today, but was common in the Midwestern United States in the early 1800s.
Alcohol Fermentation
Another familiar fermentation process is alcohol fermentation (Figure $3$) that produces ethanol, an alcohol. The first chemical reaction of alcohol fermentation is the following (CO2 does not participate in the second reaction):
$\text{Pyruvic} \enspace \text{acid} \rightarrow \ce{CO_2} + \text{acetaldehyde} + \text{NADH} \rightarrow \text{ethanol} + \text{NAD}^+ \nonumber$
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, making 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.
Other Types of Fermentation
Other fermentation methods occur in bacteria. Many prokaryotes are facultatively anaerobic. This means that they can switch between aerobic respiration and fermentation, depending on the availability of oxygen. Certain prokaryotes, like 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. It should be noted 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, that step would not occur and no ATP would be harvested from the breakdown of glucose.
Summary
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.
Glossary
anaerobic cellular respiration
process in which organisms convert energy for their use in the absence of oxygen
fermentation
process of regenerating NAD+ with either an inorganic or organic compound serving as the final electron acceptor, occurs in the absence; occurs in the absence of oxygen | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/07%3A_Cellular_Respiration/7.5%3A_Metabolism_without_Oxygen.txt |
Skills to Develop
• 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 more 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 \(2\)). 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.
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 shunted into glycogen for storage. Glycogen is made and stored in both liver and muscle. The glycogen will be hydrolyzed into glucose 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 G-1-P and converted into 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 (which is part of the milk sugar, the 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 \(1\)). 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.
Connections of Lipid and Glucose Metabolisms
The lipids that are connected to the glucose pathways are 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 are a form of long-term energy storage in animals. Triglycerides are made of glycerol and three fatty acids. 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 that 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.
Evolution Connection: Pathways of Photosynthesis and Cellular Metabolism
The 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—probably on the surface of some porous clays. 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). (Early photosynthesis did not produce free oxygen because it did not use water as the source of hydrogen ions; instead, it used materials like 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 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.
Summary
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.
Contributors and Attributions
• 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]). | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/07%3A_Cellular_Respiration/7.6%3A_Connections_of_Carbohydrate_Protein_and_Lipid_Metabolic_Pathways.txt |
Skills to Develop
• 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 stand still 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 proteins that transport glucose (Figure \(1\)). Different forms of the GLUT protein control passage of glucose into the cells of specific tissues.
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 feedback. 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 non-reversible 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 \(2\)). 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.
Phosphofructokinase is the main enzyme controlled in glycolysis. High levels of ATP, citrate, or a lower, more acidic pH decrease 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 like 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 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 accumulate, 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. 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. α-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 is the relative concentration of ADP to ATP triggers the cell to slow down the electron transport chain.
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 \(1\).
Table \(1\): 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
Summary
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, 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.
Glossary
GLUT protein
integral membrane protein that transports glucose | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/07%3A_Cellular_Respiration/7.7%3A_Regulation_of_Cellular_Respiration.txt |
7.1: 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.
Review Questions
The energy currency used by cells is ________.
1. ATP
2. ADP
3. AMP
4. adenosine
Answer
A
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
Answer
B
Free Response
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?
Answer
ATP provides the cell with a way to handle energy in an efficient manner. The molecule can be charged, stored, and used as needed. Moreover, the energy from hydrolyzing ATP is delivered as a consistent amount. Harvesting energy from the bonds of several different compounds would result in energy deliveries of different quantities.
7.2: 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.
Review Questions
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.
Answer
C
Free Response
Nearly all organisms on earth carry out some form of glycolysis. How does that fact support or not support the assertion that glycolysis is one of the oldest metabolic pathways?
Answer
If glycolysis evolved relatively late, it likely would not be as universal in organisms as it is. It probably evolved in very primitive organisms and persisted, with the addition of other pathways of carbohydrate metabolism that evolved later.
Red blood cells do not perform aerobic respiration, but they do perform glycolysis. Why do all cells need an energy source, and what would happen if glycolysis were blocked in a red blood cell?
Answer
All cells must consume energy to carry out basic functions, such as pumping ions across membranes. A red blood cell would lose its membrane potential if glycolysis were blocked, and it would eventually die.
7.3: 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.
Review Questions
What is removed from pyruvate during its conversion into an acetyl group?
1. oxygen
2. ATP
3. B vitamin
4. carbon dioxide
Answer
D
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.
Answer
B
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
Answer
B
How many NADH molecules are produced on each turn of the citric acid cycle?
1. one
2. two
3. three
4. four
Answer
C
Free Response
What is the primary difference between a circular pathway and a linear pathway?
Answer
In a circular pathway, the final product of the reaction is also the initial reactant. The pathway is self-perpetuating, as long as any of the intermediates of the pathway are supplied. Circular pathways are able to accommodate multiple entry and exit points, thus being particularly well suited for amphibolic pathways. In a linear pathway, one trip through the pathway completes the pathway, and a second trip would be an independent event.
7.4: 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.
Review Questions
What compound receives electrons from NADH?
1. FMN
2. ubiquinone
3. cytochrome c1
4. oxygen
Answer
A
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
Answer
C
Free Response
How do the roles of ubiquinone and cytochrome c differ from the other components of the electron transport chain?
Answer
Q and cytochrome c are transport molecules. Their function does not result directly in ATP synthesis in that they are not pumps. Moreover, Q is the only component of the electron transport chain that is not a protein. Ubiquinone and cytochrome c are small, mobile, electron carriers, whereas the other components of the electron transport chain are large complexes anchored in the inner mitochondrial membrane.
What accounts for the different number of ATP molecules that are formed through cellular respiration?
Answer
Few tissues except muscle produce the maximum possible amount of ATP from nutrients. The intermediates are used to produce needed amino acids, fatty acids, cholesterol, and sugars for nucleic acids. When NADH is transported from the cytoplasm to the mitochondria, an active transport mechanism is used, which decreases the amount of ATP that can be made. The electron transport chain differs in composition between species, so different organisms will make different amounts of ATP using their electron transport chains.
7.5: 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.
Review Questions
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
Answer
A
Free Response
What is the primary difference between fermentation and anaerobic respiration?
Answer
Fermentation uses glycolysis only. Anaerobic respiration uses all three parts of cellular respiration, including the parts in the mitochondria like the citric acid cycle and electron transport; it also uses a different final electron acceptor instead of oxygen gas.
7.6: 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.
Review Questions
A major connection for sugars in glycolysis is ________.
1. glucose-6-phosphate
2. fructose-1,6-bisphosphate
3. dihydroxyacetone phosphate
4. phosphoenolpyruvate
Answer
A
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
Answer
C
Free Response
Would you describe metabolic pathways as inherently wasteful or inherently economical, and why?
Answer
They are very economical. The substrates, intermediates, and products move between pathways and do so in response to finely tuned feedback inhibition loops that keep metabolism balanced overall. Intermediates in one pathway may occur in another, and they can move from one pathway to another fluidly in response to the needs of the cell.
7.7: 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.
Review Questions
The effect of high levels of ADP is to ________.
1. increase the activity of the enzyme
2. decrease the activity of the enzyme
3. have no effect on the activity of the enzyme
4. slow down the pathway
Answer
A
The control of which enzyme exerts the most control on glycolysis?
1. hexokinase
2. phosphofructokinase
3. glucose-6-phosphatase
4. aldolase
Answer
B
Free Response
How does citrate from the citric acid cycle affect glycolysis?
Answer
Citrate can inhibit phosphofructokinase by feedback regulation.
Why might negative feedback mechanisms be more common than positive feedback mechanisms in living cells?
Answer
Negative feedback mechanisms actually control a process; it can turn it off, whereas positive feedback accelerates the process, allowing the cell no control over it. Negative feedback naturally maintains homeostasis, whereas positive feedback drives the system away from equilibrium. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/07%3A_Cellular_Respiration/7.E%3A_Cellular_Respiration_%28Exercises%29.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.
• 8.0: Prelude to Photosynthesis
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).
• 8.1: 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.
• 8.2: 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.
• 8.3: 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.
• 8.E: Photosynthesis (Exercises)
Thumbnail: Plant cells (bounded by purple walls) filled with chloroplasts (green), which are the site of photosynthesis. Image used with permission (CC BY-SA 3.0; Kristian Peters).
08: 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.
8.1: Overview of Photosynthesis
Skills to Develop
• Explain the relevance of photosynthesis to other living things
• Describe the main structures involved in photosynthesis
• Identify the substrates and products of photosynthesis
• Summarize the process 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. 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 almost 200 million years ago.
Plants, algae, and a group of bacteria called cyanobacteria are the only organisms capable of performing photosynthesis (Figure \(1\)). 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; hence, they are referred to as chemoautotrophs.
The importance of photosynthesis is not just that it can capture sunlight’s energy. A lizard sunning itself on a cold day can use the sun’s energy to warm up. Photosynthesis is vital because it evolved as a way to store the energy in solar radiation (the “photo-” part) as high-energy electrons 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 \(2\)), the wolf is at the end of an energy path that went from nuclear reactions on the surface of the sun, to light, to photosynthesis, to vegetation, to deer, and finally to wolf.
Main Structures and Summary of Photosynthesis
Photosynthesis is a multi-step process that requires sunlight, carbon dioxide (which is low in energy), and water as substrates (Figure \(3\)). After the process is complete, it releases oxygen and produces glyceraldehyde-3-phosphate (GA3P), simple carbohydrate molecules (which are high in energy) that can subsequently 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.
The following is the chemical equation for photosynthesis (Figure \(4\)):
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.
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. 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 in the mesophyll. Chloroplasts have a double membrane envelope (composed of an outer membrane and an inner membrane). 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 \(5\), 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).
Art Connection
On a hot, dry day, 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 drive 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, 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\(6\) illustrates the components inside the chloroplast where the light-dependent and light-independent reactions take place.
Link to Learning
Click the link to learn more about photosynthesis.
Everyday Connection: Photosynthesis at the Grocery Store
Major grocery stores in the United States are organized into departments, such as dairy, meats, produce, bread, cereals, and so forth. Each aisle (Figure \(7\)) contains hundreds, if not thousands, of different products for customers to buy and consume.
Although there is a large variety, each item links 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. 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.
Summary
The process of photosynthesis transformed life on Earth. By harnessing energy from the sun, photosynthesis evolved to allow 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, called photoautotrophs, can perform photosynthesis; they require the presence of chlorophyll, a specialized pigment that absorbs certain portions 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 waste product 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.
Art Connections
Figure \(5\): On a hot, dry day, plants close their stomata to conserve water. What impact will this have on photosynthesis?
Answer
Levels of carbon dioxide (a necessary photosynthetic substrate) will immediately fall. As a result, the rate of photosynthesis will be inhibited.
Glossary
chemoautotroph
organism that can build organic molecules using energy derived from inorganic chemicals instead of sunlight
chloroplast
organelle in which photosynthesis takes place
granum
stack of thylakoids located inside a chloroplast
heterotroph
organism that consumes organic substances or other organisms for food
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, though 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
photoautotroph
organism capable of producing its own organic compounds from sunlight
pigment
molecule that is capable of absorbing certain wavelengths of light and reflecting others (which accounts for its color)
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 | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/08%3A_Photosynthesis/8.0%3A_Prelude_to_Photosynthesis.txt |
Skills to Develop
• 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 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 carbohydrate molecules (Figure \(1\)). However, autotrophs only use a few specific components of sunlight.
What Is Light Energy?
The sun emits an enormous amount of electromagnetic radiation (solar energy). Humans can see only a fraction of this energy, which portion is therefore referred 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, the distance between consecutive points of a wave. A single wave is measured from two consecutive points, such as from crest to crest or from trough to trough (Figure \(2\)).
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 \(3\)). The difference between wavelengths relates to the amount of energy carried by them.
Each type of electromagnetic radiation travels at a particular wavelength. The longer the wavelength (or the more stretched out it appears in the diagram), the less energy is carried. Short, tight waves carry the most energy. This may seem illogical, but think of it in terms of a piece of moving a 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 \(3\)) 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, explaining 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 the 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 a populatable, excited (quantum) state. Energy levels higher than those in blue light will physically tear the molecules apart, called bleaching. So retinal pigments can only “see” (absorb) 700 nm to 400 nm light, which 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 \(4\)).
Understanding Pigments
Different kinds of pigments exist, and each has evolved to absorb only certain wavelengths (colors) of visible light. Pigments reflect or transmit the wavelengths they cannot absorb, making them appear in the corresponding color.
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, which is the absorption spectrum. The graph in Figure \(5\) 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.
Many photosynthetic organisms have a mixture of pigments; using them, 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 \(6\)).
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 \(7\). Protein complexes and pigment molecules work together to produce NADPH and ATP.
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 \(7\)). 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 300–400 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.
Art Connection
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, this step in 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 and PSII is re-reduced after every photoact. Splitting one H2O molecule releases two electrons, two hydrogen atoms, and one atom of oxygen. 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. That 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 \(8\)). 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.
Link to Learning
Visit this site to view the process of photosynthesis within a leaf.
Summary
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 to the electron transport chain, which pumps hydrogen ions into the thylakoid interior. This action builds up a high concentration of ions. The ions flow through ATP synthase via 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 power carrier for the light-independent reactions.
Art Connections
Figure \(8\): What is the source of electrons for the chloroplast electron transport chain?
1. Water
2. Oxygen
3. Carbon dioxide
4. NADPH
Answer
A.
Glossary
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
carotenoid
photosynthetic pigment that functions to dispose of excess energy
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
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
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 300–400 chlorophyll a and b molecules as well as other pigments like carotenoids
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
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
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
spectrophotometer
instrument that can measure transmitted light and compute the absorption
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_1e_(OpenStax)/2%3A_The_Cell/08%3A_Photosynthesis/8.2%3A_The_Light-Dependent_Reactions_of_Photosynthesis.txt |
Skills to Develop
• 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 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.
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 reactions, because light is not directly required (Figure \(1\)). 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.
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 \(2\). RuBP has five atoms of carbon, flanked by two phosphates.
Art Connection
Which of the following statements is true?
1. In photosynthesis, oxygen, carbon dioxide, ATP, and NADPH are reactants. GA3P and water are products.
2. In photosynthesis, chlorophyll, water, and carbon dioxide are reactants. GA3P 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. GA3P 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-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 atoms from 3CO2 + 15 atoms from 3RuBP = 18 atoms in 3 atoms 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 reenergized.
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
This link leads to an animation of the Calvin cycle. Click stage 1, stage 2, and then stage 3 to see G3P and ATP regenerate to form RuBP.
Evolution Connection: Photosynthesis
During 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.
Photosynthesis in desert plants has evolved adaptations that conserve water. In the harsh dry heat, every drop of water must be used 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. A more efficient use of CO2 allows plants to adapt to living with less water. Some plants such as cacti (Figure \(3\)) 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. In addition, cacti have evolved the ability to carry out low levels of photosynthesis without opening stomata at all, an extreme mechanism to face extremely dry periods.
The Energy Cycle
Whether the organism is a bacterium, plant, or animal, all living things access energy by breaking down carbohydrate 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.
In nature, there is no such thing as waste. Every single atom of matter and energy is conserved, recycling over and over infinitely. Substances change form or move from one type of molecule to another, but their constituent atoms never disappear (Figure \(4\)).
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.
Summary
Using the energy carriers formed in the first steps of photosynthesis, the light-independent reactions, or the Calvin cycle, take in CO2 from the environment. An enzyme, RuBisCO, catalyzes a reaction with CO2 and another molecule, 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. Plants need both photosynthesis and respiration for their ability to function in both the light and dark, and to be able to interconvert essential metabolites. Therefore, plants contain both chloroplasts and mitochondria.
Art Connections
Figure \(2\): 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.
Answer
D
Glossary
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
reduction
gain of electron(s) by an atom or molecule | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/08%3A_Photosynthesis/8.3%3A_Using_Light_Energy_to_Make_Organic_Molecules.txt |
8.1: 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.
Review Questions
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
Answer
A
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
Answer
C
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
Answer
B
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.
Answer
B
Free Response
What is the overall outcome of the light reactions in photosynthesis?
Answer
The outcome of light reactions in photosynthesis is the conversion of solar energy into chemical energy that the chloroplasts can use to do work (mostly anabolic production of carbohydrates from carbon dioxide).
Why are carnivores, such as lions, dependent on photosynthesis to survive?
Answer
Because lions eat animals that eat plants.
Why are energy carriers thought of as either “full” or “empty”?
Answer
The energy carriers that move from the light-dependent reaction to the light-independent one are “full” because they bring energy. After the energy is released, the “empty” energy carriers return to the light-dependent reaction to obtain more energy. There is not much actual movement involved. Both ATP and NADPH are produced in the stroma where they are also used and reconverted into ADP, Pi, and NADP+.
8.2: 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.
Review Questions
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
Answer
A
How many photons does it take to fully reduce one molecule of NADP+ to NADPH?
1. 1
2. 2
3. 4
4. 8
Answer
B
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
Answer
C
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
Answer
B
Free Response
Describe the pathway of electron transfer from photosystem II to photosystem I in light-dependent reactions.
Answer
A photon of light hits an antenna molecule in photosystem II, and the energy released by it travels through other antenna molecules to the reaction center. The energy causes an electron to leave a molecule of chlorophyll a to a primary electron acceptor protein. The electron travels through the electron transport chain and is accepted by a pigment molecule in photosystem I.
What are the roles of ATP and NADPH in photosynthesis?
Answer
Both of these molecules carry energy; in the case of NADPH, it has reducing power that is used to fuel the process of making carbohydrate molecules in light-independent reactions.
8.3: 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.
Review Questions
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
Answer
D
Which order of molecular conversions is correct for the Calvin cycle?
1. $\text{RuBP} + \text{G3P} \rightarrow \text{3-PGA} \rightarrow \text{sugar}$
2. $\text{RuBisCo} \rightarrow \text{CO}_2 \rightarrow \text{RuBP} \rightarrow \text{G3P}$
3. $\text{RuBP} + \text{CO}_2 \rightarrow \text{[RuBisCo]} \enspace \text{3-PGA} \rightarrow \text{G3P}$
4. $\text{CO}_2 \rightarrow \text{3-PGA} \rightarrow \text{RuBP} \rightarrow \text{G3P}$
Answer
C
Where in eukaryotic cells does the Calvin cycle take place?
1. thylakoid membrane
2. thylakoid lumen
3. chloroplast stroma
4. granum
Answer
C
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
Answer
A
Free Response
Why is the third stage of the Calvin cycle called the regeneration stage?
Answer
Because RuBP, the molecule needed at the start of the cycle, is regenerated from G3P.
Which part of the light-independent reactions would be affected if a cell could not produce the enzyme RuBisCO?
Answer
None of the cycle could take place, because RuBisCO is essential in fixing carbon dioxide. Specifically, RuBisCO catalyzes the reaction between carbon dioxide and RuBP at the start of the cycle.
Why does it take three turns of the Calvin cycle to produce G3P, the initial product of photosynthesis?
Answer
Because G3P has three carbon atoms, and each turn of the cycle takes in one carbon atom in the form of carbon dioxide. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/08%3A_Photosynthesis/8.E%3A_Photosynthesis_%28Exercises%29.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.
• 9.0: Prelude to Cell Communication
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.
• 9.1: 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.
• 9.2: 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.
• 9.3: 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.
• 9.4: 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.
• 9.E: Cell Communication (Exercises)
09: Cell Communication
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 to find out more about your environment. 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 whether a cell is growing by itself in a pond or is one of many cells that form a larger organism. 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 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. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/09%3A_Cell_Communication/9.0%3A_Prelude_to_Cell_Communication.txt |
Skills to Develop
• Describe four types of signaling 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" (like 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 \(1\)). The main difference between the different categories of signaling is the distance that the signal travels through the organism to reach the target cell. Not all cells are affected by the same signals.
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 amount 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 by the presynaptic cell (the cell emitting the signal). The neurotransmitters are transported across the very small distances between nerve cells, which are called chemical synapses (Figure \(2\)). 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.
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 get 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 water-filled channels allow small signaling molecules, called intracellular mediators, to diffuse between the two cells. Small molecules, 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 \(3\)). Transcription is the process of copying the information in a cells 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.
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, in which an extracellular signal is converted into an intercellular 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, a hydrophobic membrane-spanning region, and an intracellular domain inside the cell. The ligand-binding domain is also called the extracellular domain. The size and extent of each of these domains vary widely, depending on the type of receptor.
Evolution Connection: How Viruses Recognize a Host
Unlike living cells, many viruses do not have a plasma membrane or any of the structures necessary to sustain life. Some viruses are simply composed of an inert protein shell containing 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) 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 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 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 proteins structure that allows ions such as sodium, calcium, magnesium, and hydrogen to pass through (Figure \(4\)).
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 \(5\)). 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 resultant shape change activates the G-protein, which releases GDP and picks up 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.
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 \(6\)), 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.
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 \(7\)). 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.
Art Connection
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 \(8\)). 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.
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).
Summary
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.
Art Connections
Figure \(7\): 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.
Answer
C. The downstream cellular response would be inhibited.
Footnotes
1. 1 A. 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.
Glossary
autocrine signal
signal that is sent and received by the same or similar nearby cells
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
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 organisms 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
intercellular signaling
communication between cells
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)
ligand
molecule produced by a signaling cell that binds with a specific receptor, delivering a signal in the process
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
receptor
protein in or on a target cell that bind to ligands
signaling cell
cell that releases signal molecules that allow communication with another cell
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_1e_(OpenStax)/2%3A_The_Cell/09%3A_Cell_Communication/9.1%3A_Signaling_Molecules_and_Cellular_Receptors.txt |
Skills to Develop
• 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 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. 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 or 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 \(1\)). 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.
Art Connection
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?
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.
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 \(2\)). 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.
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 use adenosine-5'-triphosphate (ATP) to remove it. 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, depending 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 \(3\)). 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.
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 \(4\)). 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.
Summary
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).
Art Connections
Figure \(1\): 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?
Answer
ERK would become permanently activated, resulting in cell proliferation, migration, adhesion, and the growth of new blood vessels. Apoptosis would be inhibited.
Glossary
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
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
kinase
enzyme that catalyzes the transfer of a phosphate group from ATP to another molecule
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 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 | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/09%3A_Cell_Communication/9.2%3A_Propagation_of_the_Signal.txt |
Skills to Develop
• 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. ERK is activated in a phosphorylation cascade when epidermal growth factor (EGF) binds the EGF receptor (see Figure 9.2.1). Upon phosphorylation, ERK enters the nucleus and activates a protein kinase that, in turn, regulates protein translation (Figure \(1\)).
The second kind of protein with which PKC can interact 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 attached to 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 glucose. (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: Cancer Biologist
Cancer 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 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 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.
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 \(2\)). 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.
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.
Summary
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.
Glossary
apoptosis
programmed cell death
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
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 | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/09%3A_Cell_Communication/9.3%3A_Response_to_the_Signal.txt |
Skills to Develop
• 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 \(1\)) 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.
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 (Figure \(2\)). 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.
Art Connection
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.
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 \(3\)) 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.
Art Connection
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
Watch geneticist Bonnie Bassler discuss her discovery of quorum sensing in biofilm bacteria in squid.
Evolution Connection: Cellular Communication in Yeasts
The first life on our planet 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 2.5 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.1
Link to Learning
Watch this collection of interview clips with biofilm researchers in “What Are Bacterial Biofilms?”
Summary
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.
Art Connections
Figure \(2\): 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.
Answer
C.
Figure \(3\): What advantage might biofilm production confer on the S. aureus inside the catheter?
Answer
S. aureus produces a biofilm because the higher cell density in the biofilm permits the formation of a dense surface that helps protect the bacteria from antibiotics.
Footnotes
1. 1 G. 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.
Glossary
autoinducer
signaling molecule secreted by bacteria to communicate with other bacteria of its kind and others
mating factor
signaling molecule secreted by yeast cells to communicate to nearby yeast cells that they are available to mate and communicating their mating orientation
quorum sensing
method of cellular communication used by bacteria that informs them of the abundance of similar (or different) bacteria in the environment | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/09%3A_Cell_Communication/9.4%3A_Signaling_in_Single-Celled_Organisms.txt |
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.
9.1: 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.
Review Questions
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.
Answer
B
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
Answer
C
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.
Answer
B
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
Answer
A
Free Response
What is the difference between intracellular signaling and intercellular signaling?
Answer
Intracellular signaling occurs within a cell, and intercellular signaling occurs between cells.
How are the effects of paracrine signaling limited to an area near the signaling cells?
Answer
The secreted ligands are quickly removed by degradation or reabsorption into the cell so that they cannot travel far.
What are the differences between internal receptors and cell-surface receptors?
Answer
Internal receptors are located inside the cell, and their ligands enter the cell to bind the receptor. The complex formed by the internal receptor and the ligand then enters the nucleus and directly affects protein production by binding to the chromosomal DNA and initiating the making of mRNA that codes for proteins. Cell-surface receptors, however, are embedded in the plasma membrane, and their ligands do not enter the cell. Binding of the ligand to the cell-surface receptor initiates a cell signaling cascade and does not directly influence the making of proteins; however, it may involve the activation of intracellular proteins.
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?
