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Cytokinins are plant hormones that are derivatives of the purine adenine. They are not to be confused with cytokines. They were discovered as an absolutely essential ingredient in medium for growing plant cells in culture. Without cytokinins in the medium, plant cells will not divide by mitosis. Cytokinins have been implicated in many plant activities; usually along with some other plant hormone such as auxin or ethylene.
Among these:
• mitosis
• chloroplast development
• differentiation of the shoot meristem
• stimulating the development of lateral buds and therefore branching
• differentiation of the tissues of the root
• leaf formation
• leaf senescence
One of the clearest examples of cytokinin activity occurs in the germination of seeds. The endosperm of monocot seeds, such as corn (maize), contains large stores of the precursor to the cytokinin zeatin (right). When the corn kernel germinates, zeatin moves from the endosperm to the root tip where it stimulates vigorous mitosis.
Steps in cytokinin signaling
The following are the steps in cytokinin signaling:
• A cytokinin, like zeatin, binds to a receptor protein embedded in the plasma membrane of the cell.
• The internal portion of the receptor then attaches a phosphate group to a protein in the cytosol.
• This protein moves into the nucleus where
• it activates one or more nuclear transcription factors.
• These bind to the promoters of genes.
• Transcription of these genes produces mRNAs that move out into the cytosol.
• Translation of these mRNAs produces the proteins that enable the cell to carry out its cytokine-induced function.
16.5D: Ethylene
Ethylene is a plant hormone that differs from other plant hormones in being a gas.
It has the molecular structure:
H2C=CH2
As they approach maturity, many fruits (e.g., apples, oranges, avocados) release ethylene. Ethylene then promotes the ripening of the fruit. Commercial fruit growers can buy equipment to generate ethylene so that their harvest ripens quickly and uniformly.
The presence of ethylene is detected by transmembrane receptors in the endoplasmic reticulum (ER) of the cells. Binding of ethylene to these receptors unleashes a signaling cascade that leads to activation of transcription factors and the turning on of gene transcription.
The ill-fated FlavrSavr tomato contains an antisense transgene that interferes with the synthesis of ethylene and hence slows ripening.
Plant functions affected by Ethylene
Ethylene also affects many other plant functions such as:
• abscission of leaves, fruits, and flower petals
• drooping of leaves
• sprouting of potato buds
• seed germination
• stem elongation in rice (by promoting the breakdown of abscisic acid (ABA) and thus relieving ABA's inhibition of gibberellic acid)
• flower formation in some species
16.5E: Gibberellins
During the 1930s Japanese scientists isolated a growth-promoting substance from cultures of a fungus that parasitizes rice plants. They called it gibberellin. After the delay caused by World War II, plant physiologists in other countries succeeded in isolating more than 30 closely-related compounds. One of the most active of these - and one found as a natural hormone in the plants themselves - is gibberellic acid (GA).
GA has a number of effects on plant growth, but the most dramatic is its effect on stem growth. When applied in low concentrations to a bush or "dwarf" bean, the stem begins to grow rapidly. The length of the internodes becomes so great that the plant becomes indistinguishable from climbing or "pole" beans. GA seems to overcome the genetic limitations in many dwarf varieties.
Synthesis of gibberellins also helps grapevines climb up toward the light by causing meristems that would have developed into flowers to develop into tendrils instead.
Note
One of the 7 pairs of traits that Mendel studied in peas as he worked out the basic rules of inheritance was dwarf-tall. The recessive gene - today called le - turns out to encode an enzyme that is defective in enabling the plant to synthesize GA. The dominant gene, Le, encodes a functioning enzyme permitting normal GA synthesis and making the "tall" phenotype.
Effects of gibberellins on gene expression
Gibberellins exert their effects by altering gene transcription, the steps for which are described below.
• Gibberellin enters the cell and binds to a soluble receptor protein called GID1 ("gibberellin-insensitive dwarf mutant 1") which now can bind to a complex of proteins (SCF) responsible for attaching ubiquitin to one or another of several DELLA proteins.
• This triggers the destruction of the DELLA proteins by proteasomes.
• DELLA proteins normally bind gibberellin-dependent transcription factors, a prominent one is designated PIF3/4, preventing them from binding to the DNA of control sequences of genes that are turned on by gibberellin.
• Destruction of the DELLA proteins relieves this inhibition and gene transcription begins.
This mechanism is another of the many cases in biology where a pathway is turned on by inhibiting the inhibitor of that pathway (a double-negative is a positive).
Another example: Auxin.
Although most of the specific proteins involved are quite different, both gibberellins and auxin affect gene expression by a similar mechanism of relief of repression.
Ligand Gibberellins Auxin
Receptor GID1 TIR1
Proteasome activator SCF SCF
Transcription factor repressor DELLA Aux/IAA
Transcription factor PIF3/4 ARF1
The dwarf varieties of rice and wheat that have played such an important part in the "green revolution" carry mutant genes that
• interfere with the synthesis of their gibberellins (in the case of rice)
• for wheat, reduce their ability to respond to their own gibberellins (because of mutant genes for a DELLA protein).
Dwarf varieties of sorghum and more recently maize (corn) also exist, but in these cases, the mutation interferes with auxin transport, not gibberellin activity.
16.5F: Strigolactones
Strigolactones are manufactured in, and secreted from, the roots and have been known for some time to
• promote the germination of some plant seeds. Unfortunately these include seeds of the genus Striga (witchweed) whose developing root invades the root of the strigolactone-secreting host plant (e.g., rice, corn, and sorghum) stealing nutrients from it and causing serious crop losses.
• signal mycorrhizal fungi to connect to the root system forming a mutualistic relationship.
However, these activities do not qualify them as plant hormones (both activities take place in the soil surrounding the roots). Only if it can be demonstrated that strigolactones are translocated in the plant from the place of manufacture (roots) to another part of the plant where they exert an effect, can they be called hormones.
Two reports in the 11 September 2008 issue of Nature come close to proving the case.
Strigolactones (or possibly molecules derived from them) suppress the development of lateral buds and thus inhibit branching of the plant. Mutations in genes needed for the synthesis of strigolactones stimulate the development of lateral buds producing a more highly-branched plant than normal. Application of a synthetic strigolactone near the base of these mutant plants inhibits development of lateral buds above and thus restores normal branching.
Auxin and, in certain circumstances, abscisic acid also inhibit branching, that is, they promote apical dominance. But both auxin and abscisic acid participate in a number of different plant functions while the effect of strigolactones on branching seems quite specific. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/16%3A_The_Anatomy_and_Physiology_of_Plants/16.05%3A_Plant_Development_-_Hormones/16.5C%3A_Cytokinins.txt |
The Input of Energy
Tropical regions every day and temperate regions during the growing season receive some 8,000 to 10,000 kilocalories (kcal) of energy each day on each square meter (1 m2) of surface. A kilocalorie is the amount of heat needed to warm 1 kg of water 1 degree Celsius (°C). Because all of the light trapped in photosynthesis is ultimately released as heat, it makes sense to follow the flow of energy through ecosystems in units of heat.
How efficient are plants at converting this energy into organic molecules?
Gross Productivity
Gross productivity is the amount of energy trapped in organic matter during a specified interval at a given trophic level.
The table shows the use of visible sunlight is a cattail marsh. The plants have trapped only 2.2% of the energy falling on them.
Photosynthesis 2.2%
Reflection 3.0
Evaporation
(including transpiration and
heating of the surroundings
94.8
Total 100.0%
However, at least half of this is lost by cellular respiration as the plants run their own metabolism.
Net Productivity
Net productivity is the amount of energy trapped in organic matter during a specified interval at a given trophic level less that lost by the respiration of the organisms at that level. One way to determine this is to collect and weigh the plant material produced on 1 m2 of land over a given interval. One gram of plant material (e.g., stems and leaves), which is largely carbohydrate, yields about 4.25 kcal of energy when burned (or respired).
The table shows representative values for the net productivity of a variety of ecosystems — both natural and managed. These values are only approximations and are subject to marked fluctuations because of variations in temperature, fertility, and availability of water.
Estimated Net Productivity of Certain Ecosystems (in kilocalories/m2/year)
Temperate deciduous forest 5,000
Tropical rain forest 15,000
Tall-grass prairie 2,000
Desert 500
Coastal marsh 12,000
Ocean close to shore 2,500
Open ocean 800
Clear (oligotrophic) lake 800
Lake in advanced state of eutrophication 2,400
Silver Springs, Florida 8,800
Field of alfalfa (lucerne) 15,000
Corn (maize) field, U.S. 4,500
Rice paddies, Japan 5,500
Lawn, Washington, D.C. 6,800
Sugar cane, Hawaii 25,000
What happens to the net productivity of a plant community?
• Some is harvested by plant-eating herbivores, e.g., insects, deer. Often this is only the start of a series of transformations as it passes through a series of heterotrophs — that together make up a food chain.
• Some is consumed by organisms of decay, e.g., fungi and bacteria.
• Some may be stored, e.g., in a growing forest or as peat in a bog.
What about humans?
Humans, like all heterotrophs, depend upon net productivity for their food both directly as we consume plant material (e.g., rice, wheat, corn) and indirectly when we eat animals that have, themselves, fed on plant material (poultry, cattle, sheep, etc.) and/or animal products (e.g., milk, eggs).
We also use the earth's net productivty to meet other needs such as:
• wood for fuel
• wood and fiber (e.g., cotton, flax) to house and clothe us
Added together it is estimated that our species now appropriates some 20% of world's net productivity for our own use. However, this figure obscures large regional variations with estimates running as high as 80% in South central Asia to as low as 6% in South America.
We also reduce the net productivity of our planet by other activities such as
• paving over land for buildings, roads, parking lots, etc.
• burning forests to clear them for agriculture | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/17%3A_Ecology/17.01%3A_Energy_Flow_through_the_Biosphere/17.1A%3A_Ecosystem_Productivity.txt |
The source of all food is the activity of autotrophs, mainly photosynthesis by plants. They are called producers because only they can manufacture food from inorganic raw materials. This food feeds herbivores, called primary consumers. Carnivores that feed on herbivores are called secondary consumers. Carnivores that feed on other carnivores are tertiary (or higher) consumers. Such a path of food consumption is called a food chain. Each level of consumption in a food chain is called a trophic level.
The table gives one example of a food chain and the trophic levels represented in it.
Grass
Grasshopper
Toad
Snake
Hawk
Bacteria of decay
In general,
Autotrophs
(Producers)
Herbivores
(Primary Consumers)
Carnivores
(Secondary, tertiary, etc. consumers)
Decomposers
Food Webs
Most food chains are interconnected. Animals typically consume a varied diet and, in turn, serve as food for a variety of other creatures that prey on them. These interconnections create food webs.
Energy Flow Through Food Chains
H. T. Odum analyzed the flow of energy through a river ecosystem in Silver Springs, Florida. His findings are shown here. The figures are given in kilocalories per square meter per year (kcal/m2/yr).
At each trophic level,
• Net production is only a fraction of gross production because the organisms must expend energy to stay alive. Note that the difference between gross and net production is greater for animals than for the producers - reflecting their greater activity.
• Much of the energy stored in net production was lost to the system by
• decay
• being carried downstream
• Note the substantial losses in net production as energy passes from one trophic level to the next.
• The ratio of net production at one level to net production at the next higher level is called the conversion efficiency. Here it varied from
• 17% from producers to primary consumers (1478/8833) to
• 4.5% from primary to secondary consumers (67/1478).
• From similar studies in other ecosystems, we can take 10% as the average conversion efficiency from producers to primary consumers.
Animal husbandry often exceeds this 10% value. For example, broilers (young chickens) can gain half a pound (227 g) of weight for every pound (454 g) of food they eat. (Since the water content of the two is not the same, the conversion efficiency is somewhat less than the apparent 50%.) Nonetheless, the loss of energy as it passes from producers to primary consumers explains, for example, why it costs more to buy a pound of beefsteak than a pound of corn.
Conversion efficiencies from primary consumers to secondary consumers (herbivores to carnivores) tend to be much lower, averaging about 1%.
• In this ecosystem, all the gross production of the producers (20,810) ultimately disappeared in respiration (14,198) and downstream export and decay (6612). So there was no storage of energy from one year to the next. This is typical of mature ecosystems, such as a mature forest.
Some ecosystems do store energy, for example,
• The slow rate of decay in bogs causes peat to accumulate (the source of the world's coal)
• A young forest accumulates organic matter as the trees grow.
The Pyramid of Energy
Conversions efficiencies are always much less than 100%. At each link in a food chain, a substantial portion of the sun's energy — originally trapped by a photosynthesizing autotroph - is dissipated back to the environment (ultimately as heat). Thus it follows that the total amount of energy stored in the bodies of a given population is dependent on its trophic level. For example, the total amount of energy in a population of toads must necessarily be far less than that in the insects on which they feed. The insects, in turn, have only a fraction of the energy stored in the plants on which they feed. This decrease in the total available energy at each higher trophic level is called the pyramid of energy.
Using Odum's data on net productivity at the various levels in Silver Springs, we get this pyramid. The figures represent net production at each trophic level expressed in kcal/m2/yr.
The Pyramid of Biomass
How does one measure the amount of energy in a population?
Since all organisms are made of roughly the same organic molecules in similar proportions, a measure of their dry weight is a rough measure of the energy they contain. A census of the population, multiplied by the weight of an average individual in it, gives an estimate of the weight of the population. This is called the biomass (or standing crop). This, too, diminishes with the distance along the food chain from the autotrophs which make the organic molecules in the first place.
The graphic shows the pyramid of biomass for Silver Springs. (It, too, is based on the data obtained by Howard T. Odum.) The figures represent the dry weight of organic matter (per square meter) at the time of sampling. Analysis of various ecosystems indicates that those with squat biomass pyramids (with conversion efficiencies between one trophic level and the next averaging 10% or better) are less likely to be disrupted by physical or biotic changes than those with tall, skinny pyramids (having conversion efficiencies less than 10%).
The Pyramid of Numbers
Small animals are more numerous than larger ones. This graph shows the pyramid of numbers resulting when a census of the populations of autotrophs, herbivores, and two levels of carnivores was taken on an acre (0.4 hectare) of grassland. The figures represent number of individuals counted at each trophic level. The pyramid is based on data acquired by Evans, Cain, and Walcott, and has been redrawn by permission from E. P. Odum, Fundamentals of Ecology, 2nd. ed., © W. B. Saunders Co., Philadelphia, 1959.
The pyramid arises because:
• Each species is limited in its total biomass by its trophic level.
• So, if the size of the individuals at a given trophic level is small, their numbers can be large and vice versa.
• Predators are usually larger than their prey.
• Occupying a higher trophic level, their biomass must be smaller.
• Hence, the number of individuals in the predator population is much smaller than that in the prey population. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/17%3A_Ecology/17.01%3A_Energy_Flow_through_the_Biosphere/17.1B%3A_Food_Chains_and_Food_Webs.txt |
A biome is a large, distinctive complex of plant communities created and maintained by climate.
How many biomes are there?
A study published in 1999 concluded that there are 150 different "ecoregions" in North America alone. But I shall cast my lot with the "lumpers" rather than the "splitters" and lump these into 8 biomes:
• tundra
• taiga
• temperate deciduous forest
• scrub forest (called chaparral in California)
• grassland
• desert
• tropical rain forest
• temperate rain forest
The figure shows the distribution of these 8 biomes around the world. A number of climatic factors interact in the creation and maintenance of a biome. Where precipitation is moderately abundant — 40 inches (about 1 m) or more per year — and distributed fairly evenly throughout the year, the major determinant is temperature. It is not simply a matter of average temperature, but includes such limiting factors as whether it ever freezes or length of the growing season. If there is ample rainfall, we find 4 characteristic biomes as we proceed from the tropics (high temperatures) to the extreme latitudes (low temperatures). In order, they are:
• tropical rain forest or jungle
• temperate deciduous forest
• taiga
• tundra
Tropical Rain Forest
In the Western Hemisphere, the tropical rain forest reaches its fullest development in the jungles of Central and South America.
• The trees are very tall and of a great variety of species.
• One rarely finds two trees of the same species growing close to one another.
• The vegetation is so dense that little light reaches the forest floor.
• Most of the plants are evergreen, not deciduous.
• The branches of the trees are festooned with vines and epiphytes (see the photo taken in the Luquillo National Forest of Puerto Rico).
Note
Epiphytes are plants that live perched on sturdier plants. They do not take nourishment from their host as parasitic plants do. Because their roots do not reach the ground, they depend on the air to bring them moisture and inorganic nutrients. Many orchids and many bromeliads (members of the pineapple family like "Spanish moss") are epiphytes.
The lushness of the tropical rain forest suggests a high net productivity, but this is illusory. Many of the frequent attempts to use the tropical rain forest for conventional crops have been disappointing. Two problems:
• The high rainfall leaches soil minerals below the reach of plant roots.
• The warmth and moisture cause rapid decay so little humus is added to the soil.
The tropical rain forest exceeds all the other biomes in the diversity of its animals as well as plants. Most of the animals - mammals and reptiles, as well as birds and insects live in the trees. The closest thing to a tropical rain forest in the continental United States are the little wooded "islands" found scattered through the Everglades in the southern tip of Florida. Their existence depends on the fact that it never freezes, and they often escape the fires that periodically sweep the Everglades.
Temperate Deciduous Forest
This biome occupies the eastern half of the United States and a large portion of Europe. It is characterized by:
• hardwood trees (e.g., beech, maple, oak, hickory) which
• are deciduous; that is, shed their leaves in the autumn.
• The number of different species is far more limited than in the jungle.
• Large stands dominated by a single species are common.
• Deer, raccoons, and salamanders are characteristic inhabitants.
• During the growing season, this biome can be quite productive in both natural and agricultural ecosystems.
The photo (by Dick Morton) shows a view of this biome in Maine in the autumn.
Taiga
Fig.17.1.3.4 Taiga
The taiga is named after the biome in Russia.
• It is a land dominated by conifers, especially spruces and firs.
• It is dotted with lakes, bogs, and marshes.
• It is populated by an even more limited variety of plants and animals than is the temperate deciduous forest.
• In North America, the moose is such a typical member that it has led to the name: "spruce-moose" biome.
• Before the long, snowy winter sets in, many of the mammals hibernate, and many of the birds migrate south.
• Although the long days of summer permit plants to grow luxuriantly, net productivity is low.
The photo (courtesy of Dr. Benjamin Dane of Tufts University) shows the "spruce-moose" biome in British Columbia.
Tundra
At extreme latitudes, the trees of the taiga become stunted by the harshness of the subarctic climate. Finally, they disappear leaving a land of bogs and lakes.
• The climate is so cold in winter that even the long days of summer are unable to thaw the permafrost beneath the surface layers of soil.
• Sphagnum moss, a wide variety of lichens, and some grasses and fast-growing annuals dominate the landscape during the short growing season.
• Caribou feed on this growth as do vast numbers of insects.
• Swarms of migrating birds, especially waterfowl, invade the tundra in the summer to raise their young, feeding them on a large variety of aquatic invertebrates and vertebrates.
• As the brief arctic summer draws to a close, the birds fly south, and
• all but a few of the permanent residents, in one way or another, prepare themselves to spend the winter in a dormant state.
Biomes established by altitude
Temperature is the major influence on the biomes discussed above. Because temperatures decline with altitude as well as latitude, similar biomes exist on mountains even when they are at low latitudes. As a rule of thumb, a climb of 1000 feet (about 300 m) is equivalent in changed flora and fauna to a trip northward of some 600 miles (966 km).
The photo is of alpine tundra at 12,000 feet (3,658 m) in the Rocky Mountains.
Field studies in various parts of the Northern Hemisphere have shown that in recent decades many species of animals and plants have
• shifted their ranges farther north (averagiing 16.9 kilometers per decade)
• shifted their ranges higher in the mountains (averaging 11.0 meters per decade)
These observations add to the growing body of evidence that global warming is affecting a broad assortment of living things.
Biomes established by rainfall
The other major biomes are controlled not so much by temperature but by the amount and seasonal distribution of rainfall.
The prevailing winds in the western half of North America blow in from the Pacific laden with moisture. Each time this air rises up from the western slopes of, successively, the Coast Ranges, the Sierras and Cascades, and finally the Rockies, it expands and cools. Its moisture condenses to rain or snow, which drenches the mountain slopes beneath. When the air reaches the eastern slopes, it is relatively dry, and much less precipitation falls. How much falls and when determine whether the biome will be
• temperate rain forest
• grassland
• desert or
• chaparral
Temperate Rain Forest
The temperate rain forest combines high annual rainfall with a temperate climate. The Olympic Peninsular in North America is a good example. An annual rainfall of as much as 150 inches (381 cm) produces a lush forest of conifers.
Grasslands
Grasslands are also known as prairie or plains. The annual precipitation in the grasslands averages 20 inches (~51 cm) per year. A large proportion of this falls as rain early in the growing season. This promotes a vigorous growth of perennial grasses and herbs, except along river valleys - is barely adequate for the growth of forests. The photo shows grassland in the Badlands National Monument in South Dakota.
Fire is probably the factor that tips the balance from forest to grasslands. Fires set by lightning and by humans regularly swept the plains in earlier times. Thanks to their underground stems and buds, perennial grasses and herbs are not harmed by fires that destroy most shrubs and trees.
The abundance of grass for food, coupled with the lack of shelter from predators, produces similar animal populations in grasslands throughout the world. The dominant vertebrates are swiftly-moving, herbivorous ungulates. In North America, bison and antelope were conspicuous members of the grassland fauna before the coming of white settlers. Now the level grasslands supply corn, wheat, and other grains, and the hillier areas support domesticated ungulates: cattle and sheep.
When cultivated carefully, the grassland biome is capable of high net productivity. A major reason: rainfall in this biome never leaches soil minerals below the reach of the roots of crop plants.
Desert
Annual rainfall in the desert is less than 10 inches (25 cm) and, in some years, may be zero. Because of the extreme dryness of the desert, its colonization is limited to
• plants such as cacti, sagebrush, and mesquite that have a number of adaptations that conserve water over long periods
• fast-growing annuals whose seeds can germinate, develop to maturity, flower, and produce a new crop of seeds all within a few weeks following a rare, soaking rain.
The photo shows the desert in the Anza-Borego park in southern California.
Many of the animals in the desert (mammals, lizards and snakes, insects, and even some birds) are adapted for burrowing to escape the scorching heat of the desert sun. Many of them limit their forays for food to the night. The net productivity of the desert is low. High productivity can sometimes be achieved with irrigation, but these gains are often only temporary. The high rates of evaporation cause minerals to accumulate near the surface and soon their concentration may reach levels toxic to plants.
Chaparral
The annual rainfall in the chaparral biome may reach 20–30 inches (64–76 cm), but in contrast to the grasslands, almost all of this falls in winter. Summers are very dry and all the plants - trees, shrubs, and grasses - are more or less dormant then.
The chaparral is found in California. (The photo shows the chaparral-clad foothills of the Sierra Nevada in California.) Similar biomes (with other names, such as scrub forest), are found around much of the Mediterranean Sea and along the southern coast of Australia.
The trees in the chaparral are mostly oaks, both deciduous and evergreen. Scrub oaks and shrubs like manzanita and the California lilac (not a relative of the eastern lilac) form dense, evergreen thickets. All of these plants are adapted to drought by such mechanisms as waxy, waterproof coatings on their leaves. The chaparral has many plants brought to it from similar biomes elsewhere. Vineyards, olives, and figs flourish just as they do in their native Mediterranean biome. So, too, do eucalyptus trees transplanted from the equivalent biome in Australia. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/17%3A_Ecology/17.01%3A_Energy_Flow_through_the_Biosphere/17.1C%3A_Biomes.txt |
Only 3% of the world's water is fresh. And 99% of this is either frozen in glaciers and pack ice or is buried in aquifers. The remainder is found in lakes, ponds, rivers, and streams.
The zone close to shore. Here light reaches all the way to the bottom. The producers are plants rooted to the bottom and algae attached to the plants and to any other solid substrate. The consumers include
• tiny crustaceans
• flatworms
• insect larvae
• snails
• frogs, fish, and turtles.
Limnetic zone
This is the layer of open water where photosynthesis can occur. As one descends deeper in the limnetic zone, the amount of light decreases until a depth is reached where the rate of photosynthesis becomes equal to the rate of respiration. At this level, net primary production no longer occurs.
The limnetic zone is shallower in turbid water than in clear and is a more prominent feature of lakes than of ponds.
Life in the limnetic zone is dominated by
• floating microorganisms - called plankton
• actively swimming animals - called nekton
The producers in this ecosystem are planktonic algae. The primary consumers include such animals as microscopic crustaceans and rotifers - the so-called zooplankton. The secondary (and higher) consumers are swimming insects and fish. These nekton usually move freely between the littoral and limnetic zones.
Profundal zone
Many lakes (but few ponds) are so deep that not enough light reaches here to support net primary productivity. Therefore, this zone depends for its calories on the drifting down of organic matter from the littoral and limnetic zones. The profundal zone is chiefly inhabited by primary consumers that are either attached to or crawl along the sediments at the bottom of the lake. Such bottom-dwelling animals are called the benthos. The sediments underlying the profundal zone also support a large population of bacteria and fungi. These decomposers break down the organic matter reaching them, releasing inorganic nutrients for recycling.
Fall overturn
Where there is a pronounced change of seasons, the warming of the surface of the lake in the summer prevents this water from mixing with deeper water. This is because warm water is less dense than cold.
The surface water becomes enriched in oxygen some from the air above it and the rest - because it is in the limnetic zone - from photosynthesis. But the water in the profundal zone - eing removed from both these sources - becomes stagnant. In the fall, however, as the surface water cools, it becomes denser and sinks to the bottom — carrying oxygen with it.
Spring overturn
A similar phenomenon occurs when the ice melts in the spring.
Rivers and Streams
The habitats available in rivers and streams differ in several ways from those in lakes and ponds.
• Because of the current, the water is usually more oxygenated.
• Photosynthesizers play a minor role in the food chains here; a large fraction of the energy available for consumers is brought from the land; e.g., in falling leaves.
Oceans, like lakes, can be described in terms of zones. There are many parallels between the two but unfortunately a separate vocabulary is used for each. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/17%3A_Ecology/17.01%3A_Energy_Flow_through_the_Biosphere/17.1D%3A_Freshwater_Ecosystems.txt |
Intertidal zone
Examples:
• sandy beaches
• rocks
• estuaries
• mangrove swamps
• coral reefs
• coastal marshes
Some of these regions are quite productive. Many of their inhabitants have adaptations that enable them to survive periodic exposure to the air and wave action.
Neritic zone
This is the relatively shallow ocean that extends to the edge of the continental shelf. Net productivity here depends on planktonic algae growing as deep as the light can reach.
Oceanic zone
Located over the ocean basins. Here, too, net productivity is pretty much limited to the depths that light can reach. The producers are planktonic algae that support secondary and higher consumers (e.g., fish) in the nekton.
Despite its diversity of life, the net productivity of the open ocean is little better than that of a desert.
Abyssal plain
The bottom of the ocean basins: This dark, relatively unvarying region is largely inhabited by sparse populations of bottom-dwelling organisms that make up the benthos. These are consumers and decomposers who depend on the organic matter drifting down from the upper portions of the sea.
An exception: the communities around rifts. Rifts are spreading cracks in the sea floor where continental drift is taking place. Although no light reaches here, net productivity does occur.
Chemoautotrophic bacteria and archaea manufacture food using energy secured by oxidizing the sulfur flowing out of the cracks ("black smokers"). These microbes support a large population of animals, e.g., tube worms. Some of these worms harbor chemoautotrophic microbes within their tissues which probably supply them with the bulk of their calories.
17.1F: Biomagnification of Pesticides
The figure shows how DDT becomes concentrated in the tissues of organisms representing four successive trophic levels in a food chain. The concentration effect occurs because DDT is metabolized and excreted much more slowly than the nutrients that are passed from one trophic level to the next. So DDT accumulates in the bodies (especially in fat). Thus most of the DDT ingested as part of gross production is still present in the net production that remains at that trophic level.
This is why the hazard of DDT to nontarget animals is particularly acute for those species living at the top of food chains.
For example,
• spraying a marsh to control mosquitoes will cause trace amounts of DDT to accumulate in the cells of microscopic aquatic organisms, the plankton, in the marsh.
• In feeding on the plankton, filter-feeders, like clams and some fish, harvest DDT as well as food. (Concentrations of DDT 10 times greater than those in the plankton have been measured in clams.)
• The process of concentration goes right on up the food chain from one trophic level to the next. Gulls, which feed on clams, may accumulate DDT to 40 or more times the concentration in their prey. This represents a 400-fold increase in concentration along the length of this short food chain.
There is abundant evidence that some carnivores at the ends of longer food chains (e.g. ospreys, pelicans, falcons, and eagles) suffered serious declines in fecundity and hence in population size because of this phenomenon in the years before use of DDT was banned (1972) in the United States. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/17%3A_Ecology/17.01%3A_Energy_Flow_through_the_Biosphere/17.1E%3A_Marine_Ecosystems.txt |
The concentration of carbon in living matter (18%) is almost 100 times greater than its concentration in the earth (0.19%). So living things extract carbon from their nonliving environment. For life to continue, this carbon must be recycled. Carbon exists in the nonliving environment as:
• carbon dioxide (CO2) in the atmosphere and dissolved in water (forming HCO3)
• carbonate rocks (limestone and coral = CaCO3)
• deposits of coal, petroleum, and natural gas derived from once-living things
• dead organic matter, e.g., humus in the soil
Carbon enters the biotic world through the action of primarily photoautotrophs, like plants and algae, that use the energy of light to convert carbon dioxide to organic matter and to a small extent, chemoautotrophs - bacteria and archaea that do the same but use the energy derived from an oxidation of molecules in their substrate. Carbon returns to the atmosphere and water by respiration (as CO2), burning, and decay (producing CO2 if oxygen is present, methane (CH4) if it is not.
The uptake and return of CO2 are not in balance
The carbon dioxide content of the atmosphere is gradually and steadily increasing. The graph shows the CO2 concentration at the summit of Mauna Loa in Hawaii from 1958 through 1999. The values are in parts per million (ppm). The seasonal fluctuation is caused by the increased uptake of CO2 by plants in the summer. (In March 2015, its average worldwide concentration reached 400 ppm.)
The increase in CO2 probably began with the start of the industrial revolution. Samples of air trapped over the centuries in the glacial ice of Greenland show no change in CO2 content until 300 years ago. Since measurements of atmospheric CO2 began late in the nineteenth century, its concentration has risen over 20%. This increase is surely "anthropogenic"; that is, caused by human activities:
• burning fossil fuels (coal, oil, natural gas) which returns to the atmosphere carbon that has been locked within the earth for millions of years.
• clearing and burning of forests, especially in the tropics. In recent decades, large areas of the Amazon rain forest have been cleared for agriculture and cattle grazing.
Where is the missing carbon?
Curiously, the increase in atmospheric CO2 is only about one-half of what would have been expected from the amount of fossil fuel consumption and forest burning. Where has the rest gone? Research has shown that increased CO2 levels lead to increased net production by photoautotrophs. There is evidence that at least some of the missing CO2 has been incorporated by: (1) increased growth of forests, especially in North America, (2) increased amounts of photoautotrophic plankton in the oceans, and (3) uptake by desert soils (mechanism as yet unknown)
The Greenhouse Effect and Global Warming
Despite these "sinks" for our greatly-increased CO2 production, the concentration of atmospheric CO2 continues to rise? Should we be worried? Carbon dioxide is transparent to light but rather opaque to heat rays. Therefore, CO2 in the atmosphere retards the radiation of heat from the earth back into space - the "greenhouse effect". Has the increase in carbon dioxide led to global warming?
Some evidence:
• Careful monitoring shows that the global air temperature in 2014 was 0.57°C higher than the average from 1961–1990, and that 14 of the 15 warmest years since records began being kept late in the 19th Century have occurred in this century (including 2005 and 2010 as well as 2014).
• Many glaciers and ice sheets are receding.
• Woody shrubs are now growing in areas of northern Alaska that 50 years ago were barren tundra.
• Many angiosperms in temperate climates are flowering earlier in the spring than they used to.
• Many species of birds and butterflies are moving north and breeding earlier in the spring.
Will continued increase in carbon dioxide lead to more global warming and, if so, how much? At this point, the answer depends on what assumptions you plug into your computer models. But as the different models have been improved, they seem to be converging on a consensus: a doubling of the CO2 concentration (expected by the end of this century) will cause the earth to warm somewhere in the range of 1.1–6.4°C.
Other Greenhouse Gases
Although their levels in the atmosphere are much lower than that of CO2,
• methane (CH4)
• nitrous oxide (N2O)
• hydrofluorocarbons (HFCs)
are also potent greenhouse gases.
Methane
Although methane ("marsh gas") is released by natural processes (e.g. from decay occurring in swamps), human activities now account for some 60% of the total.
• mining, processing, and use of coal, oil, and natural gas
• release from landfills
• growing rice in paddies
• burning forests
• raising cattle (fermentation in their rumens produces methane that is expelled from their GI tract)
So burning of the tropical rain forest adds to the atmospheric methane budget in two ways:
• incomplete combustion during burning
• release from the GI tract of the cattle that are later placed on the cleared land.
The methane concentration in Arctic air is presently some 1.9 parts per million, the highest level seen such measurements began. Although this concentration is far less than that of CO2, methane is 28 times as potent a greenhouse gas. The marked warming of the earth that occurred at the end of the Paleocene epoch is thought to have been caused by the release of large amounts of methane from the sea floor. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/17%3A_Ecology/17.02%3A_Cycles_of_Matter_in_the_Biosphere/17.2A%3A_Carbon_Cycle.txt |
All life requires nitrogen-compounds, e.g., proteins and nucleic acids. Air, which is 79% nitrogen gas (N2), is the major reservoir of nitrogen. But most organisms cannot use nitrogen in this form. Plants must secure their nitrogen in "fixed" form, i.e., incorporated in compounds such as: nitrate ions (NO3), ammonium ions (NH4+) and urea (NH2)2CO. Animals secure their nitrogen (and all other) compounds from plants (or animals that have fed on plants).
Four processes participate in the cycling of nitrogen through the biosphere: (1) nitrogen fixation, (2) decay, (3) nitrification, and (4) denitrification. Microorganisms play major roles in all four of these.
Nitrogen Fixation
The nitrogen molecule (N2) is quite inert. To break it apart so that its atoms can combine with other atoms requires the input of substantial amounts of energy. Three processes are responsible for most of the nitrogen fixation in the biosphere:
• atmospheric fixation by lightning
• biological fixation by certain microbes alone or in a symbiotic relationship with some plants and animals
• industrial fixation
Atmospheric Fixation
The enormous energy of lightning breaks nitrogen molecules and enables their atoms to combine with oxygen in the air forming nitrogen oxides. These dissolve in rain, forming nitrates, that are carried to the earth. Atmospheric nitrogen fixation probably contributes some 5– 8% of the total nitrogen fixed.
Industrial Fixation
Under great pressure, at a temperature of 600°C, and with the use of a catalyst, atmospheric nitrogen and hydrogen (usually derived from natural gas or petroleum) can be combined to form ammonia (NH3). Ammonia can be used directly as fertilizer, but most of its is further processed to urea and ammonium nitrate (NH4NO3).
Biological Fixation
The ability to fix nitrogen is found only in certain bacteria and archaea.
• Some live in a symbiotic relationship with plants of the legume family (e.g., soybeans, alfalfa).
• Some establish symbiotic relationships with plants other than legumes (e.g., alders).
• Some establish symbiotic relationships with animals, e.g., termites and "shipworms" (wood-eating bivalves).
• Some nitrogen-fixing bacteria live free in the soil.
• Nitrogen-fixing cyanobacteria are essential to maintaining the fertility of semi-aquatic environments like rice paddies.
Biological nitrogen fixation requires a complex set of enzymes and a huge expenditure of ATP. Although the first stable product of the process is ammonia, this is quickly incorporated into protein and other organic nitrogen compounds.
Decay
The proteins made by plants enter and pass through food webs just as carbohydrates do. At each trophic level, their metabolism produces organic nitrogen compounds that return to the environment, chiefly in excretions. The final beneficiaries of these materials are microorganisms of decay. They break down the molecules in excretions and dead organisms into ammonia.
Nitrification
Ammonia can be taken up directly by plants — usually through their roots. However, most of the ammonia produced by decay is converted into nitrates. Until recently this was thought always to be accomplished in two steps:
1. Bacteria of the genus Nitrosomonas oxidize \(\ce{NH3}\) to nitrites (\(\ce{NO2^{−}}\)).
2. Bacteria of the genus Nitrobacter oxidize the nitrites to nitrates (\(\ce{NO3^{−}}\)).
These two groups of autotrophic bacteria are called nitrifying bacteria. Through their activities (which supply them with all their energy needs), nitrogen is made available to the roots of plants. However, in 2015, two groups reported finding that bacteria in the genus Nitrospira were able to carry out both steps: ammonia to nitrite and nitrite to nitrate. This ability is called "comammox" (for complete ammonia oxidation).
In addition, both soil and the ocean contain archaeal microbes, assigned to the Crenarchaeota, that convert ammonia to nitrites. They are more abundant than the nitrifying bacteria and may turn out to play an important role in the nitrogen cycle.
Many legumes, in addition to fixing atmospheric nitrogen, also perform nitrification - converting some of their organic nitrogen to nitrites and nitrates. These reach the soil when they shed their leaves.
Denitrification
The three processes above remove nitrogen from the atmosphere and pass it through ecosystems. Denitrification reduces nitrates and nitrites to nitrogen gas, thus replenishing the atmosphere. In the process several intermediates are formed:
• nitric oxide (NO)
• nitrous oxide (N2O)(a greenhouse gas 300 times as potent as CO2)
• nitrous acid (HONO)
Once again, bacteria are the agents. They live deep in soil and in aquatic sediments where conditions are anaerobic. They use nitrates as an alternative to oxygen for the final electron acceptor in their respiration.
Anammox (anaerobic ammonia oxidation)
Under anaerobic conditions in marine and freshwater sediments, other species of bacteria are able to oxidize ammonia (with \(\ce{NO2^{−}}\)) forming nitrogen gas.
\[\ce{NH4^{+} + NO2^{−} → N2 + 2H2O}\]
The anammox reaction may account for as much as 50% of the denitrification occurring in the oceans. All of these processes participate in closing the nitrogen cycle.
Are the denitrifiers keeping up?
Agriculture may now be responsible for one-half of the nitrogen fixation on earth through the use of fertilizers produced by industrial fixation and the the growing of legumes like soybeans and alfalfa. This is a remarkable influence on a natural cycle. Are the denitrifiers keeping up the nitrogen cycle in balance? Probably not. Certainly, there are examples of nitrogen enrichment in ecosystems. One troubling example: the "blooms" of algae in lakes and rivers as nitrogen fertilizers leach from the soil of adjacent farms (and lawns). The accumulation of dissolved nutrients in a body of water is called eutrophication. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/17%3A_Ecology/17.02%3A_Cycles_of_Matter_in_the_Biosphere/17.2B%3A_Nitrogen_Cycle.txt |
Symbiotic nitrogen fixation occurs in plants that harbor nitrogen-fixing bacteria within their tissues. The best-studied example is the association between legumes and bacteria in the genus Rhizobium. Each of these is able to survive independently (soil nitrates must then be available to the legume), but life together is clearly beneficial to both. Only together can nitrogen fixation take place. A symbiotic relationship in which both partners benefits is called mutualism.
Rhizobia
Rhizobia are Gram-negative bacilli that live freely in the soil (especially where legumes have been grown). However, they cannot fix atmospheric nitrogen until they have invaded the roots of the appropriate legume.
The Infection Thread
The interaction between a particular strain of rhizobia and the "appropriate" legume is mediated by a "Nod factor" secreted by the rhizobia and transmembrane receptors on the cells of the root hairs of the legume. Different strains of rhizobia produce different Nod factors, and different legumes produce receptors of different specificity.
If the combination is correct, the bacteria enter an epithelial cell of the root; then migrate into the cortex. Their path runs within an intracellular channel that grows through one cortex cell after another. This infection thread is constructed by the root cells, not the bacteria, and is formed only in response to the infection. When the infection thread reaches a cell deep in the cortex, it bursts and the rhizobia are engulfed by endocytosis into membrane-enclosed symbiosomes within the cytoplasm. At this time the cell goes through several rounds of mitosis - without cytokinesis - so the cell becomes polyploid.
The above electron micrograph (courtesy of Dr. D. C. Jordan) shows a rhizobia-filled infection thread growing into the cell (from the upper left to the lower right). Note how the wall of the infection thread is continuous with the wall of the cell. The dark ovals are the symbiosomes.
The cortex cells then begin to divide rapidly forming a nodule. This response is driven by the translocation of cytokinins from epidermal cells to the cells of the cortex. The above photo in fig. 17.2.3.2 (courtesy of The Nitragin Co. Milwaukee, Wisconsin) shows nodules on the roots of the birdsfoot trefoil, a legume.
The rhizobia also go through a period of rapid multiplication within the nodule cells. Then they begin to change shape and lose their motility. The bacteroids, as they are now called, may almost fill the cell. Only now does nitrogen fixation begin. The electron micrograph in fig. 17.2.3.3(courtesy of R. R. Hebert) shows bacteroid-filled cells from a soybean nodule. The horizontal line marks the walls between two adjacent nodule cells.
Root nodules are not simply structureless masses of cells. Each becomes connected by the xylem and phloem to the vascular system of the plant. The photo in fig. 17.2.3.4 on the left shows a developing lateral root on a pea root. On its right is a segment of a pea root showing a developing nodule 12 days after the root was infected with rhizobia. Both structures are connected to the nutrient transport system of the plant (dark area extending through the center of the root). (Photomicrographs courtesy of the late John G. Torrey.) Thus the development of nodules, while dependent on rhizobia, is a well-coordinated developmental process of the plant.
Although some soil bacteria (e.g., Azotobacter) can fix nitrogen by themselves, rhizobia cannot. Clearly rhizobia and legumes are mutually dependent. The benefit to the legume host is clear. The rhizobia make it independent of soil nitrogen. But why is the legume necessary? The legume is certainly helpful in that it supplies nutrients to the bacteroids with which they synthesize the large amounts of ATP needed to convert nitrogen (N2) into ammonia (NH3). In addition, the legume host supplies one critical component of nitrogenase - the key enzyme for fixing nitrogen.
The bacteroids need oxygen to make their ATP (by cellular respiration). However, nitrogenase is strongly inhibited by oxygen. Thus the bacteroids must walk a fine line between too much and too little oxygen. Their job is made easier by another contribution from their host: hemoglobin. Nodules are filled with hemoglobin. So much of it, in fact, that a freshly-cut nodule is red. The hemoglobin of the legume (called leghemoglobin), like the hemoglobin of vertebrates, probably supplies just the right concentration of oxygen to the bacteroids to satisfy their conflicting requirements.
The metal molybdenum is a critical component of nitrogenase and so is absolutely essential for nitrogen fixation. But the amounts required are remarkably small. One ounce (28.3 g) of molybdenum broadcast over an acre (0.4 hectare) of cropland in Australia was found to be sufficient to restore fertility for over ten years.
The photo in fig. 17.2.3.5 shows that the legume clover grows normally only where the supply of molybdenum is adequate. The soil shown here (in eastern Australia) is naturally deficient in molybdenum. Although the entire fenced-in plot was seeded to clover, the plant was able to flourish and fix nitrogen only where molybdenum fertilizer had been added (foreground). (Photo courtesy of A. J. Anderson.)
Because of the specificity of the interaction between the Nod factor and the receptor on the legume, some strains of rhizobia will infect only peas, some only clover, some only alfalfa, etc. The treating of legume seeds with the proper strain of rhizobia is a routine agricultural practice. (The Nitragin Company, that supplied one of the photos above specializes in producing rhizobial strains appropriate to each leguminous crop.)
How did two such organisms ever work out such an intimate and complex living relationship? Assuming that the ancestors of the rhizobia could carry out the entire process by themselves - as many other soil bacteria still do - they must have gained some real advantage from evolving to share the duties with the legume. Perhaps the environment provided by their host, e.g., lots of food and just the right amount of oxygen, enabled the rhizobia to do the job more efficiently than before. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/17%3A_Ecology/17.02%3A_Cycles_of_Matter_in_the_Biosphere/17.2C%3A_Symbiotic_Nitrogen_Fixation.txt |
Soil is the entry point for most materials into terrestrial food webs. Through their roots, plants absorb water and minerals (e.g., nitrates, phosphates, potassium, copper, zinc). With these, they use photosynthesis to convert carbon dioxide (taken in through their leaves) into carbohydrates, proteins, lipids, nucleic acids and the vitamins on which all heterotrophs depend. Along with temperature and water, soil is a major determinant of productivity.
Topsoil
The very top layer consists of partially decayed organic debris like leaves. Beneath this is the topsoil. This horizon is usually dark in color because of humus- partially decayed organic matter - which has been incorporated in it from above. Humus gives the soil a loose texture that holds water and allows air to diffuse through it. Oxygen is essential to permit cellular respiration in plant roots, decay organisms, and other inhabitants of the soil.
Subsoil
The subsoil is usually lighter in color that topsoil and often contains an accumulation of inorganic nutrients.
Weathered parent material
This represents the first steps in the chemical breakdown of rock into soil. Often the weathered parent material is underlain by the parent material itself, although in some places it has been carried from another location by wind, water, or glaciers.
Parent material
The chemical nature of the parent material, whether granite, limestone, or sandstone, for example, has a great influence on the fertility of the soil derived from it.
The Effect of Water on Soil
The Tropical Rain Forest
The lushness of the jungle biome is somewhat illusory. While productivity is high, the soils themselves tend to be of very poor quality. Because of the high rainfall, nutrients are quickly washed out of the topsoil unless they are incorporated in the forest plants. As plant and animal debris falls to the ground, it is quickly decomposed because of the warmth and moisture there. Thus minerals are found mainly in the forest plants, not in the soil. When the plants are removed and cultivation attempted, the soils quickly lose fertility. The situation is made worse by the lack of humus (the topsoil may be no thicker than 2 in. [= 5 cm]) and the high iron and aluminum content of most of these soils. Once exposed to the sun, these lateritic soils soon bake into a bricklike material that cannot be cultivated.
The most ancient (some might say primitive) way of working these soils is still the best:
• clearing a small area of jungle
• growing crops for only a year or two, and then
• abandoning the area to jungle once again.
17.2E: Sewage Treatment
The wastes generated by some 60% of the U.S. population are collected in sewer systems and carried along by some 14 billion gallons (~53 billion liters) of water a day. Of this enormous volume, some 10% is allowed to pass untreated into rivers, streams, and the ocean. The rest receives some form of treatment to improve the quality of the water (which makes up 99.9% of sewage) before it is released for reuse.
Biochemical Oxygen Demand (BOD)
The BOD is an important measure of water quality. It is a measure of the amount of oxygen needed (in milligrams per liter or parts per million) by bacteria and other microorganisms to oxidize the organic matter present in a water sample over a period of 5 days. The BOD of drinking water should be less than 1. That of raw sewage may run to several hundred. It is also called the "biological" oxygen demand.
Basic Sewage Treatment
Primary Treatment
The simplest, and least effective, method of treatment is to allow the undissolved solids in raw sewage to settle out of suspension forming sludge. Such primary treatment removes only one-third of the BOD and virtually none of the dissolved minerals. Attempts to use digested sludge as a fertilizer have been hampered by its frequent contamination by toxic chemicals derived from industrial wastes.
Secondary Treatment
However, many treatment plants in North America then pass the effluent from primary treatment to secondary treatment. Here the effluent is brought in contact with oxygen and aerobic microorganisms. They break down much of the organic matter to harmless substances such as carbon dioxide. Primary and secondary treatment together can remove up to 90% of the BOD. After chlorination to remove its content of bacteria, the effluent from secondary treatment is returned to the local surface water.
Advanced Waste Treatment
The combination of primary and secondary treatment removes most of the organic matter in sewage and thus lowers the BOD. However, most of the nitrogen and phosphorus in sewage remains in the effluent from secondary treatment. These inorganic nutrients can cause eutrophication of surface water receiving the effluent causing blooms of algae. To avoid this, a few communities add a third stage of treatment called tertiary or advanced waste treatment.
Several techniques are available to remove dissolved salts from sewage effluent, but all are quite expensive. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/17%3A_Ecology/17.02%3A_Cycles_of_Matter_in_the_Biosphere/17.2D%3A_Soil.txt |
Chlorination is the adding of chlorine to water in order to kill any dangerous bacteria that might be present. Most municipal water supplies are chlorinated with chlorine gas, Cl2. Swimming pools, hot tubs, and the like are usually chlorinated with chlorine-containing substances like
• calcium hypochlorite, Ca(HClO)2
• sodium hypochlorite, NaHClO (bleach)
• trichloro-s-triazinetrione
In every case, the effectiveness of chlorination as a germicide is a result of chlorine's powerful oxidizing action. The widespread chlorination of municipal water supplies has been one of the public health triumphs of the past century. However, chlorine also reacts with any organic matter present in the water. Among the products formed are chloroform and a variety of other trihalomethanes (THMs). Although these substances are normally present only in the range of parts per billion (ppb), they nevertheless have caused considerable anxiety because several of them are known or suspected carcinogens.
The U.S. Environmental Protection Agency (EPA) sets a limit of <1 ppb of THMs in major water systems and an absolute limit of 100 ppb in any water system.
Assuming:
• that laboratory animals respond the same as humans when fed these chemicals (they may not; when methylene chloride, a THM, is fed to mice, it increases their incidence of cancer, but it is not carcinogenic when fed to rats),
• that we know how to scale up from doses in rats and mice to the equivalent dose in humans (there is still controversy about how best to do this),
• that there is no threshold below which doses of THMs are safe and thus
• that the concept of collective dose applies,
the EPA estimates that if everyone in the U.S. drank water containing 100 ppb of THMs for their entire lives, their chance of developing cancer (currently about 25%, representing some 500,000 cancer deaths per year) would increase by some 700 cases per year.
Turn off the chlorinators?
Claiming that they were responding to the questions raised by the U.S. EPA over the safety of THMs, officials in Peru began, in the late 80s, shutting down some of the chlorinators in the capital city, Lima, as well as in other cities and towns.
In January 1991, an outbreak of cholera began in several towns just north of Lima. Within weeks the epidemic of this dangerous disease (the first epidemic of cholera in the Western hemisphere in a century) spread throughout Peru and eventually through much of South and Central America. Once introduced into a city, town, or village, the disease spread rapidly through contaminated, but now unchlorinated, water supplies.
By Dec. 31, 1992 — 23 months after the epidemic began, a total of 731,312 cases had been recorded with 6,323 deaths. Worst hit was Peru itself. Barely 10 months into the epidemic (Nov. 13, 1991), 2,720 of its people had died of cholera. With a population of 22 million, that works out to 140 deaths per million people. Even taking the EPA's gloomiest prediction, a lifetime of drinking water containing 100 ppb of THMs would increase the rate of cancer deaths each year in Peru by less than 3 deaths per million.
What's to be done?
After the appalling devastation caused in Central and South America by misguided risk analysis, one might have hoped that the choices would be clear.
• Certainly don't suddenly stop disinfecting municipal water supplies!
• Continue to explore alternatives to chlorination.
• For example, many water systems in France and some in the U.S. use ozone as the disinfectant. However, this strong oxidant also interacts with organic matter to produce undesirable contaminants.
• Adding ammonia (NH3) as well as chlorine to water produces chloramine, which is an effective disinfectant but has the disadvantage of producing carcinogenic nitrosamines and leaching lead from ancient water pipes.
• Irradiation with ultraviolet light is least likely to produce unwanted contaminants.
• Whatever method(s) used, treat the water to reduce the amount of organic matter in it.
• Keep a cool head and try to evaluate the size of the risks involved before taking action. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/17%3A_Ecology/17.02%3A_Cycles_of_Matter_in_the_Biosphere/17.2F%3A_Chlorination_and_the_Law_of_Unintended_Consequences.txt |
Human activities add a number of ingredients to the air:
• particles. In industrial areas and where there is heavy vehicular traffic, these contain carbon and hydrocarbons from the incomplete combustion of fuels. The hydrocarbons include a variety of polycyclic aromatic hydrocarbons (PAHs) that have been shown to cause mutations.
Inhaled particles smaller than 2.5 µm ("PM2.5") are taken deep into the lungs and may be deposited there. Chronic exposure to these small particles has been linked to
• reduced lung development and function in adolescents;
• an increased risk of asthma;
• increases in the incidence of heart disease and lung cancer later in life;
• a significant increase in the frequency of germline mutations in the sperm of exposed mice.
The U.S. Environmental Protection Agency (EPA) has established an air quality standard of an annual average of no more than 15 µg of these particles in a cubic meter of air. (Los Angeles averaged 20 µg/m3 in 1999 and 2000.) A survey of 217 counties in the U.S. showed an association between a reduction of 10 µg PM2.5 with an increase in life expectancy of almost 1 year. Conversely, studies in Europe showed that an increase of 10 µg PM2.5 was associated with a decrease in life expectancy of about 1 year.
• sulfur dioxide (SO2). These are produced from the oxidation of fuels (e.g., coal and oil) containing sulfur compounds.
• carbon monoxide (CO). Also produced from the incomplete combustion of fuels.
• various volatile hydrocarbons including PAHs like benzopyrene, a notorious carcinogen). These are produced from the incomplete combustion of gasoline.
• nitrogen oxides ("NOX". These are produced by the chemical union of O2 and N2 in the cylinders of internal combustion engines.
Photochemical smog
In bright sunlight nitrogen oxides, hydrocarbons and oxygen interact chemically to produce powerful oxidants like ozone (O3) and peroxyacetyl nitrate (PAN). These secondary pollutants are damaging to plant life and lead to the formation of photochemical smog. PAN is primarily responsible for the eye irritation so characteristic of this type of smog. The figure outlines representative reactions leading to the formation of photochemical smog. Radicals are atoms or molecules with unpaired electrons. They are very reactive chemically. The catalytic converter in automobile exhaust systems reduces air pollution by oxidizing hydrocarbons to CO2 and H2O and, to a lesser extent, converting nitrogen oxides to N2 and O2.
17.2H: Acid Rain
Is rain more acid than normal. Natural rain and snow is slightly acidic (pH 5.6) because of the carbon dioxide (CO2) dissolved in it. But over recent decades, rain in North America and Europe downwind of industrial areas has had a pH close to 4.5 and sometimes as low as 2.1 (equivalent to lemon juice).
Sulfur dioxide
The evidence is very strong that most of this acidity is caused by sulfur dioxide (SO2) released from the smokestacks of coal-burning power plants and other industrial sources. The sulfur dioxide is converted into sulfuric acid (H2SO4). This may be carried to the ground in rain or snow, but often particles containing sulfuric acid settle out of dry air. So the problem of acid rain is really one of acid deposition in dry weather as well as wet.
Nitrogen oxides
Nitrogen oxides ("NOx"), which are converted into nitric acid, also contribute to acid deposition. Automobile exhaust accounts for 50% or more of the nitrogen oxides in polluted air.
Types of damage
Acid rain has been held responsible for damaging buildings and statues made of limestone, damaging aquatic life in lakes (true), causing a decline in the vigor of U.S. and European forests (may be partially responsible), and harming human health (doubtful).
Sensitive areas
There is solid evidence that lakes in certain "sensitive" areas of North America and Europe have become more acid in recent decades. Sensitive areas are downwind of major industrial areas and where the underlying rock is granite rather than limestone. In North America, the Adirondacks of New York, the mountains of northern New England as well as large areas of southern Quebec have been particularly hard-hit. Both the plant and animal life in a lake become altered as the pH drops. The productivity of the lakes, and their content of desirable fish, decline.
The role of smokestacks
Coal burning by heavy industry was going on long before the lakes of northeastern North America began to show signs of damage. Their acidification seems to have coincided with the trend to build very tall smokestacks - often more than 500 feet (152 m) high. This was done to reduce local air pollution, but the result has been simply to transfer the problem further downwind.
Polluted air masses can cross political boundaries
Acid rain does not respect political boundaries. The lakes of Norway and Sweden suffer from the air pollution generated by the industrial areas to their south and southwest. Canadians are distressed by the damage from the air pollution generated by the industrial heartland of the U.S. The U.S. is not entirely to blame for their problems, however. Sensitive areas in Quebec are also downwind of the smelters in Sudbury, Ontario, which have the dubious distinction of generating more sulfur dioxide pollution than any other place in the entire world.
Current trends
Since the early 1980s, emissions of sulfur dioxide have been reduced in both Europe and North America. Even though nitrogen oxides have not been reduced proportionally, the result has been a reduction in the amount of acid deposition. This seems to have stopped the acidification of lakes but not yet reversed it. The technology exists to generate electricity from coal with greatly reduced emissions and as this technology comes into use, that aspect of the problem should improve.
What about forests?
Not enough is yet known to be certain, but my guess is that sulfur dioxide will turn out to have only a supporting role to play and that the major culprit will turn out to be ozone. Air pollution by ozone, like that by nitrogen oxides, is largely a matter of automobile exhaust. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/17%3A_Ecology/17.02%3A_Cycles_of_Matter_in_the_Biosphere/17.2G%3A_Air_Pollution.txt |
Ozone is a highly active form of oxygen (O3 rather than O2). Ozone is made when a electric spark passes through air, and this accounts for the characteristic odor give off by some electrical motors. Ozone presents two quite different biological problems: too much at low levels of the atmosphere (the troposphere); too little at high altitudes (the stratosphere).
Ozone in the Troposphere
Ozone is produced by the reaction of sunlight, oxygen, and automobile exhaust (which contains hydrocarbons and nitrogen oxides). Ozone is largely responsible for the discomfort associated with photochemical smog. This form of smog, long familiar to people in the Los Angeles basin, is now common wherever sunlight and stagnant air occur in urban areas (Mexico City is a dramatic example with ozone levels that often exceed 100 ppb and sometimes rise above 350 ppb). High levels of ozone during smog build-up can cause difficulty to people with respiratory ailments like emphysema and asthma. Ozone also damages plants and may be an important factor in the damage that is occurring to forests in Europe and North America.
Ozone in the Stratosphere
While we often have too much ozone around us, the concentration of ozone high in the stratosphere (which begins about 7 miles [11 km] up — where airliners cruise) has declined over the past two decades. Satellite monitoring of the stratosphere, which began in 1978, has revealed a marked decline. The most serious decline occurs over Antarctica in spring (October) when a precipitous drop in ozone causes an ozone hole. The figure (courtesy of NASA) shows a map of the ozone hole measured over Antarctica on 5 October 1987 by a device carried on the Nimbus 7 satellite. The tips of South America (upper right quadrant ) and Africa (lower right) are drawn in, as is the outline of Australia and New Zealand (lower left).
The Dobson unit is a measure of the number of molecules of ozone in a vertical column of the atmosphere. You can see that the concentration of ozone decreases in ever-smaller concentric circles with the lowest reading centered over the South Pole. Despite an anomalous increase in October 2015 (attributed to a volcanic eruption in Chile), the hole has been steadily shrinking over the last 14 years. This is probably the result of phasing out the manufacture and use of chlorofluorocarbons.
The Ozone Shield
The spreading of this ozone-depleted air may account for the more gradual and more protracted declines that are being seen at midlatitudes. From 1978-1990, average ozone levels declined 8% over Europe and about 5% over the United States. This is ominous because ozone shields the earth's surface from much of the ultraviolet radiation reaching the earth from the sun. Ultraviolet rays can cause skin cancer, cataracts, and may depress the immune system.
The graph (from C. R. Roy, et. al., in Nature 347:235, 1990) shows measurements of the intensity of ultraviolet light and the concentration of ozone on several sunny days in Melbourne, Australia during December 1987 and January 1988. When ozone levels were low, ultraviolet light was more intense and vice versa. The drop in ozone, which lasted about a month, was probably caused by ozone-depleted air drifting in from the ozone hole over the South Pole. Most of the ultraviolet light that reaches the earth is ultraviolet "B" (UV-B), which includes wavelengths from 280 to 320 nm.
Chlorofluorocarbons (CFCs)
Chlorofluorocarbons (CFCs) are synthetic gases in which the hydrogen atoms of methane are replaced by atoms of fluorine and chlorine (e.g., CHF2Cl, CFCl3, CF2Cl2). These gases are noninflammable, nontoxic, and very stable. They were widely used in industry as refrigerants (e.g., in refrigerators and air conditioners), solvents, propellants in aerosol cans (now banned in some countries), and in the manufacture of plastic foams. CFCs escape to the air from all of these uses (e.g., from leaky and discarded refrigeration units). Their chemical inertness, which makes CFCs so desirable for industry, also makes them a threat to the atmosphere. Once in the atmosphere, it may take 60–100 years for them to decompose and disappear. In the meantime, they pose a threat to the ozone shield.
Although some of the recent depletion of ozone in the stratosphere was probably due to natural causes (volcanic eruptions, fewer sunspots), some is most likely caused by chlorofluorocarbons (CFCs). However, a multi-nation agreement drawn up in 1987 - the Montreal Protocol - established a schedule for reducing the use of these materials. And, in fact, monitoring shows that the concentration of CFCs in the stratosphere has been decreasing since the mid-90s.
CFCs have largely been replaced by hydrofluorocarbons (HFCs) in air conditioners and refrigerators. HFCs do not destroy ozone but are potent greenhouse gases. While the ozone hole over the Antarctic still persists, there are signs of recovery of ozone levels at mid-latitudes (where we live). Whether this trend continues may depend on the contribution to ozone-depletion by nitrous oxide. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/17%3A_Ecology/17.02%3A_Cycles_of_Matter_in_the_Biosphere/17.2I%3A_Ozone.txt |
Ecology studies the interactions among organisms and their environment. Objects of study include interactions of organisms with each other and with abiotic components of their environment. Topics of interest include the biodiversity, distribution, biomass, and populations of organisms, as well as cooperation and competition within and between species. Ecosystems are dynamically interacting systems of organisms, the communities they make up, and the non-living components of their environment. Ecosystem processes, such as primary production, pedogenesis, nutrient cycling, and niche construction, regulate the flux of energy and matter through an environment.
17: Ecology
• 17.3A: The Human Population
• 17.3B: Principles of Population Growth
The vagaries of the physical environment, for example drought, freezes, hurricane, floods, and forest fires are often check population growth. Not only may they limit population growth but they often drive existing populations well below their previous level. (And also make it unlikely that many animals will survive long enough to show signs of aging.)
17.03: The Growth of Populations
The Rate of Natural Increase ( r )
Birth rate (b) − death rate (d) = rate of natural increase (r)
• birth rate expressed as number of births per 1000 per year (currently 13 in the U.S.)
• death rate expressed as the number of deaths per 1000 per year (currently 8 in the U.S.)
• So the rate of natural increase is 5 per thousand (0.005 or 0.5%).
Although the value of r is affected by both birth rate and death rate, the recent history of the human population has been affected more by declines in death rates than by increases in birth rates.
The graph shows birth and death rates in Mexico since 1930. The introduction of public health measures, such as better nutrition, greater access to medical care, improved sanitation, and more widespread immunization has produced a rapid decline in death rates, but until recently there was no corresponding decline in birth rates. In 2012, r is 1.5%. (Data from the Population Reference Bureau.) Although death rates declined in all age groups, the reduction among infants and children had — and will continue to have — the greatest impact on population growth. This is because they will soon be having children of their own. This situation, resulting in a rapid rate of population growth, is characteristic of many of the poorer regions of the world.
The Demographic Transition
Slowly declining birth rates following an earlier sharp decline in death rates are today characteristic of most of the less-developed regions of the world. The shift from high birth and death rates to low birth as well as death rates is called the demographic transition.
This graph (based on data from the Population Reference Bureau) shows that the demographic transition began much earlier in Sweden than in Mexico and was, in fact, completed by the end of the nineteenth century. The spike in deaths in the interval between 1901 and 1926 was caused by the worldwide influenza pandemic of 1918–1919. The birth rate in Sweden is now (2012) 12/1000; the death rate 10/1000, giving a rate of natural increase (r) of 0.2%.
The Story of Sri Lanka
Prior to World War II, advances in public health has been largely limited to affluent, industrialized countries. But since then, improvements in public health have been made in many of the poorer countries of the world - always with dramatic effect on death rates.
• In 1945, the death rate in Sri Lanka (then called Ceylon) was 22/1000.
• In 1946, a large-scale program of mosquito control - using DDT - was started.
• By eliminating its vector, the incidence of malaria dropped sharply.
• After 9 years, the death rate dropped to 10/1000, and by 2012 was 6.
• But a compensating decline in birth rates has come more slowly (18/1000 in 2012).
• So by 2012 the population was increasing at an annual rate of 1.2% (12/1000/year).
• At this rate the population would double in 57.5 years.
Let's see why.
Exponential Growth
The prediction that Sri Lanka will double its population in 57.5 years is based on:
• the assumption that r will remain unchanged (which is surely false)
• the mathematics of exponential growth.
The product of growth grows itself. So the growth of populations is a problem in "compound interest". At the end of each year (or whatever period you choose to use), the base against which the rate is applied has grown. Whatever figures you pick, as long as r is positive, a plot of population as time elapses will produce an exponential growth curve like this one.
The rate of population growth at any instant is given by the equation
$\dfrac{dN}{dt} = rN$
where
• r is the rate of natural increase in
• t — some stated interval of time, and
• N is the number of individuals in the population at a given instant.
The algebraic solution of this differential equation is
$N = N_0e^{rt} \label{exgr}$
where
• N0 is the starting population
• N is the population after
• a certain time, t, has elapsed, and
• e is the constant 2.71828... (the base of natural logarithms).
Plotting the results gives this exponential growth curve, so-called because it reflects the growth of a number raised to an exponent (rt).
Doubling Times
When a population has doubled,
$N = N_0 \times 2.$
Putting this in our exponential growth equation (Equation \ref{exgr})
$2N_0 = N_0e^{rt}$
ert = 2
rt = ln (natural logarithm) of 2 = 0.69
doubling time,
$t = \dfrac{0.69}{r}$
So Sri Lanka with an r of 1.2% (0.012) has a doubling time
$t = \dfrac{0.69}{0.012} = 57.5.$
(You can use the same equation to calculate how quickly an investment in, for example, a certificate of deposit will enable you to double your money.)
The Population of the World
The solid line in this graph shows estimates of the size of the world's population over the last two millennia. The estimates from 1800 to 1991 are based on more accurate data than those before. The dotted line shows what would happen if exponential growth continued to the year 2100. As you can see, the world's population has been growing exponentially (except during the years of the black death). How long will it continue to do so? (Since the graph was drawn, the world's population has reached 7.1 billion; that is, in 2012 we are still on course.) But can it continue indefinitely? Surely not.
Predicting Future Population Size
With a 2012 rate of natural increase in Mexico of 1.5%, its population would be expected to double in 46 years (0.69/0.015 = 46) from its 116.1 million people now to some 232 million in 2058. Will it? No one knows for certain. What actually happens to population growth depends on a number of factors. Some of these can be estimated with some confidence, some cannot. Two that can are:
• the age structure of the population and
• the total fertility rate (TFR).
Total Fertility Rate (TFR)
The total fertility rate is the average number of children that each woman will have during her lifetime. The TFR is an average because, of course, some women will have more, some fewer, and some no children at all. Theoretically, when the TFR = 2, each pair of parents just replaces itself. Actually it takes a TFR of 2.1 or 2.2 to replace each generation - this number is called the replacement rate - because some children will die before they grow up to have their own two children. In countries with low life expectancies, the replacement rate is even higher (2.2–3).
Age Structure of Populations
But even a TFR of 2.1 may not ensure zero population growth (ZPG). If at one period a population has an unusually large number of children, they will — as they pass through their childbearing years — increase the r of the population even if their TFR goes no higher than 2.
Most childbearing is done by women between the ages of 15 and 49. So if a population has a large number of young people just entering their reproductive years, the rate of growth of that population is sure to rise.
These pyramids compare the age structure of the populations of France and India in 1984. The relative number (%) of males and females is shown in 5-year cohorts. Almost 20% of India's population were children — 15 years or less in age — who had yet to begin reproduction. When the members of a large cohort like this begin reproducing, they add greatly to birth rates. In France, in contrast, each cohort is about the size of the next until close to the top when old age begins to take its toll. Broad-based pyramids like India's are characteristic of populations
• with high birth rates
• low life expectancies (where many people die before reaching old age)
• advances in public health have recently reduced infant and childhood mortality
The age structure of a population also reflects the recent pattern of mortality. In countries where injuries, starvation, and disease, etc. take a heavy toll throughout life, a plot of the age cohorts produces a broad based pyramid like that of India. In France (and other countries in western Europe) almost everyone survives until old age, and a plot of the age cohorts is scarcely a pyramid at all. So even if the TFRs were the same in both countries (they are not - in India it is 2.5, in France, 2.0), India is in for more years of rapid population growth, France is not.
The U.S. Baby Boom
The TFR in the United States declined from more than 4 late in the nineteenth century to less than replacement in the early 1930s. However, when the small numbers of children born in the depression years reached adulthood, they went on a childbearing spree that produced the baby-boom generation. In 1957 more children were born in the United States than ever before (or since). These population pyramids show the baby-boom generation in 1970 and again in 1985 (green ovals).
Profound changes (e.g. enrollments in schools and colleges) have occurred — and continue to occur — in U.S. society as this bulge passes into ever-older age brackets. The baby boomers seem not to be headed for the high TFRs of their parents. They are marrying later and having smaller families than their parents. So it looks as though the TFR for the baby-boom generation will not exceed replacement rate. But this is not the same as zero population growth. Even with the current TFR of 1.9, this large cohort of people will keep the U.S. population growing during their reproductive years (current value for r = 0.5%).
Looking Ahead
Exponential growth cannot continue indefinitely. If the current world value for r (1.2%) remains unchanged, the world population would grow from its current 7.1 billion to 9.6 billion over the next 38 years (2050).
• Could the earth's resources sustain such a population?
• If not, how large a human population can live decently on this planet?
Some demographers (students of population) say we have already exceeded the number. Others say the earth can hold billions more.
Whatever the case, there are grounds for some optimism about future population growth.
The world value for r peaked around 1990 and has declined since. This is a reflection of the decline in total fertility rates (TFRs) in undeveloped countries, presumably as the various factors involved in the demographic transition take hold, e.g.,
• improved standard of living
• increased confidence that your children will survive to maturity
• improved status of women
• increased use of birth control measures
The projection of future TFRs in the upper graph (from the Population Reference Bureau) predicts that the less developed countries of the world will reach replacement fertility around the year 2020. In fact, they will probably reach it sooner because by 2012 the world TFR has dropped to 2.4. Even so, will the world reach zero population growth (ZPG) then?
The right graph (based on data from the UN Long-Range World Population Projections, 1991) gives 5 estimates of the growth of the world population from now until 2150, assuming that TFRs decline from the 1991 value of 3.4 to the values shown.
• A value of 2.06 will produce a stable population of about 11.5 billion.
• A value 5% below that (1.96) will cause the population to drop back to close to 6.1 billion while
• a value of only 5% above (2.17) would produce a population of over 20 billion and still rising.
A consensus?
The several agencies that try to predict future population seem to be moving closer to a consensus that the world population will continue to grow until after the middle of this century reaching a peak of some 9.6 billion (up from the current 7.1 billion) and then perhaps declining in the waning years of this century. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/17%3A_Ecology/17.03%3A_The_Growth_of_Populations/17.3A%3A_The_Human_Population.txt |
Density-Independent Checks on Population Growth
The vagaries of the physical environment, for example drought, freezes, hurricane, floods, and forest fires are often check population growth. Not only may they limit population growth but they often drive existing populations well below their previous level. (And also make it unlikely that many animals will survive long enough to show signs of aging.)
These factors are described as density-independent because they exert their effect irrespective of the size of the population when the catastrophe struck.
Fig.17.3.2.1 Population Density
This graph (from P. T. Boag and P.R. Grant in Science, 214:82, 1981) shows the decline in the population of one of Darwin's finches (Geospiza fortis) on Daphne Major, a tiny (100 acres = 40 hectares) member of the Galapagos Islands. The decline (from 1400 to 200 individuals) occurred because of a severe drought that reduced the quantity of seeds on which this species feeds. The drought ended in 1978, but even with ample food once again available the finch population recovered only slowly.
Catastrophic declines are particularly risky for populations living on islands. The smaller the island, the smaller the population of each species on it, and the greater the risk that a catastrophe will so decimate the population that it becomes extinct. This appears to be one reason for the clear relationship between size of island and the number of different species it contains.
The graph (redrawn from R. H. MacArthur and E. O. Wilson, The Theory of Island Biogeography, Princeton University Press) shows the number of species of reptiles and amphibians on various islands in the West Indies. In general, if one island has 10 times the area of another, it will contain approximately twice the number of species.
The same principle applies to many habitats. In a sense, most habitats are islands. A series of ponds, a range of mountain tops, scattered groves of citrus trees, even individual trees within a grove, all are made up of patches of habitat separated by barriers to the free migration of their inhabitants.
This has practical as well as theoretical importance. As the human population grows, jungles are cleared for agriculture, farms are paved for shopping centers, rivers are dammed for hydroelectric power and irrigation, etc. Although wildlife sanctuaries are being established, they must be made large enough so that they can support populations large enough to survive density-independent checks when they strike.
An example: Lake Guri
In 1986, the closing of a dam in Venezuela flooded over a thousand square miles (>2,500 km2) turning hundreds of hilltops into islands. These ranged in size from less than 1 hectare (2.5 acres) to more than 150 hectares (370 acres).
Within 8 years:
• The tiniest islands (<1 hectare) lost 75% of the species that had lived there.
• The larger the island, the fewer species it lost.
• But all the islands - even the largest - lost their top predators; that is carnivores like pumas, jaguars (image), and eagles at the ends of food chains.
• Those animal species that did remain - mostly herbivores and small carnivores - greatly increased their populations because of
• a reduction in competition for resources
• no longer being eaten by predators
The intense grazing by the increased herbivore populations is degrading the variety of plant life on the smaller islands.
Density-Dependent Checks on Population Growth
Intra specific Competition
Intraspecific competition is competition between members of the same species.
In the summer of 1980, much of southern New England was struck by an infestation of the gypsy moth (Porthetria dispar). As the summer wore on,
• the larvae (caterpillars) pupated
• the hatched adults mated
• the females laid masses of eggs (each mass containing several hundred eggs) on virtually every tree in the region
• In early May of 1981, the young caterpillars that hatched from these eggs began feeding and molting.