Answer
An ion channel receptor opened up a pore in the membrane, which allowed the ionic dye to move into the cell.
9.2: 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.
Review Questions
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.
Answer
D
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.
Answer
C
Free Response
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?
Answer
Different cells produce different proteins, including cell-surface receptors and signaling pathway components. Therefore, they respond to different ligands, and the second messengers activate different pathways. Signal integration can also change the end result of signaling.
What would happen if the intracellular domain of a cell-surface receptor was switched with the domain from another receptor?
Answer
The binding of the ligand to the extracellular domain would activate the pathway normally activated by the receptor donating the intracellular domain.
9.3: 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.
Review Questions
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.
Answer
B
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.
Answer
B
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
Answer
D
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.
Answer
C
Free Response
What is a possible result of a mutation in a kinase that controls a pathway that stimulates cell growth?
Answer
If a kinase is mutated so that it is always activated, it will continuously signal through the pathway and lead to uncontrolled growth and possibly cancer. If a kinase is mutated so that it cannot function, the cell will not respond to ligand binding.
How does the extracellular matrix control the growth of cells?
Answer
Receptors on the cell surface must be in contact with the extracellular matrix in order to receive positive signals that allow the cell to live. If the receptors are not activated by binding, the cell will undergo apoptosis. This ensures that cells are in the correct place in the body and helps to prevent invasive cell growth as occurs in metastasis in cancer.
9.4: 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.
Review Questions
Which type of molecule acts as a signaling molecule in yeasts?
1. steroid
2. autoinducer
3. mating factor
4. second messenger
Answer
C
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
Answer
D
Free Response
What characteristics make yeasts a good model for learning about signaling in humans?
Answer
Yeasts are eukaryotes and have many of the same systems that humans do; however, they are single-celled, so they are easy to grow, grow rapidly, have a short generation time, and are much simpler than humans.
Why is signaling in multicellular organisms more complicated than signaling in single-celled organisms?
Answer
Multicellular organisms must coordinate many different events in different cell types that may be very distant from each other. Single-celled organisms are only concerned with their immediate environment and the presence of other cells in the area. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/09%3A_Cell_Communication/9.E%3A_Cell_Communication_%28Exercises%29.txt |
• 10.0: 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.
• 10.1: 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.
• 10.2: 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.
• 10.3: 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.
• 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 damage
• 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 is not necessary in bacterial cell division.
• 10.E: Cell Reproduction (Exercises)
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]).
10: Cell Reproduction
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. For example, new blood and skin cells are constantly being produced. All multicellular organisms use cell division for growth and the maintenance and repair of cells and tissues. Cell division is tightly regulated, and the occasional failure of regulation can have life-threatening consequences. Single-celled organisms use cell division as their method of reproduction. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/10%3A_Cell_Reproduction/10.0%3A_Introduction.txt |
Skills to Develop
• 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 daughter cells. The mechanisms involved in the cell cycle are highly regulated.
Genomic DNA
Before discussing the steps a cell must undertake to replicate, 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 \(1\)). 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.
In eukaryotes, the genome consists of several double-stranded linear DNA molecules (Figure \(2\)). Each species of eukaryotes has a characteristic number of chromosomes in the nuclei of its cells. Human body cells have 46 chromosomes, while human gametes (sperm or eggs) have 23 chromosomes each. A typical body cell, or somatic cell, contains two matched sets of chromosomes, a configuration known as diploid. 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.
Matched pairs of chromosomes in a diploid organism are 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.
Each copy of a homologous pair of chromosomes originates from a different parent; therefore, the genes themselves are not identical. 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 which two versions of the marker gene 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.
Minor variations of traits, such as blood type, eye color, and handedness, contribute to the natural variation found within a species. However, if the entire DNA sequence from any pair of human homologous chromosomes is compared, the difference is 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 was 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. During some stages of the cell cycle, the long strands of DNA are condensed into compact chromosomes. 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 \(3\)). 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 next level of compaction occurs as the nucleosomes and the linker DNA between them are coiled into a 30-nm chromatin fiber. This coiling further shortens the chromosome so that it is now about 50 times shorter than the extended form. In the third level of packing, 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 \(2\)).
DNA replicates in the S phase of interphase. 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
This animation illustrates the different levels of chromosome packing.
Summary
Prokaryotes have a single circular chromosome composed of double-stranded DNA, whereas eukaryotes have multiple, linear chromosomes composed of chromatin 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. This is the n or haploid state. Genes are segments of DNA that code for a specific protein. 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.
Glossary
cell cycle
ordered sequence of events that a cell passes through between one cell division and the next
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
diploid
cell, nucleus, or organism containing two sets of chromosomes (2n)
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
locus
position of a gene on a chromosome
nucleosome
subunit of chromatin composed of a short length of DNA wrapped around a core of histone proteins | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/10%3A_Cell_Reproduction/10.1%3A_Cell_Division.txt |
Skills to Develop
• Describe the three stages of interphase
• Discuss the behavior of chromosomes during karyokinesis
• 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 division that produces two identical (clone) cells. The cell cycle has two major phases: interphase and the mitotic phase (Figure \(1\)). During interphase, the cell grows and DNA is replicated. During the mitotic phase, the replicated DNA and cytoplasmic contents are separated, and the cell divides.
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 aspect, 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 to the centromeric region. The centrosome is 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. At the center of each animal cell, the centrosomes of animal cells are associated with a pair of rod-like objects, the centrioles, which are at right angles to each other. Centrioles help organize cell division. Centrioles are not present in the centrosomes of other eukaryotic species, 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. 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. The second portion of the mitotic phase, called cytokinesis, is the physical separation of the cytoplasmic components into the two daughter cells.
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 \(2\)). Karyokinesis is also called mitosis.
Exercise \(1\)
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.
Answer
D. 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.
During prophase, the “first phase,” the nuclear envelope starts to dissociate into small vesicles, and the membranous organelles (such as the Golgi complex or Golgi apparatus, and endoplasmic reticulum), fragment and disperse toward the periphery of the cell. The nucleolus disappears (disperses). 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 become visible under a light microscope.
During prometaphase, the “first change phase,” many processes that were begun in prophase continue to advance. The remnants of the nuclear envelope fragment. The mitotic spindle continues to develop as more microtubules assemble and stretch across the length of the former nuclear area. Chromosomes become more condensed and discrete. Each sister chromatid develops a protein structure called a kinetochore in the centromeric region (Figure \(3\)). The proteins of the kinetochore attract and bind 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.
During metaphase, the “change phase,” all the chromosomes are aligned in a plane called the metaphase plate, or the equatorial plane, 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.
During anaphase, the “upward phase,” the cohesin proteins degrade, and the sister chromatids separate at the centromere. Each chromatid, now called a 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.
During telophase, the “distance phase,” the chromosomes reach the opposite poles and begin to decondense (unravel), relaxing into a 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
Cytokinesis, or “cell motion,” is 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. 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 cells such as animal cells that lack cell walls, cytokinesis follows the onset of 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, or “crack,” is called the cleavage furrow. The furrow deepens as the actin ring contracts, and eventually the membrane is cleaved in two (Figure \(4\)).
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 \(4\)).
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. 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 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: 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 blastula cross-sections will show cells arrested in various stages of the cell cycle. 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 scanning objective of your microscope. Notice that the section is a circle composed of dozens of closely packed individual cells.
3. Switch to the low-power objective and refocus. With this objective, individual cells are visible.
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 \(5\)). 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.
5. Practice identifying the various stages of the cell cycle, using the drawings of the stages as a guide (Figure \(2\)).
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.
7. Keep a tally of your observations and stop when you reach 100 cells identified.
8. 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 the Table \(1\) in which you record your observations.
Table \(1\): Results of cell stage identification.
Phase or Stage Individual Totals Group Totals Percent
Interphase
Prophase
Metaphase
Anaphase
Telophase
Cytokinesis
Totals 100 100 100 percent
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 the Table \(2\) to illustrate your data.
Table \(2\): Estimate of cell stage length.
Phase or Stage Percent (as Decimal) Time in Hours
Interphase
Prophase
Metaphase
Anaphase
Telophase
Cytokinesis
Draw a conclusion: Did your results support your estimated times? Were any of the outcomes unexpected? If so, discuss which events in that stage might contribute to the calculated time.
Summary
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. 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 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).
Glossary
anaphase
stage of mitosis during which sister chromatids are separated from each other
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
centriole
rod-like structure constructed of microtubules at the center of each animal cell centrosome
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
cytokinesis
division of the cytoplasm following mitosis that forms two daughter cells.
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
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
metaphase plate
equatorial plane midway between the two poles of a cell where the chromosomes align during metaphase
metaphase
stage of mitosis during which chromosomes are aligned at the metaphase plate
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
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
quiescent
refers to a cell that is performing normal cell functions and has not initiated preparations for cell division
S phase
second, or synthesis, stage of interphase during which DNA replication occurs
telophase
stage of mitosis during which chromosomes arrive at opposite poles, decondense, and are surrounded by a new nuclear envelope | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/10%3A_Cell_Reproduction/10.2%3A_The_Cell_Cycle.txt |
Skills to Develop
• Understand how the cell cycle is controlled by mechanisms 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 fast-dividing mammalian cells are grown in culture (outside the body under optimal growing conditions), the length of the 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. In early embryos of fruit flies, the cell cycle is completed in about eight minutes. The timing of events in the cell cycle 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 a nearby cell or as sweeping as the release of growth-promoting hormones, such as human growth hormone (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. Another factor that can initiate cell division is the size of the cell; as a cell grows, it becomes 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 \(1\)).
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
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. Conversely, 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 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 \(2\)). 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.
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. Like all kinases, Cdks are enzymes (kinases) that 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 \(3\)). 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.
Since the cyclic fluctuations of cyclin levels are 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. Negative regulators halt 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. The 53 and 21 designations refer to the functional molecular masses of the proteins (p) in kilodaltons. 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 (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 recruits 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 exerts its regulatory influence on other positive regulator proteins. Chiefly, Rb monitors cell size. In the active, dephosphorylated state, Rb binds to proteins called transcription factors, most commonly, E2F (Figure \(4\)). 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.”
Exercise \(1\)
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?
Answer
Rb and other negative regulatory proteins control cell division and therefore prevent the formation of tumors. Mutations that prevent these proteins from carrying out their function can result in cancer.
Summary
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. Negative regulator molecules monitor cellular conditions and can halt the cycle until specific requirements are met.
Glossary
cell cycle checkpoint
mechanism that monitors the preparedness of a eukaryotic cell to advance through the various cell cycle stages
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
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
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
retinoblastoma protein (Rb)
regulatory molecule that exhibits negative effects on the cell cycle by interacting with a transcription factor (E2F) | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/10%3A_Cell_Reproduction/10.3%3A_Control_of_the_Cell_Cycle.txt |
Skills to Develop
• 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.
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 will probably 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 one-half 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 \(1\)). 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.
Exercise \(1\)
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
Answer
D. 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
Go to this website to watch an animation of how cancer results from errors in the cell cycle.
Summary
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).
Glossary
oncogene
mutated version of a normal gene involved in the positive regulation of the cell cycle
proto-oncogene
normal gene that when mutated becomes an oncogene
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_1e_(OpenStax)/2%3A_The_Cell/10%3A_Cell_Reproduction/10.4%3A_Cancer_and_the_Cell_Cycle.txt |
Skills to Develop
• Describe the process of binary fission in prokaryotes
• Explain how FtsZ and tubulin proteins are examples of homology
Prokaryotes, such as bacteria, propagate 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 machinery to sustain life. In 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 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, called binary fission, is a less complicated and much more rapid process than cell division in eukaryotes. The single, circular DNA chromosome of bacteria is not enclosed in a nucleus, but instead occupies a specific location, the nucleoid, within the cell (Figure \(1\)). 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 \(1\)). 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 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 nucleoids, extending gradually from the periphery toward the center of the cell. When the new cell walls are in place, the daughter cells separate.
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 that make up the mitotic spindle fibers that are necessary for eukaryotes. 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 homologous structures derived from common evolutionary origins. In this example, FtsZ is the ancestor protein to tubulin (a modern 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 \(1\): Cell Division Apparatus among Various Organisms
Structure of genetic material Division of nuclear material Separation of daughter cells
Prokaryotes There 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 protists Linear 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 protists Linear chromosomes 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 cells Linear 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.
Summary
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. 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.
Glossary
binary fission
prokaryotic cell division process
FtsZ
tubulin-like protein component of the prokaryotic cytoskeleton that is important in prokaryotic cytokinesis (name origin: Filamenting temperature-sensitive mutant Z)
origin
(also, ORI) region of the prokaryotic chromosome where replication begins (origin of replication)
septum
structure formed in a bacterial cell as a precursor to the separation of the cell into two daughter cells | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/10%3A_Cell_Reproduction/10.5%3A_Prokaryotic_Cell_Division.txt |
10.1: 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.
Review Questions
A diploid cell has_______ the number of chromosomes as a haploid cell.
1. one-fourth
2. half
3. twice
4. four times
Answer
C
An organism’s traits are determined by the specific combination of inherited _____.
1. cells.
2. genes.
3. proteins.
4. chromatids.
Answer
B
The first level of DNA organization in a eukaryotic cell is maintained by which molecule?
1. cohesin
2. condensin
3. chromatin
4. histone
Answer
D
Identical copies of chromatin held together by cohesin at the centromere are called _____.
1. histones.
2. nucleosomes.
3. chromatin.
4. sister chromatids.
Answer
D
Free Response
Compare and contrast a human somatic cell to a human gamete.
Answer
Human somatic cells have 46 chromosomes: 22 pairs and 2 sex chromosomes that may or may not form a pair. This is the 2n or diploid condition. Human gametes have 23 chromosomes, one each of 23 unique chromosomes, one of which is a sex chromosome. This is the n or haploid condition.
What is the relationship between a genome, chromosomes, and genes?
Answer
The genome consists of the sum total of an organism’s chromosomes. Each chromosome contains hundreds and sometimes thousands of genes, segments of DNA that code for a polypeptide or RNA, and a large amount of DNA with no known function.
Eukaryotic chromosomes are thousands of times longer than a typical cell. Explain how chromosomes can fit inside a eukaryotic nucleus.
Answer
The DNA double helix is wrapped around histone proteins to form structures called nucleosomes. Nucleosomes and the linker DNA in between them are coiled into a 30-nm fiber. During cell division, chromatin is further condensed by packing proteins.
10.2: 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.
Review Questions
Chromosomes are duplicated during what stage of the cell cycle?
1. G1 phase
2. S phase
3. prophase
4. prometaphase
Answer
B
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
Answer
D
The mitotic spindles arise from which cell structure?
1. centromere
2. centrosome
3. kinetochore
4. cleavage furrow
Answer
B
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
Answer
B
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
Answer
D
Separation of the sister chromatids is a characteristic of which stage of mitosis?
1. prometaphase
2. metaphase
3. anaphase
4. telophase
Answer
C
The chromosomes become visible under a light microscope during which stage of mitosis?
1. prophase
2. prometaphase
3. metaphase
4. anaphase
Answer
A
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
Answer
A
Free Response
Briefly describe the events that occur in each phase of interphase.
Answer
During G1, the cell increases in size, the genomic DNA is assessed for damage, and the cell stockpiles energy reserves and the components to synthesize DNA. During the S phase, the chromosomes, the centrosomes, and the centrioles (animal cells) duplicate. During the G2 phase, the cell recovers from the S phase, continues to grow, duplicates some organelles, and dismantles other organelles.
Chemotherapy drugs such as vincristine and colchicine 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?
Answer
The mitotic spindle is formed of microtubules. Microtubules are polymers of the protein tubulin; therefore, it is the mitotic spindle that is disrupted by these drugs. Without a functional mitotic spindle, the chromosomes will not be sorted or separated during mitosis. The cell will arrest in mitosis and die.
Describe the similarities and differences between the cytokinesis mechanisms found in animal cells versus those in plant cells.
Answer
There are very few similarities between animal cell and plant cell cytokinesis. In animal cells, a ring of actin fibers is formed around the periphery of the cell at the former metaphase plate (cleavage furrow). The actin ring contracts inward, pulling the plasma membrane toward the center of the cell until the cell is pinched in two. In plant cells, a new cell wall must be formed between the daughter cells. Due to the rigid cell walls of the parent cell, contraction of the middle of the cell is not possible. Instead, a phragmoplast first forms. Subsequently, a cell plate is formed in the center of the cell at the former metaphase plate. The cell plate is formed from Golgi vesicles that contain enzymes, proteins, and glucose. The vesicles fuse and the enzymes build a new cell wall from the proteins and glucose. The cell plate grows toward and eventually fuses with the cell wall of the parent cell.
List some reasons why a cell that has just completed cytokinesis might enter the G0 phase instead of the G1 phase.
Answer
Many cells temporarily enter G0 until they reach maturity. Some cells are only triggered to enter G1 when the organism needs to increase that particular cell type. Some cells only reproduce following an injury to the tissue. Some cells never divide once they reach maturity.
What cell cycle events will be affected in a cell that produces mutated (non-functional) cohesin protein?
Answer
If cohesin is not functional, chromosomes are not packaged after DNA replication in the S phase of interphase. It is likely that the proteins of the centromeric region, such as the kinetochore, would not form. Even if the mitotic spindle fibers could attach to the chromatids without packing, the chromosomes would not be sorted or separated during mitosis.
10.3: 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.
Review Questions
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
Answer
A
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
Answer
C
If the M checkpoint is not cleared, what stage of mitosis will be blocked?
1. prophase
2. prometaphase
3. metaphase
4. anaphase
Answer
D
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)
Answer
D
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
Answer
C
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)
Answer
A
Free Response
Describe the general conditions that must be met at each of the three main cell cycle checkpoints.
Answer
The G1 checkpoint monitors adequate cell growth, the state of the genomic DNA, adequate stores of energy, and materials for S phase. At the G2 checkpoint, DNA is checked to ensure that all chromosomes were duplicated and that there are no mistakes in newly synthesized DNA. Additionally, cell size and energy reserves are evaluated. The M checkpoint confirms the correct attachment of the mitotic spindle fibers to the kinetochores.
Explain the roles of the positive cell cycle regulators compared to the negative regulators.
Answer
Positive cell regulators such as cyclin and Cdk perform tasks that advance the cell cycle to the next stage. Negative regulators such as Rb, p53, and p21 block the progression of the cell cycle until certain events have occurred.
What steps are necessary for Cdk to become fully active?
Answer
Cdk must bind to a cyclin, and it must be phosphorylated in the correct position to become fully active.
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?
Answer
Rb is active when it is dephosphorylated. In this state, Rb binds to E2F, which is a transcription factor required for the transcription and eventual translation of molecules required for the G1/S transition. E2F cannot transcribe certain genes when it is bound to Rb. As the cell increases in size, Rb becomes phosphorylated, inactivated, and releases E2F. E2F can then promote the transcription of the genes it controls, and the transition proteins will be produced.
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 damage
Review Questions
___________ 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
Answer
C
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.
Answer
C
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.
Answer
D
Which molecule is a Cdk inhibitor that is controlled by p53?
1. cyclin
2. anti-kinase
3. Rb
4. p21
Answer
D
Free Response
Outline the steps that lead to a cell becoming cancerous.
Answer
If one of the genes that produces regulator proteins becomes mutated, it produces a malformed, possibly non-functional, cell cycle regulator, increasing the chance that more mutations will be left unrepaired in the cell. Each subsequent generation of cells sustains more damage. The cell cycle can speed up as a result of the loss of functional checkpoint proteins. The cells can lose the ability to self-destruct and eventually become “immortalized.”
Explain the difference between a proto-oncogene and a tumor suppressor gene.
Answer
A proto-oncogene is a segment of DNA that codes for one of the positive cell cycle regulators. If that gene becomes mutated so that it produces a hyperactivated protein product, it is considered an oncogene. A tumor suppressor gene is a segment of DNA that codes for one of the negative cell cycle regulators. If that gene becomes mutated so that the protein product becomes less active, the cell cycle will run unchecked. A single oncogene can initiate abnormal cell divisions; however, tumor suppressors lose their effectiveness only when both copies of the gene are damaged.
List the regulatory mechanisms that might be lost in a cell producing faulty p53.
Answer
Regulatory mechanisms that might be lost include monitoring of the quality of the genomic DNA, recruiting of repair enzymes, and the triggering of apoptosis.
p53 can trigger apoptosis if certain cell cycle events fail. How does this regulatory outcome benefit a multicellular organism?
Answer
If a cell has damaged DNA, the likelihood of producing faulty proteins is higher. The daughter cells of such a damaged parent cell would also produce faulty proteins that might eventually become cancerous. If p53 recognizes this damage and triggers the cell to self-destruct, the damaged DNA is degraded and recycled. No further harm comes to the organism. Another healthy cell is triggered to divide instead.
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 is not necessary in bacterial cell division.
Review Questions
Which eukaryotic cell cycle event is missing in binary fission?
1. cell growth
2. DNA duplication
3. karyokinesis
4. cytokinesis
Answer
C
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
Answer
B
Free Response
Name the common components of eukaryotic cell division and binary fission.
Answer
The common components of eukaryotic cell division and binary fission are DNA duplication, segregation of duplicated chromosomes, and division of the cytoplasmic contents.
Describe how the duplicated bacterial chromosomes are distributed into new daughter cells without the direction of the mitotic spindle.
Answer
As the chromosome is being duplicated, each origin moves away from the starting point of replication. The chromosomes are attached to the cell membrane via proteins; the growth of the membrane as the cell elongates aids in their movement. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/10%3A_Cell_Reproduction/10.E%3A_Cell_Reproduction_%28Exercises%29.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.
• 5.0: Prelude to Structure and Function of Plasma Membranes
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.
• 5.1: 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.
• 5.2: 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.
• 5.3: 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.
• 5.4: 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.
• 5.E: Structure and Function of Plasma Membranes (Exercises)
Thumbnail: The cell membrane. (Public Domain; LadyofHats via Wikimedia Commons).
5: 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. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/5%3A_Structure_and_Function_of_Plasma_Membranes/5.0%3A_Prelude_to_Structure_and_Function_of_Plasma_Membranes.txt |
Skills to Develop
• Understand the fluid mosaic model of cell membranes
• Describe the functions of phospholipids, proteins, and carbohydrates 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 \(1\) 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 blood cells and white blood cells, to change shape as they pass through narrow capillaries. These are the more obvious functions of a plasma membrane. In addition, the surface of the plasma membrane 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 “self” versus “non-self” distinction of the immune response.
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. Occasionally, receptors are hijacked by viruses (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 process of signal transduction to malfunction with disastrous consequences.
Fluid Mosaic Model
The existence of the plasma membrane was identified in the 1890s, and its chemical components were identified in 1915. The principal components identified at that time were lipids and proteins. The first widely accepted model of the plasma membrane’s structure was proposed in 1935 by Hugh Davson and James Danielli; it was based on the “railroad track” appearance of the plasma membrane in early electron micrographs. They theorized that the structure of the plasma membrane resembles a sandwich, with protein being analogous to the bread, and lipids being analogous to the filling. In the 1950s, advances in microscopy, notably transmission electron microscopy (TEM), allowed researchers to see that the core of the plasma membrane consisted of a double, rather than a single, layer. A new model that better explains both the microscopic observations and the function of that plasma membrane was proposed by S.J. Singer and Garth L. Nicolson in 1972.
The explanation proposed by Singer and Nicolson is called the fluid mosaic model. The model has evolved somewhat over time, but it still best accounts for the structure and functions of the plasma membrane as we now understand them. The fluid mosaic model describes the structure of the plasma membrane 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 \(1\)).
The principal components of a plasma membrane are lipids (phospholipids and cholesterol), proteins, and carbohydrates attached to some of the lipids and some of the proteins. A phospholipid is a molecule consisting of glycerol, two fatty acids, and a phosphate-linked head group. Cholesterol, another lipid composed of four fused carbon rings, is found alongside the phospholipids in the core of the membrane. The proportions of proteins, lipids, and carbohydrates 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 of the composition by mass, with the remaining 10 percent of the composition by mass being carbohydrates. However, the concentration of proteins and lipids varies with different cell membranes. For example, myelin, an outgrowth of the membrane of specialized cells that insulates the axons of the peripheral nerves, 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 exterior surface of the plasma membrane and are attached to proteins, forming glycoproteins, or attached to lipids, forming glycolipids.
Phospholipids
The main fabric of the membrane is composed of 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 \(1\)) 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 hydrophilic regions of the phospholipids tend to form hydrogen bonds with water and other polar molecules on both the exterior and interior of the cell. Thus, the membrane surfaces that face the interior and exterior of the cell are hydrophilic. In contrast, the interior of the cell membrane 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 of the cell.
A phospholipid molecule (Figure \(2\)) 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 an area described as its head (the phosphate-containing group), which has a polar character or negative charge, and an area called the tail (the fatty acids), which has no charge. The head can form hydrogen bonds, but the tail cannot. A molecule with this arrangement of a positively or negatively charged area and an uncharged, or non-polar, area is referred to as amphiphilic or “dual-loving.”