• The results were dramatic:
• In 72 hours, a 50-ft beech tree or a 25-ft white pine tree would be completely defoliated.
• Large patches of forest began to take on a winter appearance with their skeletons of bare branches.
• In fact the infestation was so heavy that many trees were completely defoliated before the caterpillars could complete their larval development.
• The result: a massive die-off of the animals; very few succeeded in completing metamorphosis.
Here, then, was a dramatic example of how competition among members of one species for a finite resource - in this case, food - caused a sharp drop in population.
The effect was clearly density-dependent. The lower population densities of the previous summer had permitted most of the animals to complete their life cycle. The graph shows a similar population crash; in this case of reindeer on two islands in the Bering Sea. Why the population on St. Paul Island went through so much more severe a boom-and-bust cycle than that on St. George Island is unknown. Many rodent populations (e.g., lemmings in the Arctic) go through such boom-and-bust cycles.
Inter specific Competition
All the ecological requirements of a species constitutes its ecological niche. The dominant requirement is usually food, but others, such as nesting sites and a place in the sun (for plants) may be important as well. When two species share overlapping ecological niches, they may be forced into competition for the resource(s) of that niche. This interspecific competition is another density-dependent check on the growth of one or both populations.
Like so many factors in ecology, interspecific competition is more easily studied in the laboratory than in the field. This graph (based on the work of G. F. Gause) shows the effect of interspecific competition on the population size of two species of paramecia, Paramecium aurelia and Paramecium caudatum.
When either species was cultured alone — with fresh food added regularly — the population grew exponentially at first and then leveled off.
However, when the two species were cultured together, P. caudatum proved to be the weaker competitor. After a brief phase of exponential growth, its population began to decline and ultimately it became extinct. The population of P. aurelia reached a plateau, but so long as P. caudatum remained, this was below the population density it achieved when grown alone.
The habitat of most natural populations is far more complex than a culture vessel. In a natural habitat, the species at a competitive advantage in one part of the habitat might be at a disadvantage in another. In addition, the presence of predators and parasites would limit population growth of the more successful as well as the less successful species. So, in a natural setting, the less effective competitor is usually not driven to extinction.
Character Displacement: an evolutionary response that lessens interspecific competition
When two closely-related species find themselves occupying the same geographic location (sympatric), their requirements for the necessities of life are probably so similar that they are forced into intense interspecific competition. This can lead to one of two possible outcomes.
1. The competition may be so intense that one species becomes eliminated entirely; that is, it is driven to extinction there.
2. Alternatively, the increased selection pressure may lead to character displacement — the evolutionary divergence of a trait they both use to exploit the resources they both depend on. Such character displacement lessens the competition between them.
Over the past several years, the research teams led by Peter and Rosemary Grant have been able to observe character displacement as it occurred between two species of Darwin's finches. This is their story.
• For many years, G. fortis, the medium ground finch, lived on Daphne Major without its relatives, G. fulginosa, the small ground finch, and G. magnirostris, the large one.
• However, in 1982, G. magnirostris arrived and over the following years grew in population.
• These were good years, with plenty of food, and the two species coexisted nicely.
• However, a severe drought in 2003–2004, sharply reduced the available food including the large seeds that magnirostris and the larger-beaked members of the fortis population competed intensely for.
• The result was a massive die-off of both species with the larger-beaked members of the fortis population suffering greater mortality than the smaller-beaked members of the species.
• The offspring of the fortis survivors, born in 2005, had beaks that averaged over 5% smaller than the average of the parental population. (After the drought of 1977, when G. magnirostris was not on the island to compete with fortis, their beak size increased rather than decreased.)
• This study of character displacement is described in the 14 July 2006 issue of Science.
Reproductive Competition
Declining birth rates also lead to reduced population growth.
We know that humans make deliberate family planning choices, but analogous behavior is found in other animals as well.
• Fruit flies living under crowded conditions lay fewer eggs.
• Laboratory rats in a confined area soon reach a stable population size even though abundant food is available. The main cause is a sharp rise in infant mortality. Reduced maternal care and even cannibalism take a heavy toll of the newborn.
• The honeybee queen regulates her rate of egg laying to the availability of food: reducing it during periods of poor flowering and ceasing entirely in the late summer.
An alternative to limiting the number of offspring per pair of parents is to limit the number of parents. Some mammals and birds achieve this by establishing breeding territories. Each mating pair occupies an area of a size sufficient to supply its needs including those of its offspring. One or both members defend this territory against intrusion from other members of the same species. This behavior not only ensures that the resources on which they depend will not be exceeded but may keep the population in check by preventing breeding among its surplus members.
Social conventions among humans (e.g., attitudes about the proper age of marriage and desirable family size) also have a marked influence on birth rates. However social conventions - and the birth control techniques that may supplement them — have been most successful at reducing birth rates among just those people least in need of it. In the poorer countries, early marriage, a desire for large families, and failure to employ birth control methods reliably are common.
Migration
Migration is often an important density-dependent factor in reducing populations. As the population increases, many of its members emigrate.
Predation
As a population increases, its predators are able to harvest it more easily. These graphs (based on data from Crombie, A. C., Journal of Animal Ecology, 16:44, 1947) show the population changes among flour beetles grown in plain flour (left) and in flour containing pieces of glass tubing.
Each culture was started with four adults of each species. In plain medium, after an initial spurt of both populations, Tribolium continued to expand its numbers while the Oryzaephilus population declined and was eventually driven to extinction (left). Several factors were at work, but predation was by far the most important.
• Tribolium adults feed voraciously on the eggs and pupae of Oryzaephilus.
• But Oryzaephilus adults do not feed so vigorously on Tribolium eggs and do not eat their larvae at all.
Glass tubing provided a refuge for some Oryzaephilus larvae enabling them to complete their life cycle. This reduction in the intensity of predation permitted the two populations to coexist indefinitely (right).
Parasitism
Parasites are able to pass from host to host more easily as the population density of the host increases. For this reason, epidemics among humans are particularly severe in cities. In fact, for most of the period since humans began living in cities, city populations have been maintained only through continual immigration from the countryside. Not until the development of community sanitation, immunization, and other public health measures did cities avoid periodic sharp drops in population as a result of epidemics.
The recurrent epidemics of the "black death" in Europe that began in the fourteenth century caused a sharp decline in population. In just 3 years (1348–1350), at least one-quarter of the population of Europe died from the disease (probably plague). More recently, the great influenza pandemic of 1918–1919 is thought to have killed over 20 million people worldwide.
The house finch, Carpodacus mexicanus, — native to western North America — is a recent immigrant to the eastern United States where it is parasitized by a mycoplasma that reduces the lifespan and fecundity of the birds. Data collected by amateur bird watchers show that the arrival of the disease (in the mid-90s) in areas with a high population of the birds drove their numbers down more than it did in regions of low finch populations. Whatever the starting value, all infected populations ended up with similar populations. This is a clear example of the density-dependent effect of parasitism on a population.
Population Cycles
Some populations go through repeated and regular periods of boom followed by bust.
This graph shows the 10-year cyclical fluctuations in the populations (measured by counting the hides offered for sale at the Hudson Bay trading posts in Canada) of the varying hare ("snowshoe rabbit") and its chief predator, the lynx, from 1850 to 1910. The size of the lynx population was closely dependent on the size of its prey (hare) population. The factors causing the hare population to go through its boom-and-bust cycles are still debated, but predation by lynxes was probably only one factor.
Recent field studies have provided clearer answers for three other cyclical populations, voles (a small rodent) in Finland, the red grouse in Scotland, and lemmings (another small rodent) in Greenland.
Voles
The vole population in Finland regularly goes through 3-year cycles of boom-and-bust. When Korpimäki and Norrdahl removed all their predators (both mammals and birds) from their test areas, the cycles ceased. Here, then, the cycles were driven by the density-dependent check of predation.
Red grouse
The red grouse population in Scotland goes through cycles of 4–8 years. From peak to trough, the population may decline by a factor of 1000. These cycles do not appear to be caused by the hunting of this popular game bird.
The birds are parasitized by a nematode, and infected birds have lower fecundity (birth rates down) and higher mortality (death rates up) than uninfected birds.
P. J. Hudson and his colleagues treated large numbers of birds in several test areas with a drug to prevent or cure an infection. The populations in the treatment areas ceased to cycle. It was not necessary to treat all the birds; 20% of them seem enough to prevent epidemics (just as immunization of humans doesn't have to reach 100% to put an end to pathogen transmission).
Here, then, the cycles were driven by the density-dependent check of parasitism.
Lemmings
A 15-year study of the population of lemmings in northeast Greenland was reported by Gilg, O., et al., in Science, 31 October 2003. These workers showed that the lemming population rises and falls with a cycle of 4 years. The population of the shorttail weasel (aka ermine, stoat), the principal predator of the lemming, does as well but with a 1-year lag behind the lemming population.
Because of this lag, one might expect that the lemming population would continue to outstrip the weasel population until the lemmings bumped into the carrying capacity of their environment (e.g., availability of food and nesting sites). But this does not occur because as the lemming population grows, other predators (e.g., foxes and owls) shift their diet in favor of lemmings.
As the lemming population then begins to decline,
• these flexible predators return to their former food sources while
• the more "picky" weasels decline in numbers as their sole food source, the lemmings, have.
The Carrying Capacity of the Environment (K)
This graph shows the growth of a yeast population in culture. After a period of exponential growth, the size of the population begins to level off and soon reaches a stable value. This type of growth curve is called sigmoid or S-shaped. If we add fresh culture medium to the container, exponential growth resumes until a new, higher plateau is reached. Evidently the growth rate (r) declines as the density of the population approaches a certain limiting value.
When r = 0, dN/dt = 0 and the population ceases to grow. The yeasts have reached zero population growth or ZPG.
The causes:
• running out of food
• accumulation of ethanol. (When its concentration reaches 12–14%, the yeast die (which explains the maximum alcohol content of natural alcoholic beverages like wine).
The limiting value of the population that can be supported in a particular environment is called its carrying capacity and is designated K. When the population is far below K, its growth is exponential, but as the population approaches K, it begins to encounter ever-stronger "environmental resistance". Let us use the expression
KN
K
as a "growth realization factor", that is, a factor representing the degree to which the population can actually realize its maximum possible rate of increase. Introducing this factor into our original (exponential) growth equation, we get
dN = rN
dt
( KN
K
)
The equation tells us that
• If the size of the population (N) is far below the carrying capacity of the environment (K), the growth realization factor will be close to 1, and the population will show exponential growth.
• But as N begins to approach K, the growth realization factor approaches zero, and the rate of population growth drops to zero:
dN = 0 = "ZPG" (zero population growth)
dt
Plotting the growth of a population from an initial growth realization factor of 1 to a final factor of 0 produces a curve like this, called the logistic growth curve or S-shaped curve of growth. Although actual populations are unlikely to follow the theoretical logistic growth curve exactly, the curve can provide us with valuable guidance in managing populations.
Example 1: The logistic curve tells you that you are unlikely to rid your house of a large rat population by setting rat traps. No matter how many you put out, the r for rats is so high (perhaps 0.0147 per day) that they will reproduce faster than you can catch them. What you must do instead is to prevent them from getting food in and around your house. With a sharply-reduced K, their population will decline.
Example 2: The converse of the pest problem is how to keep endangered species from becoming extinct. But outlawing hunting will have no appreciable impact if the habitat on which that species depends for its K — pasture or woods or whatever — disappears under the parking lot of a shopping plaza.
Example 3: Modern intensive fishing methods have repeatedly produced ominous declines in the catch of many species as the populations have been unable to maintain themselves. The logistic curve provides a goal to managing fisheries: harvest at only such a rate that the population is maintained at K/2. At this size, the population is able to grow most rapidly. The value K/2 is known as the maximum sustainable yield.
r -Strategists and K -Strategists
r-strategists
I once plowed up an old field and allowed it to lie fallow. In the first season it grew a large crop of ragweed.
Ragweed is well-adapted to exploiting its environment in a hurry - before competitors can become established. It grows rapidly and produces a huge number of seeds (after releasing its pollen, the bane of many hay fever sufferers). Because ragweed's approach to continued survival is through rapid reproduction, i.e., a high value of r, it is called an r-strategist. Other weeds, many insects, and many rodents are also r-strategists. If fact, if we consider an organism a pest, it is probably an r-strategist.
In general r-strategists share a number of features:
1. They are usually found in disturbed and/or transitory habitats. In the second season of my field, perennial grasses and wildflowers had produced a dense carpet of mixed vegetation and not a ragweed plant was to be found.
2. They have short life spans. The house mouse, with a maximum life span of 3 years, is an r-strategist.
3. They begin breeding early in life.
4. They usually have short generation times; that is, they have short gestation periods and are soon ready to produce another crop of young. The housefly can produce 7 generations each year (each of about 120 young).
5. They produce large numbers of offspring. The American oyster, releasing a million eggs in one season, is an r-strategist. Most of its offspring will die, but the sheer size of its output increases the likelihood that some offspring will disperse to new habitats.
6. They take little care of their offspring, and infant mortality is huge. If we plot a survivorship curve for an r-strategist, it is apt to take the form of the curve labeled D. Although humans are not r-strategists, the higher birth rate in some countries may well be a response to their higher rates of infant mortality (curve B).
7. They have efficient means of dispersal to new habitats.
For r-strategists, alleles that enhance any of the traits listed above will be favored by natural selection. Hence, r-strategists are said to be the product of r-selection.
The graph shows 4 representative survivorship curves. The vertical axis gives the fraction of survivors at each age.
• Curve A is characteristic of organisms that have low mortality until late in life when aging takes its toll.
• Cure B is typical of populations in which such factors as starvation and disease obscure the effects of aging, and infant mortality is high.
• Curve C is a theoretical curve for organisms for which the chance of death is equal at all ages. This might be the case for organisms that do not age (some fishes) or those that suffer severe random mortality throughout life (e.g., many songbirds). K-strategists usually have survivorship curves somewhere between A and C.
• Curve D is typical of organisms, oysters for example, that produce huge numbers of offspring accompanied by high rates of infant mortality. Many r-strategists have such a curve.
K-strategists
When a habitat becomes filled with a diverse collection of creatures competing with one another for the necessities of life, the advantage shifts to K-strategists. K-strategists have stable populations that are close to K. There is nothing to be gained from a high r. The species will benefit most by a close adaptation to the conditions of its environment.
Typically, K-strategists share these qualities:
1. They are usually found in stable habitats. Most of the species in a mature forest will be K-strategists.
2. They have long life spans. The elephant and the tortoise are K-strategists.
3. They begin breeding later in life.
4. They usually have long generation times. It takes 9 months to produce a human baby.
5. Most produce small numbers of offspring. Birds are K-strategists, most species producing fewer than a dozen young each year.
6. They take good care of their young. Infant mortality tends to be low. If we plot a survivorship curve for a K-strategist, it usually lies somewhere between curve A (above), where most of the population dies of old age, and curve C, where all ages are equally at risk of being struck down by random hazards.
7. K-strategists typically have evolved in such a way that they become increasingly efficient at exploiting an ever-narrower slice of their environment. Thus it is not surprising that many endangered species are K-strategists.
For K-strategists, alleles that enhance their ability to exploit the resources of their habitat; that is, to increase the carrying capacity, K, of their environment, will be favored by natural selection. Hence, K-strategists are said to be the product of K-selection.
Population density can cause shifts in strategy
A team at the Santa Cruz campus of the University of California (Sinervo et al., in the 21 August 2001 issue of Nature) studied the boom-and-bust cycles of the native side-blotched lizard. They found that the lizard population went through 2-year cycles of boom and bust.
Year 1 = Boom
• A low population of adults
• living well below the carrying capacity (K) of their environment
• produced large numbers of young (an r-strategy)
• leading to rapid overcrowding and
Year 2 = Bust
• A large population of adults
• living close to or above the K of their environment
• produced fewer surviving young
• leading to a sharp decline in population and
Year 3 = another Boom year, and so on.
They also found that the population is polymorphic containing:
• females with orange throats that produced as many as 5 clutches of eggs (averaging 6 eggs per clutch) a season. It takes lots of food reserves to make eggs and the eggs of these highly-prolific orange-throated females tended to be smaller — and to hatch into smaller lizards — than those of the
• females with yellow throats. These females tend to lay fewer, but larger, eggs, and the young lizards that hatch from them are larger than those produced by orange-throated mothers.
As they predicted, it turned out that:
• Orange-throated lizards are r-strategists. In boom years, they were more successful than the yellow. The population explosion of young lizards produced by them led to next year's bust.
• Yellow-throated lizards are K-strategists. Producing smaller numbers of larger lizards, they were more successful at leaving surviving offspring to lay the groundwork for the next boom year.
Here, then, intraspecific competition has created a population cycle alternately favoring r-strategists and K-strategists. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/17%3A_Ecology/17.03%3A_The_Growth_of_Populations/17.3B%3A_Principles_of_Population_Growth.txt |
Most of the interactions between species involve food, i.e., competing for the same food supply, eating (predation) and avoiding being eaten (avoiding predation). These interactions are often brief. There are many cases, however, where two species live in close association for long periods. Such associations are called symbiotic ("living together"). In symbiosis, at least one member of the pair benefits from the relationship. The other member may be injured (parasitism), relatively unaffected (commensalism) or may also benefit (mutualism). (Some people restrict the term symbiosis to only these mutually beneficial interactions, but we shall not.)
Mutualism
Symbiotic relationships in which each species benefits are mutualistic. There are hundreds of examples of mutualism between a heterotroph and an alga.
• Paramecium bursaria is a ciliate that engulfs unicellular green algae into vacuoles within its cell.
• The paramecium certainly benefits from the food synthesized by the alga. It can be cultured apart from the alga but then must be given extra food.
• The alga presumably benefits from the carbon dioxide produced by its host as well as the host's ability to transport it to a spot where there is ample light.
• Many other aquatic heterotrophs
• sponges
• sea anemones
• planarians
• clams
also harbor algae within their cells.
Mutualistic relations between plants and fungi are very common. The fungus invades and lives in or among the cortex cells of the secondary roots. The association is called a mycorrhiza. The fungus helps the host plant absorb inorganic nitrogen and phosphorus from the soil. Some mycorrhizal fungi also secrete antibiotics which may help protect their host from invasion by parasitic fungi and bacteria. Many mushrooms are the spore-forming bodies of mycorrhizal fungi. The truffle is often found in oak forests because the fungus that produces it establishes mycorrhiza on oak roots.
Endosymbiosis
Endosymbiosis is a mutualistic relationship between a host and an organism living within its body or cells.
The pea aphid and its endosymbiont
The pea aphid, Acyrthosiphon pisum, is an insect pest that sucks the juices from its host plant. However, plant sap is deficient in several essential amino acids. The pea aphid thrives nonetheless thanks to specialized cells within its body that contain the gamma proteobacterium, Buchnera aphidicola, that can live nowhere else. The genome of this obligate intracellular Gram-negative bacterium encodes a number of enzymes needed to complete the synthesis of the amino acids needed by its host. In return, the aphid's genome encodes enzymes needed by Buchnera to synthesize its lipopolysaccharide cell wall and has lost genes that might otherwise repel infection by Gram-negative bacteria.
Symbiotic nitrogen fixation
One of the most important examples of mutualism in the overall economy of the biosphere is the endosymbiotic relationship between certain nitrogen-fixing bacteria and their legume hosts. A large body of evidence supports the view that intracellular endosymbiotic relationships gave rise to eukaryotes with their mitochondria and chloroplasts.
Cleaning Symbiosis
The drawing shows the Nile crocodile opening its mouth to permit the Egyptian plover to feed on any leeches attached to its gums. Cleaning symbiosis is more common in fish.
Commensalism
Commensalism means "at table together". It is used for symbiotic relationships in which one organism consumes the unused food of another. Some examples:
• the remora and the shark. The dorsal fin of the remora (a bony fish) is modified into a sucker with which it forms a temporary attachment to the shark. When the shark feeds, the remora picks up scraps. The shark makes no attempt to prey on the remora.
• Some species of barnacles are found only as commensals on the jaws of whales. And there are other species of barnacles found only as commensals on those barnacles!
• Many of the bacteria living in our large intestine. They feed on food which we cannot digest and do not harm us. And some help us; that is, the relationship is mutualistic. Animals (e.g., mice) raised under germfree conditions are abnormal in several ways, e.g.,
• they have elevated levels of a subset of NKT cells
• reduced levels of regulatory T cells (Treg) - both effects predisposing the animals to
• asthma and inflammation of the intestine
So it is now standard practice to deliberately infect them with several species of microorganisms so that the animals develop normally.
Epiphytes
Epiphytes are plants that live perched on sturdier plants. They do not take any nourishment from their host and simply benefit from being better exposed to sunlight. Some examples include many orchids and many bromeliads (e.g., "Spanish moss" and other members of the pineapple family).
Parasitism
A parasite is an organism that lives on or in the body of another organism (the host) from whose tissues it gets its nourishment, and to whom it does some damage. Animals are parasitized by viruses, bacteria, fungi, protozoans, flatworms (tapeworms and flukes), nematodes, insects (fleas, lice), and arachnids (mites). Plants are parasitized by viruses, bacteria, fungi, nematodes, and a few other plants. Parasites damage their host in two major ways:
• consuming its tissues, e.g., hookworms
• liberating toxins, for example,
• Tetanus bacilli secrete tetanus toxin which interferes with synaptic transmission.
• Diphtheria bacilli secrete a toxin that inhibits protein synthesis by ribosomes.
The relationship between parasite and host varies along a spectrum that extends from "hit and run" parasites that live in their host for a brief period and then move on to another with or without killing the first to parasites that establish chronic infections. Both parasite and host must evolve to ensure the survival of both because if the parasite kills its host before it can move on, it destroys its own meal ticket
Rabbits in Australia
In 1859, the European rabbit was introduced into Australia for sport. With no important predator there, it multiplied explosively. The raising of sheep (another imported species) suffered badly as the rabbits competed with them for forage. This picture (courtesy of Dunston from Black Star) gives you the idea. Having removed all forage plants, which ordinarily supply them with water as well as food, the rabbits had to drink from a pool.
In 1950, the myxoma virus was brought from Brazil and released. The epidemic that followed killed off millions of rabbits (perhaps 99.5% of the population). Green grass returned and sheep raising once again became profitable. But the rabbits were not eliminated. In fact, although small epidemics still occur, the rabbit population has recovered somewhat (although nowhere near its pre-1950 levels). What happened? Thanks to careful planning, we know.
• The rabbits today are more resistant to infection than their predecessors. This can be measured by infecting them with the original strain that has been maintained in the laboratory.
• At the same time, the virus circulating in the wild rabbits has become less virulent. This can be measured by determining the % mortality of laboratory rabbits when they are infected with the current strain of virus.
The graph (based on data of Sir Macfarlane Burnet and D. O. White) shows these mutual evolutionary adaptations over the first six years after the introduction of the virus.
The "Degeneracy" of Parasites
During the course of adapting to conditions in their host, parasites often lose structures and functions that were essential for their ancestors (and any free-living relatives). The tapeworm has no eyes, no digestive tract, and only vestiges of nervous, excretory, and muscular systems. While you may call them degenerate, these losses represent a gain in efficiency and improved specialization. What good would these structures be anyway in the human intestine? On the other hand, the tapeworm produces hundreds of proglottids: egg-forming machines that improve the likelihood that the tapeworm will leave descendants that reach another host.
This emphasis on reproduction is also seen in
• Rafflesia, a parasitic angiosperm found in Malaysia. It has no roots, stems, or leaves, although it does have tubes which penetrate the tissues of its host. But it has a huge flower (~3 feet or 1 meter in diameter).
• Sacculina, a barnacle that parasites crabs. The adult consists of little more than a sac (hence the name) containing reproductive organs. Not until its larvae were discovered could it even be determined that Sacculina was a crustacean.
Mycobacterium leprae: pseudogenes
M. leprae causes leprosy (Hansen's disease). It is an intracellular parasite, taking up residence in Schwann cells where, in due course, it triggers an autoimmune attack on them that leads to their destruction. The resulting loss of sensation makes it difficult to avoid injury to the extremities. M. leprae is a mycobacterium and a close relative of M. tuberculosis, the cause of TB.
M. leprae infection also occurs naturally in the wild armadillos living in a band of southern states extending from Alabama through Texas. A survey of 39 human leprosy patients in that region revealed 25 of them infected with the identical strain found in the local armadillos. Although it was the first bacterium to be identified as a cause of human disease (in 1873), no bacteriologist has ever succeeded in cultivating it in vitro. It can, however, be propagated (slowly) in the nine-banded armadillo, and this has provided enough material to sequence its entire genome.
Its sequence, which was published in the 22 February 2001 issue of Nature (Cole, S. T. et al.) — when compared to that of M. tuberculosis — provides a vivid demonstration of degeneracy at the level of the genes. Although its genome is only about 25% smaller than that of M. tuberculosis, it has only 40% of the genes of its cousin. Many of the missing genes are still detectible, but they are now pseudogenes — genes that have mutated so that they can no longer be expressed in a protein product.
M. tuberculosis M. leprae
Size of genome (bp) 4,411,532 3,268,203
Protein-coding genes 3,959 1,604
citrate synthase genes (for citric acid cycle) 3 1
pyruvate dehydrogenase genes (for citric acid cycle) 6 2
lactate dehydrogenase genes (cellular respiration) 2 1
phosphofructokinase genes (glycolysis) 2 1
M. leprae is not an exception. The many bacterial genomes that have now been sequenced show that bacteria that are obligate intracellular parasites express far fewer proteins than bacteria that can live on culture medium.
A collection of links to examples of parasites
• Viruses
• Retroviruses, incl HIV-1, the cause of AIDS
• Influenza
• an assortment of others
• Bacteria, the agents of
• tetanus, botulism, and anthrax
• typhoid, cholera, and plague
• staphylococcal and streptococcal infections
• gonorrhea
• tuberculosis, leprosy, and diphtheria
• syphilis and Lyme disease
• typhus fever and Rocky Mountain spotted fever
• Protists
• Plasmodium (agents of malaria)
• Trypanosomes
• Invertebrates
• Tapeworms
• Blood flukes
• Games Parasites Play (some interesting interactions between host and parasite).
The Evolution of Symbiosis
It seems plausible that what begins as a parasitic relationship might over the course of time evolve into a mutualistic one as the two organisms evolve to minimize the damage to the host.
And there is some evidence for this. In 1966, K. W. Jeon discovered a culture of amoebas that had become infected with bacteria (60,00 to 150,000 per cell). The infection slowed their rate of growth and made them much more fragile. But five years later, the amoebas still were infected but now no ill effects could be seen. Most interesting for our question, the amoebas — or at least their nuclei — had become dependent on the bacteria.
• When the nucleus was removed from an infected amoeba and replaced with one from a uninfected strain, the combination worked fine.
• But when the nucleus from an uninfected cell was replaced with one from an infected cell, the combination usually failed to survive.
Evidently, after 5 years, the nuclei had become dependent on a bacterial function (an enzyme produced by the bacteria but no longer by the host). What started as parasitism had evolved into mutualism (the bacteria could not be grown outside their host). But it doesn't always work like that. There are other examples where a mutualistic relationship seems to have evolved into a commensalistic or even parasitic one. Some parasitic fungi seem to have evolved from ancestors living in the mutualistic partnership of a lichen.
Some of the bacteria living in our large intestine supply us with vitamin K, thus evolving from commensalism to mutualism.
Mutually beneficial symbiotic relationships can lead to "degeneracy" also. Some marine annelid worms have completely lost the digestive tract of their relatives (like the common earthworm). One species gets its nourishment from a large population of at least 5 different species of bacteria living underneath its outer skin. The most abundant of these are chemoautotrophs (but these bacteria are gamma- and delta- proteobacteria not beta-proteobacteria) that manufacture food from carbon dioxide using the energy provided by oxidizing inorganic substances (H2S, H2) in the sediments in which the worm lives.
The nature of a symbiotic relationship can also change as circumstances change. Some fungi, bacteria, and protozoans that live harmlessly in most of us can cause opportunistic infections — that is become parasitic — in immunodeficient people, e.g., those with AIDS. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/17%3A_Ecology/17.04%3A_Interactions_between_Species/17.4A%3A_Symbiosis.txt |
Inorganics
Inorganic compounds of arsenic, such as lead arsenate, have long been used against insect pests. However, these materials are highly toxic to nontarget organisms and persist in the environment. (Years after apple growers stopped using lead arsenate, high concentrations of lead can still be found in orchard soils.)
Botanicals
These are organic molecules (or mixtures) extracted from plants. Popular examples:
• pyrethrins
• rotenone
• nicotine
• azadirachtin. This extract from the neem tree affects insect growth and is discussed further under growth regulators.
Features:
• very toxic to insects
• relatively harmless to other organisms (except fish!)
• decompose readily so residues do not accumulate on crops or in the soil
• expensive, but you can get
• more bang for the buck by adding a synergist like piperonyl butoxide. Synergists have little toxicity themselves but enhance the effectiveness of the insecticide with which they are mixed.
Pyrethroids
Pyrethrins break down so rapidly in sunlight that they are of little use outdoors on crops. However, a number of synthetic pyrethrin-like substances — called pyrethroids — do not have this defect and are effective.
Example:
• permethrin (Ambush®, Pounce®)
Bacillus thuringiensis (B.t.)
This bacterium parasitizes many caterpillars. Its spores and/or mixtures of its protein toxins are now being used against a variety of insect pests. Examples:
• Dipel®
• Javelin®
• Agree®
These are all stomach poisons; that is, they must be ingested to work.
Chlorinated Hydrocarbons
DDT was the first of a long line of insecticides based on hydrocarbons with chlorine atoms replacing some of the hydrogen atoms. Its chemical name is dichloro, diphenyl, trichloroethane (see figure).
Some others:
• methoxychlor
• dieldrin (see figure)
• dicofol (Kelthane®)
• endosulfan (Thiodan®, Phaser®)
DDT was introduced during World War II and, along with penicillin and the sulfa drugs, was responsible for the fact that this was the first war in history where trauma killed more people - combatants and noncombatants alike - than infectious disease.
DDT is effective against
• vectors of human diseases such as
• malaria and yellow fever (both transmitted by mosquitoes)
• plague (transmitted by fleas)
• many crop pests
Prior to the introduction of DDT, the number of cases of malaria in Ceylon (now Sri Lanka) was more than a million a year. By 1963 the disease had been practically eliminated from the island. However, growing concern about the hazards of DDT led to its abandonment there in the mid-1960s, and soon thereafter malaria became common once again.
DDT was especially effective against malarial mosquitoes because of its persistence and resistance to breakdown in the environment. One or two sprays a year on the walls of homes kept them free of mosquitoes. But DDT has several serious drawbacks.
Insecticide resistance
As early as 1946, Swedish workers discovered populations of houseflies resistant to DDT. This was quickly followed by many other reports of developing resistance. Other chlorinated hydrocarbons (like dieldrin and methoxychlor) were developed as substitutes, but in time insects developed resistance to these as well.
Persistence
DDT is stable and fat soluble. These properties cause it to accumulate in fat tissue. People who were heavily exposed to DDT (during its manufacture or application) often showed concentrations of DDT in their fat 1000 times higher than that in their blood. Even these high levels were probably of little harm to the workers. In the early stages of exposure, the blood levels of DDT (and its metabolite DDE) rise rapidly at first and then reach a steady level. From that point on, the body excretes it as fast as it acquires it.
Biomagnification
Although no harmful effects from average exposures to DDT have been seen in humans, DDT and other chlorinated hydrocarbons have been shown to harm other species, such as fishes, earthworms, and robins. The hazard of DDT to nontarget animals is particularly acute for those species living at the top of food chains. Carnivores at the ends of long food chains (e.g., ospreys, pelicans, falcons, and eagles) once suffered serious declines in fecundity and hence in population size because of this. High levels of chlorinated hydrocarbons interfere with forming eggshells of normal thickness.
Correlation between DDE concentrations in the eggs of Alaskan falcons and hawks and reduction in the thickness of their eggshells (compared with shells collected prior to 1947). DDE is a metabolite of DDT. Data from T. J. Cade, et. al., Science 172:955, 1971.
Species Location Average Concentration
of DDE in Eggs (ppm)
Reduction in
Shell Thickness
Peregrine falcon Alaskan tundra (north slope) 889 -21.7%
Peregrine falcon Central Alaska 673 -16.8%
Peregrine falcon Aleutian Islands 167 -7.5%
Rough-legged hawk Alaskan tundra (north slope) 22.5 -3.3%
Gyrfalcon Seward Peninsular, Alaska 3.88 0
Another group of nontarget victims of DDT (and other pesticides) are insects that prey upon insect pests; that is, the natural enemies of the pests. Killing these has serious ecological and economic effects. For example, once apple growers began controlling pests with DDT, they quickly found their orchards being attacked by scale insects and mites. The reason: DDT had killed off their natural enemies.
Organophosphates
The organophosphates, e.g., parathion (right), are related to the nerve gases developed during World War II. They react irreversibly with the enzyme acetylcholinesterase, which is responsible for inactivating acetylcholine (ACh) at neuromuscular junctions and at certain synapses in the central and peripheral nervous systems.
Some other examples:
• malathion
• diazinon
• phosmet (Imidan®)
• chlorpyrifos (Lorsban®)
Some of the organophosphates are very toxic. Parathion, for example, is 30 times more toxic than DDT. Each year organophosphates poison thousands of humans throughout the world, causing hundreds of deaths. Medical personnel caring for poisoning victims are also at risk. They may be seriously poisoned by the excretions of, and even the vapors emanating from, their patients.
This table gives the LD50 values for some insecticides. In each case, the chemical was fed to laboratory rats. Note that the lower the LD50, the more toxic the chemical.
Chemical Category Oral LD50 in Rats
(mg/kg)
Aldicarb ("Temik") Carbamate 1
Carbaryl ("Sevin") Carbamate 307
DDT Chlorinated hydrocarbon 87
Dieldrin Chlorinated hydrocarbon 40
Diflubenzuron ("Dimilin") Chitin inhibitor 10,000
Malathion Organophosphate 885
Methoprene JH mimic 34,600
Methoxychlor Chlorinated hydrocarbon 5,000
Parathion Organophosphate 3
Piperonyl butoxide Synergist 7,500
Pyrethrins Plant extract 200
Rotenone Plant extract 60
Unlike chlorinated hydrocarbons,
• Organophosphates break down quickly in the environment, and thus residues on crops are less likely to be a problem.
• They are not stored in animal tissue, so biomagnification has not been a problem either.
For these reasons, their use has greatly reduced the hazard to nontarget species like ospreys and eagles (at the price of a much greater hazard to humans). Development of resistance is just as much a problem as it is with the chlorinated hydrocarbons. The carbamates were introduced in an attempt to keep ahead.
Carbamates
Carbamate insecticides are also inhibitors of acetylcholinesterase, but their action is reversible.
Some examples:
• carbaryl (Sevin®)
• aldicarb (Temik®)
• methomyl (Lannate®)
Features:
• These compounds are rapidly detoxified and excreted so their risk to warm-blooded animals is less than the other agents we have looked at.
• They are degraded rapidly in the environment so persistence is not a problem.
• They are, however, a danger to many useful insects, especially honeybees.
Growth Regulators
The members of this diverse group interfere in one way or another with insect development. Although most insect growth regulators do not affect adults, for many pests, it is the larval stages that are the most destructive.
Chitin Inhibitors
These substances, diflubenzuron (Dimilin®) is an example, interfere with the synthesis of chitin, the material that makes up the insect exoskeleton. It seems to have very low toxicity for vertebrates, but is harmful to crustaceans as well as insects. Its effect on fungi, which also synthesize chitin, needs to be studied.
Molting Disruptors
Insects must periodically shed their exoskeleton — called molting — in order to grow. Each molt is triggered by a steroid hormone called ecdysone.
A few synthetic ecdysone
• agonists, e.g.,
• tebufenozide (Confirm®)
• methoxyfenozide (Intrepid®)
• inhibitors, e.g., azadirachtin (Neemix®)
are now used as insecticides.
Juvenile Hormone (JH)
In some insects, the final molt produces an adult that looks pretty much like the earlier larval stages. In others, like moths and butterflies, the final molt of the larva (caterpillar) produces a pupa. After a period of metamorphosis, the adult moth emerges.
Ecdysone triggers larva-to-larva molts as long as another hormone, called juvenile hormone (JH), is present. In its absence, ecdysone promotes the pupa-to-adult molt. Thus normal metamorphosis seems to occur when the output of JH diminishes spontaneously in the mature caterpillar.
When solutions of JH are sprayed on mature caterpillars, or on the foliage upon which they are feeding, their normal development is upset. This raises the possibility of using JH as an insecticide (one that might avoid the problem of developing resistance).
As it turns out, JH is too unstable to be practical, but some synthetic JH mimics, e.g.,
• methoprene (Altosid®)
• pyriproxyfen (Esteem®, Knack®, Distance®)
• diofenolan
are now being used.
Precocenes
These are substances, first discovered in plants, that damage the corpora allata thus preventing juvenile hormone (JH) from doing its normal job. Applied to early larval stages, precocenes induce premature or precocious metamorphosis (like that induced by the surgical removal of the corpora allata). Not only does precocious metamorphosis cut short the destructive larval phase of the insect, but the adults are abnormal (besides being small). The females, for example, are sterile (because JH is needed for development of the ovaries).
Summary
It is often said that the evolution of insecticide resistance requires the introduction of ever more powerful insecticides. But what is really needed is a new substance that attacks some other chink in the insect's armor. Whether gram for gram the new substance is more or less toxic to the insect (and whether its LD50 for mammals is lower or higher) is quite a separate issue. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/17%3A_Ecology/17.04%3A_Interactions_between_Species/17.4B%3A_Insecticides.txt |
The biological control of pests involves using natural enemies of the pest to control it — instead of chemical agents like insecticides and herbicides. Not only should this be safer for the environment, but once established - the natural enemies might be able to sustain their population avoiding the need for future treatments.
Most of the species that we consider pests are plants ("weeds") or animals (especially insects) that have invaded a new habitat without being accompanied by the natural enemies that kept them in check in their original home. With increasing international travel and trade, this problem becomes increasingly severe.
The Biological Control of Insects
Cottony Cushion Scale Insect
In 1887, this insect - an import from Australia, was devastating the citrus groves of California. A U.S. entomologist went to Australia to find a natural enemy and came back with the vedalia beetle, a species of lady beetle. Released in California, the beetle quickly brought the scale under control.
At least until 1946. In that year the pest made a dramatic comeback. This coincided with the first use of DDT in the groves. DDT not only killed the target pest insects but the vedalia beetle as well. Only by altering spray procedures and reintroducing the beetle was the scale insect again controlled.
The Sterile Male Technique
This technique was first applied against the screwworm fly, a serious pest of cattle. The female flies lay their eggs in sores or other open wounds on the animals. After hatching, the larvae eat the tissues of their host. As they do so, they expose a still larger area to egg laying, often finally killing the host.
Prior to its eradication from the southeastern United States, the screwworm was causing huge annual livestock losses. The sterile male technique involves releasing factory-reared and sterilized flies into the natural population. Sterilization is done by exposing the factory flies to just enough gamma radiation to make them sterile but not enough to reduce their general vigor.
Starting in early 1958, up to 50 million sterilized flies were released each week from aircraft flying over Florida and parts of the adjoining states. Each time a fertile female in the natural population mated with a sterile male, the female layed sterile eggs. Since the females mate only once, her reproductive career was at an end. By early 1959, the pest was totally eliminated east of the Mississippi River. Success depended only on the sterile males. In fact, the presence of sterile females was a drawback (because they competed with the intended target), but it was difficult to separate the sexes.
The southwestern states presented a harder problem because the fly winters in Mexico and with each new season could move across the border. Even so, by expanding the program to include Mexico as well, the screwworm fly was finally eliminated from both countries by 1991.
The sterile male technique has also been used with success against several other insect pests, including
• The "medfly", a destructive fruit fly (not Drosophila) in California
• The tsetse fly, the vector of African sleeping sickness.
Using Genetic Engineering to Improve the Sterile Male Technique
There are two problems with the sterile male technique
• The factory produces both males and females in equal numbers. But if you release the females along with the males, many males will mate with them rather than with wild females. For this reason, the sexes are now separated - an expensive operation - and only males released.
• Irradiation may harm the males in subtle ways - reducing their breeding effectiveness.
Genetic engineering may solve both these problems.
A group of British entomologists (see Thomas, D. D., et al., in the 31 March 2000 issue of Science) have engineered Drosophila so that
• Only males are produced.
• When these mate with normal females, the females give birth only to males (thus ending the population).
The system works like this:
• Transgenic flies are created containing a chromosome with an enhancer (En) for a gene (tet TA) that encodes a transcription factor (green disk) that binds the response element (tet RE), which is part of the promoter for a gene (Toxin gene) encoding a protein whose product is lethal to the insect.
• Only females produce the transcription factor that binds En.
• If the antibiotic tetracycline is given to the insects, it binds to the tet TA transcription factor, producing an allosteric change that prevents the transcription factor from binding the tetracycline response element (tet RE).
• The toxin gene is repressed and viable females are made.
• In the absence of tetracycline, the tet TA transcription factor (green disk) turns on the toxin promoter and no females are produced.
• Because the tet TA enhancer (En) responds to a transcription factor made only by females, males are produced whether tetracycline is present or not.
If this system could be applied to an insect pest (and most seem to produce the same female-specific transcription factor [red oval]),
• removing tetracycline from the food of a batch of flies in the factory would produce a new generation containing only males.
• Released into the wild, these would pass their transgenic chromosome on to the offspring of all the wild females they mated with.
• The genes are dominant so even though the next generation would be heterozygous, only males would be produced.
• Thus the pest population would soon die out.
In 2010, release of male mosquitoes Aedes aegypti, the vector of dengue fever - genetically modified (GM) with a similar system reduced the resident mosquito population in part of Grand Cayman (Caribbean) by 80%.
Gene Drive
Techniques have now been developed which greatly increase the frequency of any desired gene in a population. So far, the uncertainties of quickly spreading an engineered gene through an entire wild population has kept the process strictly confined to the laboratory. The process, called gene drive or the mutagenic chain reaction, is described on a separate page.
Male Confusion
Insect sex attractants have also been enlisted in the fight against harmful insects. Distributing a sex attractant throughout an area masks the female's own attractant so the sexes fail to get together. This is called "communication disruption" or "male confusion". In some cotton-growing areas, male confusion with the sex attractant of the pink bollworm reduced the need for conventional chemical insecticides by 90%. It has been used successfully against pests that attack tomatoes, grapes, and peaches.
Parasites vs Insect Pests
Parasites, as well as predators, have been used to achieve control over destructive insects.
• The bacterium Bacillus popilliae is supplied commercially to help control the Japanese beetle by infecting it with "milky disease".
• Bacillus thuringiensis ("Bt") is sold commercially to aid in controlling a number of harmful insects. In some cases, the bacterium itself infects the pests and eventually kills them. But in most cases, it is the toxin manufactured by the bacterium while it is growing in culture that does the job.
The Biological Control of Plants
Prickly-pear Cactus (Opuntia)
Introduced into Australia, this cactus soon spread over millions of hectares of range land driving out forage plants. In 1924, the cactus moth, Cactoblastis cactorum, was introduced (from Argentina) into Australia. The caterpillars of the moth are voracious feeders on prickly-pear cactus, and within a few years, the caterpillars had reclaimed the range land without harming a single native species. However, its introduction into the Caribbean in 1957 did not produce such happy results. By 1989, the cactus moth had reached Florida, and now threatens 5 species of native cacti there.
Klamath Weed
In 1946 two species of Chrysolina beetles were introduced into California to control the Klamath weed (also known as St. Johnswort, and the same plant that yields the popular herbal concoction) that was ruining millions of acres of range land in California and the Pacific Northwest. Before their release, the beetles were carefully tested to make certain that they would not turn to valuable plants once they had eaten all the Klamath weed they could find.
The beetles succeeded beautifully, restoring about 99% of the endangered range land and earning them a commemorative plaque at the Agricultural Center Building in Eureka, California. (Photo courtesy of John V. Lenz.)
Rules to Live By
• Pick only candidates that have a very narrow target preference; i.e., eat only a sharply-limited range of hosts
• Test each candidate carefully to be sure that once it has cleaned up the intended target, it doesn't turn to desirable species.
• Don't use bio controls against native species.
• Avoid introducing alien species into the environment. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/17%3A_Ecology/17.04%3A_Interactions_between_Species/17.4C%3A_Biological_Control_of_Pests.txt |
• 18.1: Evolution and Adaptation
Evolution involves two interrelated phenomena: adaptation and speciation. In adaptation, over the course of time, species modify their phenotypes in ways that permit them to succeed in their environment. In speciation, over the course of time, the number of species multiplies; that is, a single species can give rise to two or more descendant species. In fact, Darwin maintained that all species are related; that is, any two species on earth today have shared a common ancestor.
• 18.2: Speciation
A species is an actually or potentially interbreeding population that does not interbreed with other such populations when there is opportunity to do so.
• 18.3: The Evolution of Body Form in Animals
Advances in genetics - especially the sequencing of entire genomes from a wide variety of animals - has revealed an unexpected paradox. While the animal kingdom contains an extraordinary diversity of body types, the great structural diversity of animals is not reflected in their genetic makeup. Throughout the animal kingdom, one finds thousands of orthologous genes; that is, genes that have similar sequences and encode similar products.
• 18.4: Recapitulation
The embryonic development of all vertebrates shows remarkable similarities. Recapitulation is the idea that embryonic development repeats that of one's ancestors. It is often expressed as "ontogeny recapitulates phylogeny"; that is, embryonic development (ontogeny) repeats phylogeny (the genealogy of the species).
• 18.5: Mutation and Evolution
So how can the small changes in genes caused by mutations, especially single-base substitutions ("point mutations"), lead to the large changes that distinguish one species from another? These questions have, as yet, only tentative answers.
• 18.6: The Hardy-Weinberg Equilibrium
The Hardy-Weinberg law argues that the gene frequencies and genotype ratios in a randomly-breeding population remain constant from generation to generation. Evolution involves changes in the gene pool, while a population in Hardy-Weinberg equilibrium shows no change. Hence, populations are able to maintain a reservoir of variability so that if future conditions require it, the gene pool can change.
• 18.7: Polymorphisms
A polymorphism is a genetic variant that appears in at least 1% of a population. (e.g., the human ABO blood groups, the human Rh factor, and the human major histocompatibility complex (MHC)). By setting the cutoff at 1%, it excludes spontaneous mutations that may have occurred in - and spread through the descendants of - a single family.
• 18.8: Kin Selection
In the discussion of natural selection, the emphasis was on how natural selection works on individuals to favor the more fit and disfavor the less fit in a population. The emphasis was on the survival (mortality selection), mating success (sexual selection), or family size (fecundity selection) of individuals. But what of the worker honeybee who gives up her life when danger threatens her hive? Or the mother bird who, feigning injury, flutters away from her nestful of young, thus risking death
• 18.9: The Origin of Life
To account for the origin of life on our earth requires solving several problems: How the organic molecules that define life, e.g. amino acids, nucleotides, were created. How these were assembled into macromolecules, e.g. proteins and nucleic acids, - a process requiring catalysts. How these were able to reproduce themselves. How these were assembled into a system delimited from its surroundings (i.e., a cell). A number of theories address each of these problems.
• 18.10: Mars
There have been efforts to identify signs of life on Mars.
• 18.11: Endosymbiosis
The endosymbiosis theory postulates that the mitochondria of eukaryotes evolved from an aerobic bacterium (probably related to the rickettsias) living within an archaeal host cell and the chloroplasts of red algae, green algae, and plants evolved from an endosymbiotic cyanobacterium living within a mitochondria-containing eukaryotic host cell.
• 18.12: Geologic Eras
Evolutionary changes coincide with geologic changes on the earth. But consider that changes in geology (e.g., mountain formation or lowering of the sea level) cause changes in climate, and together these alter the habitats available for life. Two types of geologic change seem to have had especially dramatic effects on life: continental drift and the impact of asteroids
Thumbnail: A silhouette of human evolution. (CC BY SA 3.0 Unported; Tkgd2007).
18: Evolution
In 1859 the English naturalist Charles Darwin published The Origin of Species. The book contained two major arguments: First, Darwin presented a wealth of evidence of evolution. He said that all living things on earth today are the descendants - with modifications - of earlier species. Second, he proposed a mechanism - natural selection - to explain how evolution takes place.
Evolution involves two interrelated phenomena: adaptation and speciation. In adaptation, over the course of time, species modify their phenotypes in ways that permit them to succeed in their environment. In speciation, over the course of time, the number of species multiplies; that is, a single species can give rise to two or more descendant species. In fact, Darwin maintained that all species are related; that is, any two species on earth today have shared a common ancestor at some point in their history.
Natural Selection
• Living things produce more offspring than the finite resources available to them can support.
• Thus living things face a constant struggle for existence.
• The individuals in a population vary in their phenotypes.
• Some of this variation is inheritable; that is, it is a reflection of variations in genotype.
• Those variants best adapted to the conditions of their life are most likely to survive and reproduce themselves ("survival of the fittest").
• To the extent that their adaptations are inheritable, they will be passed on to their offspring.
The forces of natural selection act on phenotypes, but only if there is a change in the genotypes of a population has evolution occurred.
The Measure of "Fitness"
Fitness is a measure of reproductive success. Those individuals who leave the largest number of mature offspring are the fittest. This can be achieved in several ways:
• Survival (mortality selection)
• Mating success (sexual selection)
• Family size (fecundity selection)
Survival
Any trait that promotes survival - at least until one's reproductive years are over - increases fitness. Such traits are adaptations.
Sexual Selection
In sexual selection, one sex - usually the female - chooses among the available males. Any inherited trait that improves the mating success of certain individuals will become more pronounced in succeeding generations. Some examples:
• When ready to mate, female three-spined sticklebacks (fish) choose males with many Class II MHC alleles over males with fewer alleles. Class II alleles encode the proteins that present antigens to the immune system. Presumably, the more of them you have, the greater the diversity of parasite antigens your immune system can recognize and defend against.The females distinguish between the males by soluble molecules ("odors") the males release into the water. How these "odors" are controlled by the MHC alleles is not known.
• A culture of Drosophila set up with equal numbers of red-eyed and white-eyed flies of both sexes will, after 25 generations or so, end up having only red-eyed (the "normal") flies in it. This despite the fact that white-eyed flies are just as healthy and live just as long as red-eyed flies, i.e., they are equal in terms of survival. But, as it turns out, not only do red-eyed females prefer red-eyed males, but white-eyed females do also.
In other cases of sexual selection, one phenotype prefers to mate with others of the same phenotype. This is called assortative mating.
Fecundity Selection
The production of a large number of mature offspring is a measure of fitness. I stress mature because only they can pass these traits on to another generation. Some ways to do this:
• Earlier breeding. If some females become sexually mature earlier than others, their chances of leaving offspring are enhanced.
• For some species (e.g., fish, oysters), which provide little or no care for their young, fitness is measured by the number of fertilized eggs they produce.
• For species (such as ourselves) that take care of their young, selection acts to reduce family size (to a point). A large study in Utah (U.S.A) showed that in the 19th century, families with fewer children had more surviving grandchildren.
All the forces of natural selection outlined above work on individuals. But there is an increasing body of evidence that natural selection can also act on groups. Natural selection that appears to work counter to the benefit of some individuals while enhancing the prospects of their relatives is called kin selection. It is discussed on a separate page.
Are Humans Exempt from Natural Selection?
It has been argued that advances in medicine, sanitation, etc. have removed humans from the rigors of natural selection. There is probably some truth to this, but consider that of all the human eggs that are fertilized, fewer than half will ever reproduce themselves. The others are eliminated as follows:
• Mortality selection
• Approximately 30% of pregnancies end by spontaneous abortion of embryos and fetuses or by stillbirth.
• Death in infancy and childhood claims another 5% or more.
• Sexual selection
• Another 20% will survive to adulthood but never marry.
• Fecundity selection
• Of those that do marry, 10% will have no children.
Continuous Variation
Most traits in a population such as height and body weight vary in a continuous way from one extreme to the other.
A plot of the distribution of the trait in a population often produces a bell-shaped curve like this one that shows the distribution of heights among a group of male secondary-school seniors. Such a distribution could arise from environmental factors - perhaps the continuous height variation in the boys is simply a result of variation in their diet as they grew up or genetic factors - tall parents tend to have tall children or - most likely - both.
Heritability
One can sort out the relative contribution of genetic and environmental factors by comparing the range of a trait in the offspring compared with the average value of that trait in their parents. If the offspring of selected parents occupy the same range as the entire population, environmental factors are working alone. The trait has a zero heritability. Example: The length of the seeds of a pure strain of beans may vary over several millimeters. However, if extra-large beans are mated, the new crop shows no shift to a larger size. So the heritability of length is zero. On the other hand, if the offspring of two extra-large mice are just as large as they are, genes are probably at work. The trait is said to have a heritability of 1.
The Effects of Selection on Populations
The pressures of natural selection can affect the distribution of phenotypes in a population in several ways.
Stabilizing Selection
Natural selection often works to weed out individuals at both extremes of a range of phenotypes resulting in the reproductive success of those near the mean. In such cases, the result is to maintain the status quo. It is not always easy to see why both extremes should be handicapped; perhaps sexual selection or liability to predation is at work. In any case, stabilizing selection is common. In humans, for example, the incidence of infant mortality is higher for very heavy as well as for very light babies.
Directional Selection
A population may find itself in circumstances where individuals occupying one extreme in the range of phenotypes are favored over the others. Since 1973, Peter and Rosemary Grant - aided by a succession of colleagues - have studied Darwin's finches in the Galapagos Islands. When rainfall, and thus food, are plentiful, the ground finches tend to have a varied diet, e.g., eat seeds of a range of sizes and show considerable variation in body and beak size (large beaks are better for large seeds but can handle small seeds as well as small beaks).
From 1976 through 1977, a severe drought struck the islands, with virtually no rainfall for over a year. This caused a precipitous decline in the production of the seeds that are the dietary mainstay of Geospiza fortis, the medium ground finch. The graph (from P. T. Boag and P. R. Grant in Science 214:82, 1981) shows how the population declined from 1400 to 200 on the island of Daphne Major, a tiny (10-acre = 4 hectares) member of the Galapagos Islands.
One of the plants to make it through the drought produces seeds in large, tough fruits that are virtually impossible for birds with a beak smaller than 10.5 mm to eat. Sampling the birds that died as well as those that survived showed that he larger birds were favored over the smaller ones and Those with larger beaks were favored over those with smaller ones.
Beak length (mm) Beak depth (mm)
Dead birds 10.68 9.42
Survivors 11.07 9.96
Here, then was natural selection at work. But did it produce evolution? The answer turned out to be yes. As the population of G. fortis recovered after the rains returned, the average body size and beak depth of their offspring was greater than before (an increase of 4–5% for beak depth). The bell-shaped curve had been shifted to the right — directional selection.
More recently, the Grants and colleagues at Harvard Medical School have shown that
• beak width and depth in the ground finches are correlated with the timing and intensity of expression of the gene, Bmp4, (that encodes bone morphogenetic protein-4) in the tissue that will form the upper beak. Bmp4 expression appears earlier in development and with greater intensity in the large-beaked Geospiza magnirostris (the large ground finch) than in its smaller-beaked relatives, Geospiza fortis (the medium ground finch) and Geospiza fuliginosa (the small ground finch). See Abzhanov, A., et al., Science, 3 September 2004.
• However, beak length is correlated with the intensity of expression of the gene CaM that encodes the Ca2+-binding protein calmodulin in the tissue that will form the upper beak. CaM expression is much higher in the embryonic tissue of the cactus finches (G. scandens and G. conirostris - both with long beaks) than in their short-beaked relatives, the ground finches G. fortis and G. magnirostris. (See Abzhanov, A., et al., Nature, 3 August 2006.)
Industrial Melanism
Many species of moths in the British Isles began to become darker in color in the 19th century. The best-studied example is the peppered moth, Biston betularia. The moth gets its name from the scattered dark markings on its wings and body. In 1849, a coal-black mutant was found near Manchester, England. Within a century, this black form had increased to 90% of the population in this region. The moth flies at night and rests by day on tree trunks. In areas far from industrial activity, the trunks of trees are encrusted with lichens. As the photos show, the light form (circled in red) is practically invisible against this background.
In areas where air pollution is severe, the combination of toxic gases and soot has killed the lichens and blackened the trunks. Against such a background, the light form stands out sharply. The moth is preyed upon by birds that pluck it from its resting place by day. In polluted woods, the dark form has a much better chance of surviving undetected. When the English geneticist H. B. D. Kettlewell (who supplied the photos) released moths of both types in the woods, he observed that birds did, indeed, eat a much higher fraction of the light moths he released than of the dark. Since pollution abatement programs were put in place after World War II, the light form has been making a comeback in the Liverpool and Manchester areas.
Disruptive Selection
In some circumstances, individuals at both extremes of a range of phenotypes are favored over those in the middle. This is called disruptive selection.
An example:
The residues ("tailings") of mines often contain such high concentrations of toxic metals (e.g., copper, lead) that most plants are unable to grow on them. However, some hardy species (e.g. certain grasses) are able to spread from the surrounding uncontaminated soil onto such waste heaps. These plants develop resistance to the toxic metals while their ability to grow on uncontaminated soil decreases. Because grasses are wind pollinated, breeding between the resistant and nonresistant populations goes on. But evidently, disruptive selection is at work. Higher death rates of both less resistant plants growing on contaminated soil and more resistant plants growing on uncontaminated soil leads to increasing divergence of the populations into two subpopulations with the extreme manifestations of this trait.
The evolutionary significance of disruptive selection lies in the possibility that the gene pool may become split into two distinct gene pools. This may be a way in which new species are formed. The formation of one or more species from a single precursor species is called speciation. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/18%3A_Evolution/18.01%3A_Evolution_and_Adaptation.txt |
One of the best definition os species is that of the evolutionary biologist Ernst Mayr: "A species is an actually or potentially interbreeding population that does not interbreed with other such populations when there is opportunity to do so." However, sometimes breeding may take place (as it can between a horse and a donkey) but if so, the offspring are not so fertile and/or well adapted as the parents (the mule produced is sterile).
Allopatric Speciation: the Role of Isolation in Speciation
The formation of two or more species often (some workers think always!) requires geographical isolation of subpopulations of the species. Only then can natural selection or perhaps genetic drift produce distinctive gene pools. It is no accident that the various races (or "subspecies") of animals almost never occupy the same territory. Their distribution is allopatric ("other country").
The seven distinct subspecies or races of the yellowthroat Geothlypis trichas (a warbler) in the continental U.S. would soon merge into a single homogeneous population if they occupied the same territory and bred with one another.
Darwin's Finches
As a young man of 26, Charles Darwin visited the Galapagos Islands off the coast of Ecuador. Among the animals he studied were what appeared to be 13 species* of finches found nowhere else on earth.
• Some have stout beaks for eating seeds of one size or another (#2, #3, #6).
• Others have beaks adapted for eating insects or nectar.
• One (#7) has a beak like a woodpecker's. It uses it to drill holes in wood, but lacking the long tongue of a true woodpecker, it uses a cactus spine held in its beak to dig the insect out.
• One (#12) looks more like a warbler than a finch, but its eggs, nest, and courtship behavior is like that of the other finches.
Darwin's finches. The finches numbered 1–7 are ground finches. They seek their food on the ground or in low shrubs. Those numbered 8–13 are tree finches. They live primarily on insects.
1. Large cactus finch (Geospiza conirostris)
2. Large ground finch (Geospiza magnirostris)
3. Medium ground finch (Geospiza fortis)
4. Cactus finch (Geospiza scandens)
5. Sharp-beaked ground finch (Geospiza difficilis)
6. Small ground finch (Geospiza fuliginosa)
7. Woodpecker finch (Cactospiza pallida)
8. Vegetarian tree finch (Platyspiza crassirostris)
9. Medium tree finch (Camarhynchus pauper)
10. Large tree finch (Camarhynchus psittacula)
11. Small tree finch (Camarhynchus parvulus)
12. Warbler finch (Certhidia olivacea)
13. Mangrove finch (Cactospiza heliobates)
(From BSCS, Biological Science: Molecules to Man, Houghton Mifflin Co., 1963)
* Genetic analysis provides evidence that:
• There are actually two species of warbler finch — Certhidia olivacea now called the green warbler finch and Certhidia fusca, the gray warbler finch.
• The various populations of Geospiza difficilis found on the different islands belong to one or another of three clades so genetically distinct that they deserve full species status.
Whether the number is 13 or 17, since Darwin's time, these birds have provided a case study of how a single species reaching the Galapagos from Central or South America could - over a few million years - give rise to the various species that live there today. Several factors have been identified that may contribute to speciation.
Ecological opportunity
When the ancestor of Darwin's finches reached the Galapagos, it found no predators (There were no mammals and few reptiles on the islands.) and few, if any, competitors. There were only a handful of other types of songbirds. In fact, if true warblers or woodpeckers had been present, their efficiency at exploiting their niches would surely have prevented the evolution of warblerlike and woodpeckerlike finches.
Geographical Isolation (allopatry)
The proximity of the various islands has permitted enough migration of Darwin's finches between them to enable distinct island populations to arise. But the distances between the islands is great enough to limit interbreeding between populations on different islands. This has made possible the formation of distinctive subspecies (= races) on the various islands.
The importance of geographical isolation is illuminated by a single, fourteenth, species of Darwin's finches that lives on Cocos Island, some 500 miles (800 km) to the northeast of the Galapagos. The first immigrants there must also have found relaxed selection pressures with few predators or competitors. How different the outcome, though. Where one immigrant species gave rise to at least 13 on the scattered Galapagos Islands, no such divergence has occurred on the single, isolated Cocos Island.
Evolutionary Change
In isolation, changes in the gene pool can occur through some combination of natural selection, genetic drift, and founder effect. These factors may produce distinct subpopulations on the different islands. So long as they remain separate (allopatric) we consider them races or subspecies. In fact, they might not be able to interbreed with other races but so long as we don't know, we assume that they could.
How much genetic change is needed to create a new species? Perhaps not as much as you might think. For example, changes at one or just a few gene loci might do the trick. For example, a single mutation altering flower color or petal shape could immediately prevent cross-pollination between the new and the parental types (a form of prezygotic isolating mechanism).
Reunion
The question of their status - subspecies or true species - is resolved if they ever do come to occupy the same territory again (become sympatric). If successful interbreeding occurs, the differences will gradually disappear, and a single population will be formed again. Speciation will not have occurred. If, on the other hand, two subspecies reunite but fail to resume breeding, speciation has occurred and they have become separate species.
An example: The medium tree finch Camarhynchus pauper is found only on Floreana Island. Its close relative, the large tree finch, Camarhynchus psittacula, is found on all the central islands including Floreana. Were it not for its presence on Floreana, both forms would be considered subspecies of the same species. Because they do coexist and maintain their separate identity on Floreana, we know that speciation has occurred.
Isolating Mechanisms
What might keep two subpopulations from interbreeding when reunited geographically? There are several mechanisms.
Prezygotic Isolating Mechanisms act before fertilization occurs. Sexual selection - a failure to elicit mating behavior. On Floreana, Camarhynchus psittacula has a longer beak than Camarhynchus pauper, and the research teams led by Peter and Rosemary Grant have demonstrated that beak size is an important criterion by which Darwin's finches choose their mates. Two subpopulations may occupy different habitats in the same area and thus fail to meet at breeding time. In plants, a shift in the time of flowering can prevent pollination between the two subpopulations. Structural differences in the sex organs may become an isolating mechanism. The sperm may fail to reach or fuse with the egg.
Postzygotic Isolating Mechanisms act even if fertilization does occur. Even if a zygote is formed, genetic differences may have become so great that the resulting hybrids are less viable or less fertile than the parental types. The sterile mule produced by mating a horse with a donkey is an example. Sterility in the males produced by hybridization is more common than in females. In fact, it is the most common postzygotic isolating mechanism. When Drosophila melanogaster attempts to mate with its relative Drosophila simulans, no viable males are even produced. Mutations in a single gene (encoding a component of the nuclear pore complex) are responsible.
Reinforcement
When two species that have separated in allopatry become reunited, their prezygotic and postzygotic isolating mechanisms may become more stringent than those between the same species existing apart from each other. This phenomenon is called reinforcement. It arises from natural selection working to favor individuals that avoid interspecific matings, which would produce less-fit hybrids, when the two species are first reunited.
Speciation by Hybridization
Hybridization between related angiosperms is sometimes followed by a doubling of the chromosome number. The resulting polyploids are now fully fertile with each other although unable to breed with either parental type - a new species has been created. This appears to have been a frequent mechanism of speciation in angiosperms. Even without forming a polyploid, interspecific hybridization can occasionally lead to a new species of angiosperm. Two species of sunflower, the "common sunflower", Helianthus annuus, and the "prairie sunflower", H. petiolaris, grow widely over the western half of the United States. They can interbreed, but only rarely are fertile offspring produced.
However, Rieseberg and colleagues have found evidence that successful hybridization between them has happened naturally in the past. They have shown that three other species of sunflower (each growing in a habitat too harsh for either parental type) are each the product of an ancient hybridization between Helianthus annuus and H. petiolaris. Although each of these species has the same diploid number of chromosomes as the parents (2n = 34), they each have a pattern of chromosome segments that have been derived, by genetic recombination, from both the parental genomes. They demonstrated this in several ways, notably by combining RFLP analysis with the polymerase chain reaction (PCR).
They even went on to produce (at a low frequency) annuus x petiolaris hybrids in the greenhouse that mimicked the phenotypes and genotypes of the natural hybrids. (These monumental studies were described in the 29 August 2003 issue of Science.)
Another example. In Pennsylvania, hybrids between a species of fruit fly (not Drosophila) that feeds on blueberries and another species (again, not Drosophila) that feeds on snowberries feed on honeysuckle where they neither encounter competition from their parental species nor have an opportunity to breed with them (no introgression). This study was published in the 28 July 2005 issue of Nature. So speciation can occur as a result of hybridization between two related species, if the hybrid
• receives a genome that enables it to breed with other such hybrids but not breed with either parental species,
• can escape to a habitat where it does not have to compete with either parent,
• is adapted to live under those new conditions.
Adaptive Radiation
The processes described in this page can occur over and over. In the case of Darwin's finches, they must have been repeated a number of times forming new species that gradually divided the available habitats between them. From the first arrival have come a variety of ground-feeding and tree-feeding finches as well as the warblerlike finch and the tool-using woodpeckerlike finch. The formation of a number of diverse species from a single ancestral one is called an adaptive radiation.
Speciateion in theHouse mice on the island of Madeira
A report in the 13 January 2000 issue of Nature describes a study of house mouse populations on the island of Madeira off the Northwest coast of Africa. These workers (Janice Britton-Davidian et al) examined the karyotypes of 143 house mice (Mus musculus domesticus) from various locations along the coast of this mountainous island.
Their findings:
• There are 6 distinct populations (shown by different colors)
• Each of these has a distinct karyotype, with a diploid number less than the "normal" (2n = 40).
• The reduction in chromosome number has occurred through Robertsonian fusions. Mouse chromosomes tend to be acrocentric; that is, the centromere connects one long and one very short arm. Acrocentric chromosomes are at risk of translocations that fuse the long arms of two different chromosomes with the loss of the short arms.
• The different populations are allopatric; isolated in different valleys leading down to the sea.
• The distinct and uniform karyotype found in each population probably arose from genetic drift rather than natural selection.
• The 6 different populations are technically described as races because there is no opportunity for them to attempt interbreeding.
• However, they surely meet the definition of true species. While hybrids would form easily (no prezygotic isolating mechanisms), these would probably be infertile as proper synapsis and segregation of such different chromosomes would be difficult when the hybrids attempted to form gametes by meiosis.
Sympatric Speciation
Sympatric speciation refers to the formation of two or more descendant species from a single ancestral species all occupying the same geographic location. Some evolutionary biologists don't believe that it ever occurs. They feel that interbreeding would soon eliminate any genetic differences that might appear. But there is some compelling (albeit indirect) evidence that sympatric speciation can occur.
Speciation in three-spined sticklebacks
The three-spined sticklebacks, freshwater fishes that have been studied by Dolph Schluter (who received his Ph.D. for his work on Darwin's finches with Peter Grant) and his current colleagues in British Columbia, provide an intriguing example that is best explained by sympatric speciation.
They have found:
• Two different species of three-spined sticklebacks in each of five different lakes.
• a large benthic species with a large mouth that feeds on large prey in the littoral zone
• a smaller limnetic species with a smaller mouth that feeds on the small plankton in open water.
• DNA analysis indicates that each lake was colonized independently, presumably by a marine ancestor, after the last ice age.
• DNA analysis also shows that the two species in each lake are more closely related to each other than they are to any of the species in the other lakes.
• Nevertheless, the two species in each lake are reproductively isolated; neither mates with the other.
• However, aquarium tests showed that
• The benthic species from one lake will spawn with the benthic species from the other lakes and likewise the limnetic species from the different lakes will spawn with each other.
• These benthic and limnetic species even display their mating preferences when presented with sticklebacks from Japanese lakes; that is, a Canadian benthic prefers a Japanese benthic over its close limnetic cousin from its own lake.
• Their conclusion: in each lake, what began as a single population faced such competition for limited resources that
• disruptive selection — competition favoring fishes at either extreme of body size and mouth size over those nearer the mean — coupled with
• assortative mating — each size preferred mates like it
favored a divergence into two subpopulations exploiting different food in different parts of the lake.
• The fact that this pattern of speciation occurred the same way on three separate occasions suggests strongly that ecological factors in a sympatric population can cause speciation.
Sympatric speciation driven by ecological factors may also account for the extraordinary diversity of crustaceans living in the depths of Siberia's Lake Baikal.
How many genes are needed to start down the path to sympatric speciation?
Perhaps not very many. The European corn borer, Ostrinia nubilalis, (which despite its common name is a major pest in the U.S. as well) exists as two distinct races designated Z and E. Both can be found in the same area; that is, they are sympatric. But in the field, they practice assortative mating - only breeding with mates of their own race.
The females of both races synthesize and release a pheromone that is a sex attractant for the males. Both races use the same substance but different isomers of it. Which isomer is produced is under the control of a single enzyme-encoding gene locus. The ability of the males to respond to one isomer or the other is controlled by 2 loci.
The Problem of Clines
There is another possible way for new species to arise in the absence of geographical barriers. If a population ranges over a large area and if the individuals in that population can disperse over only a small portion of this range, then gene flow across these great distances would be reduced. The occurrence of gradual phenotypic (and genotypic) differences in a population across a large geographical area is called a cline. Successful interbreeding occurs freely at every point along the cline, but individuals at the ends of the cline may not be able to interbreed. This can be tested in the laboratory.
And, on occasions, it is tested in nature. If a cline bends around so that the ends meet, and the populations reunited at the junction cannot interbreed, then the definition of separate species has been met. Such species are called ring species and this type of speciation is called parapatric speciation.
Two examples:
1. The Caribbean slipper spurge Euphorbia tithymaloides.
Genetic analysis shows that this wildflower originated in Central America where Mexico and Guatemala share a common boundary. From there it spread in two directions
• northeast through the Yucatan peninsula and then island-hopped through Jamaica, the Dominican Republic, Puerto Rico and into the Virgin Islands;
• south through Central America, on through Venezuela, and then north through Barbados and the other islands of the Lesser Antilles finally also reaching the Virgin Islands.
Reunited in the Virgin Islands, the two populations have diverged sufficiently that they retain their distinctive genotypic and phenotypic traits. Ongoing studies will determine to what degree they may be reproductively isolated.
2. The large-blotched salamander Ensatina eschscholtzii.
This animal is found in California where it occurs in a number of different subspecies or races. A single subspecies is found in Northern California, and it is thought to be the founder of all the others. Over time that original population spread southward in two directions:
• down the Sierra Nevada mountains east of the great central San Joaquin Valley and
• down the coast range of mountains west of the valley.
South of the valley, the eastern group has moved west and now meets the western group, closing the ring. Here the two populations fail to interbreed successfully, maintaining their distinct identities. But each subspecies interbreeds in an unbroken chain up the two paths their ancestors took.
Ring species present a difficult problem in assigning species designations. It is easy to say that the populations at the ends of the cline represent separate species, but where did one give rise to the other? At every point along the cline, interbreeding goes on successfully.
The same problem faces paleontologists examining the gradual phenotypic changes seen in an unbroken line of ever-younger fossils from what one presumes to be a single line of descent. If one could resurrect the ancestral species (A) and the descendant species (B) and they could not interbreed, then they meet the definition of separate species. But there was no moment in time when one could say that A became B. So the clines of today are a model in space of Darwin's descent with modification occurring over time.
Although clines present a problem for classifiers, they are a beautiful demonstration of Darwin's conviction that the accumulation of small inherited differences can lead to the formation of new species. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/18%3A_Evolution/18.02%3A_Speciation.txt |
Advances in genetics - especially the sequencing of entire genomes from a wide variety of animals - has revealed an unexpected paradox. While the animal kingdom contains an extraordinary diversity of body types, the great structural diversity of animals is not reflected in their genetic makeup. Throughout the animal kingdom, one finds thousands of orthologous genes; that is, genes that have similar sequences and encode similar products.
Advances in genetics - especially the sequencing of entire genomes from a wide variety of animals - has revealed an unexpected paradox. While the animal kingdom contains an extraordinary diversity of body types:
• with sizes ranging from the microscopic daphnia (a crustacean) to the great blue whale
• with body plans as diverse as those of Drosophila and humans,
the great structural diversity of animals is not reflected in their genetic makeup. Throughout the animal kingdom, one finds thousands of orthologous genes; that is, genes that have similar sequences and encode similar products.
At the level of the cell, and even of tissues, this perhaps should not be surprising. After all, most types of cells - from whatever animal - are quite similar in their structure and function. Thus we would expect that their genes that encode ribosomal proteins, cytochromes, histones, etc., etc. would be similar.
In trying to resolve the paradox that these findings present, it is useful to distinguish between
• "housekeeping" genes - genes that encode proteins (e.g. cytochromes) and RNAs (e.g. ribosomal RNAs) that function in all cells and
• "toolkit" genes
• genes that control the expression of other genes by encoding transcription factors
• genes that encode cell-signaling proteins that signal the cell to turn on (or off) a genetic program.