This characteristic is vital to the structure of a plasma membrane because, in water, phospholipids tend to become arranged with their hydrophobic tails facing each other and their hydrophilic heads facing out. In this way, they form a lipid bilayer—a barrier composed of a double layer of phospholipids that separates the water and other materials on one side of the barrier from the water and other materials on the other side. In fact, phospholipids heated in an aqueous solution tend to spontaneously form small spheres or droplets (called micelles or liposomes), with their hydrophilic heads forming the exterior and their hydrophobic tails on the inside (Figure \(3\)).
Proteins
Proteins make up the second major component of plasma membranes. Integral proteins (some specialized types are called integrins) are, as their name suggests, integrated completely into the membrane structure, and their hydrophobic membrane-spanning regions interact with the hydrophobic region of the the phospholipid bilayer (Figure \(1\)). 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 of the membrane to the other, and are exposed on either side. Some complex proteins are composed of up to 12 segments of a single protein, which are extensively folded and embedded in the membrane (Figure \(4\)). This type of protein has a hydrophilic region or regions, and one or several mildly hydrophobic regions. This arrangement of regions of the protein tends to orient the protein alongside the phospholipids, with the hydrophobic region of the protein adjacent to the tails of the phospholipids and the hydrophilic region or regions of the protein protruding from the membrane and in contact with the cytosol or extracellular fluid.
Peripheral proteins are found on the exterior and interior surfaces of membranes, attached either to integral proteins or to phospholipids. Peripheral proteins, along with integral proteins, may serve as enzymes, as structural attachments for the fibers of the cytoskeleton, or as part of the cell’s recognition sites. These are sometimes referred to as “cell-specific” proteins. The body recognizes its own proteins and attacks foreign proteins associated with invasive pathogens.
Carbohydrates
Carbohydrates are the third major component of plasma membranes. They are always found on the exterior surface of cells and are bound either to proteins (forming glycoproteins) or to lipids (forming glycolipids) (Figure \(1\)). 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 the cell to be recognized, much the way that the facial features unique to each person allow him or her to be recognized. This recognition function is very important to cells, as it allows the immune system to differentiate between body cells (called “self”) and foreign cells or tissues (called “non-self”). Similar types of glycoproteins and glycolipids are found on the surfaces of viruses and may change frequently, preventing immune cells from recognizing and attacking them.
These carbohydrates on the exterior surface of the cell—the carbohydrate components of both glycoproteins and glycolipids—are collectively referred to as the glycocalyx (meaning “sugar coating”). The glycocalyx is highly hydrophilic and attracts large amounts of water to the surface of the cell. This aids in the interaction of the cell with its watery environment and in the cell’s ability to obtain substances dissolved in the water. As discussed above, the glycocalyx is also important for cell identification, self/non-self determination, and embryonic development, and is used in cell-cell attachments to form tissues.
Evolution Connection: How Viruses Infect Specific Organs
Glycoprotein and glycolipid patterns on the surfaces of cells 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 \(5\)). 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 activity of the virus. Unfortunately, these recognition sites on HIV change at a rapid rate because of mutations, making the production of 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 are distinguished by differences in these recognition sites. 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 new variations of the surface patterns. In the case of HIV, the problem is compounded by the fact that the virus specifically infects and destroys cells involved in the immune response, further incapacitating the host.
Membrane Fluidity
The mosaic characteristic of the membrane, described in the fluid mosaic model, 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 the needle is extracted.
The mosaic characteristics of the membrane 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 string of carbons of approximately 30 degrees (Figure \(2\)).
Thus, if saturated fatty acids, with their straight tails, are compressed by decreasing temperatures, 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 relative fluidity of the membrane is particularly important in a cold environment. A cold environment tends to compress membranes composed 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 the lowering of the temperature.
Link to Learning
Visit this site to see animations of the fluidity and mosaic quality of membranes.
Animals have an additional membrane constituent that assists in maintaining fluidity. Cholesterol, which lies alongside the phospholipids in the membrane, tends to dampen the effects of temperature 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 range of temperature 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.
Table \(1\): The Components and Functions of the Plasma Membrane.
Component Location
Phospholipid Main fabric of the membrane
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 inner or outer surface of the phospholipid bilayer; not embedded within the phospholipids
Carbohydrates (components of glycoproteins and glycolipids) Generally attached to proteins on the outside membrane layer
Career Connection: Immunologist
The variations in peripheral proteins and carbohydrates that affect a cell’s recognition sites are of prime interest in immunology. These changes are taken into consideration in vaccine development. Many infectious diseases, such as smallpox, polio, diphtheria, and tetanus, were conquered by the use of vaccines.
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 his or her 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 are called in to 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, the importance of having a healthy immune system in preventing cancer was not at all understood.
To work as an immunologist, a PhD or MD is required. In addition, immunologists undertake at least 2–3 years of training in an accredited program and must pass an examination given by the American Board of Allergy and Immunology. Immunologists must possess knowledge of the functions of the human body as they relate to issues beyond immunization, and knowledge of pharmacology and medical technology, such as medications, therapies, test materials, and surgical procedures.
Summary
The modern understanding of the plasma membrane is referred to as the fluid mosaic model. The plasma membrane is composed of a bilayer of phospholipids, with their hydrophobic, fatty acid tails in contact with each other. The landscape of the membrane is studded with proteins, some of 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 outward-facing surface of the membrane, forming complexes that function to identify the cell to other cells. The fluid nature of the membrane is due to temperature, the configuration of the fatty acid tails (some kinked by double bonds), the presence of cholesterol 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 borders of cells, but rather than being a static bag, they are dynamic and constantly in flux.
Glossary
amphiphilic
molecule possessing a polar or charged area and a nonpolar or uncharged area capable of interacting with both hydrophilic and hydrophobic environments
fluid mosaic model
describes the structure of the plasma membrane 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”
integral protein
protein integrated into the membrane structure that interacts extensively with the hydrocarbon chains of membrane lipids and often spans the membrane; these proteins can be removed only by the disruption of the membrane by detergents
peripheral protein
protein found at the surface of a plasma membrane either on its exterior or interior side; these proteins can be removed (washed off of the membrane) by a high-salt wash | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/5%3A_Structure_and_Function_of_Plasma_Membranes/5.1%3A_Components_and_Structure.txt |
Skills to Develop
• Explain why and how passive transport occurs
• Understand the processes of osmosis and diffusion
• Define tonicity and describe 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—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; 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. All cells spend the majority of their energy to maintain an imbalance of sodium and potassium ions between the interior and exterior of the cell.
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 range of concentrations of a single substance is said to have a concentration gradient.
Selective Permeability
Plasma membranes are asymmetric: the interior of the membrane is not identical to the exterior of the membrane. In fact, there is a considerable difference between the array of phospholipids and proteins between the two leaflets that form a membrane. On the interior of the membrane, some proteins serve to anchor the membrane to fibers of the cytoskeleton. There are peripheral proteins on the exterior of the membrane that bind elements of the extracellular matrix. Carbohydrates, attached to lipids or proteins, are also found on the exterior surface of the plasma membrane. These carbohydrate complexes help the cell bind substances that the cell needs in the extracellular fluid. This adds considerably to the selective nature of plasma membranes (Figure \(1\)).
Recall that plasma membranes are amphiphilic: They have hydrophilic and hydrophobic regions. This characteristic helps the movement of some materials through the membrane and hinders the movement of others. Lipid-soluble material with a low molecular weight can easily slip through the hydrophobic lipid core of the membrane. 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 are readily transported into the body’s tissues and organs. Molecules of oxygen and carbon dioxide have no charge and so pass through membranes by simple diffusion.
Polar substances present problems for the membrane. While some polar molecules connect easily with the outside of a cell, they cannot readily pass through the lipid core of the plasma membrane. Additionally, while small ions could easily slip through the spaces in the mosaic of the membrane, 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 help with transport across plasma membranes, achieved by various transmembrane proteins (channels).
Diffusion
Diffusion is a passive process of transport. A single substance tends to move from an area of high concentration to an area of low concentration 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 edges of the room. The ammonia vapor will diffuse, or spread away, from the bottle, and gradually, more and 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 \(2\)). Diffusion expends no energy. On the contrary, concentration gradients are a form of potential energy, dissipated as the gradient is eliminated.
Each separate substance in a medium, such as the extracellular fluid, has its own concentration gradient, independent of the concentration gradients of other materials. In addition, each substance will diffuse according to that gradient. Within a system, there will be different rates of diffusion of the different 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 the diffusion of molecules through whatever medium in which they are localized. A substance will tend to move into any space available to it until it is evenly distributed throughout it. 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. This lack of a concentration gradient in which there is no net movement of a substance is known as dynamic equilibrium. While diffusion will go forward in the presence of a concentration gradient of a substance, several factors affect the rate of diffusion.
• 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 rate of diffusion becomes.
• 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 movement of the molecules, increasing the rate of diffusion. Lower temperatures decrease the energy of the molecules, thus decreasing the rate of diffusion.
• Solvent density: As the density of a solvent increases, the rate of diffusion decreases. The molecules slow down because they have a more difficult time getting 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 rate of diffusion 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 discussed earlier, nonpolar or lipid-soluble materials pass through plasma membranes more easily than polar materials, allowing a faster rate of diffusion.
• Surface area and thickness of the plasma membrane: Increased surface area increases the rate of diffusion, whereas a thicker membrane reduces it.
• Distance travelled: The greater the distance that a substance must travel, the slower the rate of diffusion. This places an upper limitation on cell size. A large, spherical cell will die because nutrients or waste cannot reach or leave the center of the cell, 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 the rate of diffusion is enhanced by pressure, 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 rate of diffusion 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 is “squeezed through” by the abnormally high pressure.
Facilitated transport
In facilitated transport, also called 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 ions are polar molecules that are repelled by the hydrophobic parts of the cell membrane. Facilitated transport proteins shield these materials from the repulsive force of the membrane, allowing them to diffuse into the cell.
The material being transported is first attached to protein or glycoprotein receptors on the exterior surface of the plasma membrane. This allows the material that is needed by the cell to be removed from the extracellular fluid. The substances are then passed 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 collectively referred to as 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 substance that is being transported. Channel proteins have hydrophilic domains exposed to the intracellular and extracellular fluids; they additionally have a hydrophilic channel through their core that provides a hydrated opening through the membrane layers (Figure \(3\)). Passage through the channel allows polar compounds to avoid the nonpolar central layer of the plasma membrane 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.
Channel proteins are either open at all times or they are “gated,” which controls the opening of the channel. The attachment of a particular ion to the channel protein 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 be opened to allow passage. An example of this occurs in the kidney, where both forms of channels are found in different parts of the renal tubules. Cells involved in the transmission of electrical impulses, such as nerve and muscle cells, have gated channels for sodium, potassium, and calcium in their membranes. Opening and closing of these channels changes the relative concentrations on opposing sides of the membrane of these ions, resulting in the facilitation of 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, in doing so, triggers a change of its own shape, moving the bound molecule from the outside of the cell to its interior (Figure \(4\)); 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 overall selectivity of the plasma membrane. The exact mechanism for the change of shape is poorly understood. 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 of the 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 rate of transport.
An example of this process occurs in the kidney. Glucose, water, salts, ions, and amino acids needed by the body are filtered in one part of the kidney. This filtrate, which includes glucose, is then reabsorbed 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 it is excreted from the body in the urine. In a diabetic individual, this is described as “spilling glucose into the urine.” A different group of carrier proteins called 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 do 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 water through a semipermeable membrane according to the concentration gradient of water across the membrane, which is inversely proportional to the concentration of solutes. While diffusion transports material across membranes and within cells, osmosis transports only water across a membrane and the membrane limits the diffusion of solutes 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 to one of low 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 \(5\)). On both sides of the membrane the water level is the same, but there are different concentrations of a dissolved substance, or solute, that cannot cross the membrane (otherwise the concentrations on each side would be balanced by the solute crossing the membrane). If the volume of the solution on both sides of the membrane is the same, but the concentrations of solute are different, then there are different amounts of water, the solvent, on either side of the membrane.
To illustrate this, imagine two full glasses of water. 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 amount of sugar 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 mixture of solutes 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 concentration gradient of water goes to zero or until the hydrostatic pressure of the water balances the osmotic pressure. Osmosis proceeds constantly in living systems.
Tonicity
Tonicity describes how an extracellular solution can change the volume of a cell by affecting osmosis. A solution's tonicity often directly correlates with the osmolarity of the solution. Osmolarity describes the total solute concentration of the solution. 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 solutions of two different osmolarities are separated by a membrane permeable to water, though not to the solute, water will move from the side of the membrane 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
Three terms—hypotonic, isotonic, and hypertonic—are used to relate the osmolarity of a cell to the osmolarity of the extracellular fluid 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 concentration of solutes, or a lower osmolarity, than the cell cytoplasm.) It also means that the extracellular fluid has a higher concentration of water 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 concentration of water, water will leave the cell.
Isotonic Solutions
In an isotonic solution, the extracellular fluid has the same osmolarity as the cell. If the osmolarity of the cell 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 \(6\)).
Art Connection
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
For a video illustrating the process of diffusion 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 concentrations of solute and solvent are equal on both sides of the membrane. There is no net water movement; therefore, there is no change in the size of the cell. 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 composing 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 amounts of water 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 death of the cell.
Various living things have ways of controlling the effects of osmosis—a mechanism called 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 limit of the cell wall, so the cell will not lyse. In fact, the cytoplasm in plants is always slightly hypertonic to the cellular environment, and water will always enter a cell if water is available. This inflow of water produces turgor pressure, which stiffens the cell walls of the plant (Figure \(8\)). In nonwoody plants, turgor pressure supports the plant. Conversly, if the plant is not watered, 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. This is called plasmolysis. Plants lose turgor pressure in this condition and wilt (Figure \(9\)).
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.
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 amount of water in the body. Osmoreceptors are specialized cells in the brain that monitor the concentration of solutes in the blood. If the levels of solutes increase beyond a certain range, a hormone is released that retards water loss through the kidney and dilutes the blood to safer levels. Animals also have high concentrations of albumin, which is produced by the liver, 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.
Summary
The passive forms of transport, diffusion and osmosis, move materials of small molecular weight across membranes. Substances diffuse from areas of high concentration to areas of lower concentration, and this process continues until the substance is evenly distributed in a system. In solutions containing more than one substance, each type of molecule diffuses according to its own concentration gradient, independent of the diffusion of other substances. Many factors can affect the rate of diffusion, including concentration gradient, size of the particles that are diffusing, temperature of the system, and so on.
In living systems, diffusion of substances into and out of cells is mediated by the plasma membrane. Some materials diffuse readily through the membrane, but others are hindered, and their passage is made possible by 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, diffusion of some substances would be slow or difficult without membrane proteins that facilitate transport.
Art Connections
Figure \(6\): 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?
Answer
No, it must have been hypotonic as a hypotonic solution would cause water to enter the cells, thereby making them burst.
Glossary
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
channel protein
membrane protein that allows a substance to pass through its hollow core across the plasma membrane
concentration gradient
area of high concentration adjacent to an area of low concentration
diffusion
passive process of transport of low-molecular weight material according to its concentration gradient
facilitated transport
process by which material moves down a concentration gradient (from high to low concentration) using integral membrane proteins
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
isotonic
situation in which the extracellular fluid has the same osmolarity as the fluid inside the cell, resulting in no net movement of water into or out of the cell
osmolarity
total amount of substances dissolved in a specific amount of solution
osmosis
transport of water through a semipermeable membrane according to the concentration gradient of water 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
plasmolysis
detaching of the cell membrane from the cell wall and constriction of the cell membrane when a plant cell is in a hypertonic solution
selectively permeable
characteristic of a membrane that allows some substances through but not others
solute
substance dissolved in a liquid to form a solution
tonicity
amount of solute in a solution
transport protein
membrane protein that facilitates passage of a substance across a membrane by binding it | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/5%3A_Structure_and_Function_of_Plasma_Membranes/5.2%3A_Passive_Transport.txt |
Skills to Develop
• Understand how electrochemical gradients affect ions
• Distinguish between primary active transport and secondary 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. Other mechanisms transport much larger molecules.
Electrochemical Gradient
We have discussed simple concentration gradients—differential concentrations of a substance 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 does the extracellular fluid. So in a living cell, the concentration gradient of Na+ tends to drive it into the cell, and the electrical gradient of Na+ (a positive ion) also tends to drive it inward to the negatively charged interior. The situation is more complex, however, for other elements such as potassium. The electrical gradient of K+, a positive ion, also tends to drive it into the cell, but the concentration gradient of K+ tends to drive K+ out of the cell (Figure \(1\)). The combined gradient of concentration and electrical charge that affects an ion is called its electrochemical gradient.
Art Connection
Injection of a potassium solution into a person’s blood is lethal; this is used in capital punishment and euthanasia. Why do you think a potassium solution injection is lethal?
Moving Against a Gradient
To move substances against a concentration or electrochemical gradient, the cell must use energy. This energy is harvested from ATP generated through the cell’s metabolism. Active transport mechanisms, collectively called pumps, work against electrochemical gradients. Small substances constantly pass through plasma membranes. Active transport maintains concentrations of ions and other substances needed by living cells in the face of these passive movements. Much of a cell’s supply of metabolic energy may be spent maintaining these processes. (Most of a red blood cell’s metabolic energy is used to maintain the imbalance between exterior and interior sodium and potassium levels required by the cell.) Because active transport mechanisms depend on a cell’s metabolism for energy, they are sensitive to many metabolic poisons that interfere with the supply of ATP.
Two mechanisms exist for the transport of 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 describes the movement of material that is due to the electrochemical gradient established by primary active transport that does not directly require ATP.
Carrier Proteins for Active Transport
An important membrane adaption for active transport is the presence of specific carrier proteins or pumps to facilitate movement: there are three types of these proteins or transporters (Figure \(2\)). 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 found 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.
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 considered active because it depends on the use of energy as does primary transport (Figure \(3\)).
One of the most important pumps in animals 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 interior or exterior of the cell and its affinity for either sodium or potassium ions. The process consists of the following six steps.
1. With the enzyme oriented towards the interior of the cell, the carrier has a high affinity for sodium ions. Three ions bind to the protein.
2. ATP is hydrolyzed by the protein carrier and a low-energy phosphate group attaches to it.
3. As a result, the carrier changes shape and re-orients itself towards the exterior of the membrane. 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 interior of the cell.
6. The carrier protein, in its new configuration, has a decreased affinity for potassium, and the two ions are released 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 of the cell than inside and more potassium ions inside than out. For every three ions of sodium that move out, two ions of potassium 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
Visit the site to see a simulation of active transport in a sodium-potassium ATPase.
Secondary Active Transport (Co-transport)
Secondary active transport brings sodium ions, and possibly other compounds, into the cell. As sodium ion concentrations build outside of the plasma membrane because of the action of the primary active transport process, an electrochemical gradient is created. If a channel protein exists and is open, the sodium ions will be pulled through the membrane. This movement is used to transport other substances that can attach themselves to the transport protein through the membrane (Figure \(4\)). Many amino acids, as well as glucose, enter a cell this way. This secondary process is also used to store high-energy hydrogen ions in the mitochondria of plant and animal cells for the production of ATP. The potential energy that accumulates in the stored hydrogen ions is translated into kinetic energy as the ions surge through the channel protein ATP synthase, and that energy is used to convert ADP into ATP.
Art Connection
If the pH outside the cell decreases, would you expect the amount of amino acids transported into the cell to increase or decrease?
Summary
The combined gradient that affects an ion includes its concentration gradient and its electrical gradient. A positive ion, for example, might tend to diffuse into a new area, down its concentration gradient, but if it is diffusing into an area of net positive charge, its diffusion will be hampered by its electrical gradient. When dealing with ions in aqueous solutions, a combination of the electrochemical and concentration gradients, rather than just the concentration gradient alone, must be considered. 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 be used to move another substance into the cell and up its concentration gradient.
Art Connections
Figure \(1\): Injection of a potassium solution into a person’s blood is lethal; this is used in capital punishment and euthanasia. Why do you think a potassium solution injection is lethal?
Answer
Cells typically have a high concentration of potassium in the cytoplasm and are bathed in a high concentration of sodium. Injection of potassium dissipates this electrochemical gradient. In heart muscle, the sodium/potassium potential is responsible for transmitting the signal that causes the muscle to contract. When this potential is dissipated, the signal can’t be transmitted, and the heart stops beating. Potassium injections are also used to stop the heart from beating during surgery.
Figure \(4\): If the pH outside the cell decreases, would you expect the amount of amino acids transported into the cell to increase or decrease?
Answer
A decrease in pH means an increase in positively charged H+ ions, and an increase in the electrical gradient across the membrane. The transport of amino acids into the cell will increase.
Glossary
active transport
method of transporting material that requires energy
antiporter
transporter that carries two ions or small molecules in different directions
electrochemical gradient
gradient produced by the combined forces of an electrical gradient and a chemical gradient
electrogenic pump
pump that creates a charge imbalance
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
secondary active transport
movement of material that is due to the electrochemical gradient established by primary active transport
symporter
transporter that carries two different ions or small molecules, both in the same direction
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_1e_(OpenStax)/2%3A_The_Cell/5%3A_Structure_and_Function_of_Plasma_Membranes/5.3%3A_Active_Transport.txt |
Skills to Develop
• 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 \(1\) for examples). 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.
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 variations of endocytosis, but all share a common characteristic: The plasma membrane of the cell invaginates, forming a pocket around the target particle. The pocket pinches off, resulting in the particle being contained in a newly created intracellular vesicle formed from the plasma membrane.
Phagocytosis
Phagocytosis (the condition of “cell eating”) is the process by which large particles, such as cells or relatively large particles, are taken in by a cell. For example, when microorganisms invade the human body, a type of white blood cell called a neutrophil will remove the invaders through this process, surrounding and engulfing the microorganism, which is then destroyed by the neutrophil (Figure \(1\)).
In preparation for phagocytosis, a portion of the inward-facing surface of the plasma membrane becomes coated with a protein called clathrin, which stabilizes this section of the membrane. The coated portion of the membrane then extends from the body of the cell 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 the breakdown of the material in the newly formed compartment (endosome). When accessible nutrients from the degradation of the vesicular contents 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 called pinocytosis. This literally means “cell drinking” and was named at a time when the assumption was 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 \(2\)).
A variation of pinocytosis is called potocytosis. This process uses a coating protein, called caveolin, on the cytoplasmic side of the plasma membrane, 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 is used to bring small molecules into the cell and to transport these molecules through the cell for their release on the other side of the cell, a process called transcytosis.
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 \(3\)).
In receptor-mediated endocytosis, as in phagocytosis, clathrin is attached to the cytoplasmic side of the plasma membrane. If uptake of a compound 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. Some human diseases are caused by the failure of receptor-mediated endocytosis. For example, the form of cholesterol termed low-density lipoprotein or LDL (also referred to as “bad” cholesterol) is removed from the blood by receptor-mediated endocytosis. 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 from their blood.
Although receptor-mediated endocytosis is designed to bring specific substances that are normally found 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
Video \(1\): 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 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 interior of the plasma membrane. This fusion opens the membranous envelope on the exterior of the cell, and the waste material is expelled into the extracellular space (Figure \(4\)). Other examples of cells releasing molecules via exocytosis include the secretion of proteins of the extracellular matrix and secretion of neurotransmitters into the synaptic cleft by synaptic vesicles.
Table \(1\): Methods of transport, Energy requirements and types of Material transported.
Transport Method Active/Passive Material Transported
Diffusion Passive Small-molecular weight material
Osmosis Passive Water
Facilitated transport/diffusion Passive Sodium, potassium, calcium, glucose
Primary active transport Active Sodium, potassium, calcium
Secondary active transport Active Amino acids, lactose
Phagocytosis Active Large macromolecules, whole cells, or cellular structures
Pinocytosis and potocytosis Active Small molecules (liquids/water)
Receptor-mediated endocytosis Active Large quantities of macromolecules
Summary
Active transport methods require the direct use of ATP to fuel the transport. Large particles, such as macromolecules, parts of cells, or whole cells, can be engulfed by other cells in a process called phagocytosis. In phagocytosis, a portion of the membrane invaginates and flows around the particle, eventually pinching off and leaving the particle entirely enclosed by an envelope of plasma membrane. Vesicle contents are broken down by the cell, 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.
Glossary
caveolin
protein that coats the cytoplasmic side of the plasma membrane and participates in the process of liquid update by potocytosis
clathrin
protein that coats the inward-facing surface of the plasma membrane and assists in the formation of specialized structures, like coated pits, for phagocytosis
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
pinocytosis
a variation of endocytosis that imports macromolecules that the cell needs from the extracellular fluid
potocytosis
variation of pinocytosis that uses a different coating protein (caveolin) on the cytoplasmic side of the plasma membrane
receptor-mediated endocytosis
variation of endocytosis that involves the use of specific binding proteins in the plasma membrane for specific molecules or particles, and clathrin-coated pits that become clathrin-coated vesicles | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/5%3A_Structure_and_Function_of_Plasma_Membranes/5.4%3A_Bulk_Transport.txt |
5.1: 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.
Review Questions
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
Answer
A
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
Answer
D
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
Answer
A
Free Response
Why is it advantageous for the cell membrane to be fluid in nature?
Answer
The fluid characteristic of the cell membrane allows greater flexibility to the cell than it would if the membrane were rigid. It also allows the motion of membrane components, required for some types of membrane transport.
Why do phospholipids tend to spontaneously orient themselves into something resembling a membrane?
Answer
The hydrophobic, nonpolar regions must align with each other in order for the structure to have minimal potential energy and, consequently, higher stability. The fatty acid tails of the phospholipids cannot mix with water, but the phosphate “head” of the molecule can. Thus, the head orients to water, and the tail to other lipids.
5.2: 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.
Review Questions
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 one of higher concentration
Answer
C
The principal force driving movement in diffusion is the __________.
1. temperature
2. particle size
3. concentration gradient
4. membrane surface area
Answer
C
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.
Answer
A
Free Response
Discuss why the following affect the rate of diffusion: molecular size, temperature, solution density, and the distance that must be traveled.
Answer
Heavy molecules move more slowly than lighter ones. It takes more energy in the medium to move them along. Increasing or decreasing temperature increases or decreases the energy in the medium, affecting molecular movement. The denser a solution is, the harder it is for molecules to move through it, causing diffusion to slow down due to friction. Living cells require a steady supply of nutrients and a steady rate of waste removal. If the distance these substances need to travel is too great, diffusion cannot move nutrients and waste materials efficiently to sustain life.
Why does water move through a membrane?
Answer
Water moves through a membrane in osmosis because there is a concentration gradient across the membrane of solute and solvent. The solute cannot effectively move to balance the concentration on both sides of the membrane, so water moves to achieve this balance.
Both of the regular intravenous solutions administered in medicine, normal saline and lactated Ringer’s solution, are isotonic. Why is this important?
Answer
Injection of isotonic solutions ensures that there will be no perturbation of the osmotic balance, and no water taken from tissues or added to them from the blood.
5.3: 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.
Review Questions
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
Answer
D
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
Answer
C
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
Answer
D
Free Response
Where does the cell get energy for active transport processes?
Answer
The cell harvests energy from ATP produced by its own metabolism to power active transport processes, such as the activity of pumps.
How does the sodium-potassium pump contribute to the net negative charge of the interior of the cell?
Answer
The sodium-potassium pump forces out three (positive) Na+ ions for every two (positive) K+ ions it pumps in, thus the cell loses a positive charge at every cycle of the pump.
5.4: 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 (see Table 5.4.1 for examples). 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.
Review Questions
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.
Answer
C
Which transport mechanism can bring whole cells into a cell?
1. pinocytosis
2. phagocytosis
3. facilitated transport
4. primary active transport
Answer
B
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.
Answer
C
Free Response
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?
Answer
The proteins allow a cell to select what compound will be transported, meeting the needs of the cell and not bringing in anything else.
Why do ions have a difficult time getting through plasma membranes despite their small size?
Answer
Ions are charged, and consequently, they are hydrophilic and cannot associate with the lipid portion of the membrane. Ions must be transported by carrier proteins or ion channels. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/2%3A_The_Cell/5%3A_Structure_and_Function_of_Plasma_Membranes/5.E%3A_Structure_and_Function_of_Plasma_Membranes_%28Exercises%29.txt |
• 11.0: Prelude to Meiosis and Sexual Reproduction
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.
• 11.1: 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.
• 11.2: 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.
• 11.E: Meiosis and Sexual Reproduction (Exercises)
Thumbnail: Example of a Punnett square. (CC BY-SA 3.0; Pbroks13 via Wikimedia Commons).
11: Meiosis and Sexual Reproduction
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. Whereas many unicellular organisms and a few multicellular organisms can produce genetically identical clones of themselves through cell division, many single-celled organisms and most multicellular organisms reproduce regularly using another method. Sexual reproduction is the production by parents of two haploid cells and the fusion of two haploid cells to form a single, unique diploid cell. In most plants and animals, through tens of rounds of mitotic cell division, this diploid cell will develop into an adult organism. Haploid cells that are part of the sexual reproductive cycle are produced by a type of cell division called meiosis. Sexual reproduction, specifically 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.
11.1: The Process of Meiosis
Skills to Develop
• Describe the behavior of chromosomes during meiosis
• Describe cellular events during meiosis
• Explain the differences between meiosis and mitosis
• Explain the mechanisms within meiosis that generate genetic variation among the products 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. If the reproductive cycle is to continue, then the diploid cell must somehow reduce its number of chromosome sets before fertilization can occur again, or there will be a continual doubling in the number of chromosome sets in every generation. So, in addition to fertilization, sexual reproduction includes a nuclear division that reduces the number of chromosome sets.
Most animals and plants are diploid, containing 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. Somatic cells are sometimes referred to as “body” cells. Homologous chromosomes are matched pairs containing the same genes in identical locations along their length. Diploid organisms inherit one copy of each homologous chromosome from each parent; all together, they are considered a full set of chromosomes. Haploid cells, containing a single copy of each homologous chromosome, are found only within structures that give rise to either gametes or spores. Spores are haploid cells that can produce a haploid organism or can fuse with another spore to form a diploid cell. All animals and most plants produce eggs and sperm, or gametes. Some plants and all fungi produce spores.
The nuclear division that forms haploid cells, which is called meiosis, is related to mitosis. As you have learned, mitosis is the part of a cell reproduction cycle that results in identical daughter nuclei that are also genetically identical to the original parent nucleus. In mitosis, both the parent and the daughter nuclei are at the same ploidy level—diploid for most plants and animals. Meiosis employs many of the same mechanisms as mitosis. However, the starting nucleus is always diploid and the nuclei that result at the end of a meiotic cell division are haploid. To achieve this reduction in chromosome number, meiosis consists of one round of chromosome duplication and two rounds of nuclear division. Because the 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. Meiosis II, in which the second round of meiotic division takes place, includes prophase II, prometaphase II, and so on.
Meiosis I
Meiosis is preceded by an interphase consisting of the G1, S, and G2 phases, which are nearly identical to the phases preceding mitosis. The G1 phase, which is also called the first gap phase, is the first phase of the interphase and is focused on cell growth. The S phase is the second phase of interphase, during which the DNA of the chromosomes is replicated. Finally, the G2 phase, also called the second gap phase, is the third and final phase of interphase; in this 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, called sister chromatids, that are held together at the centromere by cohesin proteins. Cohesin holds the chromatids together until anaphase II. The centrosomes, which are the structures that organize the microtubules of the meiotic spindle, also replicate. This prepares the cell to enter prophase I, the first meiotic phase.
Prophase I
Early in prophase I, before the chromosomes can be seen clearly microscopically, 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 close to each other. Recall that, in mitosis, homologous chromosomes do not pair together. In mitosis, homologous chromosomes line up end-to-end so that when they divide, each daughter cell receives a sister chromatid from both members of the homologous pair. The synaptonemal complex, a lattice of proteins between the homologous chromosomes, first forms at specific locations and then spreads 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 non-sister homologous chromatids, a process called crossing over. Crossing over can be observed visually after the exchange as chiasmata (singular = chiasma) (Figure \(1\)).
In species such as humans, even though the X and Y sex chromosomes are not homologous (most of their genes differ), they have 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.
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 non-sister chromatids. Near the recombination nodule on each chromatid, the double-stranded DNA is cleaved, the cut ends are modified, and a new connection is made between the non-sister 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 also removed. At the end of prophase I, the pairs are held together only at the chiasmata (Figure \(2\)) and are called tetrads because the 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 non-sister chromatids leads to a reciprocal exchange of equivalent DNA between a maternal chromosome and a paternal chromosome. Now, when that sister chromatid is moved into a gamete cell it will carry some DNA from one parent of the individual and some DNA from the other parent. The sister recombinant chromatid has a combination of maternal and paternal genes that did not exist before the crossover. Multiple crossovers in an arm of the chromosome have the same effect, exchanging segments of DNA to create recombinant 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 centrosomes placed at opposite poles of the cell. The microtubules move toward the middle of the cell and attach to one of the two fused homologous chromosomes. The microtubules attach at each chromosomes' kinetochores. With each member of the homologous pair attached to opposite poles of the cell, 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 chiasmata. In addition, the nuclear membrane has broken down entirely.
Metaphase I
During metaphase I, the homologous chromosomes are arranged in the center of the cell with the kinetochores facing opposite poles. The homologous pairs orient themselves 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 slight differences in their genetic information, causing each gamete to have a unique genetic makeup.
This randomness is the physical basis for the creation of the second form of genetic variation in offspring. Consider 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 donated by the mother. The father provides the other set of 23 chromosomes in the sperm that fertilizes the egg. Every cell of the multicellular offspring has copies of the original two sets of homologous chromosomes. 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. Any maternally inherited chromosome may face either pole. 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, where n is the number of chromosomes per set. Humans have 23 chromosome pairs, which results in over eight million (223) possible genetically-distinct gametes. This number does not include the variability that was previously created in the sister chromatids by crossover. Given these two mechanisms, it is highly unlikely that any two haploid cells resulting from meiosis will have the same genetic composition (Figure \(3\)).
To summarize the genetic consequences of meiosis I, the maternal and paternal genes are recombined by crossover events that occur between each homologous pair during prophase I. In addition, the random assortment of tetrads on the metaphase plate produces a unique combination of maternal and paternal chromosomes that will make their way into the gametes.
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 \(4\)).
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 chromatids in 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 end result of the first meiotic division. 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 homolog 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
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 is similar to mitosis, except that each dividing cell has only one set of homologous chromosomes. Therefore, each cell has half the number of sister chromatids to separate out as a diploid cell undergoing mitosis.
Prophase II
If the chromosomes decondensed in telophase I, they condense again. If nuclear envelopes were formed, they fragment into vesicles. The centrosomes 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. Non-kinetochore microtubules elongate the cell.
Telophase II and Cytokinesis
The chromosomes arrive at opposite poles and begin to decondense. Nuclear envelopes form around the chromosomes. Cytokinesis separates the two cells into four unique haploid cells. At this point, the newly formed nuclei are both haploid. The cells produced are genetically unique because of the random assortment of paternal and maternal homologs and because of the recombining 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 \(5\).
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 distinct differences that lead to very different outcomes (Figure \(6\)). 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 most plants and all animal species, it is typically diploid cells that undergo mitosis to form new diploid cells. In contrast, meiosis consists of two nuclear divisions resulting in four nuclei that are usually partitioned into four new cells. The nuclei resulting from meiosis are not genetically identical and they contain one chromosome set only. This is half the number of chromosome sets in 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 become associated with each other, are bound together with the synaptonemal complex, develop chiasmata and undergo crossover between sister chromatids, and line up along the metaphase plate in tetrads with kinetochore fibers from opposite spindle poles attached to each kinetochore of a homolog in a tetrad. All of these events occur only in meiosis I.
When the chiasmata resolve and the tetrad is broken up with the homologs 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 reduction division. There is no such reduction in ploidy level during mitosis.
Meiosis II is much more 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 (like 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.
Evolution Connection: The Mystery of the Evolution of Meiosis
Some characteristics of organisms are so widespread and fundamental that it is sometimes difficult to remember that they evolved like other simpler traits. Meiosis is such an extraordinarily complex series of cellular events that biologists have had trouble hypothesizing and testing 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, 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.
Summary
Sexual reproduction requires that diploid organisms produce haploid cells that can fuse during fertilization to form diploid offspring. As with mitosis, DNA replication occurs prior to meiosis during the S-phase of the cell cycle. Meiosis is a series of events that arrange and separate chromosomes and chromatids into daughter cells. During the interphases of meiosis, each chromosome is duplicated. 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 separates homologs, and the second—like mitosis—separates chromatids into individual chromosomes. During meiosis, variation in the daughter nuclei is introduced because of crossover in prophase I and random alignment of tetrads at metaphase I. The cells that are produced by meiosis are genetically unique.
Meiosis and mitosis share similarities, but have distinct outcomes. Mitotic divisions are single nuclear divisions that produce daughter nuclei that are genetically identical and have the same number of chromosome sets as the original cell. Meiotic divisions include two nuclear divisions that produce four daughter nuclei that are genetically different and have one chromosome set instead of the two sets of chromosomes in the parent cell. The main differences between the processes occur in the first division of meiosis, in which homologous chromosomes are paired and exchange non-sister 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 more similar to a mitotic division, except that the daughter cells do not contain identical genomes because of crossover.
Footnotes
1. 1 Adam S. Wilkins and Robin Holliday, “The Evolution of Meiosis from Mitosis,” Genetics 181 (2009): 3–12.
2. 2 Marilee 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.
Glossary
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 non-sister chromatids resulting in chromosomes that incorporate genes from both parents of the organism
fertilization
union of two haploid cells from two individual organisms
interkinesis
(also, interphase II) brief period of rest between meiosis I and meiosis II
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 non-sister chromatids
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
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 | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/11%3A_Meiosis_and_Sexual_Reproduction/11.0%3A_Prelude_to_Meiosis_and_Sexual_Reproduction.txt |
Skills to Develop
• Explain that meiosis and sexual reproduction are evolved traits
• Identify variation among offspring as a potential evolutionary advantage to sexual reproduction
• Describe the three different life-cycle types among sexual multicellular organisms and their commonalities
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. If the parent organism is successfully occupying a habitat, offspring with the same traits would 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 asexual eggs. These methods of reproduction do not require another organism of the opposite sex. 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 in theory an asexual population could grow twice as fast.
However, multicellular organisms that exclusively depend on asexual reproduction are exceedingly rare. Why is sexuality (and meiosis) so common? This is one of the important unanswered questions in biology and has been the focus of much research beginning in the latter half of the twentieth 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. This is the ultimate source of variation in sexual organisms, but in addition, those different mutations are 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: The Red Queen Hypothesis
It is not in dispute that sexual reproduction provides evolutionary advantages to organisms that employ this mechanism to produce offspring. But why, even in the face of fairly stable conditions, does sexual reproduction persist when it is more difficult and costly for individual organisms? Variation is the outcome of sexual reproduction, but why are ongoing variations necessary? Enter the Red Queen hypothesis, first proposed by Leigh Van Valen in 1973.1 The concept was named in reference to the Red Queen's race in Lewis Carroll's book, Through the Looking-Glass.
All species co-evolve 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 an edge over close competitors, predators, parasites, or even prey. The only method that will allow a co-evolving species to maintain its own share of the resources is to also continually improve its fitness. 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 co-evolution 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. The process of meiosis reduces the chromosome number by half. Fertilization, the joining of two haploid gametes, restores the diploid condition. There are three main categories of life cycles in multicellular organisms: diploid-dominant, in which the multicellular diploid stage is the most obvious life stage, such as with most animals including humans; haploid-dominant, in which the multicellular haploid stage is the most obvious life stage, such as with all fungi and some algae; and alternation of generations, in which the two stages are apparent to different degrees depending on the group, as with plants and some algae.
Diploid-Dominant Life Cycle
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 cell line and meiosis to produce 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 \(1\)).
Haploid-Dominant Life Cycle
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 haploid like the “parents,” these spores contain a new genetic combination from two parents. The spores can remain dormant for various time periods. Eventually, when conditions are conducive, the spores form multicellular haploid structures by many rounds of mitosis (Figure \(2\)).
Art Connection
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?
Alternation of Generations
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 a 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 \(3\)).
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. However, at some point in each type of life cycle, meiosis produces haploid cells that will fuse with the haploid cell of another organism. The mechanisms of variation—crossover, random assortment of homologous chromosomes, and random fertilization—are present in all versions of sexual reproduction. 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.
Summary
Nearly all eukaryotes undergo sexual reproduction. The variation introduced into the reproductive cells by meiosis appears to be one of the advantages of sexual reproduction that has made it so 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. Fertilization, the fusion of haploid gametes from two individuals, restores the diploid condition. Thus, 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. There are three main categories of life cycles: diploid-dominant, demonstrated by most animals; haploid-dominant, demonstrated by all fungi and some algae; and the alternation of generations, demonstrated by plants and some algae.
Art Connections
Figure \(2\): 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?
Answer
Yes, it will be able to reproduce asexually.
Footnotes
1. 1 Leigh Van Valen, “A New Evolutionary Law,” Evolutionary Theory 1 (1973): 1–30
Glossary
alternation of generations
life-cycle type in which the diploid and haploid stages alternate
diploid-dominant
life-cycle type in which the multicellular diploid stage is prevalent
haploid-dominant
life-cycle type in which the multicellular haploid stage is prevalent
gametophyte
a multicellular haploid life-cycle stage that produces gametes
germ cells
specialized cell line that produces gametes, such as eggs or sperm
life cycle
the sequence of events in the development of an organism and the production of cells that produce offspring
sporophyte
a multicellular diploid life-cycle stage that produces haploid spores by meiosis | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/11%3A_Meiosis_and_Sexual_Reproduction/11.2%3A_Sexual_Reproduction.txt |
11.1: 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.
Review Questions
Meiosis produces ________ daughter cells.
1. two haploid
2. two diploid
3. four haploid
4. four diploid
Answer
C
What structure is most important in forming the tetrads?
1. centromere
2. synaptonemal complex
3. chiasma
4. kinetochore
Answer
B
At which stage of meiosis are sister chromatids separated from each other?
1. prophase I
2. prophase II
3. anaphase I
4. anaphase II
Answer
D
At metaphase I, homologous chromosomes are connected only at what structures?
1. chiasmata
2. recombination nodules
3. microtubules
4. kinetochores
Answer
A
Which of the following is not true in regard to crossover?
1. Spindle microtubules guide the transfer of DNA across the synaptonemal complex.
2. Non-sister chromatids exchange genetic material.
3. Chiasmata are formed.
4. Recombination nodules mark the crossover point.
Answer
C
What phase of mitotic interphase is missing from meiotic interkinesis?
1. G0 phase
2. G1 phase
3. S phase
4. G2 phase
Answer
C
The part of meiosis that is similar to mitosis is ________.
1. meiosis I
2. anaphase I
3. meiosis II
4. interkinesis
Answer
C
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
Answer
B
Free Response
Describe the process that results in the formation of a tetrad.
Answer
During the meiotic interphase, each chromosome is duplicated. The sister chromatids that are formed during synthesis are held together at the centromere region by cohesin proteins. All chromosomes are attached to the nuclear envelope by their tips. As the cell enters prophase I, the nuclear envelope begins to fragment, and the proteins holding homologous chromosomes locate each other. The four sister chromatids align lengthwise, and a protein lattice called the synaptonemal complex is formed between them to bind them together. The synaptonemal complex facilitates crossover between non-sister chromatids, which is observed as chiasmata along the length of the chromosome. As prophase I progresses, the synaptonemal complex breaks down and the sister chromatids become free, except where they are attached by chiasmata. At this stage, the four chromatids are visible in each homologous pairing and are called a tetrad.
Explain how the random alignment of homologous chromosomes during metaphase I contributes to the variation in gametes produced by meiosis.
Answer
Random alignment leads to new combinations of traits. The chromosomes that were originally inherited by the gamete-producing individual came equally from the egg and the sperm. In metaphase I, the duplicated copies of these maternal and paternal homologous chromosomes line up across the center of the cell. The orientation of each tetrad is random. There is an equal chance that the maternally derived chromosomes will be facing either pole. The same is true of the paternally derived chromosomes. The alignment should occur differently in almost every meiosis. As the homologous chromosomes are pulled apart in anaphase I, any combination of maternal and paternal chromosomes will move toward each pole. The gametes formed from these two groups of chromosomes will have a mixture of traits from the individual’s parents. Each gamete is unique.
What is the function of the fused kinetochore found on sister chromatids in prometaphase I?
Answer
In metaphase I, the homologous chromosomes line up at the metaphase plate. In anaphase I, the homologous chromosomes are pulled apart and move to opposite poles. Sister chromatids are not separated until meiosis II. The fused kinetochore formed during meiosis I ensures that each spindle microtubule that binds to the tetrad will attach to both sister chromatids.
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?
Answer
All of the stages of meiosis I, except possibly telophase I, are unique because homologous chromosomes are separated, not sister chromatids. In some species, the chromosomes do not decondense and the nuclear envelopes do not form in telophase I. All of the stages of meiosis II have the same events as the stages of mitosis, with the possible exception of prophase II. In some species, the chromosomes are still condensed and there is no nuclear envelope. Other than this, all processes are the same.
11.2: 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.
Review Questions
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.
Answer
C
Which type of life cycle has both a haploid and diploid multicellular stage?
1. asexual
2. diploid-dominant
3. haploid-dominant
4. alternation of generations
Answer
D
Fungi typically display which type of life cycle?
1. diploid-dominant
2. haploid-dominant
3. alternation of generations
4. asexual
Answer
B
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
Answer
A
Free Response
List and briefly describe the three processes that lead to variation in offspring with the same parents.
Answer
a. Crossover occurs in prophase I between non-sister homologous chromosomes. Segments of DNA are exchanged between maternally derived and paternally derived chromosomes, and new gene combinations are formed. b. Random alignment during metaphase I leads to gametes that have a mixture of maternal and paternal chromosomes. c. Fertilization is random, in that any two gametes can fuse.
Compare the three main types of life cycles in multicellular organisms and give an example of an organism that employs each.
Answer
a. In the haploid-dominant life cycle, the multicellular stage is haploid. The diploid stage is a spore that undergoes meiosis to produce cells that will divide mitotically to produce new multicellular organisms. Fungi have a haploid-dominant life cycle. b. In the diploid-dominant life cycle, the most visible or largest multicellular stage is diploid. The haploid stage is usually reduced to a single cell type, such as a gamete or spore. Animals, such as humans, have a diploid-dominant life cycle. c. In the alternation of generations life cycle, there are both haploid and diploid multicellular stages, although the haploid stage may be completely retained by the diploid stage. Plants have a life cycle with alternation of generations. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/11%3A_Meiosis_and_Sexual_Reproduction/11.E%3A_Meiosis_and_Sexual_Reproduction_%28Exercises%29.txt |
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.
• 12.0: Prelude to Mendel's Experiments and Heredity
Genetics is the study of heredity. Johann Gregor Mendel set the framework for genetics long before chromosomes or genes had been identified, at a time when meiosis was not well understood. Mendel selected a simple biological system and conducted methodical, quantitative analyses using large sample sizes. Because of Mendel’s work, the fundamental principles of heredity were revealed.
• 12.1: Mendel’s Experiments and the Laws of Probability
In 1865, Mendel presented the results of his experiments with nearly 30,000 pea plants to the local Natural History Society. He demonstrated that traits are transmitted faithfully from parents to offspring independently of other traits and in dominant and recessive patterns.
• 12.2: Characteristics and Traits
The genetic makeup of peas consists of two similar or homologous copies of each chromosome, one from each parent. Each pair of homologous chromosomes has the same linear order of genes; hence peas are diploid organisms. The same is true for many other plants and for virtually all animals. Diploid organisms utilize meiosis to produce haploid gametes, which contain one copy of each homologous chromosome that unite at fertilization to create a diploid zygote.
• 12.3: Laws of Inheritance
Mendel generalized the results of his pea-plant experiments into four postulates, some of which are sometimes called “laws,” that describe the basis of dominant and recessive inheritance in diploid organisms. As you have learned, more complex extensions of Mendelism exist that do not exhibit the same F2 phenotypic ratios (3:1). Nevertheless, these laws summarize the basics of classical genetics.
• 12.E: Mendel's Experiments and Heredity (Exercises)
Thumbnail: Pea plants were used by Gregor Mendel to discover some fundamental laws of genetics. (Flicker-Christian Guthier-CC:A).
12: Mendel's Experiments and Heredity
Genetics is the study of heredity. Johann Gregor Mendel set the framework for genetics long before chromosomes or genes had been identified, at a time when meiosis was not well understood. Mendel selected a simple biological system and conducted methodical, quantitative analyses using large sample sizes. Because of Mendel’s work, the fundamental principles of heredity were revealed. We now know that genes, carried on chromosomes, are the basic functional units of heredity with the capability to be replicated, expressed, or mutated. Today, the postulates put forth by Mendel form the basis of classical, or Mendelian, genetics. Not all genes are transmitted from parents to offspring according to Mendelian genetics, but Mendel’s experiments serve as an excellent starting point for thinking about inheritance.
12.1: Mendels Experiments and the Laws of Probability
Skills to Develop
• Describe the scientific reasons for the success of Mendel’s experimental work
• Describe the expected outcomes of monohybrid crosses involving dominant and recessive alleles
• Apply the sum and product rules to calculate probabilities
Johann Gregor Mendel (1822–1884) (Figure $1$) was a lifelong learner, teacher, scientist, and man of faith. As a young adult, he joined the Augustinian Abbey of St. Thomas in Brno in what is now the Czech Republic. Supported by the monastery, he taught physics, botany, and natural science courses at the secondary and university levels. In 1856, he began a decade-long research pursuit involving inheritance patterns in honeybees and plants, ultimately settling on pea plants as his primary model system (a system with convenient characteristics used to study a specific biological phenomenon to be applied to other systems). In 1865, Mendel presented the results of his experiments with nearly 30,000 pea plants to the local Natural History Society. He demonstrated that traits are transmitted faithfully from parents to offspring independently of other traits and in dominant and recessive patterns. In 1866, he published his work, Experiments in Plant Hybridization,1 in the proceedings of the Natural History Society of Brünn.