Housekeeping genes generally
• show modest sequence differences from animal to animal. Some of these are neutral in their effect on the gene's function while others are the result of evolutionary adaptation. Both can be used to trace taxonomic relationships.
• have simple control regions, i.e. promoters and enhancers.
• are expressed in all types of cells in the body (almost half of our protein-encoding genes are expressed in every cell - liver, neurons, muscle, etc.).
Toolkit genes generally
• show very slight sequence differences between different animal species in their coding regions (exons) while
• they have very elaborate control regions with many promoter and enhancer sites each of which has a binding site for one or another different transcription factors.
The proteins (transcription factors and cell-signaling molecules) of toolkit genes are identical in whatever cells they are expressed in. However, the function of that protein can vary greatly
• in different tissues of the animal - a phenomenon called mosaic pleiotropy
• at different times in the embryonic development of the animal - a phenomenon called heterochrony
Even such primitive animals as sponges and cnidarians have hundreds of toolkit genes that are clear orthologs to genes of humans. Some examples are genes whose products are involved in cell signaling (e.g., Wnt and β-catenin, Hedgehog, Notch, Receptor Tyrosine Kinases (RTKs), components of JAK/STAT pathways, and Transforming Growth Factor-beta TGF-β receptors).
In fact the sequences of many of these genes from different animal phyla are so similar that they can be interchanged. This similarity can be tested in animals that can be made transgenic. Some examples:
• The mouse gene Pax6 (also known as small eyes [Sey] for the mutant phenotype) can substitute for the mutant eyeless gene in Drosophila while the human PAX6 gene can restore normal eye development in the mutant small eyes (Sey) mouse.
• The mouse homeobox gene HoxB6 can substitute for the Drosophila homeobox gene Antennapedia (Antp) and when introduced into Drosophila give rise to legs in place of antennae just as mutant Antp genes do.
Mosaic Pleiotropy
Pleiotropy is the production by a single gene of more than one effect on the phenotype. Mosaic refers to the patchy distribution of cells and tissues expressing that phenotype.
An example:
Pitx1 is a
• Homeobox gene (similar to bicoid in Drosophila) with orthologs found in all vertebrates.
• It contains 3 exons that encode a protein of some 283 amino acids (varying slightly in different species) which is
• A transcription factor that regulates the expression of other genes involved in the differentiation and function of
• the anterior lobe of the pituitary gland (Pitx1 = "Pituitary homeobox1");
• jaw development (mutations are associated with cleft palate in mammals);
• development of the thymus and some types of mechanoreceptors;
• development of the hind limbs.
• Its activity in these regions is controlled by regulatory regions (promoters and/or enhancers) specific to each region (and presumably turned on by other transcription factors in the cells of those regions).
When we consider the dramatically-different activities that a given toolkit gene product can perform in different parts of the same animal, it is easier to understand how easy it must be for these same genes to alter the structure of the same body part in different species, e.g., the human arm and the wing of the bat.
Mutations in Regulatory Regions
Not all genes need to be expressed in all cells. In which cells and when a given gene will be expressed is controlled by the interaction of:
• extracellular signals turning on (or off)
• transcription factors, which turn on (or off)
• particular genes
A mutation that would be lethal in the protein coding region of a gene need not be if it occurs in a control region (e.g. promoters and/or enhancers) of that gene. In fact, there is increasing evidence that mutations in control regions have played an important part in evolution. Examples:
• Humans have a gene (LCT) encoding lactase; the enzyme that digests lactose (e.g. in milk). In most of the world's people, LCT is active in young children but is turned off in adults. However, northern Europeans and three different tribes of African pastoralists, for whom milk remains a part of the adult diet, carry a mutation in the control region of their lactase gene that permits it to be expressed in adults. The mutation is different in each of the 4 cases — examples of convergent evolution.
• There are very few differences in the coding sequences between genes of humans and chimpanzees. However, many of their shared genes differ in their control regions.
• The story of Prx1. Prx1 encodes a transcription factor that is essential for forelimb growth in mammals. When mice have the enhancer region of their Prx1 replaced with the enhancer region of Prx1 from a bat (whose front limbs are wings), the front legs of resulting mice are 6% longer than normal. Here, then is a morphological change not driven by a change in the Prx1 protein but by a change in the expression of its gene.
• The story of Pitx1.
In a remarkable study of three-spined sticklebacks published in the 15 April 2004 issue of Nature, Michael Shapiro, Melissa Marks, Catherine Peichel, and their colleagues report that a mutation in a noncoding region of the Pitx1 gene accounts for most of the difference in the structure of the pelvic bones of the marine stickleback and its close freshwater cousins.
The marine sticklebacks
• have prominent spines jutting out in their pelvic region (red arrow) as well as the spines along the back (that give the fish its name). These spines may help protect them from being eaten by predators. (Drawing courtesy of the Parks Administration in the Emilia-Romagna region of Italy.)
• express the Pitx1 gene in various tissues, including
• thymus
• mechanoreceptors
• the pelvic region
The freshwater sticklebacks
• have no or very much smaller spines in their pelvic region
• express the identical Pitx1 gene in all the same tissues except those that develop into the pelvic structures
• The reason: a deletion in an enhancer of Pitx1 responsible for turning on Pitx1 in the developing pelvic area. (Mice homozygous for a mutation in this control region have deformed hind limbs.)
Here then is a remarkable demonstration of how a single gene mutation can not only be viable but can lead to a major change in phenotype - adaptive evolution. (The changes seem not to have produce true speciation as yet. The marine and freshwater forms can interbreed. In fact, that is how the differences in their hind limbs were found to be primarily due to the expression of Pitx1.)
Heterochrony
What toolkit proteins do is governed not only by what tissue they are being produced in but also by when they are produced - a phenomenon called heterochrony.
Examples:
• The transcription factor decapentaplegic (DPP) plays a wide variety of roles in the development of Drosophila from laying the foundation for the future central nervous system in the early embryo to the elaboration of wings, legs, antennae, etc. in the adult.
• The formation of vertebrae. As their name implies, a key feature of all vertebrates is their backbone of vertebrae. However, the number of these can vary greatly. Humans have 33 while snakes can have several hundred. However, the toolkit genes (e.g., Wnt, Notch, FGF-β) responsible for forming vertebrae appear to be the same for all. What makes the difference is the timing (rate) at which pulses of these proteins are produced relative to the rate at which the embryo grows.
The Tc1 Mouse
So the evidence is increasing that what makes the difference between a human and a chimpanzee (or any other pair of animals) is in large measure
• not a matter of their inheritance of different genes and their encoded proteins and RNAs but
• their inheritance of mutations in the control regions - promoters and enhancers - that regulate where and when these genes will be expressed.
A vivid example of this is the work reported by Wilson et al. in the 17 October 2008 issue of Science. Their experimental material was liver cells (hepatocytes) taken from
• normal humans
• normal mice
• the Tc1 mouse
The Tc1 mouse is more than simply transgenic, it carries in most of its cells a human chromosome #21. This small chromosome is the one that, when present in a triple dose (trisomy 21), produces Down syndrome in humans. Mice have a similar chromosome that is designated #16.
The question that this remarkable animal could answer: will the genes on human chromosome #21 (105 of them) when present in a mouse nucleus and surrounded by mouse transcription factors and signaling pathways respond as the mouse #16 does or as #21 does in human liver cells or something quite different from either?
The answer turned out that the #21 responded pretty much as it does in its normal human cellular environment.
One line of evidence
Several transcription factors turn on gene activity in liver cells. As seems to be the case with all transcription factors, the human and mouse versions are close orthologs (95% identical in sequence). Using ChIP analysis, they found that the mouse transcription factors bound to sites along the human chromosome much as the human transcription factors do. (Chromosome #21 does not encode any transcription factors, so all those available in the mouse nucleus were of mouse origin.)
Tissue Chromosome Transcription Factors (TFs) Sites Bound by TFs Gene Expression
human liver cells #21 human TFs human pattern human pattern
Tc1 liver cells #21 mouse TFs human pattern human pattern
#16 mouse TFs mouse pattern mouse pattern
normal mouse liver cells #16 mouse TFs mouse pattern mouse pattern
A second line of evidence: gene expression
These workers also examined the pattern of gene expression; that is, the production of messenger RNAs, in the various combinations. They did this using microarrays. The human genes expressed on chromosome #21 by mouse transcription factors in the Tc1 mouse cells were mostly the same as those turned on by human transcription factors in human cells.
The Bottom Line
All these lines of evidence point to the following:
Throughout the animal kingdom,
• Genes encoding "housekeeping" proteins (histones, enzymes, etc., etc.) are remarkably conserved; that is, their products vary only slightly - certainly not enough to account for the vast range of bodies seen in animals from sea anemones to humans.
• Genes encoding "toolkit" proteins (transcription factors, cell signaling molecules) are also highly conserved (even more so).
• So the key to the fabulous diversity in the animal kingdom must lie in what evolution has done to the DNA sequences that control where and when genes are expressed in the developing animal.
So after years of looking for and sequencing open reading frames, the task now will be to analyze the sequence differences - arisen by mutation and evolution - in the intergenic regions that serve as control regions of those genes. An early result of genome analysis: during the radiation of the various mammalian orders, enhancers have diversified (evolved) much more rapidly than have promoters and their associated protein-encoding genes. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/18%3A_Evolution/18.03%3A_The_Evolution_of_Body_Form_in_Animals.txt |
The embryonic development of all vertebrates shows remarkable similarities as you can see from these drawings (supplied by Open Court Publishing Company). The drawings in the top row are of the embryonic stage called the pharyngula. At this stage ("I") they all contain a notochord, dorsal hollow nerve cord, a tail extending behind the anus, and a series of paired branchial grooves.
The branchial grooves are matched on the inside by a series of paired gill pouches. In fishes, the pouches and grooves eventually meet and form the gill slits, which allow water to pass from the pharynx over the gills and out the body. In the other vertebrates shown here, the grooves and pouches disappear. In humans, the chief trace of their existence is the eustachian tube and auditory canal which (interrupted only by the eardrum) connect the pharynx with the outside of the head.
Anatomical Recapitulation
The idea that embryonic development repeats that of one's ancestors is called recapitulation. It is often expressed as "ontogeny recapitulates phylogeny"; that is, embryonic development (ontogeny) repeats phylogeny (the genealogy of the species). This is a distortion of the truth and implies that early in our embryonic development we go through a fishlike stage. We do not. Rather, we pass through some (not all) of the embryonic stages that our ancestors passed through. Therefore, we find that the more distantly related two vertebrates are, the shorter the period during which they pass through similar embryonic stages (fish and human) and vice versa (fish and salamander).
We should also keep in mind that embryonic development prior to the pharyngula (stage I) may also be very different in the different groups. For example, while the pharyngulas of the human and the salamander look quite similar, their earlier development, starting with their fertilized eggs, are very different. The idea that "ontogeny recapitulates phylogeny" was proposed over a century ago by the biologist Ernst Haeckel. He also made the drawings on which the drawings above are based. Periodically, people rediscover that in making them, he altered certain details to emphasize his theory. Though they are schematic, the story they illustrate here has stood the test of time.
Another Example
Fossil evidence suggests that the ancestors of the insects had a pair of legs on each of their body segments. In this, they resembled today's millipedes (which may represent a second line of descent from these early forms). In any case, during embryonic development of insects, limb buds appear on the abdomen just as they must have in their multilegged ancestors. But by the time the larva hatches, only the six legs on the thorax (color) remain. The ones in the head become mouth parts. The ones in the abdomen disappear. Both these changes appear to be controlled by the expression of HOX genes.
Biochemical Recapitulation
Fish excrete a large part of their waste nitrogen as ammonia (NH3), while amphibians have the less toxic urea as their nitrogenous waste. Actually, the fish-like tadpole excretes ammonia until it undergoes metamorphosis into the adult frog. Only then does its chief nitrogenous waste become urea.
As for reptiles and birds, they convert their waste nitrogen compounds into the almost insoluble uric acid. During its development within the egg, however, the chicken embryo first passes through a stage of ammonia excretion followed by a period in which it excretes urea before finally turning to uric acid. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/18%3A_Evolution/18.04%3A_Recapitulation.txt |
Mutations are the raw materials of evolution. Evolution absolutely depends on mutations because this is the only way that new alleles and new regulatory regions are created. However, this seems paradoxical because most mutations that we observe are harmful (e.g., many missense mutations) or, at best, neutral, For example, "silent" mutations encoding the same amino acid. Also, many of the mutations in the vast amounts of DNA that lie between genes. Morevoer, most mutations in genes affect a single protein product (or a small set of related proteins produced by alternative splicing of a single gene transcript) while much evolutionary change involves myriad structural and functional changes in the phenotype.
So how can the small changes in genes caused by mutations, especially single-base substitutions ("point mutations"), lead to the large changes that distinguish one species from another? These questions have, as yet, only tentative answers.
One Solution: Duplication of Genes and Genomes
Mutations that would be harmful in a single pair of genes can be tolerated if those genes have first been duplicated. Gene duplication in a diploid organism provides a second pair of genes so that one pair can be safely mutated and tested in various combinations while the essential functions of the parent pair are kept intact.
Possible benefits:
• Over time, one of the duplicates can acquire a new function. This can provide the basis for adaptive evolution.
• But even while two paralogous genes are still similar in sequence and function, their existence provides redundancy ("belt and suspenders"). This may be a major reason why knocking out genes in yeast, "knockout mice", etc. so often has such a mild effect on the phenotype. The function of the knocked out gene can be taken over by a paralog.
• After gene duplication, random loss of these genes at a later time in one group of descendants different from the loss in another group could provide a barrier (a "post-zygotic isolating mechanism") to their interbreeding. Such a barrier could cause speciation: the evolution of two different species from a single ancestral species.
Evidence:
• Paralogous genes. Genes in one species that have arisen by duplication of an ancestral gene. Example: genes encoding olfactory receptors.
• Duplication of the entire genome. Examples:
• Polyploid angiosperms.
• Genome analysis of three ascomycetes show that early in the evolution of the budding yeast, Saccharomyces cerevisiae, its entire genome was duplicated. Each chromosome of the other ascomycetes contains stretches of genes whose orthologs are distributed over two Saccharomyces cerevisiae chromosomes.
• There is also evidence that vertebrate evolution has involved at least two duplications of the entire genome. Example: both the invertebrate Drosophila and the invertebrate chordate Amphioxus contain a single HOX gene cluster while mice and humans have four.
A Second Solution: Mutations in Regulatory Regions
Not all genes are expressed in all cells. In which cells and when a given gene will be expressed is controlled by the interaction of (1) extracellular signals turning on (or off),(2) transcription factors, which turn on (or off), and (3) particular genes. A mutation that would be lethal in the protein coding region of a gene need not be if it occurs in a control region (e.g. promoters and/or enhancers) of that gene. In fact, there is increasing evidence that mutations in control regions have played an important part in evolution. Examples:
• Humans have a gene (LCT) encoding lactase; the enzyme that digests lactose (e.g. in milk). In most of the world's people, LCT is active in young children but is turned off in adults. However, northern Europeans and three different tribes of African pastoralists, for whom milk remains a part of the adult diet, carry a mutation in the control region of their lactase gene that permits it to be expressed in adults. The mutation is different in each of the 4 cases examples of convergent evolution.
• There are very few differences in the coding sequences between genes of humans and chimpanzees. However, many of their shared genes differ in their control regions.
• The story of Prx1. Prx1 encodes a transcription factor that is essential for forelimb growth in mammals. When mice have the enhancer region of their Prx1 replaced with the enhancer region of Prx1 from a bat (whose front limbs are wings), the front legs of resulting mice are 6% longer than normal. Here, then is a morphological change not driven by a change in the Prx1 protein but by a change in the expression of its gene.
• The story of Pitx1
• The story of Style2.1 in the domestic tomato
A Third Solution?
Another theoretically-possible way by which a point mutation might give rise to a new gene is if the point mutation in a previously noncoding section of DNA converts a triplet of nucleotides into ATG thus creating a new open reading frame (ORF). It is increasingly evident that much of noncoding DNA is transcribed into a heterogeneous collection of RNAs. Transcription of DNA with its newly-acquired ATG codon would produce an RNA molecule with a translation start codon (AUG). Translation of this RNA would create a protein that most likely would be useless, perhaps even harmful but might, on rare occasions, provide the starting point for the acquisition of a new useful gene.
Large Changes in Phenotype can come from small changes in Genotype
Selector Genes
The building of an organ requires the coordinated activity of many genes. However, these are often organized in hierarchies so that "upstream genes" regulate the activity of "downstream genes". The closer you get to the top with a mutation, the greater the changes affected downstream.
Follow these links to see examples of the influence of "master" (selector) genes on the phenotype.
• Embryonic Development: Getting Started (especially the story of bicoid and nanos)
• Organizing the Embryo: The Central Nervous System Organizing the Embryo: Segmentation (more on bicoid and nanos)
• Embryonic Development: Putting on the finishing touches (especially the discussion of homeobox genes)
The Story of Pitx1
Pitx1 is homeobox gene (similar to bicoid in Drosophila) with orthologs found in all vertebrates. It contains 3 exons that encode a protein of some 283 amino acids (varying slightly in different species) which is a transcription factor that regulates the expression of other genes involved in the differentiation and function of multiple features including:
1. the anterior lobe of the pituitary gland (Pitx1 = "Pituitary homeobox1");
2. jaw development (mutations are associated with cleft palate);
3. development of the thymus and some types of mechanoreceptors;
4. development of the hind limbs.
Its activity in these regions is controlled by regulatory regions (promoters and/or enhancers) specific to each region (and presumably turned on by other transcription factors in the cells of those regions).
Pitx1 is an essential gene. Mutations in the coding regions are lethal when homozygous (shown in mice). However, mutations in noncoding regions need not be. All vertebrates have a pelvic girdle with associated bones which make up the pelvic fins of fishes and the hind legs of the tetrapods. Pitx1 is needed by them all for the proper development of these structures (as well as the other functions of Pitx1).
In a remarkable study of three-spined sticklebacks published in the 15 April 2004 issue of Nature, Michael Shapiro, Melissa Marks, Catherine Peichel, and their colleagues report that a mutation in a noncoding region of the Pitx1 gene accounts for most of the difference in the structure of the pelvic bones of the marine stickleback and its close freshwater cousins.
The marine sticklebacks have prominent spines jutting out in their pelvic region (red arrow) as well as the spines along the back (that give the fish its name). These spines may help protect them from being eaten by predators. (Drawing courtesy of the Parks Administration in the Emilia-Romagna region of Italy.) The also express the Pitx1 gene in various tissues, including thymus, mechanoreceptors, and the pelvic region.
The four species of stickleback that inhabit the Atlantic coast of North America. These species are sympatric between Newfoundland, Canada and Long Island, New York, United States. Image used iwth permission (CC BY-SA 3.0; Ghegeman).
The freshwater sticklebacks have no — or very much smaller — spines in their pelvic region. They express the identical Pitx1 gene in all the same tissues except those that develop into the pelvic structures. The reason: a mutation in an enhancer upstream of the Pitx1 exons. The unmutated enhancer turns on Pitx1 in the developing pelvic area. (Mice homozygous for a mutation in this control region have deformed hind limbs.)
Here then is a remarkable demonstration of how a single gene mutation can not only be viable but can lead to a major change in phenotype - adaptive evolution. (The changes seem not to have produce true speciation as yet. The marine and freshwater forms can interbreed. In fact, that is how the differences in their hind limbs were found to be primarily due to the expression of Pitx1.)
A survey of 21 different populations of sticklebacks - both freshwater and marine - from different regions of North America, Europe, and Japan has revealed a pattern of consistent genetic differences that distinguish the freshwater from the marine forms. However, only 17% of the distinguishing mutations were found in exons that alter the amino acid sequence of the encoded proteins. All the rest were "silent" and most, 41% or more, of these occurred in intergenic regions. These results further demonstrate the importance of mutations in regulatory regions - promoters and enhancers - in the evolution of adaptive phenotypes. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/18%3A_Evolution/18.05%3A_Mutation_and_Evolution.txt |
If two individuals mate that are heterozygous (e.g., Bb) for a trait, we find that
• 25% of their offspring are homozygous for the dominant allele (BB)
• 50% are heterozygous like their parents (Bb)
• 25% are homozygous for the recessive allele (bb) and thus, unlike their parents, express the recessive phenotype.
This is what Mendel found when he crossed monohybrids. It occurs because meiosis separates the two alleles of each heterozygous parent so that 50% of the gametes will carry one allele and 50% the other and when the gametes are brought together at random, each B (or b)-carrying egg will have a 1 in 2 probability of being fertilized by a sperm carrying B (or b). (Left table)
Results of random union of the two gametes produced by two individuals, each heterozygous for a given trait. As a result of meiosis, half the gametes produced by each parent with carry allele B; the other half allele b. Results of random union of the gametes produced by an entire population with a gene pool containing 80% B and 20% b.
0.5 B 0.5 b 0.8 B 0.2 b
0.5 B 0.25 BB 0.25 Bb 0.8 B 0.64 BB 0.16 Bb
0.5 b 0.25 Bb 0.25 bb 0.2 b 0.16 Bb 0.04 bb
However, the frequency of two alleles in an entire population of organisms is unlikely to be exactly the same. Let us take as a hypothetical case, a population of hamsters in which 80% of all the gametes in the population carry a dominant allele for black coat (B) and 20% carry the recessive allele for gray coat (b).
Random union of these gametes (right table) will produce a generation:
• 64% homozygous for BB (0.8 x 0.8 = 0.64)
• 32% Bb heterozygotes (0.8 x 0.2 x 2 = 0.32)
• 4% homozygous (bb) for gray coat (0.2 x 0.2 = 0.04)
So 96% of this generation will have black coats; only 4% gray coats.
Will gray coated hamsters eventually disappear? No. Let's see why not.
• All the gametes formed by BB hamsters will contain allele B as will one-half the gametes formed by heterozygous (Bb) hamsters.
• So, 80% (0.64 + .5*0.32) of the pool of gametes formed by this generation with contain B.
• All the gametes of the gray (bb) hamsters (4%) will contain b but one-half of the gametes of the heterozygous hamsters will as well.
• So 20% (0.04 + .5*0.32) of the gametes will contain b.
So we have duplicated the initial situation exactly. The proportion of allele b in the population has remained the same. The heterozygous hamsters ensure that each generation will contain 4% gray hamsters. Now let us look at an algebraic analysis of the same problem using the expansion of the binomial (p+q)2.
$(p+q)^2 = p^2 + 2pq + q^2$
The total number of genes in a population is its gene pool.
• Let $p$ represent the frequency of one gene in the pool and $q$ the frequency of its single allele.
• So, $p + q = 1$
• $p^2$ = the fraction of the population homozygous for $p$
• $q^2$ = the fraction homozygous for $q$
• $2pq$ = the fraction of heterozygotes
• In our example, p = 0.8, q = 0.2, and thus $(0.8 + 0.2)^2 = (0.8)^2 + 2(0.8)(0.2) + (0.2)^2 = 064 + 0.32 + 0.04$
The algebraic method enables us to work backward as well as forward. In fact, because we chose to make B fully dominant, the only way that the frequency of B and b in the gene pool could be known is by determining the frequency of the recessive phenotype (gray) and computing from it the value of q.
q2 = 0.04, so q = 0.2, the frequency of the b allele in the gene pool. Since p + q = 1, p = 0.8 and allele B makes up 80% of the gene pool. Because B is completely dominant over b, we cannot distinguish the Bb hamsters from the BB ones by their phenotype. But substituting in the middle term (2pq) of the expansion gives the percentage of heterozygous hamsters. 2pq = (2)(0.8)(0.2) = 0.32
So, recessive genes do not tend to be lost from a population no matter how small their representation.
Hardy-Weinberg law
So long as certain conditions are met (discussed below), gene frequencies and genotype ratios in a randomly-breeding population remain constant from generation to generation. This is known as the Hardy-Weinberg law.
The Hardy-Weinberg law is named in honor of the two men who first realized the significance of the binomial expansion to population genetics and hence to evolution. Evolution involves changes in the gene pool. A population in Hardy-Weinberg equilibrium shows no change. What the law tells us is that populations are able to maintain a reservoir of variability so that if future conditions require it, the gene pool can change. If recessive alleles were continually tending to disappear, the population would soon become homozygous. Under Hardy-Weinberg conditions, genes that have no present selective value will nonetheless be retained.
When the Hardy-Weinberg Law Fails
To see what forces lead to evolutionary change, we must examine the circumstances in which the Hardy-Weinberg law may fail to apply. There are five:
1. mutation
2. gene flow
3. genetic drift
4. nonrandom mating
5. natural selection
Mutation
The frequency of gene B and its allele b will not remain in Hardy-Weinberg equilibrium if the rate of mutation of B -> b (or vice versa) changes. By itself, this type of mutation probably plays only a minor role in evolution; the rates are simply too low. However, gene (and whole genome) duplication - a form of mutation - probably has played a major role in evolution. In any case, evolution absolutely depends on mutations because this is the only way that new alleles are created. After being shuffled in various combinations with the rest of the gene pool, these provide the raw material on which natural selection can act.
Gene Flow
Many species are made up of local populations whose members tend to breed within the group. Each local population can develop a gene pool distinct from that of other local populations. However, members of one population may breed with occasional immigrants from an adjacent population of the same species. This can introduce new genes or alter existing gene frequencies in the residents.
In many plants and some animals, gene flow can occur not only between subpopulations of the same species but also between different (but still related) species. This is called hybridization. If the hybrids later breed with one of the parental types, new genes are passed into the gene pool of that parent population. This process is called introgression. It is simply gene flow between species rather than within them.
Comparison of the genomes of contemporary humans with the genome recovered from Neanderthal remains shows that from 1–3% of our genes were acquired by introgression following mating between members of the two populations tens of thousands of years ago.
Whether within a species or between species, gene flow increases the variability of the gene pool.
Genetic Drift
As we have seen, interbreeding often is limited to the members of local populations. If the population is small, Hardy-Weinberg may be violated. Chance alone may eliminate certain members out of proportion to their numbers in the population. In such cases, the frequency of an allele may begin to drift toward higher or lower values. Ultimately, the allele may represent 100% of the gene pool or, just as likely, disappear from it.
Drift produces evolutionary change, but there is no guarantee that the new population will be more fit than the original one. Evolution by drift is aimless, not adaptive.
Nonrandom Mating
One of the cornerstones of the Hardy-Weinberg equilibrium is that mating in the population must be random. If individuals (usually females) are choosy in their selection of mates, the gene frequencies may become altered. Darwin called this sexual selection.
Nonrandom mating seems to be quite common. Breeding territories, courtship displays, "pecking orders" can all lead to it. In each case certain individuals do not get to make their proportionate contribution to the next generation.
Assortative mating
Humans seldom mate at random preferring phenotypes like themselves (e.g., size, age, ethnicity). This is called assortative mating. Marriage between close relatives is a special case of assortative mating. The closer the kinship, the more alleles shared and the greater the degree of inbreeding. Inbreeding can alter the gene pool. This is because it predisposes to homozygosity. Potentially harmful recessive alleles — invisible in the parents — become exposed to the forces of natural selection in the children.
It turns out that many species - plants as well as animals - have mechanisms be which they avoid inbreeding. Examples:
• Link to discussion of self-incompatibility in plants.
• Male mice use olfactory cues to discriminate against close relatives when selecting mates. The preference is learned in infancy - an example of imprinting. The distinguishing odors are controlled by the MHC alleles of the mice and are detected by the vomeronasal organ (VNO).
Natural Selection
If individuals having certain genes are better able to produce mature offspring than those without them, the frequency of those genes will increase. This is simply expressing Darwin's natural selection in terms of alterations in the gene pool. (Darwin knew nothing of genes.) Natural selection results from differential mortality and/or differential fecundity.
Mortality Selection
Certain genotypes are less successful than others in surviving through to the end of their reproductive period. The evolutionary impact of mortality selection can be felt anytime from the formation of a new zygote to the end (if there is one) of the organism's period of fertility. Mortality selection is simply another way of describing Darwin's criteria of fitness: survival.
Fecundity Selection
Certain phenotypes (thus genotypes) may make a disproportionate contribution to the gene pool of the next generation by producing a disproportionate number of young. Such fecundity selection is another way of describing another criterion of fitness described by Darwin: family size. In each of these examples of natural selection, certain phenotypes are better able than others to contribute their genes to the next generation. Thus, by Darwin's standards, they are more fit. The outcome is a gradual change in the gene frequencies in that population.
Calculating the Effect of Natural Selection on Gene Frequencies
The effect of natural selection on gene frequencies can be quantified. Let us assume a population containing
• 36% homozygous dominants (AA)
• 48% heterozygotes (Aa) and
• 16% homozygous recessives (aa)
The gene frequencies in this population are $p = 0.6$ and $q = 0.4$. The heterozygotes are just as successful at reproducing themselves as the homozygous dominants, but the homozygous recessives are only 80% as successful. That is, for every 100 AA (or Aa) individuals that reproduce successfully only 80 of the aa individuals succeed in doing so. The fitness ($w$) of the recessive phenotype is thus 80% or 0.8.
Their relative disadvantage can also be expressed as a selection coefficient, $s$, where
$s = 1 − w$
In this case,
$s = 1 − 0.8 = 0.2.$
The change in frequency of the dominant allele ($Δp$) after one generation is expressed by the equation
$Δp = \dfrac{s p_0 q_0^2}{1 - s q_0^2}$
where $p_0$ and $q_0$ are the initial frequencies of the dominant and recessive alleles respectively. Substituting, we get
\begin{align} Δp & = \dfrac{(0.2)(0.6)(0.4)^2}{1 − (0.2)(0.4)^2} \[5pt] &=\dfrac{0.019}{0.968} \[5pt] &=0.02 \end{align}
So, in one generation, the frequency of allele A rises from its initial value of 0.6 to 0.62 and that of allele a declines from 0.4 to 0.38 ($q = 1 − p$).
The new equilibrium produces a population of
• 38.4% homozygous dominants (an increase of 2.4%) (p2 = 0.384)
• 47.1% heterozygotes (a decline of 0.9%)(2pq = 0.471) and
• 14.4% homozygous recessives (a decline of 1.6%)(q2 = 0.144)
If the fitness of the homozygous recessives continues unchanged, the calculations can be reiterated for any number of generations. If you do so, you will find that although the frequency of the recessive genotype declines, the rate at which a is removed from the gene pool declines; that is, the process becomes less efficient at purging allele a. This is because when present in the heterozygote, a is protected from the effects of selection. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/18%3A_Evolution/18.06%3A_The_Hardy-Weinberg_Equilibrium.txt |
A polymorphism is a genetic variant that appears in at least 1% of a population. (e.g., the human ABO blood groups, the human Rh factor, and the human major histocompatibility complex). By setting the cutoff at 1%, it excludes spontaneous mutations that may have occurred in - and spread through the descendants of - a single family.
Protein Polymorphisms
All the examples above are of the protein products of alleles. These can be identified by serology - that is, using antibodies to detect the different versions of the protein. (Antibodies caused the clumping of the red blood cells in this test) and electrophoresis - if amino acid changes in the protein alter its net electrical charge, it will migrate more or less rapidly in an electrical field. Enzymes are frequently polymorphic. A population may contain two or more variants of an enzyme encoded by a single locus. The variants differ slightly in their amino acid sequence and often this causes them to migrate differently under electrophoresis. By treating the gel with the substrate for the enzyme, its presence can be visualized.
Electrophoresis of tissue extracts from 15 different green treefrogs (Hyla cinerea) reveals 4 allelic versions of the enzyme aconitase (one of the enzymes of the citric acid cycle). The results:
• Eight frogs (#2, 3, 4, 6, 7, 9, 12, and 14) were homozygous for allele M.
• Frog #8 was homozygous for allele E.
• Three frogs (#1, 11, 15) are heterozygous for the M and S alleles.
• Two (#5, 13) were heterozygous for M and E.
• Frog #10 was heterozygous for M and F.
Electrophoretic variants of an enzyme occurring in a population are called allozymes.
Restriction Fragment Length Polymorphisms (RFLPs)
Proteins are gene products and so polymorphic versions are simply reflections of allelic differences in the gene; that is, allelic differences in DNA. Often these changes create new - or abolish old - sites for restriction enzymes to cut the DNA. Digestion with the enzyme then produces DNA fragments of a different length. These can be detected by electrophoresis. Most* RFLPs are created by a change in a single nucleotide in the gene, and so these are called single nucleotide polymorphisms (SNPs).
Single Nucleotide Polymorphisms (SNPs)
Developments in DNA sequencing now make it easy to look for allelic versions of a gene by sequencing samples of the gene taken from different members of a population (or from a heterozygous individual). Alleles whose sequence reveals only a single changed nucleotide are called single nucleotide polymorphisms or SNPs. SNPs can occur in noncoding parts of the gene so they would not be seen in the protein product. They might not alter the cutting site for any known restriction enzymes so they would not be seen by RFLP analysis. As of October 2005, over one million SNPs had been identified across the human genome.
Copy Number Polymorphisms (CNPs)
Genetic analysis (using DNA chips and FISH) has revealed another class of human polymorphisms. These copy number polymorphisms are large (thousands of base pairs) duplications or deletions that are found in some people but not in others. On average, one person differs from another by 11 of these. One or more have been found on most chromosomes, and the list is probably incomplete. While most of this DNA is non-coding, functional genes are embedded in some of it. Example: AMY1, the gene encoding salivary amylase, an enzyme that digests starch. Humans vary in the number of copies of AMY1 in their genome.
• Populations whose diet is rich in starches (e.g., many Americans, Japanese) have an average of 7 copies of the gene.
• Populations with low-starch diets (e.g., nomadic tribes in Siberia whose diet is dominated by dairy products and fish) average only 5 copies.
In the case of AMY1, the more copies present, the more enzyme that is produced. How a person adapts to a change in gene number for autosomal genes is unknown (in contrast to the way that human females adjust the activity of the genes on their two X chromosomes to match that of males with their solitary X chromosome).
How are polymorphisms useful?
Polymorphism analysis is in widespread use. In tissue typing, it is use to find the best match between the donor, e.g., of a kidney, and the recipient. It is used to find disease genes (e.g., the gene for Huntington's disease was located when the presence of the disease was found to be linked to a RFLP whose location on the chromosome was known). In population studies, it is used to assess the degree of genetic diversity in a population, including:
• The McAlpine study, which produced the photo above, found that the heterozygous frogs were more successful breeders than homozygous ones.
• A search for polymorphisms in elephant seals and cheetahs has revealed that they have few or none.
• Determining whether two populations represent separate species or races of the same species. This is often critical to applying laws protecting endangered species.
Tracking migration patterns of a species (e.g., whales).
How do polymorphisms arise and persist?
They arise by mutation. But what keeps them in the population? Several factors may maintain polymorphism in a population.
• Founder Effect: If a population began with a few individuals — one or more of whom carried a particular allele — that allele may come to be represented in many of the descendants. In the 1680s Ariaantje and Gerrit Jansz emigrated from Holland to South Africa, one of them bringing along an allele for the mild metabolic disease porphyria. Today more than 30000 South Africans carry this allele and, in every case examined, can trace it back to this couple — a remarkable example of the founder effect.
• Genetic Drift: An allele may increase - or decrease - in frequency simply through chance. Not every member of the population will become a parent and not every set of parents will produce the same number of offspring. The effect, called random genetic drift, is particularly strong in small populations (e.g., 100 breeding pairs or fewer) and when the allele is neutral; that is, is neither helpful nor deleterious
Eventually the entire population may become homozygous for the allele or - equally likely - the allele may disappear. Before either of these fates occurs, the allele represents a polymorphism.
Two examples of reduced polymorphism because of genetic drift:
• By 1900, hunting of the northern elephant seal off the Pacific coast had reduced its population to only 20 survivors. Since hunting ended, the population has rebounded from this population bottleneck to some 100,000 animals today. However, these animals are homozygous at every one of the gene loci that have been examined.
• Cheetahs, the fastest of the land animals, seem to have passed through a similar period of small population size with its accompanying genetic drift. Examination of 52 different loci has failed to reveal any polymorphisms; that is, these animals are homozygous at all 52 loci. The lack of genetic variability is so profound that cheetahs will accept skin grafts from each other just as identical twins (and inbred mouse strains) do. Whether a population with such little genetic diversity can continue to adapt to a changing environment remains to be seen.
Natural Selection
Copy Number Polymorphisms
The varying number of copies of the AMY1 gene in different human populations appears to have arisen from the evolutionary pressure of the differences in the starch content of their diet.
Balanced Polymorphism
In regions of the world (e.g., parts of Africa) where malaria caused by Plasmodium falciparum is common, the allele for sickle-cell hemoglobin is also common. This is because children who inherit one gene for the "normal" beta chain of hemoglobin and one sickle gene are more likely to survive than either homozygote. Children homozygous for the sickle allele die young from sickle-cell disease but children homozygous for the "normal" beta chain are more susceptible to illness and death from falciparum malaria than are heterozygotes. Hence the relatively high frequency of the allele in malarial regions. When natural selection favors heterozygotes over both homozygotes, the result is balanced polymorphism. It accounts for the persistence of an allele even though it is deleterious when homozygous.
Another example: prion proteins
All human populations are polymorphic for the prion protein PrPC. It is encoded by the prion protein gene (PRNP). Two of the alleles have different codons at position 129 - one encoding methionine; the other valine. Homozygosity for either allele increases the susceptibility to prion diseases. People who are heterozygous are more resistant. A study of elderly women who had survived the kuru epidemic of the first half of the 20th century (eating the tissues of the deceased was banned in 1950) showed that 76.7% of them were heterozygotes. This table compares the gene frequencies in this population as well as in a population that never practiced mortuary feasts.