Mendel’s work went virtually unnoticed by the scientific community that believed, incorrectly, that the process of inheritance involved a blending of parental traits that produced an intermediate physical appearance in offspring; this hypothetical process appeared to be correct because of what we know now as continuous variation. Continuous variation results from the action of many genes to determine a characteristic like human height. Offspring appear to be a “blend” of their parents’ traits when we look at characteristics that exhibit continuous variation. The blending theory of inheritance asserted that the original parental traits were lost or absorbed by the blending in the offspring, but we now know that this is not the case. Mendel was the first researcher to see it. Instead of continuous characteristics, Mendel worked with traits that were inherited in distinct classes (specifically, violet versus white flowers); this is referred to as discontinuous variation. Mendel’s choice of these kinds of traits allowed him to see experimentally that the traits were not blended in the offspring, nor were they absorbed, but rather that they kept their distinctness and could be passed on. In 1868, Mendel became abbot of the monastery and exchanged his scientific pursuits for his pastoral duties. He was not recognized for his extraordinary scientific contributions during his lifetime. In fact, it was not until 1900 that his work was rediscovered, reproduced, and revitalized by scientists on the brink of discovering the chromosomal basis of heredity.
Mendel’s Model System
Mendel’s seminal work was accomplished using the garden pea, Pisum sativum, to study inheritance. This species naturally self-fertilizes, such that pollen encounters ova within individual flowers. The flower petals remain sealed tightly until after pollination, preventing pollination from other plants. The result is highly inbred, or “true-breeding,” pea plants. These are plants that always produce offspring that look like the parent. By experimenting with true-breeding pea plants, Mendel avoided the appearance of unexpected traits in offspring that might occur if the plants were not true breeding. The garden pea also grows to maturity within one season, meaning that several generations could be evaluated over a relatively short time. Finally, large quantities of garden peas could be cultivated simultaneously, allowing Mendel to conclude that his results did not come about simply by chance.
Mendelian Crosses
Mendel performed hybridizations, which involve mating two true-breeding individuals that have different traits. In the pea, which is naturally self-pollinating, this is done by manually transferring pollen from the anther of a mature pea plant of one variety to the stigma of a separate mature pea plant of the second variety. In plants, pollen carries the male gametes (sperm) to the stigma, a sticky organ that traps pollen and allows the sperm to move down the pistil to the female gametes (ova) below. To prevent the pea plant that was receiving pollen from self-fertilizing and confounding his results, Mendel painstakingly removed all of the anthers from the plant’s flowers before they had a chance to mature.
Plants used in first-generation crosses were called P0, or parental generation one, plants (Figure $2$). Mendel collected the seeds belonging to the P0 plants that resulted from each cross and grew them the following season. These offspring were called the F1, or the first filial (filial = offspring, daughter or son), generation. Once Mendel examined the characteristics in the F1 generation of plants, he allowed them to self-fertilize naturally. He then collected and grew the seeds from the F1 plants to produce the F2, or second filial, generation. Mendel’s experiments extended beyond the F2 generation to the F3 and F4 generations, and so on, but it was the ratio of characteristics in the P0−F1−F2 generations that were the most intriguing and became the basis for Mendel’s postulates.
Garden Pea Characteristics Revealed the Basics of Heredity
In his 1865 publication, Mendel reported the results of his crosses involving seven different characteristics, each with two contrasting traits. A trait is defined as a variation in the physical appearance of a heritable characteristic. The characteristics included plant height, seed texture, seed color, flower color, pea pod size, pea pod color, and flower position. For the characteristic of flower color, for example, the two contrasting traits were white versus violet. To fully examine each characteristic, Mendel generated large numbers of F1 and F2 plants, reporting results from 19,959 F2 plants alone. His findings were consistent.
What results did Mendel find in his crosses for flower color? First, Mendel confirmed that he had plants that bred true for white or violet flower color. Regardless of how many generations Mendel examined, all self-crossed offspring of parents with white flowers had white flowers, and all self-crossed offspring of parents with violet flowers had violet flowers. In addition, Mendel confirmed that, other than flower color, the pea plants were physically identical.
Once these validations were complete, Mendel applied the pollen from a plant with violet flowers to the stigma of a plant with white flowers. After gathering and sowing the seeds that resulted from this cross, Mendel found that 100 percent of the F1 hybrid generation had violet flowers. Conventional wisdom at that time would have predicted the hybrid flowers to be pale violet or for hybrid plants to have equal numbers of white and violet flowers. In other words, the contrasting parental traits were expected to blend in the offspring. Instead, Mendel’s results demonstrated that the white flower trait in the F1 generation had completely disappeared.
Importantly, Mendel did not stop his experimentation there. He allowed the F1 plants to self-fertilize and found that, of F2-generation plants, 705 had violet flowers and 224 had white flowers. This was a ratio of 3.15 violet flowers per one white flower, or approximately 3:1. When Mendel transferred pollen from a plant with violet flowers to the stigma of a plant with white flowers and vice versa, he obtained about the same ratio regardless of which parent, male or female, contributed which trait. This is called a reciprocal cross—a paired cross in which the respective traits of the male and female in one cross become the respective traits of the female and male in the other cross. For the other six characteristics Mendel examined, the F1 and F2 generations behaved in the same way as they had for flower color. One of the two traits would disappear completely from the F1 generation only to reappear in the F2 generation at a ratio of approximately 3:1 (Table $1$).
Table $1$: The Results of Mendel’s Garden Pea Hybridizations
Characteristic Contrasting P0 Traits F1 Offspring Traits F2 Offspring Traits F2 Trait Ratios
Flower color Violet vs. white 100 percent violet
• 705 violet
• 224 white
3.15:1
Flower position Axial vs. terminal 100 percent axial
• 651 axial
• 207 terminal
3.14:1
Plant height Tall vs. dwarf 100 percent tall
• 787 tall
• 277 dwarf
2.84:1
Seed texture Round vs. wrinkled 100 percent round
• 5,474 round
• 1,850 wrinkled
2.96:1
Seed color Yellow vs. green 100 percent yellow
• 6,022 yellow
• 2,001 green
3.01:1
Pea pod texture Inflated vs. constricted 100 percent inflated
• 882 inflated
• 299 constricted
2.95:1
Pea pod color Green vs. yellow 100 percent green
• 428 green
• 152 yellow
2.82:1
Upon compiling his results for many thousands of plants, Mendel concluded that the characteristics could be divided into expressed and latent traits. He called these, respectively, dominant and recessive traits. Dominant traits are those that are inherited unchanged in a hybridization. Recessive traits become latent, or disappear, in the offspring of a hybridization. The recessive trait does, however, reappear in the progeny of the hybrid offspring. An example of a dominant trait is the violet-flower trait. For this same characteristic (flower color), white-colored flowers are a recessive trait. The fact that the recessive trait reappeared in the F2 generation meant that the traits remained separate (not blended) in the plants of the F1 generation. Mendel also proposed that plants possessed two copies of the trait for the flower-color characteristic, and that each parent transmitted one of its two copies to its offspring, where they came together. Moreover, the physical observation of a dominant trait could mean that the genetic composition of the organism included two dominant versions of the characteristic or that it included one dominant and one recessive version. Conversely, the observation of a recessive trait meant that the organism lacked any dominant versions of this characteristic.
So why did Mendel repeatedly obtain 3:1 ratios in his crosses? To understand how Mendel deduced the basic mechanisms of inheritance that lead to such ratios, we must first review the laws of probability.
Probability Basics
Probabilities are mathematical measures of likelihood. The empirical probability of an event is calculated by dividing the number of times the event occurs by the total number of opportunities for the event to occur. It is also possible to calculate theoretical probabilities by dividing the number of times that an event is expected to occur by the number of times that it could occur. Empirical probabilities come from observations, like those of Mendel. Theoretical probabilities come from knowing how the events are produced and assuming that the probabilities of individual outcomes are equal. A probability of one for some event indicates that it is guaranteed to occur, whereas a probability of zero indicates that it is guaranteed not to occur. An example of a genetic event is a round seed produced by a pea plant. In his experiment, Mendel demonstrated that the probability of the event “round seed” occurring was one in the F1 offspring of true-breeding parents, one of which has round seeds and one of which has wrinkled seeds. When the F1 plants were subsequently self-crossed, the probability of any given F2 offspring having round seeds was now three out of four. In other words, in a large population of F2 offspring chosen at random, 75 percent were expected to have round seeds, whereas 25 percent were expected to have wrinkled seeds. Using large numbers of crosses, Mendel was able to calculate probabilities and use these to predict the outcomes of other crosses.
The Product Rule and Sum Rule
Mendel demonstrated that the pea-plant characteristics he studied were transmitted as discrete units from parent to offspring. As will be discussed, Mendel also determined that different characteristics, like seed color and seed texture, were transmitted independently of one another and could be considered in separate probability analyses. For instance, performing a cross between a plant with green, wrinkled seeds and a plant with yellow, round seeds still produced offspring that had a 3:1 ratio of green:yellow seeds (ignoring seed texture) and a 3:1 ratio of round:wrinkled seeds (ignoring seed color). The characteristics of color and texture did not influence each other.
The product rule of probability can be applied to this phenomenon of the independent transmission of characteristics. The product rule states that the probability of two independent events occurring together can be calculated by multiplying the individual probabilities of each event occurring alone. To demonstrate the product rule, imagine that you are rolling a six-sided die (D) and flipping a penny (P) at the same time. The die may roll any number from 1–6 (D#), whereas the penny may turn up heads (PH) or tails (PT). The outcome of rolling the die has no effect on the outcome of flipping the penny and vice versa. There are 12 possible outcomes of this action (Table $2$), and each event is expected to occur with equal probability.
Table $2$: Twelve Equally Likely Outcomes of Rolling a Die and Flipping a Penny
Rolling Die Flipping Penny
D1 PH
D1 PT
D2 PH
D2 PT
D3 PH
D3 PT
D4 PH
D4 PT
D5 PH
D5 PT
D6 PH
D6 PT
Of the 12 possible outcomes, the die has a 2/12 (or 1/6) probability of rolling a two, and the penny has a 6/12 (or 1/2) probability of coming up heads. By the product rule, the probability that you will obtain the combined outcome 2 and heads is: (D2) x (PH) = (1/6) x (1/2) or 1/12 (table above). Notice the word “and” in the description of the probability. The “and” is a signal to apply the product rule. For example, consider how the product rule is applied to the dihybrid cross: the probability of having both dominant traits in the F2 progeny is the product of the probabilities of having the dominant trait for each characteristic, as shown here:
$\frac{3}{4} * \frac{3}{4} = \frac{9}{16}\nonumber$
On the other hand, the sum rule of probability is applied when considering two mutually exclusive outcomes that can come about by more than one pathway. The sum rule states that the probability of the occurrence of one event or the other event, of two mutually exclusive events, is the sum of their individual probabilities. Notice the word “or” in the description of the probability. The “or” indicates that you should apply the sum rule. In this case, let’s imagine you are flipping a penny (P) and a quarter (Q). What is the probability of one coin coming up heads and one coin coming up tails? This outcome can be achieved by two cases: the penny may be heads (PH) and the quarter may be tails (QT), or the quarter may be heads (QH) and the penny may be tails (PT). Either case fulfills the outcome. By the sum rule, we calculate the probability of obtaining one head and one tail as
$\mathrm{[(P_H) × (Q_T)] + [(Q_H) × (P_T)] = [(1/2) × (1/2)] + [(1/2) × (1/2)] = 1/2.}\nonumber$
You should also notice that we used the product rule to calculate the probability of PH and QT, and also the probability of PT and QH, before we summed them. Again, the sum rule can be applied to show the probability of having just one dominant trait in the F2 generation of a dihybrid cross:
$\frac{3}{16} + \frac{3}{4} = \frac{15}{16}\nonumber$
Table $3$: The Product rule and the Sum rule
Product Rule Sum Rule
For independent events A and B, the probability (P) of them both occurring (A and B) is (PA × PB) For mutually exclusive events A and B, the probability (P) that at least one occurs (A or B) is (PA + PB)
To use probability laws in practice, it is necessary to work with large sample sizes because small sample sizes are prone to deviations caused by chance. The large quantities of pea plants that Mendel examined allowed him calculate the probabilities of the traits appearing in his F2 generation. As you will learn, this discovery meant that when parental traits were known, the offspring’s traits could be predicted accurately even before fertilization.
Summary
Working with garden pea plants, Mendel found that crosses between parents that differed by one trait produced F1 offspring that all expressed the traits of one parent. Observable traits are referred to as dominant, and non-expressed traits are described as recessive. When the offspring in Mendel’s experiment were self-crossed, the F2 offspring exhibited the dominant trait or the recessive trait in a 3:1 ratio, confirming that the recessive trait had been transmitted faithfully from the original P0 parent. Reciprocal crosses generated identical F1 and F2 offspring ratios. By examining sample sizes, Mendel showed that his crosses behaved reproducibly according to the laws of probability, and that the traits were inherited as independent events.
Two rules in probability can be used to find the expected proportions of offspring of different traits from different crosses. To find the probability of two or more independent events occurring together, apply the product rule and multiply the probabilities of the individual events. The use of the word “and” suggests the appropriate application of the product rule. To find the probability of two or more events occurring in combination, apply the sum rule and add their individual probabilities together. The use of the word “or” suggests the appropriate application of the sum rule.
Footnotes
1. 1 Johann Gregor Mendel, Versuche über Pflanzenhybriden Verhandlungen des naturforschenden Vereines in Brünn, Bd. IV für das Jahr, 1865 Abhandlungen, 3–47. [for English translation see www.mendelweb.org/Mendel.plain.html]
Glossary
blending theory of inheritance
hypothetical inheritance pattern in which parental traits are blended together in the offspring to produce an intermediate physical appearance
continuous variation
inheritance pattern in which a character shows a range of trait values with small gradations rather than large gaps between them
discontinuous variation
inheritance pattern in which traits are distinct and are transmitted independently of one another
dominant
trait which confers the same physical appearance whether an individual has two copies of the trait or one copy of the dominant trait and one copy of the recessive trait
F1
first filial generation in a cross; the offspring of the parental generation
F2
second filial generation produced when F1 individuals are self-crossed or fertilized with each other
hybridization
process of mating two individuals that differ with the goal of achieving a certain characteristic in their offspring
model system
species or biological system used to study a specific biological phenomenon to be applied to other different species
P0
parental generation in a cross
product rule
probability of two independent events occurring simultaneously can be calculated by multiplying the individual probabilities of each event occurring alone
recessive
trait that appears “latent” or non-expressed when the individual also carries a dominant trait for that same characteristic; when present as two identical copies, the recessive trait is expressed
reciprocal cross
paired cross in which the respective traits of the male and female in one cross become the respective traits of the female and male in the other cross
sum rule
probability of the occurrence of at least one of two mutually exclusive events is the sum of their individual probabilities
trait
variation in the physical appearance of a heritable characteristic | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/12%3A_Mendel's_Experiments_and_Heredity/12.0%3A_Prelude_to_Mendel%27s_Experiments_and_Heredity.txt |
Skills to Develop
• Explain the relationship between genotypes and phenotypes in dominant and recessive gene systems
• Develop a Punnett square to calculate the expected proportions of genotypes and phenotypes in a monohybrid cross
• Explain the purpose and methods of a test cross
• Identify non-Mendelian inheritance patterns such as incomplete dominance, codominance, recessive lethals, multiple alleles, and sex linkage
The seven characteristics that Mendel evaluated in his pea plants were each expressed as one of two versions, or traits. The physical expression of characteristics is accomplished through the expression of genes carried on chromosomes. The genetic makeup of peas consists of two similar or homologous copies of each chromosome, one from each parent. Each pair of homologous chromosomes has the same linear order of genes. In other words, peas are diploid organisms in that they have two copies of each chromosome. The same is true for many other plants and for virtually all animals. Diploid organisms utilize meiosis to produce haploid gametes, which contain one copy of each homologous chromosome that unite at fertilization to create a diploid zygote.
For cases in which a single gene controls a single characteristic, a diploid organism has two genetic copies that may or may not encode the same version of that characteristic. Gene variants that arise by mutation and exist at the same relative locations on homologous chromosomes are called alleles. Mendel examined the inheritance of genes with just two allele forms, but it is common to encounter more than two alleles for any given gene in a natural population.
Phenotypes and Genotypes
Two alleles for a given gene in a diploid organism are expressed and interact to produce physical characteristics. The observable traits expressed by an organism are referred to as its phenotype. An organism’s underlying genetic makeup, consisting of both physically visible and non-expressed alleles, is called its genotype. Mendel’s hybridization experiments demonstrate the difference between phenotype and genotype. When true-breeding plants in which one parent had yellow pods and one had green pods were cross-fertilized, all of the F1 hybrid offspring had yellow pods. That is, the hybrid offspring were phenotypically identical to the true-breeding parent with yellow pods. However, we know that the allele donated by the parent with green pods was not simply lost because it reappeared in some of the F2 offspring. Therefore, the F1 plants must have been genotypically different from the parent with yellow pods.
The P1 plants that Mendel used in his experiments were each homozygous for the trait he was studying. Diploid organisms that are homozygous at a given gene, or locus, have two identical alleles for that gene on their homologous chromosomes. Mendel’s parental pea plants always bred true because both of the gametes produced carried the same trait. When P1 plants with contrasting traits were cross-fertilized, all of the offspring were heterozygous for the contrasting trait, meaning that their genotype reflected that they had different alleles for the gene being examined.
Dominant and Recessive Alleles
Our discussion of homozygous and heterozygous organisms brings us to why the F1 heterozygous offspring were identical to one of the parents, rather than expressing both alleles. In all seven pea-plant characteristics, one of the two contrasting alleles was dominant, and the other was recessive. Mendel called the dominant allele the expressed unit factor; the recessive allele was referred to as the latent unit factor. We now know that these so-called unit factors are actually genes on homologous chromosome pairs. For a gene that is expressed in a dominant and recessive pattern, homozygous dominant and heterozygous organisms will look identical (that is, they will have different genotypes but the same phenotype). The recessive allele will only be observed in homozygous recessive individuals (Table \(1\)).
Table \(1\): Human Inheritance in Dominant and Recessive Patterns
Dominant Traits Recessive Traits
Achondroplasia Albinism
Brachydactyly Cystic fibrosis
Huntington’s disease Duchenne muscular dystrophy
Marfan syndrome Galactosemia
Neurofibromatosis Phenylketonuria
Widow’s peak Sickle-cell anemia
Wooly hair Tay-Sachs disease
Several conventions exist for referring to genes and alleles. For the purposes of this chapter, we will abbreviate genes using the first letter of the gene’s corresponding dominant trait. For example, violet is the dominant trait for a pea plant’s flower color, so the flower-color gene would be abbreviated as V (note that it is customary to italicize gene designations). Furthermore, we will use uppercase and lowercase letters to represent dominant and recessive alleles, respectively. Therefore, we would refer to the genotype of a homozygous dominant pea plant with violet flowers as VV, a homozygous recessive pea plant with white flowers as vv, and a heterozygous pea plant with violet flowers as Vv.
The Punnett Square Approach for a Monohybrid Cross
When fertilization occurs between two true-breeding parents that differ in only one characteristic, the process is called a monohybrid cross, and the resulting offspring are monohybrids. Mendel performed seven monohybrid crosses involving contrasting traits for each characteristic. On the basis of his results in F1 and F2 generations, Mendel postulated that each parent in the monohybrid cross contributed one of two paired unit factors to each offspring, and every possible combination of unit factors was equally likely.
To demonstrate a monohybrid cross, consider the case of true-breeding pea plants with yellow versus green pea seeds. The dominant seed color is yellow; therefore, the parental genotypes were YY for the plants with yellow seeds and yy for the plants with green seeds, respectively. A Punnett square, devised by the British geneticist Reginald Punnett, can be drawn that applies the rules of probability to predict the possible outcomes of a genetic cross or mating and their expected frequencies. To prepare a Punnett square, all possible combinations of the parental alleles are listed along the top (for one parent) and side (for the other parent) of a grid, representing their meiotic segregation into haploid gametes. Then the combinations of egg and sperm are made in the boxes in the table to show which alleles are combining. Each box then represents the diploid genotype of a zygote, or fertilized egg, that could result from this mating. Because each possibility is equally likely, genotypic ratios can be determined from a Punnett square. If the pattern of inheritance (dominant or recessive) is known, the phenotypic ratios can be inferred as well. For a monohybrid cross of two true-breeding parents, each parent contributes one type of allele. In this case, only one genotype is possible. All offspring are Yy and have yellow seeds (Figure \(1\)).
A self-cross of one of the Yy heterozygous offspring can be represented in a 2 × 2 Punnett square because each parent can donate one of two different alleles. Therefore, the offspring can potentially have one of four allele combinations: YY, Yy, yY, or yy (Figure \(1\)). Notice that there are two ways to obtain the Yy genotype: a Y from the egg and a y from the sperm, or a y from the egg and a Y from the sperm. Both of these possibilities must be counted. Recall that Mendel’s pea-plant characteristics behaved in the same way in reciprocal crosses. Therefore, the two possible heterozygous combinations produce offspring that are genotypically and phenotypically identical despite their dominant and recessive alleles deriving from different parents. They are grouped together. Because fertilization is a random event, we expect each combination to be equally likely and for the offspring to exhibit a ratio of YY:Yy:yy genotypes of 1:2:1 (Figure \(1\)). Furthermore, because the YY and Yy offspring have yellow seeds and are phenotypically identical, applying the sum rule of probability, we expect the offspring to exhibit a phenotypic ratio of 3 yellow:1 green. Indeed, working with large sample sizes, Mendel observed approximately this ratio in every F2 generation resulting from crosses for individual traits.
Mendel validated these results by performing an F3 cross in which he self-crossed the dominant- and recessive-expressing F2 plants. When he self-crossed the plants expressing green seeds, all of the offspring had green seeds, confirming that all green seeds had homozygous genotypes of yy. When he self-crossed the F2 plants expressing yellow seeds, he found that one-third of the plants bred true, and two-thirds of the plants segregated at a 3:1 ratio of yellow:green seeds. In this case, the true-breeding plants had homozygous (YY) genotypes, whereas the segregating plants corresponded to the heterozygous (Yy) genotype. When these plants self-fertilized, the outcome was just like the F1 self-fertilizing cross.
The Test Cross Distinguishes the Dominant Phenotype
Beyond predicting the offspring of a cross between known homozygous or heterozygous parents, Mendel also developed a way to determine whether an organism that expressed a dominant trait was a heterozygote or a homozygote. Called the test cross, this technique is still used by plant and animal breeders. In a test cross, the dominant-expressing organism is crossed with an organism that is homozygous recessive for the same characteristic. If the dominant-expressing organism is a homozygote, then all F1 offspring will be heterozygotes expressing the dominant trait (Figure \(2\)). Alternatively, if the dominant expressing organism is a heterozygote, the F1 offspring will exhibit a 1:1 ratio of heterozygotes and recessive homozygotes (Figure \(2\)). The test cross further validates Mendel’s postulate that pairs of unit factors segregate equally.
Exercise
In pea plants, round peas (R) are dominant to wrinkled peas (r). You do a test cross between a pea plant with wrinkled peas (genotype rr) and a plant of unknown genotype that has round peas. You end up with three plants, all which have round peas. From this data, can you tell if the round pea parent plant is homozygous dominant or heterozygous? If the round pea parent plant is heterozygous, what is the probability that a random sample of 3 progeny peas will all be round?
Answer
You cannot be sure if the plant is homozygous or heterozygous as the data set is too small: by random chance, all three plants might have acquired only the dominant gene even if the recessive one is present. If the round pea parent is heterozygous, there is a one-eighth probability that a random sample of three progeny peas will all be round.
Many human diseases are genetically inherited. A healthy person in a family in which some members suffer from a recessive genetic disorder may want to know if he or she has the disease-causing gene and what risk exists of passing the disorder on to his or her offspring. Of course, doing a test cross in humans is unethical and impractical. Instead, geneticists use pedigree analysis to study the inheritance pattern of human genetic diseases (Figure \(3\)).
Exercise
What are the genotypes of the individuals labeled 1, 2 and 3?
Answer
Individual 1 has the genotype aa. Individual 2 has the genotype Aa. Individual 3 has the genotype Aa.
Alternatives to Dominance and Recessiveness
Mendel’s experiments with pea plants suggested that: (1) two “units” or alleles exist for every gene; (2) alleles maintain their integrity in each generation (no blending); and (3) in the presence of the dominant allele, the recessive allele is hidden and makes no contribution to the phenotype. Therefore, recessive alleles can be “carried” and not expressed by individuals. Such heterozygous individuals are sometimes referred to as “carriers.” Further genetic studies in other plants and animals have shown that much more complexity exists, but that the fundamental principles of Mendelian genetics still hold true. In the sections to follow, we consider some of the extensions of Mendelism. If Mendel had chosen an experimental system that exhibited these genetic complexities, it’s possible that he would not have understood what his results meant.
Incomplete Dominance
Mendel’s results, that traits are inherited as dominant and recessive pairs, contradicted the view at that time that offspring exhibited a blend of their parents’ traits. However, the heterozygote phenotype occasionally does appear to be intermediate between the two parents. For example, in the snapdragon, Antirrhinum majus (Figure \(4\)), a cross between a homozygous parent with white flowers (CWCW) and a homozygous parent with red flowers (CRCR) will produce offspring with pink flowers (CRCW). (Note that different genotypic abbreviations are used for Mendelian extensions to distinguish these patterns from simple dominance and recessiveness.) This pattern of inheritance is described as incomplete dominance, denoting the expression of two contrasting alleles such that the individual displays an intermediate phenotype. The allele for red flowers is incompletely dominant over the allele for white flowers. However, the results of a heterozygote self-cross can still be predicted, just as with Mendelian dominant and recessive crosses. In this case, the genotypic ratio would be 1 CRCR:2 CRCW:1 CWCW, and the phenotypic ratio would be 1:2:1 for red:pink:white.
Codominance
A variation on incomplete dominance is codominance, in which both alleles for the same characteristic are simultaneously expressed in the heterozygote. An example of codominance is the MN blood groups of humans. The M and N alleles are expressed in the form of an M or N antigen present on the surface of red blood cells. Homozygotes (LMLM and LNLN) express either the M or the N allele, and heterozygotes (LMLN) express both alleles equally. In a self-cross between heterozygotes expressing a codominant trait, the three possible offspring genotypes are phenotypically distinct. However, the 1:2:1 genotypic ratio characteristic of a Mendelian monohybrid cross still applies.
Multiple Alleles
Mendel implied that only two alleles, one dominant and one recessive, could exist for a given gene. We now know that this is an oversimplification. Although individual humans (and all diploid organisms) can only have two alleles for a given gene, multiple alleles may exist at the population level such that many combinations of two alleles are observed. Note that when many alleles exist for the same gene, the convention is to denote the most common phenotype or genotype among wild animals as the wild type (often abbreviated “+”); this is considered the standard or norm. All other phenotypes or genotypes are considered variants of this standard, meaning that they deviate from the wild type. The variant may be recessive or dominant to the wild-type allele.
An example of multiple alleles is coat color in rabbits (Figure \(5\)). Here, four alleles exist for the c gene. The wild-type version, C+C+, is expressed as brown fur. The chinchilla phenotype, cchcch, is expressed as black-tipped white fur. The Himalayan phenotype, chch, has black fur on the extremities and white fur elsewhere. Finally, the albino, or “colorless” phenotype, cc, is expressed as white fur. In cases of multiple alleles, dominance hierarchies can exist. In this case, the wild-type allele is dominant over all the others, chinchilla is incompletely dominant over Himalayan and albino, and Himalayan is dominant over albino. This hierarchy, or allelic series, was revealed by observing the phenotypes of each possible heterozygote offspring.
The complete dominance of a wild-type phenotype over all other mutants often occurs as an effect of “dosage” of a specific gene product, such that the wild-type allele supplies the correct amount of gene product whereas the mutant alleles cannot. For the allelic series in rabbits, the wild-type allele may supply a given dosage of fur pigment, whereas the mutants supply a lesser dosage or none at all. Interestingly, the Himalayan phenotype is the result of an allele that produces a temperature-sensitive gene product that only produces pigment in the cooler extremities of the rabbit’s body.
Alternatively, one mutant allele can be dominant over all other phenotypes, including the wild type. This may occur when the mutant allele somehow interferes with the genetic message so that even a heterozygote with one wild-type allele copy expresses the mutant phenotype. One way in which the mutant allele can interfere is by enhancing the function of the wild-type gene product or changing its distribution in the body. One example of this is the Antennapedia mutation in Drosophila (Figure \(6\)). In this case, the mutant allele expands the distribution of the gene product, and as a result, the Antennapedia heterozygote develops legs on its head where its antennae should be.
Evolution Connection: Multiple Alleles Confer Drug Resistance in the Malaria Parasite
Malaria is a parasitic disease in humans that is transmitted by infected female mosquitoes, including Anopheles gambiae (Figure \(7\)a), and is characterized by cyclic high fevers, chills, flu-like symptoms, and severe anemia. Plasmodium falciparum and P. vivax are the most common causative agents of malaria, and P. falciparum is the most deadly (Figure \(7\)b). When promptly and correctly treated, P. falciparum malaria has a mortality rate of 0.1 percent. However, in some parts of the world, the parasite has evolved resistance to commonly used malaria treatments, so the most effective malarial treatments can vary by geographic region.
In Southeast Asia, Africa, and South America, P. falciparum has developed resistance to the anti-malarial drugs chloroquine, mefloquine, and sulfadoxine-pyrimethamine. P. falciparum, which is haploid during the life stage in which it is infectious to humans, has evolved multiple drug-resistant mutant alleles of the dhps gene. Varying degrees of sulfadoxine resistance are associated with each of these alleles. Being haploid, P. falciparum needs only one drug-resistant allele to express this trait.
In Southeast Asia, different sulfadoxine-resistant alleles of the dhps gene are localized to different geographic regions. This is a common evolutionary phenomenon that occurs because drug-resistant mutants arise in a population and interbreed with other P. falciparum isolates in close proximity. Sulfadoxine-resistant parasites cause considerable human hardship in regions where this drug is widely used as an over-the-counter malaria remedy. As is common with pathogens that multiply to large numbers within an infection cycle, P. falciparum evolves relatively rapidly (over a decade or so) in response to the selective pressure of commonly used anti-malarial drugs. For this reason, scientists must constantly work to develop new drugs or drug combinations to combat the worldwide malaria burden.1
X-Linked Traits
In humans, as well as in many other animals and some plants, the sex of the individual is determined by sex chromosomes. The sex chromosomes are one pair of non-homologous chromosomes. Until now, we have only considered inheritance patterns among non-sex chromosomes, or autosomes. In addition to 22 homologous pairs of autosomes, human females have a homologous pair of X chromosomes, whereas human males have an XY chromosome pair. Although the Y chromosome contains a small region of similarity to the X chromosome so that they can pair during meiosis, the Y chromosome is much shorter and contains many fewer genes. When a gene being examined is present on the X chromosome, but not on the Y chromosome, it is said to be X-linked.
Eye color in Drosophila was one of the first X-linked traits to be identified. Thomas Hunt Morgan mapped this trait to the X chromosome in 1910. Like humans, Drosophila males have an XY chromosome pair, and females are XX. In flies, the wild-type eye color is red (XW) and it is dominant to white eye color (Xw) (Figure \(8\)). Because of the location of the eye-color gene, reciprocal crosses do not produce the same offspring ratios. Males are said to be hemizygous, because they have only one allele for any X-linked characteristic. Hemizygosity makes the descriptions of dominance and recessiveness irrelevant for XY males. Drosophila males lack a second allele copy on the Y chromosome; that is, their genotype can only be XWY or XwY. In contrast, females have two allele copies of this gene and can be XWXW, XWXw, or XwXw.
In an X-linked cross, the genotypes of F1 and F2 offspring depend on whether the recessive trait was expressed by the male or the female in the P1 generation. With regard to Drosophila eye color, when the P1 male expresses the white-eye phenotype and the female is homozygous red-eyed, all members of the F1 generation exhibit red eyes (Figure \(9\)). The F1 females are heterozygous (XWXw), and the males are all XWY, having received their X chromosome from the homozygous dominant P1 female and their Y chromosome from the P1 male. A subsequent cross between the XWXw female and the XWY male would produce only red-eyed females (with XWXW or XWXw genotypes) and both red- and white-eyed males (with XWY or XwY genotypes). Now, consider a cross between a homozygous white-eyed female and a male with red eyes. The F1 generation would exhibit only heterozygous red-eyed females (XWXw) and only white-eyed males (XwY). Half of the F2 females would be red-eyed (XWXw) and half would be white-eyed (XwXw). Similarly, half of the F2 males would be red-eyed (XWY) and half would be white-eyed (XwY).
Exercise
What ratio of offspring would result from a cross between a white-eyed male and a female that is heterozygous for red eye color?
Answer
Half of the female offspring would be heterozygous (XWXw) with red eyes, and half would be homozygous recessive (XwXw) with white eyes. Half of the male offspring would be hemizygous dominant (XWY) withe red yes, and half would be hemizygous recessive (XwY) with white eyes.
Discoveries in fruit fly genetics can be applied to human genetics. When a female parent is homozygous for a recessive X-linked trait, she will pass the trait on to 100 percent of her offspring. Her male offspring are, therefore, destined to express the trait, as they will inherit their father's Y chromosome. In humans, the alleles for certain conditions (some forms of color blindness, hemophilia, and muscular dystrophy) are X-linked. Females who are heterozygous for these diseases are said to be carriers and may not exhibit any phenotypic effects. These females will pass the disease to half of their sons and will pass carrier status to half of their daughters; therefore, recessive X-linked traits appear more frequently in males than females.
In some groups of organisms with sex chromosomes, the gender with the non-homologous sex chromosomes is the female rather than the male. This is the case for all birds. In this case, sex-linked traits will be more likely to appear in the female, in which they are hemizygous.
Human Sex-linked Disorders
Sex-linkage studies in Morgan’s laboratory provided the fundamentals for understanding X-linked recessive disorders in humans, which include red-green color blindness, and Types A and B hemophilia. Because human males need to inherit only one recessive mutant X allele to be affected, X-linked disorders are disproportionately observed in males. Females must inherit recessive X-linked alleles from both of their parents in order to express the trait. When they inherit one recessive X-linked mutant allele and one dominant X-linked wild-type allele, they are carriers of the trait and are typically unaffected. Carrier females can manifest mild forms of the trait due to the inactivation of the dominant allele located on one of the X chromosomes. However, female carriers can contribute the trait to their sons, resulting in the son exhibiting the trait, or they can contribute the recessive allele to their daughters, resulting in the daughters being carriers of the trait (Figure \(10\)). Although some Y-linked recessive disorders exist, typically they are associated with infertility in males and are therefore not transmitted to subsequent generations.
Link to Learning
Watch this video to learn more about sex-linked traits.
Lethality
A large proportion of genes in an individual’s genome are essential for survival. Occasionally, a nonfunctional allele for an essential gene can arise by mutation and be transmitted in a population as long as individuals with this allele also have a wild-type, functional copy. The wild-type allele functions at a capacity sufficient to sustain life and is therefore considered to be dominant over the nonfunctional allele. However, consider two heterozygous parents that have a genotype of wild-type/nonfunctional mutant for a hypothetical essential gene. In one quarter of their offspring, we would expect to observe individuals that are homozygous recessive for the nonfunctional allele. Because the gene is essential, these individuals might fail to develop past fertilization, die in utero, or die later in life, depending on what life stage requires this gene. An inheritance pattern in which an allele is only lethal in the homozygous form and in which the heterozygote may be normal or have some altered non-lethal phenotype is referred to as recessive lethal.
For crosses between heterozygous individuals with a recessive lethal allele that causes death before birth when homozygous, only wild-type homozygotes and heterozygotes would be observed. The genotypic ratio would therefore be 2:1. In other instances, the recessive lethal allele might also exhibit a dominant (but not lethal) phenotype in the heterozygote. For instance, the recessive lethal Curly allele in Drosophila affects wing shape in the heterozygote form but is lethal in the homozygote.
A single copy of the wild-type allele is not always sufficient for normal functioning or even survival. The dominant lethal inheritance pattern is one in which an allele is lethal both in the homozygote and the heterozygote; this allele can only be transmitted if the lethality phenotype occurs after reproductive age. Individuals with mutations that result in dominant lethal alleles fail to survive even in the heterozygote form. Dominant lethal alleles are very rare because, as you might expect, the allele only lasts one generation and is not transmitted. However, just as the recessive lethal allele might not immediately manifest the phenotype of death, dominant lethal alleles also might not be expressed until adulthood. Once the individual reaches reproductive age, the allele may be unknowingly passed on, resulting in a delayed death in both generations. An example of this in humans is Huntington’s disease, in which the nervous system gradually wastes away (Figure \(11\)). People who are heterozygous for the dominant Huntington allele (Hh) will inevitably develop the fatal disease. However, the onset of Huntington’s disease may not occur until age 40, at which point the afflicted persons may have already passed the allele to 50 percent of their offspring.
Summary
When true-breeding or homozygous individuals that differ for a certain trait are crossed, all of the offspring will be heterozygotes for that trait. If the traits are inherited as dominant and recessive, the F1 offspring will all exhibit the same phenotype as the parent homozygous for the dominant trait. If these heterozygous offspring are self-crossed, the resulting F2 offspring will be equally likely to inherit gametes carrying the dominant or recessive trait, giving rise to offspring of which one quarter are homozygous dominant, half are heterozygous, and one quarter are homozygous recessive. Because homozygous dominant and heterozygous individuals are phenotypically identical, the observed traits in the F2 offspring will exhibit a ratio of three dominant to one recessive.
Alleles do not always behave in dominant and recessive patterns. Incomplete dominance describes situations in which the heterozygote exhibits a phenotype that is intermediate between the homozygous phenotypes. Codominance describes the simultaneous expression of both of the alleles in the heterozygote. Although diploid organisms can only have two alleles for any given gene, it is common for more than two alleles of a gene to exist in a population. In humans, as in many animals and some plants, females have two X chromosomes and males have one X and one Y chromosome. Genes that are present on the X but not the Y chromosome are said to be X-linked, such that males only inherit one allele for the gene, and females inherit two. Finally, some alleles can be lethal. Recessive lethal alleles are only lethal in homozygotes, but dominant lethal alleles are fatal in heterozygotes as well.
Footnotes
1. 1 Sumiti Vinayak, et al., “Origin and Evolution of Sulfadoxine Resistant Plasmodium falciparum,” Public Library of Science Pathogens 6, no. 3 (2010): e1000830, doi:10.1371/journal.ppat.1000830.
Glossary
allele
gene variations that arise by mutation and exist at the same relative locations on homologous chromosomes
autosomes
any of the non-sex chromosomes
codominance
in a heterozygote, complete and simultaneous expression of both alleles for the same characteristic
dominant lethal
inheritance pattern in which an allele is lethal both in the homozygote and the heterozygote; this allele can only be transmitted if the lethality phenotype occurs after reproductive age
genotype
underlying genetic makeup, consisting of both physically visible and non-expressed alleles, of an organism
hemizygous
presence of only one allele for a characteristic, as in X-linkage; hemizygosity makes descriptions of dominance and recessiveness irrelevant
heterozygous
having two different alleles for a given gene on the homologous chromosome
homozygous
having two identical alleles for a given gene on the homologous chromosome
incomplete dominance
in a heterozygote, expression of two contrasting alleles such that the individual displays an intermediate phenotype
monohybrid
result of a cross between two true-breeding parents that express different traits for only one characteristic
phenotype
observable traits expressed by an organism
Punnett square
visual representation of a cross between two individuals in which the gametes of each individual are denoted along the top and side of a grid, respectively, and the possible zygotic genotypes are recombined at each box in the grid
recessive lethal
inheritance pattern in which an allele is only lethal in the homozygous form; the heterozygote may be normal or have some altered, non-lethal phenotype
sex-linked
any gene on a sex chromosome
test cross
cross between a dominant expressing individual with an unknown genotype and a homozygous recessive individual; the offspring phenotypes indicate whether the unknown parent is heterozygous or homozygous for the dominant trait
X-linked
gene present on the X, but not the Y chromosome | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/12%3A_Mendel's_Experiments_and_Heredity/12.2%3A_Characteristics_and_Traits.txt |
Skills to Develop
• Explain Mendel’s law of segregation and independent assortment in terms of genetics and the events of meiosis
• Use the forked-line method and the probability rules to calculate the probability of genotypes and phenotypes from multiple gene crosses
• Explain the effect of linkage and recombination on gamete genotypes
• Explain the phenotypic outcomes of epistatic effects between genes
Mendel generalized the results of his pea-plant experiments into four postulates, some of which are sometimes called “laws,” that describe the basis of dominant and recessive inheritance in diploid organisms. As you have learned, more complex extensions of Mendelism exist that do not exhibit the same F2 phenotypic ratios (3:1). Nevertheless, these laws summarize the basics of classical genetics.
Pairs of Unit Factors, or Genes
Mendel proposed first that paired unit factors of heredity were transmitted faithfully from generation to generation by the dissociation and reassociation of paired factors during gametogenesis and fertilization, respectively. After he crossed peas with contrasting traits and found that the recessive trait resurfaced in the F2 generation, Mendel deduced that hereditary factors must be inherited as discrete units. This finding contradicted the belief at that time that parental traits were blended in the offspring.
Alleles Can Be Dominant or Recessive
Mendel’s law of dominance states that in a heterozygote, one trait will conceal the presence of another trait for the same characteristic. Rather than both alleles contributing to a phenotype, the dominant allele will be expressed exclusively. The recessive allele will remain “latent” but will be transmitted to offspring by the same manner in which the dominant allele is transmitted. The recessive trait will only be expressed by offspring that have two copies of this allele (Figure \(1\)), and these offspring will breed true when self-crossed.
Since Mendel’s experiments with pea plants, other researchers have found that the law of dominance does not always hold true. Instead, several different patterns of inheritance have been found to exist.
Equal Segregation of Alleles
Observing that true-breeding pea plants with contrasting traits gave rise to F1 generations that all expressed the dominant trait and F2 generations that expressed the dominant and recessive traits in a 3:1 ratio, Mendel proposed the law of segregation. This law states that paired unit factors (genes) must segregate equally into gametes such that offspring have an equal likelihood of inheriting either factor. For the F2 generation of a monohybrid cross, the following three possible combinations of genotypes could result: homozygous dominant, heterozygous, or homozygous recessive. Because heterozygotes could arise from two different pathways (receiving one dominant and one recessive allele from either parent), and because heterozygotes and homozygous dominant individuals are phenotypically identical, the law supports Mendel’s observed 3:1 phenotypic ratio. The equal segregation of alleles is the reason we can apply the Punnett square to accurately predict the offspring of parents with known genotypes. The physical basis of Mendel’s law of segregation is the first division of meiosis, in which the homologous chromosomes with their different versions of each gene are segregated into daughter nuclei. The role of the meiotic segregation of chromosomes in sexual reproduction was not understood by the scientific community during Mendel’s lifetime.
Independent Assortment
Mendel’s law of independent assortment states that genes do not influence each other with regard to the sorting of alleles into gametes, and every possible combination of alleles for every gene is equally likely to occur. The independent assortment of genes can be illustrated by the dihybrid cross, a cross between two true-breeding parents that express different traits for two characteristics. Consider the characteristics of seed color and seed texture for two pea plants, one that has green, wrinkled seeds (yyrr) and another that has yellow, round seeds (YYRR). Because each parent is homozygous, the law of segregation indicates that the gametes for the green/wrinkled plant all are yr, and the gametes for the yellow/round plant are all YR. Therefore, the F1 generation of offspring all are YyRr (Figure \(2\)).
Exercise
In pea plants, purple flowers (P) are dominant to white flowers (p) and yellow peas (Y) are dominant to green peas (y). What are the possible genotypes and phenotypes for a cross between PpYY and ppYy pea plants? How many squares do you need to do a Punnett square analysis of this cross?
Answer
The possible genotypes are PpYY, PpYy, ppYY, and ppYy. The former two genotypes would result in plants with purple flowers and yellow peas, while the latter two genotypes would result in plants with white flowers with yellow peas, for a 1:1 ratio of each phenotype. You only need a 2 × 2 Punnett square (four squares total) to do this analysis because two of the alleles are homozygous.
For the F2 generation, the law of segregation requires that each gamete receive either an R allele or an r allele along with either a Y allele or a y allele. The law of independent assortment states that a gamete into which an r allele sorted would be equally likely to contain either a Y allele or a y allele. Thus, there are four equally likely gametes that can be formed when the YyRr heterozygote is self-crossed, as follows: YR, Yr, yR, and yr. Arranging these gametes along the top and left of a 4 × 4 Punnett square (Figure \(2\)) gives us 16 equally likely genotypic combinations. From these genotypes, we infer a phenotypic ratio of 9 round/yellow:3 round/green:3 wrinkled/yellow:1 wrinkled/green (Figure \(2\)). These are the offspring ratios we would expect, assuming we performed the crosses with a large enough sample size.
Because of independent assortment and dominance, the 9:3:3:1 dihybrid phenotypic ratio can be collapsed into two 3:1 ratios, characteristic of any monohybrid cross that follows a dominant and recessive pattern. Ignoring seed color and considering only seed texture in the above dihybrid cross, we would expect that three quarters of the F2 generation offspring would be round, and one quarter would be wrinkled. Similarly, isolating only seed color, we would assume that three quarters of the F2 offspring would be yellow and one quarter would be green. The sorting of alleles for texture and color are independent events, so we can apply the product rule. Therefore, the proportion of round and yellow F2 offspring is expected to be (3/4) × (3/4) = 9/16, and the proportion of wrinkled and green offspring is expected to be (1/4) × (1/4) = 1/16. These proportions are identical to those obtained using a Punnett square. Round, green and wrinkled, yellow offspring can also be calculated using the product rule, as each of these genotypes includes one dominant and one recessive phenotype. Therefore, the proportion of each is calculated as (3/4) × (1/4) = 3/16.
The law of independent assortment also indicates that a cross between yellow, wrinkled (YYrr) and green, round (yyRR) parents would yield the same F1 and F2 offspring as in the YYRR x yyrr cross.
The physical basis for the law of independent assortment also lies in meiosis I, in which the different homologous pairs line up in random orientations. Each gamete can contain any combination of paternal and maternal chromosomes (and therefore the genes on them) because the orientation of tetrads on the metaphase plane is random.
Forked-Line Method
When more than two genes are being considered, the Punnett-square method becomes unwieldy. For instance, examining a cross involving four genes would require a 16 × 16 grid containing 256 boxes. It would be extremely cumbersome to manually enter each genotype. For more complex crosses, the forked-line and probability methods are preferred.
To prepare a forked-line diagram for a cross between F1 heterozygotes resulting from a cross between AABBCC and aabbcc parents, we first create rows equal to the number of genes being considered, and then segregate the alleles in each row on forked lines according to the probabilities for individual monohybrid crosses (Figure \(3\)). We then multiply the values along each forked path to obtain the F2 offspring probabilities. Note that this process is a diagrammatic version of the product rule. The values along each forked pathway can be multiplied because each gene assorts independently. For a trihybrid cross, the F2 phenotypic ratio is 27:9:9:9:3:3:3:1.
Probability Method
While the forked-line method is a diagrammatic approach to keeping track of probabilities in a cross, the probability method gives the proportions of offspring expected to exhibit each phenotype (or genotype) without the added visual assistance. Both methods make use of the product rule and consider the alleles for each gene separately. Earlier, we examined the phenotypic proportions for a trihybrid cross using the forked-line method; now we will use the probability method to examine the genotypic proportions for a cross with even more genes.
For a trihybrid cross, writing out the forked-line method is tedious, albeit not as tedious as using the Punnett-square method. To fully demonstrate the power of the probability method, however, we can consider specific genetic calculations. For instance, for a tetrahybrid cross between individuals that are heterozygotes for all four genes, and in which all four genes are sorting independently and in a dominant and recessive pattern, what proportion of the offspring will be expected to be homozygous recessive for all four alleles? Rather than writing out every possible genotype, we can use the probability method. We know that for each gene, the fraction of homozygous recessive offspring will be 1/4. Therefore, multiplying this fraction for each of the four genes, (1/4) × (1/4) × (1/4) × (1/4), we determine that 1/256 of the offspring will be quadruply homozygous recessive.
For the same tetrahybrid cross, what is the expected proportion of offspring that have the dominant phenotype at all four loci? We can answer this question using phenotypic proportions, but let’s do it the hard way—using genotypic proportions. The question asks for the proportion of offspring that are 1) homozygous dominant at A or heterozygous at A, and 2) homozygous at B or heterozygous at B, and so on. Noting the “or” and “and” in each circumstance makes clear where to apply the sum and product rules. The probability of a homozygous dominant at A is 1/4 and the probability of a heterozygote at A is 1/2. The probability of the homozygote or the heterozygote is 1/4 + 1/2 = 3/4 using the sum rule. The same probability can be obtained in the same way for each of the other genes, so that the probability of a dominant phenotype at A and B and C and D is, using the product rule, equal to 3/4 × 3/4 × 3/4 × 3/4, or 27/64. If you are ever unsure about how to combine probabilities, returning to the forked-line method should make it clear.
Rules for Multihybrid Fertilization
Predicting the genotypes and phenotypes of offspring from given crosses is the best way to test your knowledge of Mendelian genetics. Given a multihybrid cross that obeys independent assortment and follows a dominant and recessive pattern, several generalized rules exist; you can use these rules to check your results as you work through genetics calculations (Table \(1\)). To apply these rules, first you must determine n, the number of heterozygous gene pairs (the number of genes segregating two alleles each). For example, a cross between AaBb and AaBb heterozygotes has an n of 2. In contrast, a cross between AABb and AABb has an n of 1 because A is not heterozygous.