Table 1: M is the allele encoding the methionine; V the allele encoding valine.
MM MV VV
Survivors 0.133 0.767 0.100
Unexposed 0.221 0.514 0.264
A quick calculation will show that the gene pool of the exposed women deviates widely from what would be found if the population were in Hardy-Weinberg equilibrium. In this case, strong mortality selection is the cause. The gene pool of the unexposed population is close to being in Hardy-Weinberg equilibrium. Here, again, natural selection has favored heterozygotes over both homozygotes (and led to the speculation that cannibalism may have been common earlier in human history).
Natural vs. Sexual Selection: Balanced polymorphism in Soay sheep
Hirta is a tiny island in the North Atlantic 100 miles off the northwest coast of Scotland. In 1932 a small (107) population of domestic sheep (Ovis aries) was introduced onto the island from the neighboring island of Soay. Since then these sheep have been allowed to run wild and, since 1985, have been intensively studied. The sheep have horns and, in males, these play an important role in competition for females. The size of the horns is strongly influenced by a single gene locus, RXFP2, with two alleles: Ho+ and HoP.
• Homozygous Ho+Ho+ males have the largest horns and sire more offspring but have reduced survival.
• Homozygous HoPHoP males have smaller horns (sometime even vestigial horns called scurs). These males have less success in mating but have increased survival.
• Heterozygous Ho+HoP males are almost as successful at mating as Ho+Ho+ males and survive almost as well as HoPHoP males. On balance, then, the heterozygotes have greater overall fitness than either homozygotes — another example of balanced polymorphism. It arises as a trade-off between the opposing effects of natural selection (survival) and sexual selection (reproductive success) on a single gene locus.
You can read about these findings in Johnston, Susan. E., et al., Nature 502, 93–95, 3 October 2013. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/18%3A_Evolution/18.07%3A_Polymorphisms.txt |
In the discussion of natural selection, the emphasis was on how natural selection works on individuals to favor the more fit and disfavor the less fit in a population. The emphasis was on the survival (mortality selection), mating success (sexual selection), or family size (fecundity selection) of individuals. But what of the worker honeybee who gives up her life when danger threatens her hive? Or the mother bird who, feigning injury, flutters away from her nestful of young, thus risking death at the hands of a predator? How can evolution produce genes for such instinctive patterns of behavior when the owner of these genes risk failing the first test of fitness: survival?
A possible solution to this dilemma lies in the effect of such seemingly altruistic behavior on the overall ("inclusive") fitness of the family of the altruistic individual. Linked together be a similar genetic endowment, the altruistic member of the family enhances the chance that many of its own genes will be passed on to future generations by sacrificing itself for the welfare of its relatives. It is interesting to note that most altruistic behavior is observed where the individuals are linked by fairly close family ties. Natural selection working at the level of the family rather than the individual is called kin selection.
How good is the evidence for kin selection? Does the behavior of the mother bird really increase her chances of being killed? After all, it may be advantageous to take the initiative in an encounter with a predator that wanders near. But even if she does increase her risk, is this anything more than another example of maternal behavior? Her children are, indeed, her kin. But isn't natural selection simply operating in one of the ways Darwin described: to produce larger mature families?
Perhaps clearer examples of altruism and kin selection are to be found in those species of birds that employ "helpers". One example: Florida scrub jays (Aphelocoma coerulescens coerulescens). These birds occupy well-defined territories. When they reach maturity, many of the young birds remain for a time (one to four years) in the territory and help their parents with the raising of additional broods. How self-sacrificing! Should not natural selection have produced a genotype that leads its owners to seek mates and start raising their own families (to receive those genes)?
But the idea of kin selection suggests that the genes guiding their seemingly altruistic behavior have been selected for because they are more likely to be passed on to subsequent generations in the bodies of an increased number of younger brothers and sisters than in the bodies of their own children. To demonstrate that this is so, it is necessary to show that
1. the "helping" behavior of these unmated birds is really a help and that
2. they have truly sacrificed opportunities to be successful parents themselves.
Thanks to the patient observations of Glen Woolfenden, the first point is established. He has shown that parents with helpers raise larger broods than those without. But the second point remains unresolved. Perhaps by waiting until they have gained experience with guarding nests and feeding young and until a suitable territory becomes available, these seemingly altruistic helpers are actually improving their chances of eventually raising larger families than they would have if they started right at it. If so, then once again we are simply seeing natural selection working through one of Darwin's criteria of individual fitness: ability to produce larger mature families.
The evolutionary advantage of helping ceases if the young are not actually siblings of the helper. It is well-established (e.g., by DNA analysis) that the females of many species of birds have "extramarital" affairs; that is, produce broods where the young have been sired by more than one male. Interestingly, it turns out that the more promiscuous the females of a given species, the less likely it is that they are assisted by helpers. Conversely, those species that employ helpers tend to be monogamous. (There are a few exceptions.)
Kin Selection in Social Insects
The honeybee and other social insects provide the clearest example of kin selection. They are also particularly interesting examples because of the peculiar genetic relationships among the family members.
Male honeybees (drones) develop from the queen's unfertilized eggs and are haploid. Thus all their sperm will contain exactly the same set of genes. This means that all their daughters will share exactly the same set of paternal genes, although they will share — on average — only one-half of their mother's genes. (Human sisters, in contrast, share one-half of their father's as well as one-half of their mother's genes.) So any behavior that favors honeybee sisters (75% of genes shared) will be more favorable to their genotype than behavior that favors their children (50% of genes shared).
Since that is the case, why bother with children at all? Why not have most of the sisters be sterile workers, caring for their mother as she produces more and more younger sisters, a few of whom will someday be queens? As for their brothers, worker bees share only 25% of their genes with them. Is it surprising, then, that as autumn draws near, the workers lose patience with the lazy demanding ways of their brothers and finally drive them from the hive? | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/18%3A_Evolution/18.08%3A_Kin_Selection.txt |
To account for the origin of life on our earth requires solving several problems:
• How the organic molecules that define life, e.g. amino acids, nucleotides, were created.
• How these were assembled into macromolecules, e.g. proteins and nucleic acids, - a process requiring catalysts.
• How these were able to reproduce themselves.
• How these were assembled into a system delimited from its surroundings (i.e., a cell).
A number of theories address each of these problems. As for the first problem, four scenarios have been proposed. Organic molecules:
1. were synthesized from inorganic compounds in the atmosphere,
2. rained down on earth from outer space,
3. were synthesized at hydrothermal vents on the ocean floor,
4. were synthesized when comets or asteroids struck the early earth.
Scenario 1: Miller's Experiment
Stanley Miller, a graduate student in biochemistry, built the apparatus shown in Figure \(1\). He filled it with water (H2O), methane (CH4), ammonia (NH3) and hydrogen (H2), but no oxygen. He hypothesized that this mixture resembled the atmosphere of the early earth. The mixture was kept circulating by continuously boiling and then condensing the water. The gases passed through a chamber containing two electrodes with a spark passing between them.
At the end of a week, Miller used paper chromatography to show that the flask now contained several amino acids as well as some other organic molecules. However, it is now thought that the atmosphere of the early earth was not rich in methane and ammonia - essential ingredients in Miller's experiments. In the years since Miller's work, many variants of his procedure have been tried. Virtually all the small molecules that are associated with life have been formed:
• 17 of the 20 amino acids used in protein synthesis, and all the purines and pyrimidines used in nucleic acid synthesis.
• But abiotic synthesis of ribose - and thus of nucleotides - has been much more difficult. However, success in synthesizing pyrimidine ribonucleotides under conditions that might have existed in the early earth was reported in the 14 May 2009 issue of Nature.
• And in 2015, chemists in Cambridge England led by John Sutherland reported that they had been able to synthesize precursors of 12 of the 20 amino acids and two (of the four) ribonucleotides used by life as well as glycerol-1-phosphate, a precursor of lipids. They created all of these molecules using only hydrogen cyanide (HCN) and hydrogen sulfide (H2S) irradiated with ultraviolet light in the presence of mineral catalysts.
Scenario 2: Molecules from Outer Space
Astronomers, using infrared spectroscopy, have identified a variety of organic molecules in interstellar space, including methane (CH4), methanol (CH3OH), formaldehyde (HCHO), cyanoacetylene (HC3N) (which in spark-discharge experiments is a precursor to the pyrimidine cytosine), polycyclic aromatic hydrocarbonsas well as such inorganic building blocks as carbon dioxide (CO2), carbon monoxide (CO), ammonia (NH3), hydrogen sulfide (H2S), and hydrogen cyanide (HCN).
There have been several reports of producing amino acids and other organic molecules in laboratories by taking a mixture of molecules known to be present in interstellar space such as ammonia (NH3), carbon monoxide (CO), methanol (CH3OH) and water (H2O), hydrogen cyanide (HCN) and exposing it to a temperature close to that of space (near absolute zero) and intense ultraviolet (UV) radiation. Whether or not the molecules that formed terrestrial life arrived here from space, there is little doubt that organic matter continuously rains down on the earth (estimated at 30 tons per day).
Alternatively, organic molecules can be transport to Earth via meteorites as demonstrated with the Murchison Meteorite that that fell near Murchison, Australia on 28 September 1969. This meteorite turned out to contain a variety of organic molecules including: purines and pyrimidines, polyols - compounds with hydroxyl groups on a backbone of 3 to 6 carbons such as glycerol and glyceric acid (sugars are polyols) and the amino acids listed in Table \(1\). The amino acids and their relative proportions were quite similar to the products formed in Miller's experiments.
Murchison meteorite at the The National Museum of Natural History (Washington). (CC SA-BY 3.0; :Basilicofresco).
Table \(1\): Representative amino acids found in the Murchison meteorite. Six of the amino acids (blue) are found in all living things, but the others (yellow) are not normally found in living matter here on earth. The same amino acids are produced in discharge experiments like Miller's.
Glycine Glutamic acid
Alanine Isovaline
Valine Norvaline
Proline N-methylalanine
Aspartic acid N-ethylglycine
Contamination?
The question is if these molecules identified in the Murchison meteorite were simply terrestrial contaminants that got into the meteorite after it fell to earth? Probably not:
• Some of the samples were collected on the same day it fell and subsequently handled with great care to avoid contamination.
• The polyols contained the isotopes carbon-13 and hydrogen-2 (deuterium) in greater amounts than found here on earth.
• The samples lacked certain amino acids that are found in all earthly proteins.
• Only L amino acids occur in earthly proteins, but the amino acids in the meteorite contain both D and L forms (although L forms were slightly more prevalent).
Scenario 3: Deep-Sea Hydrothermal Vents
Some deep-sea hydrothermal vents discharge copious amounts of hydrogen, hydrogen sulfide, and carbon dioxide at temperatures around 100°C. (These are not "black smokers".) These gases bubble up through chambers rich in iron sulfides (FeS, FeS2). These can catalyze the formation of simple organic molecules like acetate. (And life today depends on enzymes that have Fe and S atoms in their active sites.)
Scenario 4: Laboratory Synthesis of Nucleobases Under Conditions Mimicking the Impact of Asteroids or Comets on the Early Earth
Researchers in the Czech Republic reported in 2014 that they had succeeded in the abiotic synthesis of adenine (A), guanine (G), cytosine (C), and uracil (U) — the four bases found in RNA (an RNA beginning?) and three of the four found in DNA. They achieved this by bombarding a mixture of formamide and clay with powerful laser pulses that mimicked the temperature and pressure expected when a large meteorite strikes the earth. Formamide is a simple substance, CH3NO, thought to have been abundant on the early earth and containing the four elements fundamental to all life.
Assembling Polymers
Another problem is how polymers - the basis of life itself - could be assembled.
• In solution, hydrolysis of a growing polymer would soon limit the size it could reach.
• Abiotic synthesis produces a mixture of L and D enantiomers. Each inhibits the polymerization of the other. (So, for example, the presence of D amino acids inhibits the polymerization of L amino acids (the ones that make up proteins here on earth).
This has led to a theory that early polymers were assembled on solid, mineral surfaces that protected them from degradation, and in the laboratory polypeptides and polynucleotides (RNA molecules) containing about ~50 units have been synthesized on mineral (e.g., clay) surfaces.
An RNA Beginning?
All metabolism depends on enzymes and, until recently, every enzyme has turned out to be a protein. But proteins are synthesized from information encoded in DNA and translated into mRNA. So here is a chicken-and-egg dilemma. The synthesis of DNA and RNA requires proteins. So proteins cannot be made without nucleic acids and nucleic acids cannot be made without proteins. The discovery that certain RNA molecules have enzymatic activity provides a possible solution. These RNA molecules — called ribozymes — incorporate both the features required of life: storage of information and the ability to act as catalysts.
While no ribozyme in nature has yet been found that can replicate itself, ribozymes have been synthesized in the laboratory that can catalyze the assembly of short oligonucleotides into exact complements of themselves. The ribozyme serves as both the template on which short lengths of RNA ("oligonucleotides" are assembled following the rules of base pairing and the catalyst for covalently linking these oligonucleotides.
In principal, the minimal functions of life might have begun with RNA and only later did proteins take over the catalytic machinery of metabolism and DNA take over as the repository of the genetic code. Several other bits of evidence support this notion of an original "RNA world":
• Many of the cofactors that play so many roles in life are based on ribose; for example:
• ATP
• NAD
• FAD
• coenzyme A
• cyclic AMP
• GTP
• In the cell, all deoxyribonucleotides are synthesized from ribonucleotide precursors.
• Many bacteria control the transcription and/or translation of certain genes with RNA molecules, not protein molecules.
Reproduction?
Perhaps the earliest form of reproduction was a simple fission of the growing aggregate into two parts - each with identical metabolic and genetic systems intact.
The First Cell?
To function, the machinery of life must be separated from its surroundings - some form of extracellular fluid (ECF). This function is provided by the plasma membrane. Today's plasma membranes are made of a double layer of phospholipids. They are only permeable to small, uncharged molecules like H2O, CO2, and O2. Specialized transmembrane transporters are needed for ions, hydrophilic, and charged organic molecules (e.g., amino acids and nucleotides) to pass into and out of the cell.
However, the same Szostak lab that produced the finding described above reported in the 3 July 2008 issue of Nature that fatty acids, fatty alcohols, and monoglycerides - all molecules that can be synthesized under prebiotic conditions - can also form lipid bilayers and these can spontaneously assemble into enclosed vesicles.
Unlike phospholipid vesicles, these
• admit from the external medium charged molecules like nucleotides
• admit from the external medium hydrophilic molecules like ribose
• grow by self-assembly
• are impermeable to, and thus retain, polymers like oligonucleotides.
These workers loaded their synthetic vesicles with a short single strand of deoxycytidine (dC) structured to provide a template for its replication. When the vesicles were placed in a medium containing (chemically modified) dG, these nucleotides entered the vesicles and assembled into a strand of Gs complementary to the template strand of Cs. Here, then, is a simple system that is a plausible model for the creation of the first cells from the primeval "soup" of organic molecules.
From Unicellular to Multicellular Organisms
This transition is probably the easiest to understand.
Several colonial flagellated green algae provide a clue. These species are called colonial because they are made up simply of clusters of independent cells. If a single cell of Gonium, Pandorina, or Eudorina is isolated from the rest of the colony, it will swim away looking quite like a Chlamydomonas cell. Then, as it undergoes mitosis, it will form a new colony with the characteristic number of cells in that colony.
(The figures are not drawn to scale. Their sizes range from Chlamydomonas which is about 10 µm in diameter - little larger than a human red blood cell - to Volvox whose sphere is some 350 µm in diameter - visible to the naked eye.)
The situation in Pleodorina and Volvox is different. In these organisms, some of the cells of the colony (most in Volvox) are not able to live independently. If a nonreproductive cell is isolated from a Volvox colony, it will fail to reproduce itself by mitosis and eventually will die. What has happened? In some way, as yet unclear, Volvox has crossed the line separating simple colonial organisms from truly multicellular ones. Unlike Gonium, Volvox cannot be considered simply a colony of individual cells. It is a single organism whose cells have lost their ability to live independently. If a sufficient number of them become damaged, the entire sphere of cells will die.
What has Volvox gained? In giving up their independence, the cells of Volvox have become specialists. No longer does every cell carry out all of life's functions (as in colonial forms); instead certain cells specialize to carry out certain functions while leaving other functions to other specialists. In Volvox this process goes no further than having certain cells specialize for reproduction while others, unable to reproduce themselves, fulfill the needs for photosynthesis and locomotion.
In more complex multicellular organisms, the degree of specialization is carried much further. Each cell has one or two precise functions to carry out. It depends on other cells to carry out all the other functions needed to maintain the life of the organism and thus its own.
The specialization and division of labor among cells is the outcome of their history of differentiation. One of the great problems in biology is how differentiation arises among cells, all of which having arisen by mitosis, share the same genes.
The genomes of both Chlamydomonas and Volvox have been sequenced. Although one is unicellular, the other multicellular, they have not only about the same number of protein-encoding genes (14,516 in Chlamydomonas, 14,520 in Volvox) but most of these are homologous. Volvox has only 58 genes that have no relatives in Chlamydomonas and even fewer unique mRNAs.
At one time, many of us would have expected that a multicellular organism like Volvox with its differentiated cells and complex life cycle would have had many more genes than a single-celled organism like Chlamydomonas. But that turns out not to be the case.
How to explain this apparent paradox? My guess is that just as we have seen in the evolution of animals, we are seeing here that the evolution of organismic complexity is not so much a matter of the evolution of new genes but rather the evolution of changes in the control elements (promoters and enhancers) that dictate how and where the basic tool kit of eukaryotic genes will be expressed .
The evidence is compelling that all these organisms are close relatives; that is, belong to the same clade. They illustrate how colonial forms could arise from unicellular ones and multicellular forms from colonial ones.
The Last Universal Common Ancestor (LUCA)?
The 3 kingdoms of contemporary life — archaea, bacteria, and eukaryotes — all share many similarities of their metabolic and genetic systems . Presumably these were present in an organism that was ancestral to these groups: the "LUCA". Although there are not enough data at present to describe LUCA, comparative genomics and proteomics reveal a closer relationship between archaea and eukaryotes than either shares with the bacteria. Except, of course, for the mitochondria and chloroplasts that eukaryotes gained from bacterial endosymbionts. Whether the endosymbionts were acquired before or after a lineage of archaea had acquired a nucleus - and thus started the lineage of eukaryotes - is still uncertain.
Creating Life?
When I headed off to college (in 1949), I wrote an essay speculating on the possibility that some day we would be able to create a living organism from nonliving ingredients. By the time I finished my formal studies in biology — having learned of the incredible complexity of even the simplest organism — I concluded that such a feat could never be accomplished.
Now I'm not so sure.
Several recent advances suggest that we may be getting close to creating life. (But note that these examples represent laboratory manipulations that do not necessarily reflect what may have happened when life first appeared.)
Examples:
• The ability to created membrane-enclosed vesicles that can take in small molecules and assemble them into polymers which remain within the "cell".
• The ability to assemble functional ribosomes — the structures that convert the information encoded in the genome into the proteins that run life — from their components.
• In 2008, scientists at the J. Craig Venter Institute (JCVI) reported (in Science 29 February 2008) that they had succeeded in synthesizing a complete bacterial chromosome — containing 582,970 base pairs — starting from single deoxynucleotides. The entire sequence of the genome of Mycoplasma genitalium was already known. Using this information, they synthesized some 10,000 short oligonucleotides (each about 50 bp long) representing the entire genitalium genome and then - step by step - assembled these into longer and longer fragments until finally they had made the entire circular DNA molecule that is the genome.
Could this be placed in the cytoplasm of a living cell and run it?
The same team showed in the previous year (see Science 3 August 2007) that they could insert an entire chromosome from one species of mycoplasma into the cytoplasm of a related species and, in due course, the recipient lost its own chromosome (perhaps destroyed by restriction enzymes encoded by the donor chromosome) and began expressing the phenotype of the donor. In short, they had changed one species into another. But the donor chromosome was made by the donor bacterium, not synthesized in the laboratory. However, there should be no serious obstacle to achieving the same genome transplantation with a chemically-synthesized chromosome.
They've done it! The same team reported on 20 May 2010 in the online Science Express that they had successfully transplanted a completely synthetic genome — based on that of Mycoplasma mycoides — into the related species Mycoplasma capricolum. The recipient strain grew well and soon acquired the phenotype of the M. mycoides donor.
• In the 4 April 2014 issue of Science (Annaluru, N. et al.), a large group of researchers - including many undergraduates at Johns Hopkins University - reported that they had successfully replaced the natural chromosome 3 in Saccharomyces cerevisiae (which has 16 chromosomes) with a totally-synthetic chromosome.
Their procedure:
1. Chemically synthesize 69- to 79-nt oligonucleotides representing all the stretches of the known chromosome 9 sequence (which contains 316,617 base pairs) except for certain sequences such as transposons, many introns, and transfer RNA genes. In addition new, non-native, sequences such as loxP sites were included to aid future manipulations of the genome.
2. Stitch these together into blocks of ~750 base pairs. This step was done in vitro by undergraduates enrolled in the "Build A Genome" class at Johns Hopkins.
3. Introduce these into yeast cells which ligated them into stretches of DNA containing 2–4 thousand base pairs.
4. Introduce these stepwise into yeast cells so that they replace the equivalent portions of the native chromosome.
5. The result: a strain of yeast that grows just as well with its new artificial chromosome (now containing only 272,871 base pairs) as it did before. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/18%3A_Evolution/18.09%3A_The_Origin_of_Life.txt |
In 1975, NASA launched two unmanned landers towards the planet Mars:
• Viking 1 settled gently on Mars on July 20, 1976
• Viking 2 landed on the opposite side of the planet on September 3, 1976.
Both Viking missions carried equipment designed to look for evidence of life. There were five different types of instruments:
Television cameras.
No images suggesting the presence of life were ever seen.
A gas chromatograph combined with a mass spectrometer
This apparatus examined the martian soil for the presence of organic molecules. Even though sensitive to concentrations in the parts per billion (ppb) range, no organic matter was detected (except for traces of the solvents that had been used on earth to clean the equipment). Even if organic molecules could be formed on Mars, the intensity of the ultraviolet light at the surface would soon destroy them.
The Labeled-Release (LR) Experiment
Metabolism is a universal property of life on earth. The LR experiment was designed to look for evidence of catabolism by any microorganisms that might have been present in the Martian soil. In this experiment, a soil sample was incubated with a dilute soup of organic molecules (such as the amino acid glycine) which had been synthesized with the radioactive isotope 14C. Over a period of 10 days, the atmosphere above the sample was monitored for the appearance of radioactive gases such as carbon dioxide (CO2). The results:
• a burst of gas production when the medium was first added
• but not when the soil had been preheated to kill off any microorganisms it might have contained.
• However, gas production did not increase as time went on (as would be expected if living organisms were growing in the medium) and
• later additions produced no additional gas.
Thus most scientists concluded that the gas was produced by nonliving chemistry (brought about by oxidizing agents in the soil). This conclusion was strengthened by similar results using soils from a dry desert in northern Chile. (See Navarro-Gonzalez, R., et al, Science, 7 November 2003)
The Pyrolytic-Release (PR) Experiment
The PR experiment was designed to look for evidence of anabolism.; specifically whether there were any microorganisms in the martian soil that could synthesize complex organic molecules from carbon dioxide (CO2) and carbon monoxide (CO). In this experiment, a mixture of radioactive CO2 and CO was introduced into a vessel containing a soil sample.
Because anabolism requires energy and the most important source of that energy here on earth is sunlight (for photosynthesis), the incubation mixture was illuminated with a bright arc lamp.
After 5 days,
• any unreacted CO2 and CO was flushed out of the system and then
• the soil sample was heated to drive off any radioactive organic molecules that might have been synthesized.
The result: organic matter was detected in 7 of 9 runs. However, some positive results were achieved even on runs where the soil had first been heated to such a high temperature that any microorganisms present would have been killed (at least here on earth).
The Gas-Exchange (GEX) Experiment
In this experiment, a known mixture of gases was placed in the chamber along with the soil sample and then analyzed periodically to see if any gases (e.g. CO2) had disappeared from - or been added to - the mixture.
• In the first part of the experiment, nutrient broth was added to the chamber but not to the soil. There was a rapid release of
• large amounts of O2 (which would not be expected from heterotrophic breakdown of organic substrates). This soon subsided.
• smaller amounts of CO2 (an expected product of catabolism).
• One week later, more nutrient broth was added; this time directly to the soil. There was another, smaller, release of CO2 but no release of O2. The conclusion: the gases were formed by nonbiological chemistry (oxidizing agents again).
So what can we conclude from these data?
The LR, PR, and GEX experiments all produced some positive results.
However:
• All of these involved puzzling ambiguities, failing to behave as similar tests done on earthly soil samples would have.
• All were later shown to be reproducible here on earth by nonbiological chemistry.
So the Viking studies probably did not reveal the presence of life on Mars. But this is not the same as saying that life does not now nor ever did exist on Mars!
Perhaps:
• The upper layers of soil are inhospitable to life.
• Other places on Mars need to be sampled.
The Curiosity Rover
On 6 August 2012, NASA's Curiosity rover landed on Mars. So far, its sampling has revealed evidence of short chains of aliphatic hydrocarbons, chlorobenzene, an aromatic hydrocarbon and nitrates.
The Evidence from Martian Meteorites
Some meteorites are thought — because of their peculiar chemistry - to have reached earth from Mars. One of these ALH84001 (found in the Allan Hills of Antarctica in 1984) has been subjected to intensive analysis for ingredients suggestive of life processes.
In it have been found:
1. polycyclic aromatic hydrocarbons (PAHs). But in most of the Martian meteorites that have been examined, these and other organic molecules have been trapped inside where no living thing could have deposited them, and PAHs and other organic molecules are also found in meteorites arriving from elsewhere in the solar system.
2. minerals within the meteorite (e.g. carbonates, magnetite) that are formed by living organisms here on earth and appear to have been deposited in the rock of the meteorite at some later time in its history;
3. objects that under the scanning electron microscope look like fossils of tiny microorganisms. However, even the largest of these "nanofossils" have diameters of only 100 nanometers (nm) (0.1 µm, about the size of a ribosome). This is smaller than the smallest microorganisms here on earth (the mycoplasmas, with diameters of about 300 nm) and is smaller than the estimates of the minimum diameter (200 nm) needed to provide the volume necessary to build a living cell.
ALH84001 is thought to have landed in Antarctica some 13,000 years ago. But in July 2011, another Martian meteorite landed in the Moroccan desert. With much less time for terrestrial contamination to occur, it may help settle some of the controversy over the significance of the features found in ALH84001.
What would answer our question?
Organic matter is, despite its name, not the exclusive product of life. Many other meteorites contain organic matter and organic molecules can, of course, be synthesized in the laboratory from inorganic precursors. What does distinguish the organic molecules produced by life is the restriction to one enantiomer or the other. For example, all proteins synthesized by living things here on earth use L-amino acids exclusively. Synthesis of amino acids in the chemistry laboratory produces a 50:50 mixture (called a racemic mixture) of the L- and the D- forms. There is nothing to suggest that life couldn't work just as well with D-amino acids. What is unlikely is the ability of proteins (e.g. enzymes) to be able to function if they are made from a mixture of L- and D- enantiomers. So if martian soil should reveal the presence of all-L (or all-D) enantiomers, this would be powerful evidence that life had produced them.
However,
• Whether tested on Mars itself, or on samples returned to earth, rigorous care must be taken to ensure that there is no contamination by terrestrial molecules.
• There is some evidence that even nonbiological synthesis in space may favor one enantiomer over the other. Four amino acids in the Murchison meteorite, which no one suggests have a biological origin, show a 7–9% excess of the L-form over the D-form.
• Over time, even in the cold, dry climate of Mars, a population of L- (or D-) enantiomers will spontaneously break down into a racemic (50:50) mixture and thus obscure a biological origin.
The case for life on Mars - whether today or in the past - is neither proven nor disproven. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/18%3A_Evolution/18.10%3A_Mars.txt |
The endosymbiosis theory postulates that the mitochondria of eukaryotes evolved from an aerobic bacterium (probably related to the rickettsias) living within an archaeal host cell and the chloroplasts of red algae, green algae, and plants evolved from an endosymbiotic cyanobacterium living within a mitochondria-containing eukaryotic host cell.
The Evidence
• Both mitochondria and chloroplasts can arise only from preexisting mitochondria and chloroplasts. They cannot be formed in a cell that lacks them because nuclear genes encode only some of the proteins of which they are made.
• Both mitochondria and chloroplasts have their own genome, and it resembles that of bacteria not that of the nuclear genome.
• Both genomes consist of a single circular molecule of DNA.
• There are no histones associated with the DNA.
• Both mitochondria and chloroplasts have their own protein-synthesizing machinery, and it more closely resembles that of bacteria than that found in the cytoplasm of eukaryotes.
• The first amino acid of their transcripts is always fMet as it is in bacteria (not methionine [Met] that is the first amino acid in eukaryotic proteins).
• A number of antibiotics (e.g., streptomycin) that act by blocking protein synthesis in bacteria also block protein synthesis within mitochondria and chloroplasts. They do not interfere with protein synthesis in the cytoplasm of the eukaryotes.
• Conversely, inhibitors (e.g., diphtheria toxin) of protein synthesis by eukaryotic ribosomes do not - sensibly enough - have any effect on bacterial protein synthesis nor on protein synthesis within mitochondria and chloroplasts.
• The antibiotic rifampicin, which inhibits the RNA polymerase of bacteria, also inhibits the RNA polymerase within mitochondria. It has no such effect on the RNA polymerase within the eukaryotic nucleus.
The Mitochondrial Genome
The genome of human mitochondria contains 16,569 base pairs of DNA organized in a closed circle (Figure \(1\)). These encode 2 ribosomal RNA (rRNA), molecules, 22 transfer RNA (tRNA) molecules, and 13 polypeptides. The 13 polypeptides participate in building several protein complexes embedded in the inner mitochondrial membrane and include 7 subunits that make up the mitochondrial NADH dehydrogenase, 3 subunits of cytochrome c oxidase, 2 subunits of ATP synthase, and cytochrome b.
All these gene products are used within the mitochondrion, but the mitochondrion also needs >900 different proteins as well as some mRNAs and tRNAs encoded by nuclear genes. The proteins (e.g., cytochrome c and the DNA polymerases used within the mitochondrion) are synthesized in the cytosol and then imported into the mitochondrion.
The Chloroplast Genome
The genome of the chloroplasts found in Marchantia polymorpha (a liverwort, one of the Bryophyta) contains 121,024 base pairs in a closed circle. These make up some 128 genes which include:
• duplicate genes encoding each of the four subunits (23S, 16S, 4.5S, and 5S) of the ribosomal RNA (rRNA) used by the chloroplast
• 37 genes encoding all the transfer RNA (tRNA) molecules used for translation within the chloroplast. Some of these are represented in the figure by black bars (a few of which are labeled).
• 4 genes encoding some of the subunits of the RNA polymerase used for transcription within the chloroplast (3 of them shown in blue)
• a gene encoding the large subunit of the enzyme RUBISCO (ribulose bisphosphate carboxylase oxygenase)
• 9 genes for components of photosystems I and II
• 6 genes encoding parts of the chloroplast ATP synthase
• genes for 19 of the ~60 proteins used to construct the chloroplast ribosome
• All these gene products are used within the chloroplast, but all the chloroplast structures also depend on proteins RUBISCO, for example, the enzyme that adds CO2 to ribulose bisphosphate to start the Calvin cycle, consists of multiple copies of two subunits:
• Encoded by nuclear genes translated in the cytosol, and imported into the chloroplast.
• A large one encoded in the chloroplast genome and synthesized within the chloroplast, and a small subunit encoded in the nuclear genome and synthesized by ribosomes in the cytosol. The small subunit must then be imported into the chloroplast.
• The arrangement of genes shown in the figure is found not only in the Bryophytes (mosses and liverworts) but also in the lycopsids (e.g., Lycopodium and Selaginella). In all other plants, however, the portion of DNA bracketed by the red arrows on the left is inverted. The same genes are present but in inverted order. The figure is based on the work of Ohyama, K., et al., Nature, 322:572, 7 Aug 1986; and Linda A. Raubeson and R. K. Jansen, Science, 255:1697, 27 March 1992.
• The evolution of the eukaryotic chloroplast by the endosymbiosis of a cyanobacterium in a mitochondria-containing eukaryotic host cell led to the evolution of the green algae and plants as described above, red algae, and glaucophytes; a small group of unicellular algae.
Secondary Endosymbiosis: Eukaryotes Engulfing Eukaryotes
The Nucleomorph
Once both heterotrophic and photosynthetic eukaryotes had evolved, the former repeatedly engulfed the latter to exploit their autotrophic way of life. Many animals living today engulf algae for this purpose. Usually the partners in these mutualistic relationships can be grown separately. However, a growing body of evidence indicates that the chloroplasts of some algae have not been derived by engulfing cyanobacteria in a primary endosymbiosis like those discussed above, but by engulfing photosynthetic eukaryotes (Figure 18.11.3). This is called secondary endosymbiosis. It occurred so long ago that these endosymbionts cannot be cultured away from their host.
In two groups, the eukaryotic nature of the endosymbiont can be seen by its retention of a vestige of a nucleus (called its nucleomorph). A group of unicellular, motile algae called cryptomonads appear to be the evolutionary outcome of a nonphotosynthetic eukaryotic flagellate (i.e., a protozoan) engulfing a red alga by endocytosis. Another tiny group of unicellular algae, called chlorarachniophytes, appear to be the outcome of a flagellated protozoan having engulfed a green alga.
The result in both cases: a motile, autotrophic cell containing its own nucleus, its own mitochondria, and its own endoplasmic reticulum. The latter of which contains the endosymbiont with:
• its own plasma membrane
• its own cytoplasm, the periplastid space
• its own ribosomes
• its own chloroplast, and
• its nucleomorph - only a vestige of its original nucleus, but still surrounded by a nuclear envelope perforated with nuclear pore complexes and containing a tiny but still-functioning genome.
The Four Genomes of Guillardia theta
The cryptomonad Guillardia theta contains four different genomes:
• its own nuclear genome; by far the largest with 87.2x106 base pairs (bp) of DNA
• the genome of its mitochondria (48,000 bp)
• the genome of the chloroplast in its endosymbiont (121,000 bp)
• the genome of the nucleomorph (551,264 bp)
Susan Douglas and her colleagues reported (in the 26 April 2001 issue of Nature) the completely-sequenced genome of the nucleomorph.
• It contains 3 small chromosomes with
• 47 genes for nonmessenger RNAs (rRNA, tRNA, snRNA)
• 464 genes for messenger RNA; that is, encoding proteins such as
• 65 proteins for its own ribosomes
• 30 for its chloroplast (a small fraction of the hundreds needed)
• a variety of proteins needed within the nucleomorph, including
• DNA licensing factors
• histones
• proteins needed for DNA replication (but no genes for DNA polymerases, which must be translated by and imported from the host ribosomes)
The genes are crowded closely on the three chromosomes. In fact, 44 of them overlap each other. Only 17 genes contain introns, and these are very small.
Genome Interactions in Guillardia theta
Millions of years of evolution have resulted in a complex but precisely-orchestrated array of interactions between the 4 genomes. For example:
• The chloroplast needs proteins synthesized by 3 different genomes: its own, the nucleomorph's, and the host's.
• The nucleomorph genome has given up all (but one) of its genes encoding enzymes for general metabolic functions; the endosymbiont now depends on those encoded by the host nucleus.
• The nucleomorph itself also depends on genes (e.g., for DNA polymerases) residing in the host nucleus.
The Apicoplast
The apicoplast (short for "apicomplexan plastid") is a solitary organelle found in the apicomplexan protists: "sporozoans" like Plasmodium falciparum (and the other agents of malaria) and Toxoplasma gondii.
Features:
• Essential - the organisms cannot survive without it.
• Encased by 4 membranes.
• Contains its own genome, a circular molecule of DNA (35,000 base pairs) which encodes
• ~ 30 proteins
• a full set of tRNAs plus some other RNAs
• Only a few functions have been discovered, but these include
• anabolic metabolism such as the synthesis of fatty acids
• repair, replication, transcription, and translation of its genes
• Clearly 30 proteins are not enough to accomplish so many functions so the apicoplast has to import from the cytosol ~500 nuclear-encoded proteins.
The apicoplast is the product of an ancient endosymbiosis in which the eukaryotic ancestor engulfed a unicellular alga - probably a red alga - with a solitary chloroplast. Over time, the nucleus was lost (no residual nucleomorph) as well as many features of the chloroplast (including its ability to perform photosynthesis).