Table \(1\): General rules for Multi-hybrid crosses
General Rule Number of Heterozygous Gene Pairs
Number of different F1 gametes 2n
Number of different F2 genotypes 3n
Given dominant and recessive inheritance, the number of different F2 phenotypes 2n
Linked Genes Violate the Law of Independent Assortment
Although all of Mendel’s pea characteristics behaved according to the law of independent assortment, we now know that some allele combinations are not inherited independently of each other. Genes that are located on separate non-homologous chromosomes will always sort independently. However, each chromosome contains hundreds or thousands of genes, organized linearly on chromosomes like beads on a string. The segregation of alleles into gametes can be influenced by linkage, in which genes that are located physically close to each other on the same chromosome are more likely to be inherited as a pair. However, because of the process of recombination, or “crossover,” it is possible for two genes on the same chromosome to behave independently, or as if they are not linked. To understand this, let’s consider the biological basis of gene linkage and recombination.
Homologous chromosomes possess the same genes in the same linear order. The alleles may differ on homologous chromosome pairs, but the genes to which they correspond do not. In preparation for the first division of meiosis, homologous chromosomes replicate and synapse. Like genes on the homologs align with each other. At this stage, segments of homologous chromosomes exchange linear segments of genetic material (Figure \(4\)). This process is called recombination, or crossover, and it is a common genetic process. Because the genes are aligned during recombination, the gene order is not altered. Instead, the result of recombination is that maternal and paternal alleles are combined onto the same chromosome. Across a given chromosome, several recombination events may occur, causing extensive shuffling of alleles.
When two genes are located in close proximity on the same chromosome, they are considered linked, and their alleles tend to be transmitted through meiosis together. To exemplify this, imagine a dihybrid cross involving flower color and plant height in which the genes are next to each other on the chromosome. If one homologous chromosome has alleles for tall plants and red flowers, and the other chromosome has genes for short plants and yellow flowers, then when the gametes are formed, the tall and red alleles will go together into a gamete and the short and yellow alleles will go into other gametes. These are called the parental genotypes because they have been inherited intact from the parents of the individual producing gametes. But unlike if the genes were on different chromosomes, there will be no gametes with tall and yellow alleles and no gametes with short and red alleles. If you create the Punnett square with these gametes, you will see that the classical Mendelian prediction of a 9:3:3:1 outcome of a dihybrid cross would not apply. As the distance between two genes increases, the probability of one or more crossovers between them increases, and the genes behave more like they are on separate chromosomes. Geneticists have used the proportion of recombinant gametes (the ones not like the parents) as a measure of how far apart genes are on a chromosome. Using this information, they have constructed elaborate maps of genes on chromosomes for well-studied organisms, including humans.
Mendel’s seminal publication makes no mention of linkage, and many researchers have questioned whether he encountered linkage but chose not to publish those crosses out of concern that they would invalidate his independent assortment postulate. The garden pea has seven chromosomes, and some have suggested that his choice of seven characteristics was not a coincidence. However, even if the genes he examined were not located on separate chromosomes, it is possible that he simply did not observe linkage because of the extensive shuffling effects of recombination.
Scientific Method Connection: Testing the Hypothesis of Independent Assortment
To better appreciate the amount of labor and ingenuity that went into Mendel’s experiments, proceed through one of Mendel’s dihybrid crosses.
Question: What will be the offspring of a dihybrid cross?
Background: Consider that pea plants mature in one growing season, and you have access to a large garden in which you can cultivate thousands of pea plants. There are several true-breeding plants with the following pairs of traits: tall plants with inflated pods, and dwarf plants with constricted pods. Before the plants have matured, you remove the pollen-producing organs from the tall/inflated plants in your crosses to prevent self-fertilization. Upon plant maturation, the plants are manually crossed by transferring pollen from the dwarf/constricted plants to the stigmata of the tall/inflated plants.
Hypothesis: Both trait pairs will sort independently according to Mendelian laws. When the true-breeding parents are crossed, all of the F1 offspring are tall and have inflated pods, which indicates that the tall and inflated traits are dominant over the dwarf and constricted traits, respectively. A self-cross of the F1 heterozygotes results in 2,000 F2 progeny.
Test the hypothesis: Because each trait pair sorts independently, the ratios of tall:dwarf and inflated:constricted are each expected to be 3:1. The tall/dwarf trait pair is called T/t, and the inflated/constricted trait pair is designated I/i. Each member of the F1 generation therefore has a genotype of TtIi. Construct a grid analogous to Figure \(2\), in which you cross two TtIi individuals. Each individual can donate four combinations of two traits: TI, Ti, tI, or ti, meaning that there are 16 possibilities of offspring genotypes. Because the T and I alleles are dominant, any individual having one or two of those alleles will express the tall or inflated phenotypes, respectively, regardless if they also have a t or i allele. Only individuals that are tt or ii will express the dwarf and constricted alleles, respectively. As shown in Figure \(5\), you predict that you will observe the following offspring proportions: tall/inflated:tall/constricted:dwarf/inflated:dwarf/constricted in a 9:3:3:1 ratio. Notice from the grid that when considering the tall/dwarf and inflated/constricted trait pairs in isolation, they are each inherited in 3:1 ratios.
Test the hypothesis: You cross the dwarf and tall plants and then self-cross the offspring. For best results, this is repeated with hundreds or even thousands of pea plants. What special precautions should be taken in the crosses and in growing the plants?
Analyze your data: You observe the following plant phenotypes in the F2 generation: 2706 tall/inflated, 930 tall/constricted, 888 dwarf/inflated, and 300 dwarf/constricted. Reduce these findings to a ratio and determine if they are consistent with Mendelian laws.
Form a conclusion: Were the results close to the expected 9:3:3:1 phenotypic ratio? Do the results support the prediction? What might be observed if far fewer plants were used, given that alleles segregate randomly into gametes? Try to imagine growing that many pea plants, and consider the potential for experimental error. For instance, what would happen if it was extremely windy one day?
Epistasis
Mendel’s studies in pea plants implied that the sum of an individual’s phenotype was controlled by genes (or as he called them, unit factors), such that every characteristic was distinctly and completely controlled by a single gene. In fact, single observable characteristics are almost always under the influence of multiple genes (each with two or more alleles) acting in unison. For example, at least eight genes contribute to eye color in humans.
In some cases, several genes can contribute to aspects of a common phenotype without their gene products ever directly interacting. In the case of organ development, for instance, genes may be expressed sequentially, with each gene adding to the complexity and specificity of the organ. Genes may function in complementary or synergistic fashions, such that two or more genes need to be expressed simultaneously to affect a phenotype. Genes may also oppose each other, with one gene modifying the expression of another.
In epistasis, the interaction between genes is antagonistic, such that one gene masks or interferes with the expression of another. “Epistasis” is a word composed of Greek roots that mean “standing upon.” The alleles that are being masked or silenced are said to be hypostatic to the epistatic alleles that are doing the masking. Often the biochemical basis of epistasis is a gene pathway in which the expression of one gene is dependent on the function of a gene that precedes or follows it in the pathway.
An example of epistasis is pigmentation in mice. The wild-type coat color, agouti (AA), is dominant to solid-colored fur (aa). However, a separate gene (C) is necessary for pigment production. A mouse with a recessive c allele at this locus is unable to produce pigment and is albino regardless of the allele present at locus A (Figure \(6\)). Therefore, the genotypes AAcc, Aacc, and aacc all produce the same albino phenotype. A cross between heterozygotes for both genes (AaCc x AaCc) would generate offspring with a phenotypic ratio of 9 agouti:3 solid color:4 albino (Figure \(6\)). In this case, the C gene is epistatic to the A gene.
Epistasis can also occur when a dominant allele masks expression at a separate gene. Fruit color in summer squash is expressed in this way. Homozygous recessive expression of the W gene (ww) coupled with homozygous dominant or heterozygous expression of the Y gene (YY or Yy) generates yellow fruit, and the wwyy genotype produces green fruit. However, if a dominant copy of the W gene is present in the homozygous or heterozygous form, the summer squash will produce white fruit regardless of the Y alleles. A cross between white heterozygotes for both genes (WwYy × WwYy) would produce offspring with a phenotypic ratio of 12 white:3 yellow:1 green.
Finally, epistasis can be reciprocal such that either gene, when present in the dominant (or recessive) form, expresses the same phenotype. In the shepherd’s purse plant (Capsella bursa-pastoris), the characteristic of seed shape is controlled by two genes in a dominant epistatic relationship. When the genes A and B are both homozygous recessive (aabb), the seeds are ovoid. If the dominant allele for either of these genes is present, the result is triangular seeds. That is, every possible genotype other than aabb results in triangular seeds, and a cross between heterozygotes for both genes (AaBb x AaBb) would yield offspring with a phenotypic ratio of 15 triangular:1 ovoid.
As you work through genetics problems, keep in mind that any single characteristic that results in a phenotypic ratio that totals 16 is typical of a two-gene interaction. Recall the phenotypic inheritance pattern for Mendel’s dihybrid cross, which considered two non-interacting genes—9:3:3:1. Similarly, we would expect interacting gene pairs to also exhibit ratios expressed as 16 parts. Note that we are assuming the interacting genes are not linked; they are still assorting independently into gametes.
Summary
Mendel postulated that genes (characteristics) are inherited as pairs of alleles (traits) that behave in a dominant and recessive pattern. Alleles segregate into gametes such that each gamete is equally likely to receive either one of the two alleles present in a diploid individual. In addition, genes are assorted into gametes independently of one another. That is, alleles are generally not more likely to segregate into a gamete with a particular allele of another gene. A dihybrid cross demonstrates independent assortment when the genes in question are on different chromosomes or distant from each other on the same chromosome. For crosses involving more than two genes, use the forked line or probability methods to predict offspring genotypes and phenotypes rather than a Punnett square.
Although chromosomes sort independently into gametes during meiosis, Mendel’s law of independent assortment refers to genes, not chromosomes, and a single chromosome may carry more than 1,000 genes. When genes are located in close proximity on the same chromosome, their alleles tend to be inherited together. This results in offspring ratios that violate Mendel's law of independent assortment. However, recombination serves to exchange genetic material on homologous chromosomes such that maternal and paternal alleles may be recombined on the same chromosome. This is why alleles on a given chromosome are not always inherited together. Recombination is a random event occurring anywhere on a chromosome. Therefore, genes that are far apart on the same chromosome are likely to still assort independently because of recombination events that occurred in the intervening chromosomal space.
Whether or not they are sorting independently, genes may interact at the level of gene products such that the expression of an allele for one gene masks or modifies the expression of an allele for a different gene. This is called epistasis.
Glossary
dihybrid
result of a cross between two true-breeding parents that express different traits for two characteristics
epistasis
antagonistic interaction between genes such that one gene masks or interferes with the expression of another
law of dominance
in a heterozygote, one trait will conceal the presence of another trait for the same characteristic
law of independent assortment
genes do not influence each other with regard to sorting of alleles into gametes; every possible combination of alleles is equally likely to occur
law of segregation
paired unit factors (i.e., genes) segregate equally into gametes such that offspring have an equal likelihood of inheriting any combination of factors
linkage
phenomenon in which alleles that are located in close proximity to each other on the same chromosome are more likely to be inherited together | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/12%3A_Mendel's_Experiments_and_Heredity/12.3%3A_Laws_of_Inheritance.txt |
12.1: Mendel’s Experiments and the Laws of Probability
In 1865, Mendel presented the results of his experiments with nearly 30,000 pea plants to the local Natural History Society. He demonstrated that traits are transmitted faithfully from parents to offspring independently of other traits and in dominant and recessive patterns.
Review Questions
Mendel performed hybridizations by transferring pollen from the _______ of the male plant to the female ova.
1. anther
2. pistil
3. stigma
4. seed
Answer
A
Which is one of the seven characteristics that Mendel observed in pea plants?
1. flower size
2. seed texture
3. leaf shape
4. stem color
Answer
B
Imagine you are performing a cross involving seed color in garden pea plants. What F1 offspring would you expect if you cross true-breeding parents with green seeds and yellow seeds? Yellow seed color is dominant over green.
1. 100 percent yellow-green seeds
2. 100 percent yellow seeds
3. 50 percent yellow, 50 percent green seeds
4. 25 percent green, 75 percent yellow seeds
Answer
B
Consider a cross to investigate the pea pod texture trait, involving constricted or inflated pods. Mendel found that the traits behave according to a dominant/recessive pattern in which inflated pods were dominant. If you performed this cross and obtained 650 inflated-pod plants in the F2 generation, approximately how many constricted-pod plants would you expect to have?
1. 600
2. 165
3. 217
4. 468
Answer
C
Free Response
Describe one of the reasons why the garden pea was an excellent choice of model system for studying inheritance.
Answer
The garden pea is sessile and has flowers that close tightly during self-pollination. These features help to prevent accidental or unintentional fertilizations that could have diminished the accuracy of Mendel’s data.
How would you perform a reciprocal cross for the characteristic of stem height in the garden pea?
Answer
Two sets of P0 parents would be used. In the first cross, pollen would be transferred from a true-breeding tall plant to the stigma of a true-breeding dwarf plant. In the second cross, pollen would be transferred from a true-breeding dwarf plant to the stigma of a true-breeding tall plant. For each cross, F1 and F2 offspring would be analyzed to determine if offspring traits were affected according to which parent donated each trait.
12.2: Characteristics and Traits
The genetic makeup of peas consists of two similar or homologous copies of each chromosome, one from each parent. Each pair of homologous chromosomes has the same linear order of genes; hence peas are diploid organisms. The same is true for many other plants and for virtually all animals. Diploid organisms utilize meiosis to produce haploid gametes, which contain one copy of each homologous chromosome that unite at fertilization to create a diploid zygote.
Review Questions
The observable traits expressed by an organism are described as its ________.
1. phenotype
2. genotype
3. alleles
4. zygote
Answer
A
A recessive trait will be observed in individuals that are ________ for that trait.
1. heterozygous
2. homozygous or heterozygous
3. homozygous
4. diploid
Answer
C
If black and white true-breeding mice are mated and the result is all gray offspring, what inheritance pattern would this be indicative of?
1. dominance
2. codominance
3. multiple alleles
4. incomplete dominance
Answer
D
The ABO blood groups in humans are expressed as the IA, IB, and i alleles. The IA allele encodes the A blood group antigen, IB encodes B, and i encodes O. Both A and B are dominant to O. If a heterozygous blood type A parent (IAi) and a heterozygous blood type B parent (IBi) mate, one quarter of their offspring will have AB blood type (IAIB) in which both antigens are expressed equally. Therefore, ABO blood groups are an example of:
1. multiple alleles and incomplete dominance
2. codominance and incomplete dominance
3. incomplete dominance only
4. multiple alleles and codominance
Answer
D
In a mating between two individuals that are heterozygous for a recessive lethal allele that is expressed in utero, what genotypic ratio (homozygous dominant:heterozygous:homozygous recessive) would you expect to observe in the offspring?
1. 1:2:1
2. 3:1:1
3. 1:2:0
4. 0:2:1
Answer
C
Free Response
The gene for flower position in pea plants exists as axial or terminal alleles. Given that axial is dominant to terminal, list all of the possible F1 and F2 genotypes and phenotypes from a cross involving parents that are homozygous for each trait. Express genotypes with conventional genetic abbreviations.
Answer
Because axial is dominant, the gene would be designated as A. F1 would be all heterozygous Aa with axial phenotype. F2 would have possible genotypes of AA, Aa, and aa; these would correspond to axial, axial, and terminal phenotypes, respectively.
Use a Punnett square to predict the offspring in a cross between a dwarf pea plant (homozygous recessive) and a tall pea plant (heterozygous). What is the phenotypic ratio of the offspring?
Answer
The Punnett square would be 2 × 2 and will have T and T along the top, and T and t along the left side. Clockwise from the top left, the genotypes listed within the boxes will be Tt, Tt, tt, and tt. The phenotypic ratio will be 1 tall:1 dwarf.
Can a human male be a carrier of red-green color blindness?
Answer
No, males can only express color blindness. They cannot carry it because an individual needs two X chromosomes to be a carrier.
12.3: Laws of Inheritance
Mendel generalized the results of his pea-plant experiments into four postulates, some of which are sometimes called “laws,” that describe the basis of dominant and recessive inheritance in diploid organisms. As you have learned, more complex extensions of Mendelism exist that do not exhibit the same F2 phenotypic ratios (3:1). Nevertheless, these laws summarize the basics of classical genetics.
Multiple Choice
Assuming no gene linkage, in a dihybrid cross of AABB x aabb with AaBb F1 heterozygotes, what is the ratio of the F1 gametes (AB, aB, Ab, ab) that will give rise to the F2 offspring?
1. 1:1:1:1
2. 1:3:3:1
3. 1:2:2:1
4. 4:3:2:1
Answer
A
The forked line and probability methods make use of what probability rule?
1. test cross
2. product rule
3. monohybrid rule
4. sum rule
Answer
B
How many different offspring genotypes are expected in a trihybrid cross between parents heterozygous for all three traits when the traits behave in a dominant and recessive pattern? How many phenotypes?
1. 64 genotypes; 16 phenotypes
2. 16 genotypes; 64 phenotypes
3. 8 genotypes; 27 phenotypes
4. 27 genotypes; 8 phenotypes
Answer
D
Free Response
Use the probability method to calculate the genotypes and genotypic proportions of a cross between AABBCc and Aabbcc parents.
Answer
Considering each gene separately, the cross at A will produce offspring of which half are AA and half are Aa; B will produce all Bb; C will produce half Cc and half cc. Proportions then are (1/2) × (1) × (1/2), or 1/4 AABbCc; continuing for the other possibilities yields 1/4 AABbcc, 1/4 AaBbCc, and 1/4 AaBbcc. The proportions therefore are 1:1:1:1.
Explain epistatis in terms of its Greek-language roots “standing upon.”
Answer
Epistasis describes an antagonistic interaction between genes wherein one gene masks or interferes with the expression of another. The gene that is interfering is referred to as epistatic, as if it is “standing upon” the other (hypostatic) gene to block its expression.
In Section 12.3, “Laws of Inheritance,” an example of epistasis was given for the summer squash. Cross white WwYy heterozygotes to prove the phenotypic ratio of 12 white:3 yellow:1 green that was given in the text.
Answer
The cross can be represented as a 4 × 4 Punnett square, with the following gametes for each parent: WY, Wy, wY, and wy. For all 12 of the offspring that express a dominant W gene, the offspring will be white. The three offspring that are homozygous recessive for w but express a dominant Y gene will be yellow. The remaining wwyy offspring will be green. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/12%3A_Mendel's_Experiments_and_Heredity/12.E%3A_Mendel%27s_Experiments_and_Heredity_%28Exercises%29.txt |
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.
• 13.0: Prelude to 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.
• 13.1: Chromosomal Theory and Genetic Linkage
The Chromosomal Theory of inheritance, proposed by Sutton and Boveri, states that chromosomes are the vehicles of genetic heredity. Neither Mendelian genetics nor gene linkage is perfectly accurate; instead, chromosome behavior involves segregation, independent assortment, and occasionally, linkage. Sturtevant devised a method to assess recombination frequency and infer the relative positions and distances of linked genes on a chromosome on the basis of the average number of crossovers.
• 13.2: Chromosomal Basis of Inherited Disorders
The number, size, shape, and banding pattern of chromosomes make them easily identifiable in a karyogram and allows for the assessment of many chromosomal abnormalities. Disorders in chromosome number, or aneuploidies, are typically lethal to the embryo, although a few trisomic genotypes are viable. Because of X inactivation, aberrations in sex chromosomes typically have milder phenotypic effects. Aneuploidies also include instances in which segments of a chromosome are duplicated or deleted.
• 13.E: Modern Understandings of Inheritance (Exercises)
Thumbnail: Chromosomes are threadlike nuclear structures consisting of DNA and proteins that serve as the repositories for genetic information. The chromosomes depicted here were isolated from a fruit fly’s salivary gland, stained with dye, and visualized under a microscope. Akin to miniature bar codes, chromosomes absorb different dyes to produce characteristic banding patterns, which allows for their routine identification. (credit: modification of work by “LPLT”/Wikimedia Commons; scale-bar data from Matt Russell)
13: 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.
13.1: Chromosomal Theory and Genetic Linkage
Skills to Develop
• Discuss Sutton’s Chromosomal Theory of Inheritance
• Describe genetic linkage
• Explain the process of homologous recombination, or crossing over
• Describe how chromosome maps are created
• Calculate the distances between three genes on a chromosome using a three-point test cross
Long before chromosomes were visualized under a microscope, the father of modern genetics, Gregor Mendel, began studying heredity in 1843. With the improvement of microscopic techniques during the late 1800s, cell biologists could stain and visualize subcellular structures with dyes and observe their actions during cell division and meiosis. With each mitotic division, chromosomes replicated, condensed from an amorphous (no constant shape) nuclear mass into distinct X-shaped bodies (pairs of identical sister chromatids), and migrated to separate cellular poles.
Chromosomal Theory of Inheritance
The speculation that chromosomes might be the key to understanding heredity led several scientists to examine Mendel’s publications and re-evaluate his model in terms of the behavior of chromosomes during mitosis and meiosis. In 1902, Theodor Boveri observed that proper embryonic development of sea urchins does not occur unless chromosomes are present. That same year, Walter Sutton observed the separation of chromosomes into daughter cells during meiosis (Figure \(1\)). Together, these observations led to the development of the Chromosomal Theory of Inheritance, which identified chromosomes as the genetic material responsible for Mendelian inheritance.
The Chromosomal Theory of Inheritance was consistent with Mendel’s laws and was supported by the following observations:
• During meiosis, homologous chromosome pairs migrate as discrete structures that are independent of other chromosome pairs.
• The sorting of chromosomes from each homologous pair into pre-gametes appears to be random.
• Each parent synthesizes gametes that contain only half of their chromosomal complement.
• Even though male and female gametes (sperm and egg) differ in size and morphology, they have the same number of chromosomes, suggesting equal genetic contributions from each parent.
• The gametic chromosomes combine during fertilization to produce offspring with the same chromosome number as their parents.
Despite compelling correlations between the behavior of chromosomes during meiosis and Mendel’s abstract laws, the Chromosomal Theory of Inheritance was proposed long before there was any direct evidence that traits were carried on chromosomes. Critics pointed out that individuals had far more independently segregating traits than they had chromosomes. It was only after several years of carrying out crosses with the fruit fly, Drosophila melanogaster, that Thomas Hunt Morgan provided experimental evidence to support the Chromosomal Theory of Inheritance.
Genetic Linkage and Distances
Mendel’s work suggested that traits are inherited independently of each other. Morgan identified a 1:1 correspondence between a segregating trait and the X chromosome, suggesting that the random segregation of chromosomes was the physical basis of Mendel’s model. This also demonstrated that linked genes disrupt Mendel’s predicted outcomes. The fact that each chromosome can carry many linked genes explains how individuals can have many more traits than they have chromosomes. However, observations by researchers in Morgan’s laboratory suggested that alleles positioned on the same chromosome were not always inherited together. During meiosis, linked genes somehow became unlinked.
Homologous Recombination
In 1909, Frans Janssen observed chiasmata—the point at which chromatids are in contact with each other and may exchange segments—prior to the first division of meiosis. He suggested that alleles become unlinked and chromosomes physically exchange segments. As chromosomes condensed and paired with their homologs, they appeared to interact at distinct points. Janssen suggested that these points corresponded to regions in which chromosome segments were exchanged. It is now known that the pairing and interaction between homologous chromosomes, known as synapsis, does more than simply organize the homologs for migration to separate daughter cells. When synapsed, homologous chromosomes undergo reciprocal physical exchanges at their arms in a process called homologous recombination, or more simply, “crossing over.”
To better understand the type of experimental results that researchers were obtaining at this time, consider a heterozygous individual that inherited dominant maternal alleles for two genes on the same chromosome (such as AB) and two recessive paternal alleles for those same genes (such as ab). If the genes are linked, one would expect this individual to produce gametes that are either AB or ab with a 1:1 ratio. If the genes are unlinked, the individual should produce AB, Ab, aB, and ab gametes with equal frequencies, according to the Mendelian concept of independent assortment. Because they correspond to new allele combinations, the genotypes Ab and aB are nonparental types that result from homologous recombination during meiosis. Parental types are progeny that exhibit the same allelic combination as their parents. Morgan and his colleagues, however, found that when such heterozygous individuals were test crossed to a homozygous recessive parent (AaBb × aabb), both parental and nonparental cases occurred. For example, 950 offspring might be recovered that were either AaBb or aabb, but 50 offspring would also be obtained that were either Aabb or aaBb. These results suggested that linkage occurred most often, but a significant minority of offspring were the products of recombination.
Art Connection
In a test cross for two characteristics such as the one shown here, can the predicted frequency of recombinant offspring be 60 percent? Why or why not?
Genetic Maps
Janssen did not have the technology to demonstrate crossing over so it remained an abstract idea that was not widely accepted. Scientists thought chiasmata were a variation on synapsis and could not understand how chromosomes could break and rejoin. Yet, the data were clear that linkage did not always occur. Ultimately, it took a young undergraduate student and an “all-nighter” to mathematically elucidate the problem of linkage and recombination.
In 1913, Alfred Sturtevant, a student in Morgan’s laboratory, gathered results from researchers in the laboratory, and took them home one night to mull them over. By the next morning, he had created the first “chromosome map,” a linear representation of gene order and relative distance on a chromosome (Figure 13.1.3).