Secondary Symbiosis can Still Occur
Two Japanese scientists have discovered a heterotrophic flagellate that engulfs a unicellular green alga that lives freely in the surrounding water. Once inside, the alga loses its flagella and cytoskeleton; the host loses its feeding apparatus. Moreover, the host switches from heterotrophic to autotrophic nutrition (photosynthesis) and the host becomes capable of phototaxis. When the host divides by mitosis, only one daughter cell gets the plastid. The other cell regrows the feeding apparatus and is ready to engulf another alga. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/18%3A_Evolution/18.11%3A_Endosymbiosis.txt |
History of life as revealed by the fossil record
With help from molecular phylogenies:
Eras Periods Epochs Aquatic Life Terrestrial Life
With approximate starting dates in millions of years ago in parentheses. Geologic features in green
Cenozoic (66)
The "Age of
Mammals"
Quaternary (2.6) Holocene Humans in the new world
Pleistocene Periodic glaciation First humans
Continental drift continues
Neogene (23) Pliocene Atmospheric oxygen reaches today's level (21%) Hominids
Miocene Adaptive radiation of birds, continued radiation of mammals
Paleogene (66) Oligocene All modern groups present
Eocene
Paleocene
Mesozoic (251)
The "Age
of Reptiles"
Cretaceous (146) Still attached: N. America & N. Europe; Australia & Antarctica; Mass extinction of both aquatic and terrestrial life at the end
Modern bony fishes Extinction of dinosaurs and pterosaurs; first snakes
Extinction of ammonites, plesiosaurs, ichthyosaurs Rise of angiosperms
Africa & S. America begin to drift apart
Jurassic (200) Plesiosaurs, ichthyosaurs abundant; first diatoms Archaeopteryx; dinosaurs dominant but mammals (Eutheria) begin to diversify
Ammonites again abundant First lizards
Skates, rays, and bony fishes abundant Adaptive radiation of dinosaurs
Pangaea splits into Laurasia and Gondwana; atmospheric oxygen drops to ~13%
Triassic (251) Mass extinctions at the end. Mass extinctions at the end.
First mammals
Adaptive radiation of reptiles: thecodonts, therapsids, turtles, crocodiles, first dinosaurs
Ammonites abundant at first
Rise of bony fishes
Paleozoic (542) Permian (299) Periodic glaciation and arid climate; atmospheric oxygen reaches ~30%. Volcanic eruptions killed off 90% of marine species at end.
Extinction of trilobites Reptiles abundant. Cycads, conifers, ginkgos
Pennsylvanian (320) Warm, humid climate
Together
the Pennsylvanian
and Mississippian
make up the
"Carboniferous";
also called the
"Age of Amphibians"
Ammonites, bony fishes First reptiles
Coal swamps
Mississippian (359) Adaptive radiation of sharks Forests of lycopsids, sphenopsids, and seed ferns
Amphibians abundant
Adaptive radiation of the insects (Hexapoda)
Atmospheric oxygen begins to rise as organic matter is buried, not respired
Devonian (416)
The "Age of Fishes"
Extensive inland seas Cartilaginous and bony fishes abundant. Ammonites, nautiloids, ostracoderms, eurypterids Ferns, lycopsids, and sphenopsids
First gymnosperms
First amphibians
Silurian (443) Mild climate; inland seas First bony fishes First myriapods and chelicerates
Ordovician (485) Mild climate, inland seas Trilobites abundant Fungi present
First plants (liverworts?) First insects
Cambrian (541) First vertebrates (jawless fishes). Eurypterids, crustaceans
mollusks, echinoderms, sponges, cnidarians, annelids, and tunicates present. Trilobites dominant.
No fossils of terrestrial eukaryotes, but phylogenetic trees suggest that lichens, mosses, perhaps even vascular plants were present.
Periodic glaciation
Proterozoic (2500) Ediacaran
(635)
Fossil evidence of multicellular algae, fungi, and bilaterian invertebrates
Evidence of eukaryotes
~1.8 x109 years ago
Archaean (3600) Evidence of archaea and bacteria
~3.5 x109 years ago
The Geologic and Evolutionary Record
A remarkable feature of the table above is how often evolutionary changes coincided with geologic changes on the earth. But consider that changes in geology (e.g., mountain formation or lowering of the sea level) cause changes in climate, and together these alter the habitats available for life. Two types of geologic change seem to have had especially dramatic effects on life: continental drift and the impact of asteroids
Continental Drift
A body of evidence, both geological and biological, supports the conclusion that 200 million years ago, at the start of the Mesozoic era, all the continents were attached to one another in a single land mass, which has been named Pangaea. This drawing of Pangaea (adapted from data of R. S. Dietz and J. C. Holden) is based on a computer-generated fit of the continents as they would look if the sea level were lowered by 6000 feet (~1800 meters). During the Triassic, Pangaea began to break up, first into two major land masses:
• Laurasia in the Northern Hemisphere
• Gondwana in the Southern Hemisphere.
The present continents separated at intervals throughout the remainder of the Mesozoic and through the Cenozoic, eventually reaching the positions they have today. Let us examine some of the evidence.
Shape of the Continents
The east coast of South America and the west coast of Africa and are strikingly complementary. This is even more dramatic when one tries to fit the continents together using the boundaries of the continental slopes, e.g., 6000 feet (~1800 meters) down, rather than the shorelines.
Geology
• In both mineral content and age, the rocks in a region on the east coast of Brazil match precisely those found in Ghana on the west coast of Africa.
• The low mountain ranges and rock types in New England and eastern Canada appear to be continued in parts of Great Britain, France, and Scandinavia.
• India and the southern part of Africa both show evidence of periodic glaciation during Paleozoic times (even though both are now close to the equator). The pattern of glacial deposits in the two regions not only match each other but also glacial deposits found in South America, Australia, and Antarctica.
Fossils
• Fossil reptiles found in South Africa are also found in Brazil and Argentina.
• Fossil amphibians and reptiles found in Antarctica are also found in South Africa, India, and China.
• Most of the marsupials alive today are confined to South America and Australia. But if these two continents were connected by Antarctica in the Mesozoic, one might expect to find fossil marsupials there. In March 1982, this prediction was fulfilled with the discovery in Antarctica of the remains of Polydolops, a 9-ft (2.7 m) marsupial.
The Impact Hypothesis
The Cretaceous period, the last period of the Mesozoic, marked the end of the Age of Reptiles. It was followed by the Cenozoic era, the Age of Mammals. Although extinctions have occurred throughout the history of life, an extraordinary number of them occurred in a relatively brief period at the end of the Cretaceous. Why?
The Alvarez Theory
Louis Alvarez, his son Walter, and their colleagues proposed that a giant asteroid or comet striking the earth some 66 million years ago caused the massive die-off at the end of the Cretaceous. Presumably, the impact generated so much dust and gases that skies were darkened all over the earth, photosynthesis declined, and worldwide temperatures dropped. The outcome was that as many as 75% of all species — including all dinosaurs — became extinct.
The key piece of evidence for the Alvarez hypothesis was the finding of thin deposits of clay containing the element iridium at the interface between the rocks of the Cretaceous and those of the Paleogene period (called the K-Pg boundary after the German word for Cretaceous). Iridium is a rare element on earth (although often discharged from volcanoes), but occurs in certain meteorites at concentrations thousands of times greater than in the earth's crust.
After languishing for many years, the Alvarez theory gained strong support from the discovery in the 1990s of the remains of a huge (180 km in diameter) crater in the Yucatan Peninsula that dated to 65 million years ago.
The abundance of sulfate-containing rock in the region suggests that the impact generated enormous amounts of sulfur dioxide (SO2), which later returned to earth as a bath of acid rain. A smaller crater in Iowa, formed at the same time, many have contributed to the devastation. Perhaps during this period the earth passed through a swarm of asteroids or a comet and the repeated impacts made the earth uninhabitable for so many creatures of the Mesozoic.
Other Impacts
A mass extinction of non-dinosaur reptiles occurred earlier, at the end of the Triassic. It was followed by a great expansion in the diversity of dinosaurs. The recent discovery of a layer enriched in iridium in rocks formed at the boundary between the Triassic and Jurassic suggests that impact from an asteroid or comet may have been responsible then just as it was at the K-Pg boundary.
The largest extinction of all time occurred still earlier at the end of the Permian period. There is evidence off the coast of Australia that a huge impact there may have contributed to the extinctions at the Permian-Triassic (P-T) boundary. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/18%3A_Evolution/18.12%3A_Geologic_Eras.txt |
At least 1.7 million species of living organisms have been discovered, and the list grows longer every year (especially of insects in the tropical rain forest). How are they to be classified? Ideally, classification should be based on homology; that is, shared characteristics that have been inherited from a common ancestor. The more recently two species have shared a common ancestor, the more homologies they share and the more similar these homologies are. Until recent decades, the study of homologies was limited to anatomical structures and pattern of embryonic development. However, since the birth of molecular biology, homologies can now also be studied at the level of proteins and DNA.
Anatomical homology: an example
The figure shows the bones in the forelimbs of three mammals: human, whale, and bat (obviously not drawn to the same scale!). Although used for such different functions as throwing, swimming, and flying, the same basic structural plan is evident in them all. In each case, the bone shown in color is the radius. Body parts are considered homologous if they have
• the same basic structure
• the same relationship to other body parts
• develop in a similar manner in the embryo
It seems unlikely that a single pattern of bones represents the best possible structure to accomplish the functions to which these forelimbs are put. However, if we interpret the persistence of the basic pattern as evidence of inheritance from a common ancestor, we see that the various modifications are adaptations of the plan to the special needs of the organism. It tells us that evolution is opportunistic, working with materials that have been handed down by inheritance.
Protein Sequences
Protein sequencing provides a tool for establishing homologies from which genealogies can be constructed and phylogenetic trees drawn. Here are two examples.
Hemoglobins
An example of molecular homology.
The numbers represent the number of amino acid differences between the beta chain of human hemoglobin and the hemoglobins of the other species. In general, the number is inversely proportional to the closeness of kinship. All the values listed are for the beta chain except for the last three, in which the distinction between alpha and beta chains does not occur. The human beta chain contains 146 amino acid residues, as do most of the others.
Cytochrome c
Cytochrome c is part of the electron transport chain down which electrons are passed to oxygen during cellular respiration. Cytochrome c is found in the mitochondria of every aerobic eukaryote - animal, plant, and protist. The amino acid sequences of many of these have been determined, and comparing them shows that they are related. Human cytochrome c contains 104 amino acids, and 37 of these have been found at equivalent positions in every cytochrome c that has been sequenced. We assume that each of these molecules has descended from a precursor cytochrome in a primitive microbe that existed over 2 billion years ago. In other words, these molecules are homologous.
The first step in comparing cytochrome c sequences is to align them to find the maximum number of positions that have the same amino acid. Sometimes gaps are introduced to maximize the number of identities in the alignment (none was needed in this table). Gaps correct for insertions and deletions that occurred during the evolution of the molecule.
This table shows the N-terminal 22 amino acid residues of human cytochrome c with the corresponding sequences from six other organisms aligned beneath. A dash indicates that the amino acid is the same one found at that position in the human molecule. All the vertebrate cytochromes (the first four) start with glycine (Gly). The Drosophila, wheat, and yeast cytochromes have several amino acids that precede the sequence shown here (indicated by <<<). In every case, the heme group of the cytochrome is attached to Cys-14. and Cys-17 (human numbering). In addition to the two Cys residues, Gly-1, Gly-6, Phe-10, and His-18 are found at the equivalent positions in every cytochrome c that has been sequenced.
We assume that the more identities there are between two molecules, the more recently they have evolved from a common ancestral molecule and thus the closer the kinship of their owners. Thus the cytochrome c of the rhesus monkey is identical to that of humans except for one amino acid, whereas yeast cytochrome c differs from that of humans at 44 positions. (There are no differences between the cytochrome c of humans and that of chimpanzees.)
Phylogenetic trees
With such information, one can reconstruct an evolutionary history of the molecule and thus of their respective owners. This requires
• using the genetic code to determine the minimum number of nucleotide substitutions in the DNA of the gene needed to derive one protein from another
• a powerful computer program to search for the shortest paths linking the molecules together
The result is a phylogenetic tree. This one (the work of Walter M. Fitch and Emanuel Margoliash) shows the relationship between 20 species of eukaryotes. The numbers represent the minimum number of nucleotide substitutions in the gene for cytochrome c needed to produce these 20 proteins from a series of hypothetical ancestral genes at the various branching points (nodes).
The tree corresponds quite well to what we have long believed to be the evolutionary relationships among the vertebrates. But there are some anomalies. It indicates, for example, that the primates (humans and monkeys) split off before the split separating the kangaroo, a marsupial, from the other placental mammals. This is certainly wrong. But sequence analysis of other proteins can resolve such discrepancies.
Cytochrome c is an ancient molecule, and it has evolved very slowly. Even after more than 2 billion years, one-third of its amino acids are unchanged. This conservatism is a great help in working out the evolutionary relationships between distantly-related creatures like fish and humans.
But what of humans and the great apes? Their cytochrome c molecules are identical and can tell us nothing about evolutionary relationships. However, some proteins have evolved much more rapidly than cytochrome c, and these can be used to decipher recent evolutionary events. During blood clotting, short peptides are cut from fibrinogen converting it into insoluble fibrin. Once removed, these fibrinopeptides have no further function. They have been pretty much free from the rigors of natural selection and have, consequently, diverged rapidly during evolution. So they provide data useful in sorting out the twigs of phylogenetic trees of mammals, for example.
DNA-DNA Hybridization
As we saw in the comparison of human and kangaroo cytochrome c, a single molecule provides only a narrow window for glimpsing evolutionary relationships.
The technique of DNA-DNA hybridization provides a way of comparing the total genome of two species. Let us examine the procedure as it might be used to assess the evolutionary relationship of species B to species A:
• The total DNA is extracted from the cells of each species and purified.
• For each, the DNA is heated so that it becomes denatured into single strands (ssDNA).
• The temperature is lowered just enough to allow the multiple short sequences of repetitive DNA to rehybridize back into double-stranded DNA (dsDNA).
• The mixture of ssDNA (representing single genes) and dsDNA (representing repetitive DNA) is passed over a column packed with hydroxyapatite. The dsDNA sticks to the hydroxyapatite; ssDNA does not and flows right through. The purpose of this step is to be able to compare the information-encoding portions of the genome — mostly genes present in a single copy — without having to worry about varying amounts of noninformative repetitive DNA.
• The ssDNA of species A is made radioactive.
• The radioactive ssDNA is then allowed to rehybridize with nonradioactive ssDNA of the same species (A) as well as — in a separate tube — the ssDNA of species B.
• After hybridization is complete, the mixtures (A/A) and (A/B) are individually heated in small (2°–3°C) increments. At each higher temperature, an aliquot is passed over hydroxyapatite. Any radioactive strands (A) that have separated from the DNA duplexes pass through the column, and the amount is measured from their radioactivity.
• A graph showing the percentage of ssDNA at each temperature is drawn.
• The temperature at which 50% of the DNA duplexes (dsDNA) have been denatured (T50H) is determined.
As the figure shows, the curve for A/B is to the left of A/A, i.e., duplexes of A/B separated at a lower temperature than those of A/A. The sequences of A/A are precisely complementary so all the hydrogen bonds between complementary base pairs (A-T, C-G) must be broken in order to separate the strands. But where the gene sequences in B differ from those in A, no base pairing will have occurred and denaturation is easier.
Thus DNA-DNA hybridization provides genetic comparisons integrated over the entire genome. Its use has cleared up several puzzling taxonomic relationships. DNA-DNA hybridization can also be used to compare genomes of mixed populations of organisms. For example, when all the bacteria are extracted from 10 g of uncontaminated soil (there are about 1010 cells in it!), the DNA extracted and purified from the bacteria and subjected to DNA-DNA hybridization analysis, the resulting curves indicate that there are over a million different species in the soil sample, although the population is dominated by only a few of these.
Chromosome Painting
Another way to compare entire genomes is to attach a fluorescent label to the DNA of individual chromosomes of one species (e.g., human) and expose the chromosomes of another species to it. Regions of gene homology will hybridize taking up the fluorescent label and the "painted" chromosomes can be examined under the microscope.
The method is a modification of fluorescence in situ hybridization (FISH) and is also called Zoo-FISH.
Chromosome painting has shown, for example, that large sections of human chromosome 6 (which includes hundreds of genes in the major histocompatibility complex (MHC) have their counterpart; i.e. homologous genes, in
• chromosome 5 of the chimpanzee
• chromosome B2 of the domestic cat
• chromosome 7 of the pig
• chromosome 23 of the cow
Comparing DNA Sequences
Proteins are the expression of genes so why not compare the actual gene sequences? There are several advantages:
• DNA is much easier to sequence than protein.
• Genes contain sites that are much freer to change during evolution than protein sequences are. These include:
• nucleotides that produce synonymous codons. For example, even if the amino acid at position 20 in two proteins is the same, the codons for that amino acid might be different in the two species.
• Introns and flanking sequences. These regions are relatively free to vary without hurting the final protein product. In other words, these regions of the genome are under much less pressure from natural selection.
• DNA is more stable than protein in the environment. This raises the possibility of doing DNA sequencing on the remains of extinct organisms. Neaderthal remains over 38,000 years old have yielded samples of DNA that were successfully sequenced.
Some of the most informative studies using comparative DNA sequencing have been done with
• rDNA genes; that is, the genes encoding the rRNA molecules (usually of the small subunit (18S in eukaryotes; 16S in bacteria) of the ribosome.
• genes on mitochondrial DNA (mtDNA).
In both cases, the genes are present in multiple copies making their isolation easier.
Cladistics
Ideally, a system of classification should reflect the genealogies of the organisms. Darwin realized this when he wrote: "our classifications will come, as far as they can be so made, genealogies". A classification based strictly on the rule that all members of a group must have shared a common ancestor more recently than they have with any species outside the group is called cladistics.
This phylogenetic tree or cladogram depicts the evolutionary relationships of 4 hypothetical species.
• They are all descended from an ancestor with 5 traits (1,2,3,4,5) to be used in drawing the tree.
• Over the course of time, 3 speciation events occurred producing the branches.
• During this time, several of the ancestral traits evolved into a modified or derived form; each one indicated by a different color.
• Taxonomists who use cladistic methods have created an extraordinary vocabulary to help them (not necessarily us).
• Ancestral traits are called plesiomorphic (shown here as black numbers).
• Derived traits are called apomorphic (shown here as colored numbers). All the members of a clade must share one or more apomorphic traits not found in any other species.
• Derived traits shared by two or more species are called synapomorphic. Here species A and B share the synapomorphic trait designated with a blue 3.
• Ancestral traits shared by two or more species are called symplesiomorphic. Here, the trait shown as black 1 is a symplesiomorphic trait retained by all 4 species.
• Note that in comparing the species, the more recent the common ancestor, the more apomorphic traits they share. Thus species C and D share 4 of the 5 traits but only three (1, 2, and 5) with species A and only two (1 and 5) with species B.
Even if we reconstruct a precise genealogy and draw a phylogenetic tree to represent it, taxonomic problems may still remain.
1. The species is the only taxonomic category that exists in nature. All higher categories (e.g., genus, family, and order) are purely arbitrary. They are created by taxonomists. For example,
• Should species C and D be placed in a single genus with A and B in another?
• Or are all four sufficiently closely related that they belong in a single genus?
• Or are all four so distantly related that they should be placed in separate genera?
• Note that none of these options (and others besides) violates the fundamental rule that all the members of any one group (or "clade") must have had a common ancestor more recent than any they share with species in other groups.
Those taxonomists who are particularly impressed by the differences between species tend to increase the number of higher categories. Those with this bias are known fondly as "splitters". "Lumpers", those taxonomists who marvel at the uniformities they see among species, tend to create fewer higher categories. Thus, splitters might put each of the 4 species in separate genera while lumpers would put them in a single genus.
1. Classifications based strictly on cladistics are too complex for convenience. In principle, a separate category has to be created for all the branches derived from each node of the tree. The box shows the conventional classification of Homo sapiens (in the order Primates of the class Mammalia). Compare it with the graphic above the box showing a classification of just the primates based more closely on cladistics.
Example
Scientific names. The Swedish naturalist Carolus Linnaeus - the "father of taxonomy" - created the system for naming species that is used by biologists throughout the world. The scientific name of each species consists of two parts:
• the name of the genus to which it is assigned and
• the "specific epithet" which identifies the particular species within the genus.
Latin names were used by Linnaeus, but so many species have been discovered since then that now taxonomists simply coin new words and cast the genus name in the form of a Latin noun and the specific epithet as a Latin adjective. By tradition, both names are printed in italics, and the genus name is capitalized, but not the specific epithet. Note, too, that the characters of the Roman alphabet are always used even by biologists in countries where different characters are used for ordinary purposes.
Here is a description of a common jellyfish as it appears in a Japanese guide to marine life.
Reprinted with permission from Hoikusha Publishing Co., Ltd., Tokyo, Japan
1. A classification based strictly on evolutionary kinship (cladistics) also may often seem to violate common sense. Thus a phylogenetic tree showing the evolutionary history that gave rise to the salmon (a fish), the lungfish, and the cow requires - according to cladistics - that the lungfish and cow be placed in a clade separate from the salmon. Even though the lungfish is a fish, the cow has shared a common ancestor with it more recently than its common ancestor with the salmon. Although it is traditional to classify the lungfish and the salmon together in the class Pisces (fishes), and to assign the cow to the class Mammalia, this violates the rule of cladistics (so Pisces is said to be a paraphyletic group). The lungfish and the cow with their apomorphic traits of internal nostrils and epiglottis are descended from a common ancestor (red arrow) that is also the ancestor of all land-living vertebrates (including ourselves!).
Even Darwin recognized that kinship alone was not always enough for a sound taxonomy so he added a second criterion - degree of similarity - to be used in assigning species to a taxonomic category.
1. Deducing the evolutionary history of animals is particularly difficult because all the 24 or more phyla of animals appeared within a short time before and during the Cambrian and have since evolved along separate lines. This means that all the branches on the phylogenetic tree are long and bunched so closely at their base that it is difficult to determine their relationships.
2. Computer power. More data would help, but as more data become available, the ability of computer programs to sort out the most likely tree becomes overwhelmed.
3. Changing rate of evolution. There is considerable evidence that mutation rates are not steady from branch to branch in phylogenetic trees. Thus a branch based on molecules that have evolved rapidly would seem longer than otherwise.
4. Back mutations. These mask the changes that preceded them and make branches look shorter than they should be.
5. Gene transfer between species. The recent availability of complete gene sequences for many bacteria have revealed genes that appear to have passed from one group to another rather than having been descended from a common ancestor. Most of these "horizontal" gene transfers are between two different species of bacteria, but the gene sequence of Mycobacterium tuberculosis reveals 8 genes that it appears to have picked up from its human host! So many horizontal gene transfers have occurred that some bacterial taxonomists despair that a proper phylogenetic tree can ever be deduced for them.
6. Convergent evolution. Evolution in which two species from different genealogies come to resemble each other is called convergent evolution and structures that resemble each other superficially (and may serve the same function) are called analogous.
There are many examples of marsupial mammals in Australia which bear a striking resemblance to placental mammals of Europe and North America. The North American woodchuck or groundhog and the Australian wombat (photo courtesy of the Australian News and Information Bureau), for examples, look superficially to be close relatives. But their similarities are analogous, not homologous, and have arisen as a result of similar selection pressures in similar ecological niches. The wombat has no placenta, cares for its young in a pouch as other marsupials do, and should be classified with them. In fact we are more closely related to the North American woodchuck than the wombat is!
In the language of cladistics, the wombat is placed in a clade with all marsupials because they share the marsupial pouch (an apomorphic trait) but are nonetheless mammals because they, too, have hair (a plesiomorphic trait).
Convergent evolution also occurs at the level of molecules.
Examples:
• Cows and langur monkeys both synthesize a lysozyme that share the same activity, but comparison of their amino acid sequences indicates that each has evolved from a different ancestral molecule.
• Cows and the bacterium Yersinia both synthesize a tyrosine phosphatase with similar three-dimensional structures around their active site and similar activity. However, each has evolved from a totally different ancestral molecule.
• The bacterium Bacillus subtilis synthesizes a serine protease that acts just like those synthesized by mammals but not only has an entirely different primary structure but its three-dimensional structure (tertiary) structure is different as well.
• Representatives of four different orders of insects, orders that last shared a common ancestor 300 million years ago, have independently evolved an identical point mutation in their Na+/K+ ATPase which protects it from inactivation by the cardiac glycosides in the plants on which they feed. Link to an illustrated discussion of how this mutation can lead to aposematic coloration and mimicry. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/19%3A_The_Diversity_of_Life/19.01%3A_Eukaryotic_Life/19.1.01%3A_Taxonomy.txt |
What are protists?
• They are eukaryotes because they all have a nucleus.
• Most have mitochondria although some have later lost theirs. Mitochondria were derived from aerobic alpha-proteobacteria that once lived within their cells.
• Many have chloroplasts with which they carry on photosynthesis. Chloroplasts were derived from photosynthetic cyanobacteria living within their cells.
• Many are unicellular and all groups (with one exception) contain some unicellular members.
• The name Protista means "the very first", and some of the 80-odd groups of organisms that we classify as protists may well have had long, independent evolutionary histories stretching as far back as 2 billion years. But genome analysis added to other criteria show that others are derived from more complex ancestors; that is, are not "primitive" at all.
• Genome analysis also shows that many of the groups placed in the Protista are not at all closely related to one another; that is, the protists do not represent a single clade.
• So we consider them here as a group more for our convenience than as a reflection of close kinship, and a better title for this page would be "Eukaryotes that are neither Animals, Fungi, nor Plants".
The Euglenozoa
Most Euglenozoa are unicellular. Many swim by means of a single flagellum. They are not encased in a cell wall so they are flexible as well as motile. Euglena is a typical member of the group (which numbers about 1600 species). Because some members of the group (like Euglena) have chloroplasts, these organisms used to be called "Euglenophytes", but in fact they are neither plants ("phytes") nor animals ("zoa"). Rather — like the other organisms on this page — they are the living descendants of some of the very earliest eukaryotes. Trypanosoma brucei, the cause of African sleeping sickness in humans, is a member of the group. The electron micrograph shows T. brucei as it occurs in the salivary gland of the tsetse fly ready to be injected into the mammalian host when the fly bites. The specimen is 12 µm long.
In Latin America, Trypanosoma cruzi, another member of the group, is the cause of Chagas disease in humans.
Ciliates, Sporozoans, and Dinoflagellates: the Alveolates
These three phyla are grouped in a clade called the alveolates because they all have a system of saclike structures ("alveoli") on the inner surface of their plasma membrane as well as close homology in their gene sequences.
Ciliates
The ciliates move by the rhythmic beating of their cilia. Although single-celled, some are large enough to be seen with the naked eye. In fact, the tiny parasitic wasp Megaphragma mymaripenne, with its tens of thousands of cells (4,600 neurons alone), is no larger than Paramecium. They feed by sweeping a stream of particle-laden water through a "mouth" and "gullet" and into a food vacuole. Undigested wastes are discharged at a permanent site. Fresh water ciliates cope with the continuous influx of water from their hypotonic surroundings by pumping it out with one or more contractile vacuoles. Parasitic ciliates, which live in isotonic surroundings, have no contractile vacuole. All of this rightly suggests that although they are unicellular, there is nothing rudimentary about the ciliates. Their single cell is far more elaborate in its organization than any cell out of which multicellular organisms are made. Examples: Paramecium, Stentor, Vorticella, Tetrahymena thermophila.
Sporozoans (Apicomplexa)
The members of this group share an "apical complex" of microtubules at one end of the cell (hence the name that many prefer to the old name of sporozoans). All the members of the phylum are parasites. The genus Plasmodium causes malaria, one of the greatest scourges of humans. There are 4 species that infect humans of which Plasmodium falciparum is the most dangerous. Malaria has probably caused more human deaths than any other infectious disease; even today it is estimated to kill a million people a year in the sub-Saharan Africa. The organism is transmitted from human to human through the bite of mosquitoes of the genus Anopheles.
The diagram shows the Plasmodium life cycle.
• The mosquito bite injects sporozoites into the human host.
• These invade the liver where they develop into merozoites.
• The merozoites invade red blood cells where they reproduce.
• Periodically, they all break out of the red cells together bringing on the chills and fever characteristic of the disease.
• Eventually some merozoites develop into either male or female gametocytes.
• These will die unless they are sucked up by the bite of an anopheline mosquito.
• Once in the stomach of the mosquito, the gametocytes form gametes: sperm and eggs.
• These fuse to form zygotes.
• The zygote invades the stomach wall of the mosquito forming thousands of sporozoites.
• These migrate to the salivary gland, ready to be injected into a new human host.
• Most forms of malaria are chronic. The organisms may coexist with their host for years (but cannot complete their life cycle there).
Toxoplasma gondii is another parasitic member of this group. Plasmodium, Toxoplasma, and some of the other members of this group contain a membrane-enclosed organelle called the apicoplast. They seem to have inherited it from a common ancestor that acquired it by engulfing a chloroplast.
Dinoflagellates
There are about 1000 species of dinoflagellates. Most are unicellular. Most use chlorophylls a and c. Unlike most eukaryotes, they lack histones on their chromosomes and have a simpler form of mitosis. They do have the eukaryotic type ("9 + 2") of flagellum (two of them in fact). Occasionally they reproduce explosively, creating poisonous red tides that may cause extensive kills of marine fish and make filter-feeding marine animals like clams unfit for human consumption.
The Stramenopiles
These organisms belong to a single clade, the stramenopiles (a/k/a heterokonts). There are four members in this group - diatoms, golden algae, brown algae and water molds. The first three members share:
• a yellow-brown pigment (which gives them their color). It is a carotenoid called fucoxanthin.
• chlorophylls a and c
• All four of them (plus a number of other groups not listed) share genes closely-homologous to those in both green and red algae. This suggests that they are all descended from a heterotrophic eukaryotic ancestor that acquired both a green alga and a red alga by a secondary endosymbiosis. (While the water molds no longer are photosynthetic, they still retain both green and red alga genes.)
Diatoms
Diatoms are unicellular. Their cell wall or shell is made of two overlapping halves. These are impregnated with silica and often beautifully ornamented. The photo (courtesy of Turtox) is of Arachnoidiscus ehrenbergi magnified some 400 times. Diatoms are major producers in aquatic environments; that is, they are responsible for as much as 40% of the photosynthesis that occurs in fresh water and in the oceans. They serve as the main base of the food chains in these habitats, supplying calories to heterotrophic protists and small animals. These, in turn, feed larger animals.
Golden Algae (Chrysophyta)
• Most are unicellular.
• Found in fresh water.
• Important producers in some aquatic food chains.
• In low light conditions, may lose their chlorophyll and turn heterotrophic feeding on bacteria and/or diatoms.
• Over 1000 species alive today; many more in the fossil record.
Brown Algae (Phaeophyta)
• The rockweeds and kelps. Some kelps grow as long as 30 meters.
• All are multicellular although without much specialization of cell types.
• Most are found in salt water.
• Used for food in some coastal areas of the world and harvested in the U. S. for fertilizer and as a source of iodine.
Water Molds (Oomycetes)
As their name suggests, water molds were once considered to be fungi. But unlike fungi, the cell wall of water molds is made of cellulose, not chitin. Furthermore, their gene sequences are very different from those of fungi (and most closely related to those of diatoms, golden and brown algae).
Some notable water molds:
• Some species (e.g., Saprolegnia, Achyla) are parasites of fishes and can be a serious problem in fish hatcheries.
• Downy mildews damage grapes and other crops.
• Phytophthora infestans, the cause of the "late blight" of potatoes. In 1845 and again in 1846, it was responsible for the almost total destruction of the potato crop in Ireland. This led to the great Irish famine of 1845–1860. During this period, approximately 1 million people starved to death and many more emigrated to the New World. By the end of the period, death and emigration had reduced the population of Ireland from 9 million to 4 million.
• Phytophthora ramorum, which is currently killing several species of oaks in California.
Red Algae
The red algae are almost exclusively marine. Some are unicellular but most are multicellular. Approximately 6000 species have been identified. They are photosynthetic using chlorophyll a. Their closest relatives are the green algae and land plants. Like the cyanobacteria, they use as antenna pigments - phycoerythrin (which makes them red) and phycocyanin. They do not have the eukaryotic "9+2" flagellum. Some are used as food in coastal regions of Asia. Agar, the base for culturing bacteria and other microorganisms, is extracted from a red alga.
Slime Molds (Mycetozoa)
Cellular Slime Molds
The organisms in this group have a complex life cycle during the course of which they go through unicellular, multicellular, funguslike (form spores) and protozoanlike (amoeboid) stages. Thousands of individual amoebalike cells aggregate into a slimy mass - each cell retaining its identity (unlike plasmodial slime molds). The aggregating cells are attracted to each other by the cyclic AMP (cAMP) that they release.
With the exception of one species that causes powdery scab on potatoes, these organisms are of little economic importance. However, their combination of traits makes them of great scientific interest. Molecular phylogenies place them in the same clade as animals (metazoa) and fungi.
Plasmodial (Acellular) Slime Molds (Myxomycetes)
At one stage in their life cycle, these organisms consist of a spreading, slimy, multinucleate mass called a plasmodium that moves slowly over its substrate (e.g., a rotting log) engulfing food and growing as it does so. Eventually, the plasmodium develops stalks that produce and release spores. If the spores land in a suitable location, they germinate forming single cells that move by both flagella and pseudopodia. These fuse in pairs and start forming a new plasmodium.
The left photo (courtesy of Prof. I. K. Ross) shows the plasmodial stage of Stemonitis just before it formed sporangia. The right photo (courtesy of Turtox) shows the fully developed sporangia of Stemonitis.
Physarum polycephalum, another member of this group, is the subject of many laboratory studies.
Protists without typical mitochondria
There are several groups of protists that were long thought to have no mitochondria. However, most (perhaps all) had them in the past. Today, only remnants of their ancestor's mitochondria - called mitosomes remain.
Some examples are:
• Microsporidia
• All are unicellular obligate intracellular parasites.
• Many are pathogenic in insects (one is even marketed commercially as a biocontrol agent).
• Some contaminate drinking water supplies and can cause gastrointestinal upsets in humans. Microsporidia, such as Encephalitozoon cuniculi, are a common cause of diarrhea in AIDS patients. Encephalitozoon cuniculi has a tiny genome with only 1,997 protein-encoding genes — fewer than many bacteria (e.g., E. coli has 4,290). Obliged to live within the cells of its host, it has lost the genes for many important functions (e.g., the citric acid cycle) depending instead on its host.
• Fungi are their closest relatives.
• Entamoeba histolytica.
• Causes amebic dysentery, the third most common parasitic disease of humans (after malaria and schistosomiasis). Its closest relatives are the slime molds.
• Giardia intestinalis (also known as Giardia lamblia)
• Frequently encountered in public water supplies contaminated by animal feces. Causes diarrhea in humans. Avoids the host immune response by periodically changing its surface protein coat.
Choanoflagellates
These are single-celled (e.g., Monosiga), aquatic (both fresh water and marine) protists that have a single flagellum surrounded by a collar ("choano" = collar) of microvilli. Some (e.g., Proterospongia) form simple colonies during part of their life. The flagellum is used for swimming and also beats bacteria-containing water through the collar for feeding.
Sponges also use collar cells to filter food from the water. Not only does this suggest a close relationship between the two groups, but other evidence indicates that choanoflagellates are the closest protistan relatives of all animals (metazoa). Although single cells, they express genes for several proteins that are essential to cell-cell interactions in metazoans, such as
• cadherins (attach cells to each other)
• tyrosine kinases (used in many examples of cell-cell signaling)
What function these proteins have in the choanoflagellates is unknown. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/19%3A_The_Diversity_of_Life/19.01%3A_Eukaryotic_Life/19.1.02%3A_Protists.txt |
Although single-celled, there is nothing primitive or simple about these protists. Not only are they large for single cells (some can be seen by the unaided eye), but they contain organelles that parallel in function the organs of multicellular creatures. In fact, some biologists consider the ciliates to be acellular (not cellular) rather than unicellular in order to emphasize that their "body" is far more elaborate in its organization than any cell out of which multicellular organisms are made.
Although single-celled, there is nothing primitive or simple about these protists. Not only are they large for single cells (some can be seen by the unaided eye), but they contain organelles that parallel in function the organs of multicellular creatures. In fact, some biologists consider the ciliates to be acellular (not cellular) rather than unicellular in order to emphasize that their "body" is far more elaborate in its organization than any cell out of which multicellular organisms are made.
Ciliates have:
• At least one small, diploid (2n) micronucleus. It contains the entire genome but is not active in gene transcription.
• A large, polyploid macronucleus that contains the active genes that run the cell.
Sexual reproduction in Ciliates
• Two parents come together and two parents separate. What kind of reproduction is that? you may well ask.
But the process they have been through is the very essence of sexual reproduction - genetic recombination. The "offspring" are not the same as the parents. They are new individuals and their macronucleus will soon reflect that fact.
Ciliated protozoans have been the source of several important discoveries in biology, for example:
• The first ribozymes were found in Tetrahymena thermophila.
• Telomerase was also discovered in Tetrahymena thermophila.
19.1.04: Volvox
Volvox Reproduction
Volvox can reproduce both asexually and sexually. In asexual reproduction, the gonidia develop into new organisms that break out of the parent (which then dies). In sexual reproduction, the presence of an inducing chemical causes
• The gonidia of the males to develop into clusters of sperm.
• The gonidia of the females to develop into new spheres each of whose own gonidia develops into a pair of eggs.
• The sperm break out of the male parent and swim to the female where they fertilize her eggs.
• The zygotes form a resting stage that enables Volvox to survive harsh conditions.
The genome of Volvox carteri consists of 14,560 protein-encoding genes - only 4 more genes than in the single-celled Chlamydomonas reinhardtii! Most of its genes are also found in Chlamydomonas. The few that are not encode the proteins needed to form the massive extracellular matrix of Volvox.