Art Connection
Which of the following statements is true?
1. Recombination of the body color and red/cinnabar eye alleles will occur more frequently than recombination of the alleles for wing length and aristae length.
2. Recombination of the body color and aristae length alleles will occur more frequently than recombination of red/brown eye alleles and the aristae length alleles.
3. Recombination of the gray/black body color and long/short aristae alleles will not occur.
4. Recombination of the red/brown eye and long/short aristae alleles will occur more frequently than recombination of the alleles for wing length and body color.
As shown in Figure \(3\), by using recombination frequency to predict genetic distance, the relative order of genes on chromosome 2 could be inferred. The values shown represent map distances in centimorgans (cM), which correspond to recombination frequencies (in percent). Therefore, the genes for body color and wing size were 65.5 − 48.5 = 17 cM apart, indicating that the maternal and paternal alleles for these genes recombine in 17 percent of offspring, on average.
To construct a chromosome map, Sturtevant assumed that genes were ordered serially on threadlike chromosomes. He also assumed that the incidence of recombination between two homologous chromosomes could occur with equal likelihood anywhere along the length of the chromosome. Operating under these assumptions, Sturtevant postulated that alleles that were far apart on a chromosome were more likely to dissociate during meiosis simply because there was a larger region over which recombination could occur. Conversely, alleles that were close to each other on the chromosome were likely to be inherited together. The average number of crossovers between two alleles—that is, their recombination frequency—correlated with their genetic distance from each other, relative to the locations of other genes on that chromosome. Considering the example cross between AaBb and aabb above, the frequency of recombination could be calculated as 50/1000 = 0.05. That is, the likelihood of a crossover between genes A/a and B/b was 0.05, or 5 percent. Such a result would indicate that the genes were definitively linked, but that they were far enough apart for crossovers to occasionally occur. Sturtevant divided his genetic map into map units, or centimorgans (cM), in which a recombination frequency of 0.01 corresponds to 1 cM.
By representing alleles in a linear map, Sturtevant suggested that genes can range from being perfectly linked (recombination frequency = 0) to being perfectly unlinked (recombination frequency = 0.5) when genes are on different chromosomes or genes are separated very far apart on the same chromosome. Perfectly unlinked genes correspond to the frequencies predicted by Mendel to assort independently in a dihybrid cross. A recombination frequency of 0.5 indicates that 50 percent of offspring are recombinants and the other 50 percent are parental types. That is, every type of allele combination is represented with equal frequency. This representation allowed Sturtevant to additively calculate distances between several genes on the same chromosome. However, as the genetic distances approached 0.50, his predictions became less accurate because it was not clear whether the genes were very far apart on the same chromosome or on different chromosomes.
In 1931, Barbara McClintock and Harriet Creighton demonstrated the crossover of homologous chromosomes in corn plants. Weeks later, homologous recombination in Drosophila was demonstrated microscopically by Curt Stern. Stern observed several X-linked phenotypes that were associated with a structurally unusual and dissimilar X chromosome pair in which one X was missing a small terminal segment, and the other X was fused to a piece of the Y chromosome. By crossing flies, observing their offspring, and then visualizing the offspring’s chromosomes, Stern demonstrated that every time the offspring allele combination deviated from either of the parental combinations, there was a corresponding exchange of an X chromosome segment. Using mutant flies with structurally distinct X chromosomes was the key to observing the products of recombination because DNA sequencing and other molecular tools were not yet available. It is now known that homologous chromosomes regularly exchange segments in meiosis by reciprocally breaking and rejoining their DNA at precise locations.
Link to Learning
Review Sturtevant’s process to create a genetic map on the basis of recombination frequencies here.
Mendel’s Mapped Traits
Homologous recombination is a common genetic process, yet Mendel never observed it. Had he investigated both linked and unlinked genes, it would have been much more difficult for him to create a unified model of his data on the basis of probabilistic calculations. Researchers who have since mapped the seven traits investigated by Mendel onto the seven chromosomes of the pea plant genome have confirmed that all of the genes he examined are either on separate chromosomes or are sufficiently far apart as to be statistically unlinked. Some have suggested that Mendel was enormously lucky to select only unlinked genes, whereas others question whether Mendel discarded any data suggesting linkage. In any case, Mendel consistently observed independent assortment because he examined genes that were effectively unlinked.
Summary
The Chromosomal Theory of inheritance, proposed by Sutton and Boveri, states that chromosomes are the vehicles of genetic heredity. Neither Mendelian genetics nor gene linkage is perfectly accurate; instead, chromosome behavior involves segregation, independent assortment, and occasionally, linkage. Sturtevant devised a method to assess recombination frequency and infer the relative positions and distances of linked genes on a chromosome on the basis of the average number of crossovers in the intervening region between the genes. Sturtevant correctly presumed that genes are arranged in serial order on chromosomes and that recombination between homologs can occur anywhere on a chromosome with equal likelihood. Whereas linkage causes alleles on the same chromosome to be inherited together, homologous recombination biases alleles toward an inheritance pattern of independent assortment.
Art Connections
Figure \(2\): In a test cross for two characteristics such as the one shown here, can the predicted frequency of recombinant offspring be 60 percent? Why or why not?
Answer
No. The predicted frequency of recombinant offspring ranges from 0% (for linked traits) to 50% (for unlinked traits).
Figure \(3\): Which of the following statements is true?
1. Recombination of the body color and red/cinnabar eye alleles will occur more frequently than recombination of the alleles for wing length and aristae length.
2. Recombination of the body color and aristae length alleles will occur more frequently than recombination of red/brown eye alleles and the aristae length alleles.
3. Recombination of the gray/black body color and long/short aristae alleles will not occur.
4. Recombination of the red/brown eye and long/short aristae alleles will occur more frequently than recombination of the alleles for wing length and body color.
Answer
D
Glossary
centimorgan (cM)
(also, map unit) relative distance that corresponds to a recombination frequency of 0.01
Chromosomal Theory of Inheritance
theory proposing that chromosomes are the vehicles of genes and that their behavior during meiosis is the physical basis of the inheritance patterns that Mendel observed
homologous recombination
process by which homologous chromosomes undergo reciprocal physical exchanges at their arms, also known as crossing over
nonparental (recombinant) type
progeny resulting from homologous recombination that exhibits a different allele combination compared with its parents
parental types
progeny that exhibits the same allelic combination as its parents
recombination frequency
average number of crossovers between two alleles; observed as the number of nonparental types in a population of progeny | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/13%3A_Modern_Understandings_of_Inheritance/13.0%3A_Prelude_to_Modern_Understandings_of_Inheritance.txt |
Skills to Develop
• Describe how a karyogram is created
• Explain how nondisjunction leads to disorders in chromosome number
• Compare disorders caused by aneuploidy
• Describe how errors in chromosome structure occur through inversions and translocations
Inherited disorders can arise when chromosomes behave abnormally during meiosis. Chromosome disorders can be divided into two categories: abnormalities in chromosome number and chromosomal structural rearrangements. Because even small segments of chromosomes can span many genes, chromosomal disorders are characteristically dramatic and often fatal.
Identification of Chromosomes
The isolation and microscopic observation of chromosomes forms the basis of cytogenetics and is the primary method by which clinicians detect chromosomal abnormalities in humans. A karyotype is the number and appearance of chromosomes, and includes their length, banding pattern, and centromere position. To obtain a view of an individual’s karyotype, cytologists photograph the chromosomes and then cut and paste each chromosome into a chart, or karyogram, also known as an ideogram (Figure \(1\)).
In a given species, chromosomes can be identified by their number, size, centromere position, and banding pattern. In a human karyotype, autosomes or “body chromosomes” (all of the non–sex chromosomes) are generally organized in approximate order of size from largest (chromosome 1) to smallest (chromosome 22). The X and Y chromosomes are not autosomes. However, chromosome 21 is actually shorter than chromosome 22. This was discovered after the naming of Down syndrome as trisomy 21, reflecting how this disease results from possessing one extra chromosome 21 (three total). Not wanting to change the name of this important disease, chromosome 21 retained its numbering, despite describing the shortest set of chromosomes. The chromosome “arms” projecting from either end of the centromere may be designated as short or long, depending on their relative lengths. The short arm is abbreviated p (for “petite”), whereas the long arm is abbreviated q (because it follows “p” alphabetically). Each arm is further subdivided and denoted by a number. Using this naming system, locations on chromosomes can be described consistently in the scientific literature.
Career Connection: Geneticists Use Karyograms to Identify Chromosomal Aberrations
Although Mendel is referred to as the “father of modern genetics,” he performed his experiments with none of the tools that the geneticists of today routinely employ. One such powerful cytological technique is karyotyping, a method in which traits characterized by chromosomal abnormalities can be identified from a single cell. To observe an individual’s karyotype, a person’s cells (like white blood cells) are first collected from a blood sample or other tissue. In the laboratory, the isolated cells are stimulated to begin actively dividing. A chemical called colchicine is then applied to cells to arrest condensed chromosomes in metaphase. Cells are then made to swell using a hypotonic solution so the chromosomes spread apart. Finally, the sample is preserved in a fixative and applied to a slide.
The geneticist then stains chromosomes with one of several dyes to better visualize the distinct and reproducible banding patterns of each chromosome pair. Following staining, the chromosomes are viewed using bright-field microscopy. A common stain choice is the Giemsa stain. Giemsa staining results in approximately 400–800 bands (of tightly coiled DNA and condensed proteins) arranged along all of the 23 chromosome pairs; an experienced geneticist can identify each band. In addition to the banding patterns, chromosomes are further identified on the basis of size and centromere location. To obtain the classic depiction of the karyotype in which homologous pairs of chromosomes are aligned in numerical order from longest to shortest, the geneticist obtains a digital image, identifies each chromosome, and manually arranges the chromosomes into this pattern (Figure \(1\)).
At its most basic, the karyogram may reveal genetic abnormalities in which an individual has too many or too few chromosomes per cell. Examples of this are Down Syndrome, which is identified by a third copy of chromosome 21, and Turner Syndrome, which is characterized by the presence of only one X chromosome in women instead of the normal two. Geneticists can also identify large deletions or insertions of DNA. For instance, Jacobsen Syndrome—which involves distinctive facial features as well as heart and bleeding defects—is identified by a deletion on chromosome 11. Finally, the karyotype can pinpoint translocations, which occur when a segment of genetic material breaks from one chromosome and reattaches to another chromosome or to a different part of the same chromosome. Translocations are implicated in certain cancers, including chronic myelogenous leukemia.
During Mendel’s lifetime, inheritance was an abstract concept that could only be inferred by performing crosses and observing the traits expressed by offspring. By observing a karyogram, today’s geneticists can actually visualize the chromosomal composition of an individual to confirm or predict genetic abnormalities in offspring, even before birth.
Disorders in Chromosome Number
Of all of the chromosomal disorders, abnormalities in chromosome number are the most obviously identifiable from a karyogram. Disorders of chromosome number include the duplication or loss of entire chromosomes, as well as changes in the number of complete sets of chromosomes. They are caused by nondisjunction, which occurs when pairs of homologous chromosomes or sister chromatids fail to separate during meiosis. Misaligned or incomplete synapsis, or a dysfunction of the spindle apparatus that facilitates chromosome migration, can cause nondisjunction. The risk of nondisjunction occurring increases with the age of the parents.
Nondisjunction can occur during either meiosis I or II, with differing results (Figure \(2\)). If homologous chromosomes fail to separate during meiosis I, the result is two gametes that lack that particular chromosome and two gametes with two copies of the chromosome. If sister chromatids fail to separate during meiosis II, the result is one gamete that lacks that chromosome, two normal gametes with one copy of the chromosome, and one gamete with two copies of the chromosome.
Art Connection
Which of the following statements about nondisjunction is true?
1. Nondisjunction only results in gametes with n+1 or n–1 chromosomes.
2. Nondisjunction occurring during meiosis II results in 50 percent normal gametes.
3. Nondisjunction during meiosis I results in 50 percent normal gametes.
4. Nondisjunction always results in four different kinds of gametes.
Aneuploidy
An individual with the appropriate number of chromosomes for their species is called euploid; in humans, euploidy corresponds to 22 pairs of autosomes and one pair of sex chromosomes. An individual with an error in chromosome number is described as aneuploid, a term that includes monosomy (loss of one chromosome) or trisomy (gain of an extraneous chromosome). Monosomic human zygotes missing any one copy of an autosome invariably fail to develop to birth because they lack essential genes. This underscores the importance of “gene dosage” in humans. Most autosomal trisomies also fail to develop to birth; however, duplications of some of the smaller chromosomes (13, 15, 18, 21, or 22) can result in offspring that survive for several weeks to many years. Trisomic individuals suffer from a different type of genetic imbalance: an excess in gene dose. Individuals with an extra chromosome may synthesize an abundance of the gene products encoded by that chromosome. This extra dose (150 percent) of specific genes can lead to a number of functional challenges and often precludes development. The most common trisomy among viable births is that of chromosome 21, which corresponds to Down Syndrome. Individuals with this inherited disorder are characterized by short stature and stunted digits, facial distinctions that include a broad skull and large tongue, and significant developmental delays. The incidence of Down syndrome is correlated with maternal age; older women are more likely to become pregnant with fetuses carrying the trisomy 21 genotype (Figure \(3\)).
Link to Learning
Visualize the addition of a chromosome that leads to Down syndrome in this video simulation.
Polyploidy
An individual with more than the correct number of chromosome sets (two for diploid species) is called polyploid. For instance, fertilization of an abnormal diploid egg with a normal haploid sperm would yield a triploid zygote. Polyploid animals are extremely rare, with only a few examples among the flatworms, crustaceans, amphibians, fish, and lizards. Polyploid animals are sterile because meiosis cannot proceed normally and instead produces mostly aneuploid daughter cells that cannot yield viable zygotes. Rarely, polyploid animals can reproduce asexually by haplodiploidy, in which an unfertilized egg divides mitotically to produce offspring. In contrast, polyploidy is very common in the plant kingdom, and polyploid plants tend to be larger and more robust than euploids of their species (Figure \(4\)).
Sex Chromosome Nondisjunction in Humans
Humans display dramatic deleterious effects with autosomal trisomies and monosomies. Therefore, it may seem counterintuitive that human females and males can function normally, despite carrying different numbers of the X chromosome. Rather than a gain or loss of autosomes, variations in the number of sex chromosomes are associated with relatively mild effects. In part, this occurs because of a molecular process called X inactivation. Early in development, when female mammalian embryos consist of just a few thousand cells (relative to trillions in the newborn), one X chromosome in each cell inactivates by tightly condensing into a quiescent (dormant) structure called a Barr body. The chance that an X chromosome (maternally or paternally derived) is inactivated in each cell is random, but once the inactivation occurs, all cells derived from that one will have the same inactive X chromosome or Barr body. By this process, females compensate for their double genetic dose of X chromosome. In so-called “tortoiseshell” cats, embryonic X inactivation is observed as color variegation (Figure \(5\)). Females that are heterozygous for an X-linked coat color gene will express one of two different coat colors over different regions of their body, corresponding to whichever X chromosome is inactivated in the embryonic cell progenitor of that region.
An individual carrying an abnormal number of X chromosomes will inactivate all but one X chromosome in each of her cells. However, even inactivated X chromosomes continue to express a few genes, and X chromosomes must reactivate for the proper maturation of female ovaries. As a result, X-chromosomal abnormalities are typically associated with mild mental and physical defects, as well as sterility. If the X chromosome is absent altogether, the individual will not develop in utero.
Several errors in sex chromosome number have been characterized. Individuals with three X chromosomes, called triplo-X, are phenotypically female but express developmental delays and reduced fertility. The XXY genotype, corresponding to one type of Klinefelter syndrome, corresponds to phenotypically male individuals with small testes, enlarged breasts, and reduced body hair. More complex types of Klinefelter syndrome exist in which the individual has as many as five X chromosomes. In all types, every X chromosome except one undergoes inactivation to compensate for the excess genetic dosage. This can be seen as several Barr bodies in each cell nucleus. Turner syndrome, characterized as an X0 genotype (i.e., only a single sex chromosome), corresponds to a phenotypically female individual with short stature, webbed skin in the neck region, hearing and cardiac impairments, and sterility.
Duplications and Deletions
In addition to the loss or gain of an entire chromosome, a chromosomal segment may be duplicated or lost. Duplications and deletions often produce offspring that survive but exhibit physical and mental abnormalities. Duplicated chromosomal segments may fuse to existing chromosomes or may be free in the nucleus. Cri-du-chat (from the French for “cry of the cat”) is a syndrome associated with nervous system abnormalities and identifiable physical features that result from a deletion of most of 5p (the small arm of chromosome 5) (Figure \(6\)). Infants with this genotype emit a characteristic high-pitched cry on which the disorder’s name is based.
Chromosomal Structural Rearrangements
Cytologists have characterized numerous structural rearrangements in chromosomes, but chromosome inversions and translocations are the most common. Both are identified during meiosis by the adaptive pairing of rearranged chromosomes with their former homologs to maintain appropriate gene alignment. If the genes carried on two homologs are not oriented correctly, a recombination event could result in the loss of genes from one chromosome and the gain of genes on the other. This would produce aneuploid gametes.
Chromosome Inversions
A chromosome inversion is the detachment, 180° rotation, and reinsertion of part of a chromosome. Inversions may occur in nature as a result of mechanical shear, or from the action of transposable elements (special DNA sequences capable of facilitating the rearrangement of chromosome segments with the help of enzymes that cut and paste DNA sequences). Unless they disrupt a gene sequence, inversions only change the orientation of genes and are likely to have more mild effects than aneuploid errors. However, altered gene orientation can result in functional changes because regulators of gene expression could be moved out of position with respect to their targets, causing aberrant levels of gene products.
An inversion can be pericentric and include the centromere, or paracentric and occur outside of the centromere (). A pericentric inversion that is asymmetric about the centromere can change the relative lengths of the chromosome arms, making these inversions easily identifiable.
When one homologous chromosome undergoes an inversion but the other does not, the individual is described as an inversion heterozygote. To maintain point-for-point synapsis during meiosis, one homolog must form a loop, and the other homolog must mold around it. Although this topology can ensure that the genes are correctly aligned, it also forces the homologs to stretch and can be associated with regions of imprecise synapsis (Figure \(8\)).
Evolution Connection: The Chromosome 18 Inversion
Not all structural rearrangements of chromosomes produce nonviable, impaired, or infertile individuals. In rare instances, such a change can result in the evolution of a new species. In fact, a pericentric inversion in chromosome 18 appears to have contributed to the evolution of humans. This inversion is not present in our closest genetic relatives, the chimpanzees. Humans and chimpanzees differ cytogenetically by pericentric inversions on several chromosomes and by the fusion of two separate chromosomes in chimpanzees that correspond to chromosome two in humans.
The pericentric chromosome 18 inversion is believed to have occurred in early humans following their divergence from a common ancestor with chimpanzees approximately five million years ago. Researchers characterizing this inversion have suggested that approximately 19,000 nucleotide bases were duplicated on 18p, and the duplicated region inverted and reinserted on chromosome 18 of an ancestral human.
A comparison of human and chimpanzee genes in the region of this inversion indicates that two genes—ROCK1 and USP14—that are adjacent on chimpanzee chromosome 17 (which corresponds to human chromosome 18) are more distantly positioned on human chromosome 18. This suggests that one of the inversion breakpoints occurred between these two genes. Interestingly, humans and chimpanzees express USP14 at distinct levels in specific cell types, including cortical cells and fibroblasts. Perhaps the chromosome 18 inversion in an ancestral human repositioned specific genes and reset their expression levels in a useful way. Because both ROCK1 and USP14 encode cellular enzymes, a change in their expression could alter cellular function. It is not known how this inversion contributed to hominid evolution, but it appears to be a significant factor in the divergence of humans from other primates.1
Translocations
A translocation occurs when a segment of a chromosome dissociates and reattaches to a different, nonhomologous chromosome. Translocations can be benign or have devastating effects depending on how the positions of genes are altered with respect to regulatory sequences. Notably, specific translocations have been associated with several cancers and with schizophrenia. Reciprocal translocations result from the exchange of chromosome segments between two nonhomologous chromosomes such that there is no gain or loss of genetic information (Figure \(9\)).
Summary
The number, size, shape, and banding pattern of chromosomes make them easily identifiable in a karyogram and allows for the assessment of many chromosomal abnormalities. Disorders in chromosome number, or aneuploidies, are typically lethal to the embryo, although a few trisomic genotypes are viable. Because of X inactivation, aberrations in sex chromosomes typically have milder phenotypic effects. Aneuploidies also include instances in which segments of a chromosome are duplicated or deleted. Chromosome structures may also be rearranged, for example by inversion or translocation. Both of these aberrations can result in problematic phenotypic effects. Because they force chromosomes to assume unnatural topologies during meiosis, inversions and translocations are often associated with reduced fertility because of the likelihood of nondisjunction.
Art Connections
Figure \(2\): Which of the following statements about nondisjunction is true?
1. Nondisjunction only results in gametes with n+1 or n–1 chromosomes.
2. Nondisjunction occurring during meiosis II results in 50 percent normal gametes.
3. Nondisjunction during meiosis I results in 50 percent normal gametes.
4. Nondisjunction always results in four different kinds of gametes.
Answer
B.
Footnotes
1. 1 Violaine Goidts et al., “Segmental duplication associated with the human-specific inversion of chromosome 18: a further example of the impact of segmental duplications on karyotype and genome evolution in primates,” Human Genetics. 115 (2004):116-122
Glossary
aneuploid
individual with an error in chromosome number; includes deletions and duplications of chromosome segments
autosome
any of the non-sex chromosomes
chromosome inversion
detachment, 180° rotation, and reinsertion of a chromosome arm
euploid
individual with the appropriate number of chromosomes for their species
karyogram
photographic image of a karyotype
karyotype
number and appearance of an individuals chromosomes; includes the size, banding patterns, and centromere position
monosomy
otherwise diploid genotype in which one chromosome is missing
nondisjunction
failure of synapsed homologs to completely separate and migrate to separate poles during the first cell division of meiosis
paracentric
inversion that occurs outside of the centromere
pericentric
inversion that involves the centromere
polyploid
individual with an incorrect number of chromosome sets
translocation
process by which one segment of a chromosome dissociates and reattaches to a different, nonhomologous chromosome
trisomy
otherwise diploid genotype in which one entire chromosome is duplicated
X inactivation
condensation of X chromosomes into Barr bodies during embryonic development in females to compensate for the double genetic dose
13.E: Modern Understandings of Inheritance (Exercises)
13.1: Chromosomal Theory and Genetic Linkage
Review Questions
X-linked recessive traits in humans (or in Drosophila) are observed ________.
1. in more males than females
2. in more females than males
3. in males and females equally
4. in different distributions depending on the trait
Answer
A
The first suggestion that chromosomes may physically exchange segments came from the microscopic identification of ________.
1. synapsis
2. sister chromatids
3. chiasmata
4. alleles
Answer
C
Which recombination frequency corresponds to independent assortment and the absence of linkage?
1. 0
2. 0.25
3. 0.50
4. 0.75
Answer
C
Which recombination frequency corresponds to perfect linkage and violates the law of independent assortment?
1. 0
2. 0.25
3. 0.50
4. 0.75
Answer
A
Free Response
Explain how the Chromosomal Theory of Inheritance helped to advance our understanding of genetics.
Answer
The Chromosomal Theory of Inheritance proposed that genes reside on chromosomes. The understanding that chromosomes are linear arrays of genes explained linkage, and crossing over explained recombination.
13.2: Chromosomal Basis of Inherited Disorders
Review Questions
Which of the following codes describes position 12 on the long arm of chromosome 13?
1. 13p12
2. 13q12
3. 12p13
4. 12q13
Answer
B
In agriculture, polyploid crops (like coffee, strawberries, or bananas) tend to produce ________.
1. more uniformity
2. more variety
3. larger yields
4. smaller yields
Answer
C
Assume a pericentric inversion occurred in one of two homologs prior to meiosis. The other homolog remains normal. During meiosis, what structure—if any—would these homologs assume in order to pair accurately along their lengths?
1. V formation
2. cruciform
3. loop
4. pairing would not be possible
Answer
C
The genotype XXY corresponds to
1. Klinefelter syndrome
2. Turner syndrome
3. Triplo-X
4. Jacob syndrome
Answer
A
Abnormalities in the number of X chromosomes tends to have milder phenotypic effects than the same abnormalities in autosomes because of ________.
1. deletions
2. nonhomologous recombination
3. synapsis
4. X inactivation
Answer
D
By definition, a pericentric inversion includes the ________.
1. centromere
2. chiasma
3. telomere
4. synapse
Answer
A
Free Response
Using diagrams, illustrate how nondisjunction can result in an aneuploid zygote.
Answer
Exact diagram style will vary; diagram should look like Figure 13.2.2. | textbooks/bio/Introductory_and_General_Biology/General_Biology_1e_(OpenStax)/3%3A_Genetics/13%3A_Modern_Understandings_of_Inheritance/13.2%3A_Chromosomal_Basis_of_Inherited_Disorders.txt |
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