19.1.05: Diversity and Evolutionary Relationships of the Plants
Evolution and Classification
The organisms we call plants are assigned to a single clade; that is, a natural grouping based on the belief that they have all evolved from a common ancestor more recent than any shared with other organisms. Among the criteria for doing this are:
• their shared use of the photosynthetic pigments chlorophyll a and chlorophyll b
• the similarities in the nucleotide sequences of the genes encoding both their small subunit (18S) and large subunit (25S) ribosomal RNA
• their shared cellulose cell wall
We shall examine here a selection of the most prominent groups.
Green Algae
The ancestors of these organisms were the most primitive members of the clade. In other words, organisms that we would put in this division were probably the ancestors of all the other plants. There are some 7000 species living today. They include:
• microscopic, unicellular forms like Chlamydomonas
• colonial forms like the filamentous Spirogyra
• multicellular forms like Volvox and Ulva, the sea lettuce
Although some of the multicellular forms are large, they never develop more than a few types of differentiated cells and their fertilized eggs do not develop into an embryo.
Green algae are an important source of food for many aquatic animals. When lakes and ponds are "fertilized" with phosphates and nitrates (e.g., from sewage and the runoff from fertilized fields and lawns), green algae often form extensive algal "blooms".
Liverworts and Mosses (Bryophytes)
These are fairly simple plants that do produce a number of differentiated cell types and whose fertilized egg develops into a distinct embryo.
However, they have neither vascular tissue (xylem and phloem) nor woody tissue and thus never grow very large. Some 16,000 living species are known. Most grow in moist places.
Lycopsids (Lycophytes)
Prominent members of this group are often called club mosses. They are not mosses at all, but vascular plants with xylem and phloem running through their roots, stems, and leaves. The leaves are quite simple and small with their vascular tissue in a single, unbranched vein. The "club" of their name comes from the appearance of their spore-forming structures called strobili. Club mosses are also sometimes called "ground pines", but they are not pines either. The photo shows Lycopodium obscurum.
About 1000 species of lycopsids exist today. All are small (those in the photo stand about 8 in. [20 cm] tall), but it was not always so. Fossil lycopsids in the Mississippian and Pennsylvanian periods (the so-called Carboniferous era) reached heights of 100 feet (30 meters). Their remains contributed to the formation of coal.
Chloroplast Genes
Chloroplasts (as well as mitochondria) have their own genome. The diagram (based on the work of Ohyama, K. et al., Nature 322:572, 1986 and Linda A. Raubeson and R. K. Jansen, Science 225:1697, 1992) shows the genome of the first chloroplast DNA to be sequenced, that of the liverwort Marchantia polymorpha. It contains 121,024 base pairs encoding 128 genes. The short lines indicate a few of the tRNA genes, some of which are labeled.
The order of the genes between the arrows (~6:30 to ~10:00) is also found in the lycopsids. But in all other vascular plants, this region is inverted and the order of the genes is precisely reversed. This provides further evidence that the other vascular plants we shall examine below, the
• horsetails
• ferns
• gymnosperms
• angiosperms
belong to a separate clade.
Horsetails
(Classified as Equisetopsida although many botanists prefer the older term Sphenopsida.)
The common name comes from the characteristic pattern of branching: whorls or rings of branchlets arising from an above-ground shoot. The shoot develops each season from an underground stem (rhizome). Horsetails often grow in sandy places and incorporate silica in their stems. This gives them an abrasive quality which caused them to once be used for cleaning pots and pans, which gave rise to another common name: scouring rush.
Only one genus, Equisetum, containing about 25 species, survives today. However, many other, much larger, species were dominant features of the Carboniferous and, like the early lycopsids, contributed to the formation of coal.
The drawing is of Equisetum palustre, a common horsetail. Spores are formed in the strobilus.
Ferns
(Assigned to the Pteridopsida although some botanisits prefer Filicopsida.)
Some 15,000 species of ferns live on earth today. Many of these are found in the tropics where some — the "tree ferns" — may grow to heights of 40 ft (13 m) or more. The ferns of temperate regions are smaller. They are usually found in damp, shady locations. Their stems — called rhizomes — as well as their roots grow underground and are perennial. Their leaves, called fronds, grow up from the rhizome each spring.
Seed Plants (Spermatophytes)
Gymnosperms
Fossil from the Devonian period reveal fernlike plants that were heterosporous; that is, produced two kinds of spores: microspores (male) and megaspores (female). The megaspores were not released from the parent sporophyte. Fertilization took place within the tissue of the parent sporophyte thus freed from dependence on surface water. However, the necessity for the microspores to be carried from one plant to another in order to reach the female gametophyte robbed them of their value as agents of dispersal. This function was taken over by seeds - dormant, protected, embryo sporophytes.
The seed ferns, as these plants are called, were among the earliest gymnosperms. Although seed ferns are now extinct, some of their living descendants, the cycads, resemble them closely. Cycads reveal their ancient lineage by the fact that after the microspore reaches the ovule, it liberates a ciliated sperm which, swimming in moisture supplied by the parent sporophyte, reaches the egg. Ginkgos are also gymnosperms that use motile sperm.
Conifers
These gymnosperms get their name from their cones: male cones in which the in which microspores develop and female cones in which megaspores develop. The microspores develop into pollen grains that are carried by the wind to the female cones. Here each germinates into a pollen tube which grows into the tissues of the female cone until it reaches the vicinity of the egg. (In pines, this may take a year.) Then the tube ruptures and a sperm nucleus fuses with the egg to form the zygote.
After fertilization, the zygote develops into a tiny embryo sporophyte plant. There are approximately 630 species of living conifers. They include the pines, spruces and firs. Conifers include the largest and the oldest of all living organisms. One redwood (genus Sequoia) growing in California is almost 400 feet (122 meters) high. Bristlecone pines growing in the mountains of eastern California are more than 4000 years old.
Although most conifers are evergreen, their leaves are modified as "needles", and these reduce snow load and transpiration during the winter in the harsh high-latitude climates where conifers are the dominant species of plants. But by retaining their needles during the winter, conifers are ready to begin photosynthesis immediately upon the return of spring.
Coniferous forests are of great economic importance producing lumber for building and pulp for paper making.
Angiosperms
Although angiosperms appear in the fossil record in Jurassic deposits, it was not until the end of the Mesozoic era that angiosperms became the dominant plants of the landscape. That they dominate the earth's flora today is clear: there are some 260,000 species of living angiosperms; the rest of the plant kingdom includes only some 47,700 species. Currently, the angiosperms are classified in some 54 orders (The names of the orders end in ..ales, e.g., Arabidopsis is in the order Brassicales.). Each order contains from one to several dozen families (Family names end in ..aceae, e.g., Arabidopsis is in the family Brassicaceae).
Monocots and Dicots
Of over 400 families of angiosperms, some 80 of them fall into a single clade, called monocots because their seeds have only a single cotyledon. The remainder are the dicots whose seeds have two cotyledons. The large majority of these occupy a single clade called the eudicots.
Monocot traits:
• a single cotyledon in their seed
• parallel venation in their leaves
• petals and sepals in 3s or some multiple thereof
• vascular bundles scattered randomly throughout the stem
Monocots include:
• palms (Arecaceae)
• orchids (Orchidaceae)
• yams, sweet potatoes (Dioscoreaceae)
• lilies, onion, asparagus (Liliaceae)
• bananas (Musaceae)
• and all the grasses (Poaceae), which include many of our most important plants such as
• corn (maize)
• wheat
• rice
• and all the other cereal grains upon which we depend so heavily for food as well as
• sugar cane and bamboo
Dicot traits:
• two cotyledons in their seeds
• netted venation in their leaves
• petals and sepals in 4s, 5s, or some multiple thereof
• vascular bundles in the stem arranged in a radial pattern like spokes of a wheel.
Here is a selection of eudicots.
Family Examples
Anacardiaceae poison ivy, cashews, pistachios
Asteraceae asters and all the other composite flowers
Brassicaceae cabbage, turnip; Arabidopsis, and other mustards
Cactaceae cacti
Cucurbitaceae squashes
Euphorbiaceae cassava (manioc)
Fabaceae beans and all the other legumes
Fagaceae oaks
Linaceae flax (source of linen)
Malvaceae cotton
Oleaceae olives, ashes, lilacs
Rosaceae roses, apples, peaches, strawberries, almonds
Rubiaceae coffee
Rutaceae oranges and other citrus fruits
Solanaceae potato, tomato, tobacco
Theaceae tea
Vitaceae grapes | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/19%3A_The_Diversity_of_Life/19.01%3A_Eukaryotic_Life/19.1.03%3A_Ciliates.txt |
Arabidopsis Thaliana has become to plant biology what Drosophila melanogaster and Caenorhabditis elegans are to animal biology. Arabidopsis is an angiosperm, a dicot from the mustard family (Brassicaceae). It is popularly known as thale cress or mouse-ear cress. While it has no commercial value - in fact is considered a weed - it has proved to be an ideal organism for studying plant development.
Some of its advantages as a model organism:
• It has one of the smallest genomes in the plant kingdom: 135 x 106 base pairs of DNA distributed in 5 chromosomes (2n = 10) and almost all of which encodes its 27,407 genes.
• Transgenic plants can be made easily using Agrobacterium tumefaciens as the vector to introduce foreign genes.
• The plant is small - a flat rosette of leaves from which grows a flower stalk 6–12 inches high.
• It can be easily grown in the lab in a relatively small space.
• Development is rapid. It only takes 5– 6 weeks from seed germination to the production of a new crop of seeds.
• It is a prolific producer of seeds (up to 10,000 per plant) making genetics studies easier.
• Mutations can be easily generated (e.g., by irradiating the seeds or treating them with mutagenic chemicals).
• It is normally self-pollinated so recessive mutations quickly become homozygous and thus expressed.
Other members of its family cannot self-pollinate. They have an active system of self-incompatibility. Arabidopsis, however, has inactivating mutations in the genes — SRK and SCR - that prevent self-pollination in other members of the family.
• However, Arabidopsis can easily be cross-pollinated to do genetic mapping and produce strains with multiple mutations.
Many of the findings about how plants work - described throughout these pages - were learned from studies with Arabidopsis.
19.1.07: Fungi
Some 100,000 species of fungi have been identified, but the true number is probably larger.
Characteristics of Fungi
Most fungi grow as tubular filaments called hyphae. An interwoven mass of hyphae is called a mycelium. The walls of hyphae are often strengthened with chitin, a polymer of N-acetylglucosamine. The linkage between the sugars is like that of cellulose and peptidoglycan and produces the same sort of structural rigidity.
Fungi disperse themselves by releasing spores, usually windblown. Fungal spores are present almost everywhere (and are a frequent cause of allergies). Spores of the wheat rust fungus have been found at 4000 m in the air and more than 1450 km (900 miles) from the place they were released. No wonder then that most fungi are worldwide in their distribution.
Fungi are heterotrophic. Some live as saprophytes, getting their nourishment from the surroundings (often having first digested it by secreting enzymes). They perform a crucial role in nature by decomposing dead organisms and releasing their nutrients for reuse by the living. Some live in a mutually beneficial symbiotic relationship with another organism, often a plant. The association of fungus and plant root is called a mycorrhiza. Some 80% of land plants benefit from symbiotic mycorrhiza. The plant benefits by more-efficient mineral (especially phosphorus) uptake and the fungus benefits by the sugars translocated to the root by the plant.
Mycorrhizal fungi may also form conduits for nutrients between plant species. The colorless, and hence heterotrophic Indian pipe (Monotropa uniflora - pictured on the right) is an angiosperm that must secure all its nourishment from mycorrhizal fungi that are attached at the same time to the roots of some autotrophic plant such as a pine tree. Radioactive carbon administered to the pine (as CO2) soon turns up in carbohydrates in nearby Indian pipes.
Some fungi are parasitic, causing serious damage to their host (a few examples are given below). Some fungi are both. Metarhizium robertsii is a soil fungus that lives symbiotically with plants but parasitizes (and kills) soil insects. Its hyphae penetrate both the roots of the plant and the corpse of the insect. It has been demonstrated that nitrogen released by the decaying insect is transported by the fungus to the plant. (See S. W. Behie, P. M. Zelisko, M. J. Bidochka in Science, 22 June 2012.) Metarhizium is an ascomycete.
Ascomycetes
Ascomycetes produce two kinds of spores: asexual spores called conidia and ascospores produced following sexual reproduction. Four or eight ascospores develop inside a saclike ascus (the group is commonly called sac fungi). Some notable examples include:
• Saccharomyces cerevisiae one of the budding yeasts. It ferments sugar to ethanol and carbon dioxide and thus is used to make alcoholic beverages like beer and wine, to make ethanol for industrial use and in baking (it is often called baker's yeast). Here, it is the carbon dioxide that is wanted (to make bread and cakes "rise" and have a spongy texture). Yeast is also used in the commercial production of some vitamins and in the production - using recombinant DNA technology - of some human therapeutic proteins.
• Neurospora crassa, another favorite "model" organism in the laboratory.
• The fungal partner in most lichens is an ascomycete.
• Powdery mildews that attack ornamental plants
• The chestnut blight, which in a few decades killed almost all of the mature American chestnut trees in the Appalachians of North America.
• The Dutch elm disease, which has killed many of the American elms in the United States.
• Pneumocystis jirovecii, which is a major cause of illness in immunosuppressed people, e.g., patients with AIDS.
• The truffle and the morel, both highly-prized food delicacies. Truffles establish a symbiotic relationship with the roots of such trees as oaks.
Lichens
Lichens are fungi that live in a symbiotic association with an autotrophic green alga or cyanobacterium (the "photobiont") or - in some cases - both. The fungal partner (the "mycobiont") in most lichens (98% of them) is an ascomycete. Zygomycetes make up the remainder. The relationship is often characterized as mutualistic; that is, both partners benefit. But recent evidence (e.g. in British soldier) suggests that while the fungus is dependent on its autotrophic partner, the photobiont is often perfectly content to live alone. Recently many lichens have been found to harbor a third partner, a single-celled basidiomycete. Its function remains to be discovered.
Lichens secrete a variety of unusual chemicals; some of these probably assist in the breakdown of rock substrates like the one shown here.
The British Solder
The below image is of the colorful lichen called British soldier. The fungus is Cladonia cristatella, an ascomycete. Its name is the name given to the lichen. The photobiont is Trebouxia erici, a green alga. It is found in many other lichens as well, and also can be found growing independently. The algal cells eventually are killed by the fungus, but are continuously replaced by new ones. So the relationship in this lichen is one of controlled parasitism rather than mutualism.
The red cap produces the spores of the fungus, but these alone cannot form new lichens. Other structures (e.g., soredia), containing both partners, are needed to disperse the lichen to new locations. Some lichens release only fungal spores. These mycobionts depend for their continued survival on finding an acceptable photobiont released from other lichens. Phylogenetic trees, based on both ribosomal RNA genes and many protein-coding genes, as well as fossils indicate that lichens have been present on the earth for at least 600 million years.
Today about 14,000 species of fungi form lichens. Lichens are extremely sensitive to air pollution. One of the best contemporary examples of evolutionary adaptation is the change in coloration of the peppered moth as the lichens in its habitat declined because of air pollution and then returned when air quality controls were put in place. Some modern fungi (e.g., Penicillium chrysogenum, the source of the antibiotic penicillin) appear to have evolved from lichen-forming ancestors — abandoning their original symbiotic way of life.
Basidiomycetes
Basidiomycetes include mushrooms, shelf fungi, puffballs, rusts, and smuts. They are dispersed by spores borne at the tips of basidia (giving rise to the name for the group). Mushrooms are masses of interwoven hyphae growing up from the main mass of the mycelium growing underground. The basidia develop on the undersides and release their spores (four from each basidium) into the air.
A single mycelium may expand outward year after year as its hyphae grow into new terrain. In some species, mushrooms are sent up once a year at the periphery producing a circle known since medieval times as a "fairy ring".
Some notable basidiomycetes:
• Armillaria bulbosa. A single specimen in northern Michigan (USA) was found to have spread over 37 acres (15 hectares) of the forest floor. RFLP analysis of samples taken from many different locations within this area showed that all the samples were from a single clone. Assuming the normal rate of vegetative growth for this species, it must have taken 1500 years to spread to that size.
• the cultivated, edible mushroom that finds its way into pizza, soups, etc.
• Amanita muscaria. Forms a beautiful mushroom but deadly when eaten.
• Smuts. Parasites of important crops like wheat, oats, and rye.
• Rusts. Some, such as
• wheat black stem rust (Puccinia graminis) and
• white pine blister rust
are serious pests. Both have complicated life cycles during which they pass through a second plant host (barberry plants for wheat black stem rust, gooseberries or wild currants for the white pine blister rust).
Zygomycetes
All the fungi assigned to this group (which probably does not represent a single clade) form spores in a sporangium. Some notable examples:
• the bread mold, Rhizopus stolonifera
• Rhizopus oryzae, used to make sake, the rice wine of Asia. Can also infect humans, especially if they are immunosuppressed (e.g., AIDS patients, transplant recipients).
• Another species of Rhizopus is used in the commercial production of glucocorticoids.
• Many mycorrhizal fungi belong to this group.
Chytrids
This small group (~1000 species) is thought to be the most primitive of the fungi. Unlike all the other fungi, its members produce flagellated gametes (for sexual reproduction) and flagellated zoospores (for asexual reproduction). They are mostly aquatic.Two species are responsible for the recent worldwide decline in amphibian populations (frogs, toads, and salamanders).
19.1.09: Barcoding
Barcoding is the term applied to a technology that is being developed to speed the identification of specimens of living things. So far, identification and classification of animals has progressed furthest. Although each individual in most species has a unique genome sequence, the differences between individuals of one species are much smaller than the differences between individuals of different species. Thus determining the genome sequence of a specimen should enable it to be positively classified if the sequences of other members of its species are already in a database.
However, sequencing entire genomes of animals is an enormous undertaking. (Most mammals have some 3 billion base pairs of DNA.) A more practical approach is to settle on the sequence of a single gene that is found in all animal life. The one that has been chosen for animals is the gene, COI, encoding the largest subunit of cytochrome c oxidase.
Advantages
• It is a mitochondrial gene and thus each cell has hundreds-to-thousands of copies of it as opposed to only two copies of each of its nuclear genes.
• It has no introns (in animals).
• Thanks to the redundancy of the genetic code, it can mutate quite freely, especially in the third position of its codons.
• Furthermore mitochondrial gene sequences vary more between related species than their nuclear genes do. For example, while the sequence differences between the nuclear genes of humans and chimpanzee is only about 1%, the difference between their mitochondrial gene sequences is some 9%.
• Within a species, however, there is little variation from specimen to specimen in their mitochondrial gene sequences.
Procedure
• The mitochondrial DNA is extracted.
• A fragment from the 5' end of COI (~648 base pairs) is isolated (the entire gene has ~1500 base pairs).
• The fragment is amplified by PCR using readily-available primers.
• The sequence is determined and compared with those already in a database.
Early Results
Barcoding analysis of several hundred different birds has shown that barcode results usually reflect the species identification based on more conventional criteria. However, a few cases have arisen where:
• specimens thought to belong to the same species differ substantially in the COI sequence and thus probably represent convergent evolution.
• specimens thought to belong to different species have similar COI sequences and thus are probably local variants of what is actually a single species.
Looking Ahead
• Development of appropriate barcoding genes for plants (whose COI genes vary little) and fungi (whose COI genes are interrupted by introns). One promising candidate for plants is the chloroplast gene rbcL which encodes the large subunit of RUBISCO.
• Development of hand-held sequencers that can barcode the DNA of a specimen in the field.
Promoting the development of barcoding is The Consortium for the Barcode of Life (CBOL). Their home page (link below) provides other links describing goals, methods, achievements, etc. As of this writing, barcodes for over 112,000 species have been entered in databases. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/19%3A_The_Diversity_of_Life/19.01%3A_Eukaryotic_Life/19.1.06%3A_Arabidopsis_Thaliana_-_A_Model_Organism.txt |
The Origin and Evolution of Animals (Metazoa)
We do not yet know from what group(s?) of eukaryotes the animals evolved. It occurred in Precambrian times. Before the Cambrian was far along, most of the animal phyla had appeared. So each of the phyla described in this section has had a long, independent history. The rapid (geologically speaking!) diversification of the animals has made it difficult to establish the genealogical relationships between them — even using molecular data. Our best guesses are shown in the cladogram below..
Sponges (Phylum Porifera)
Sponges are sessile, spending their lives anchored to a solid surface underwater. Most are marine although some live in fresh water. Diploblastic; that is, the body wall is made of two layers of cells with a jellylike mesoglea between them. The body wall is perforated with pores (hence the name Porifera) through which water containing food particles is filtered. The water is drawn in through the pores by collar cells like those found in choanoflagellates. Some sponges can process a volume of water more than 100,000 times their own volume in the course of a day!
Sponges are dispersed by small, free-swimming larvae. There are about 10,000 species known. Sponges are probably the most ancient of today's invertebrates, their fossils appear in the geological record as far back as 635 million years. Despite their simple body plan, sequencing shows that their genome (> 18,000 genes) contains many genes homologous to those found in much more complex animals.
Cnidarians (Phylum Cnidaria)
Characteristics:
• diploblastic; two layers of cells - ectoderm and endoderm - with a jellylike mesoglea between them;
• predominantly radial symmetry: body parts (e.g., tentacles) arranged in whorls. However, in some sea anemones, there is only one plane through the tubular body that divides it into two mirror-image halves; thus revealing bilateral symmetry.
• cnidoblasts: specialized cells that secrete a stinging capsule called a nematocyst.
• Food is taken through a mouth into the gastrovascular cavity. The cavity is also called a coelenteron and for many years the name of this phylum was Coelenterata. There is no anus.
• Sexual reproduction produces a free-swimming, ciliated larva called a planula.
• The phylum contains about 10,000 species distributed in 3 classes:
• Hydrozoa Although the freshwater hydra is a much-studied representative, it is not typical of the class.
Most members are
• marine
• colonial
• produce two body forms: the sessile polyp (like the hydra) and the free-floating medusa (which disperses the species)
• Scyphozoa Jellyfishes (the medusa stage is dominant). The jelly of the medusa is a much-enlarged mesoglea.
• Anthozoa Sea anemones and corals. Have only the polyp stage.
Bilaterians
All the remaining groups of animals belong in a clade whose members share:
1. bilateral symmetry (hence the name); that is, dorsal-ventral and left-right axes
2. triploblastic (three tissue layers: ectoderm, mesoderm, endoderm)
3. HOX genes in one or more clusters with the genes within a cluster arranged in the same order as the body parts they affect.
The bilaterians contain two clades, the protostomia and the deuterostomia.
Protostomia vs. Deuterostomia
Long before the days of genome analysis, taxonomists were convinced of a fundamental division in the animal kingdom between the protostomes ("first mouth") and the deuterostomes ("second mouth").
Protostomia Deuterostomia
Blastopore forms future mouth (in most groups). Blastopore forms future anus. Mouth forms later.
Few HOX genes for the posterior Multiple HOX genes for the posterior
Spiral cleavage of Lophotrochozoan embryos Perpendicular cleavage planes in embryo
Early cleavage cells committed; no identical twins Early cleavage cells totipotent; identical twins possible
Coelom arises by splitting of mesoderm Coelom arises between invaginating mesoderm during gastrulation
Lophotrochozoans and Ecdysozoans Echinoderms, Acorn worms, and Chordates
Let's first examine the protostomes. The deuterostomes are discussed below.
Lophotrochozoans vs. Ecdysozoans
Genome analysis, especially the analysis of 18S rRNA genes and HOX genes supports a major division of the Protostomia into two superphyla: Lophotrochozoans and Ecdysozoans.
Lophotrochozoans
Their name was created from the names of formerly-separated groups that have now been joined in a single clade on the basis of the similarities of their genomes. They all share a cluster of HOX genes quite different from those found in the ecdysozoans (and deuterostomes). They share similar sequences in their 18S rRNA genes. The clade contains a number of phyla of which we shall examine only 3.
• flatworms (Platyhelminthes),
• annelids (Annelida), and
• mollusks (Mollusca).
Flatworms (Phylum Platyhelminthes)
This phylum contains some 20,000 species distributed among three classes. Turbellaria, free-living forms of which the planarian is a commonly-studied example. Planaria share with the other members of the phylum (1) a flat, almost ribbonlike, shape and (2) bilateral symmetry. The bilateral symmetry of planarians is associated with active locomotion by secreting a layer of mucus underneath them and propelling themselves forward with the many cilia on their ventral surface and by swimming and a concentration of sense organs in the head (called cephalization). Planarians feed through a mouth on their ventral surface. It leads to an elaborate gastrovascular cavity. But there is no separate exit so undigested food has to leave by the mouth.
• Trematoda, a group of parasitic
• lung flukes
• liver flukes
• blood flukes (e.g., Schistosoma)
• All of these have at least two different stages in their life cycle, each parasitic in a different host - one of which is usually a snail.
The diagram gives the life cycle of the blood fluke, Schistosoma mansoni. Once within the alternate host, a snail, a single miracidium may produce as many as 200,000 infectious cercariae. Both sexes must infect the human if the cycle is to continue. With the increasing use of irrigation in tropical regions, the incidence of human infection — known as schistosomiasis or bilharzia — is rising alarmingly.
• Cestoda; the parasitic tapeworms. They, too, alternate between an intermediate host (e.g., pig, fish) and a definitive host (e.g., us). The growing popularity of sushi and sashimi made of raw Pacific salmon has caused infections by the fish tapeworm to become more common in the U.S.
Annelids (Phylum Annelida)
Characteristics:
• segmented; that is, their body is made up of repeating units. Although some structures, e.g., the digestive tract, run straight through, others like the excretory organs are repeated in each segment.
• The major nerve trunk runs along the ventral side.
• a large, fluid-filled coelom; It is lined with mesoderm and enables the internal organs to slide easily against one another making for easy locomotion.
There are >15,000 species known. Some examples:
• the common earthworm
• leeches
• marine forms such as the clam worm These animals produce a free-swimming trochophore larva (figure), which partly accounts for the name Lophotrochozoan.
Mollusks (Phylum Mollusca)
With over 100,000 living species identified so far, the mollusks must be counted as among the most successful animals on earth today. Most belong to the first 3 of the 6 classes shown here:
1. Bivalvia. Two shells encase the body. Includes the clams, mussels, oysters, and scallops.
2. Gastropoda. Snails and slugs. Snails have a single shell ("univalves') while slugs have none.
3. Cephalopoda. This marine group includes the various species of octopus, squid, as well as the chambered nautilus. A record 28-foot (8.5 m) octopus and 60-foot (18 m) squid make these the largest of all the invertebrates.
4. Scaphopoda. Marine, filter-feeding "tooth shells".
5. Monoplacophora. Until a live specimen was discovered in 1952, these animals were thought to have been extinct for millions of years. It has a single shell (hence the name) and, unlike the other mollusks, is segmented (as are its relatives the annelids).
6. Polyplacophora. The animals in this group, called chitons, have their dorsal surface protected by 8 overlapping plates or "valves".
The trochophore larvae of mollusks is also evidence that they belong in the same clade with the annelids.
Ecdysozoans
All the members of this clade
• grow by periodically molting - shedding their skin or exoskeleton
• share a unique pattern of HOX genes, e.g. Ubx and Abd-B
The clade includes a number of phyla of which we shall examine 2:
• nematodes
• arthropods.
Roundworms (Phylum Nematoda)
Features:
• A one-way digestive tract running from mouth to anus.
• A cavity between the digestive tract and the body wall. It develops from the blastocoel and is called a pseudocoel.
• Some 25,000 species have been identified but this may be less than 10% of the true number.
• Most are free-living; found in soil where they are important decomposers.
• One of these is Caenorhabditis elegans, a model laboratory animal.
• Some are parasitic, including
• hookworms (In 2003 the number of humans infected by hookworms was estimated at 740 million worldwide.)
• pinworms and whipworms
• filarial worms - threadlike worms that are transmitted to the definitive host from an intermediate host causing such human ailments as
• river blindness (Onchocerca volvulus) - acquired from the bite of infected black flies
• elephantiasis (Wuchereria bancrofti) - acquired from infected mosquitoes
• dracunculiasis (Guinea worm disease) (Dracunculus medinensis) - acquired from ingesting water containing infected "water fleas" (Cyclops)
• many parasites of commercially important plants like strawberries and oranges.
• Most are small although one that parasitizes whales reached 30 feet (9 m)!
Arthropods (Phylum Arthropoda)
Some characteristics:
• Incredible diversity. Over a million living species have been identified so far - more than all the other species of living things put together - and this is probably only a fraction of them.
• Live in every possible habitat: fresh water, salt water, soil, even in the most forbidding regions of Antarctica and high mountains.
• A jointed external skeleton made of chitin, a polymer of N-acetylglucosamine (NAG).
• Segmented.
• Pairs of jointed appendages; one pair to a segment - used for locomotion, feeding, sensation, weaponry.
• Bilateral symmetry.
• Main nerve cord runs along the ventral side.
We shall look at four groups (subphyla):
• Crustacea
• Hexapoda (the insects)
• Myriapoda
• Chelicerata
Crustacea
Figure 19.1.10.7 Crustacea
• Head and thorax fused into a cephalothorax.
• At least 40,000 species.
• Most are aquatic, found in both fresh water and in the oceans.
• Includes crayfish, lobsters, barnacles, crabs, shrimp.
Hexapoda - the insects
• Body segments grouped into head, thorax, and abdomen.
• Each of the 3 thoracic segments carries a pair of legs (hence the 6-legged "hexapoda")
• Many have wings, usually 2 pairs (only one pair in flies - diptera).
• Gas exchange through a tracheal system.
• Nitrogenous waste is uric acid thus conserving water.
• Some 950,000 species, and this may be only 10% of the number out there.
• Dominate all habitats except for the oceans.
• Most intensively-studied representative: Drosophila melanogaster.
• Representative colonial insect: the honeybee, Apis mellifera
Myriapoda
Some 13,000 species of
• centipedes
• millipedes
Neither group has the number of legs their name suggests, although one species of millipede does have 375 pairs.
Chelicerata
• Anterior segments fused into a cephalothorax.
• The first pair of appendages - the chelicerae - are used for feeding.
• There are no antennae.
• Includes:
• Merostomata. The only member alive today is Limulus, the horseshoe "crab". It has existed in the sea virtually unchanged for 200 million years.
• Arachnids (some 75,000 species)
• 8-legged
• scorpions, mites, ticks, spiders, daddy longlegs.
Evolutionary relationships of the arthropods
An ever-increasing number of arthropod gene sequences appear to have answered some long-standing questions about the evolutionary relationships of the various arthropod groups. A recent study (Regier, J. C., et al., Nature, 463:1079, 25 February 2010) examined 63 nuclear genes from 75 species of arthropods and concluded that
• the crustacea are paraphyletic; that is, the single common ancestor from which all the animals we call crustaceans are descended was also the ancestor of another group, the insects (Hexapoda). So insects are terrestrial crustaceans!
• All these groups plus the millipedes and centipedes (Myriapoda) make up a clade designated Mandibulata.
• So millipedes and centipedes are more closely related to the crustaceans than to, as once thought, the Chelicerata.
The Deuterostomes
In addition to the features listed above, the deuterostomes have (or had) gill slits. (The echinoderms have lost the gill slits of their ancestors.)
Echinoderms (Phylum Echinodermata)
Characteristics:
• radial symmetry. HOWEVER, their larvae have bilateral symmetry so the echinoderms probably evolved from bilaterally symmetrical ancestors and properly belong in the Bilateria.
• water vascular system. Seawater is taken into a system of canals and is used to extend the many tube feet. These have suckers on their tips and aid the animal in attaching itself to solid surfaces.
• no gill slits
• About 6,000 species — all of them marine.
There are 5 classes of echinoderms:
• Sea lilies (Crinoidea)
• Sea Stars (aka "Starfish") (Asteroidea) The photo (courtesy of Dr. Charles Walcott) shows a sea star that lost an arm and is in the process of regenerating a replacement.
• Brittle stars (Ophiuroidea)
• Sea cucumbers (Holothuroidea)
• Sea urchins and sand dollars (Echinoidea)
Acorn Worms (Phylum Hemichordata)
The members of this small phylum (some 90 species have been identified) are marine forms most of whom live in burrows in ocean sediments. Their closest living relatives are the echinoderms with which they share the clade Ambulacraria. However, they possess a suite of features, both in their anatomy (e.g. gill slits) and their gene expression patterns, suggesting that their ancestors also led to the evolution of the chordates.
Chordates (Phylum Chordata)
During their embryonic development, all chordates pass through a stage called the pharyngula with these features:
• a dorsal, tubular nerve cord ("1") running from anterior to posterior. At its anterior end, it becomes enlarged to form the brain.
• a flexible, rodlike notochord ("2") that runs dorsal to the digestive tract and provides internal support. In vertebrate chordates, it is replaced by a vertebral column or backbone long before maturity.
• pairs of gill pouches. These lateral outpocketings of the pharynx are matched on the exterior by paired grooves. In aquatic chordates, one or more pairs of gill pouches break through to the exterior grooves, forming gill slits ("3"). These provide an exit for water taken in through the mouth and passed over the gills.
• a tail that extends behind the anus
• The vast majority of chordates have a skull enclosing their brain (Craniata), and all but one of these (the hagfish) convert their notochord into a vertebral column or backbone. These latter are the vertebrates.
Vertebrates also differ from all the other animals by having quadrupled their HOX gene cluster; that is, vertebrates have 4 clusters of HOX genes located on 4 different chromosomes.
Here we shall examine two groups of invertebrate chordates:
• Urochordata and
• Cephalochordata
Urochordata
This group (also called Tunicata) includes animals known as ascidians (and commonly called sea squirts). They are
• marine
• sessile animals
• feed by filtering food particles from seawater taken in through one opening, or siphon, and squirted out the other.
The one on the above is Halocynthia, the sea peach (photo courtesy of Ralph Buchsbaum). It is hard to see what makes these animals chordates. The adults have neither notochord nor a dorsal tubular nervous system. However, these animals disperse themselves with free-swimming larvae that have
• dorsal tubular nervous system
• notochord
• gill slits
One of the most common species (Ciona intestinalis) has had its genome sequenced.
• It has a very small genome: ~1.6 x 108 base pairs encoding ~16,000 genes. (Some 20% of these are organized in operons.)
• Its larva is small (with ~2,600 cells) including only
• 36 muscle cells
• 40 notochord cells
• 100 neurons
• These cells (as well as the others) develop along rigid pathways which can be easily observed because the larva is
• transparent.
All these features are shared with C. elegans, but now we are talking about an animal far closer to the evolutionary line that produced us. In fact, with 80% of Ciona's genes having homologs in us, tunicates are probably our closest invertebrate relatives.
Cephalochordata
The representative member of this tiny subphylum of so-called lancelets is a small (5 cm), marine, fishlike creature called amphioxus (above). For years its genus name was Amphioxus but that has now been replaced by the name Branchiostoma. Amphioxus retains a dorsal nerve cord, notochord and gill slits throughout its life. There is a small cluster of neurons at the anterior tip of the nerve cord with certain similarities of structure and gene expression to the vertebrate fore-, mid- and hindbrain. Although able to swim, the lancelet spends most of its time partially buried in the sand while it filters microscopic food particles from the water. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/19%3A_The_Diversity_of_Life/19.01%3A_Eukaryotic_Life/19.1.10%3A_Invertebrates.txt |
Some of the reasons for its popularity:
• The flies are small and easily reared in the laboratory.
• They have a short life cycle The figure shows the various stages of the life cycle (not all drawn to the same scale). A new generation of adult flies can be produced every two weeks.
• They are fecund; a female may lay hundreds of fertilized eggs during her brief life span. The resulting large populations make statistical analysis easy and reliable.
• The giant ("polytene") chromosomes in the salivary (and other) glands of the mature larvae.
• These chromosomes show far more structural detail than do normal chromosomes
• They are present during interphase when chromosomes are normally invisible.
• More recently, Drosophila has proven in other ways to have been a happy choice.
• Its embryo grows outside the body and can easily be studied at every stage of development.
• The blastoderm stage of the embryo is a syncytium (thousands of nuclei unconfined by cells) so that, for example, macromolecules like DNA injected into the embryo have easy access to all the nuclei.
• The genome is relatively small for an animal (less than a tenth that of humans and mice).
• Mutations can targeted to specific genes.
19.1.12: Caenorhabditis Elegans
Caenorhabditis elegans is a microscopic (~1 mm) nematode (roundworm) that normally lives in soil. It has become one of the "model" organisms in biology. It is a true animal with at least rudiments of the physiological systems - feeding, nervous, muscle, reproductive - found in "higher" animals like mice and humans. However, it is so small that large numbers can be raised in petri dishes (where it is fed E. coli - another model organism). It reproduces rapidly.
It is transparent so that every cell in the living animal can be seen under the microscope from the fertilized egg to the 556 cells of the newly-hatched worm and, later, the 959 somatic cells, and a variable number of germ cells, of the adult worm. It can be easily transformed with transgenes - DNA injected into the animal. It can also be treated with antisense RNA. Before it dies (after 2–3 weeks), it shows signs of aging and thus may provide general clues as to the aging process.
Its cells contain 5 pairs of autosomes and 2 X chromosomes. These animals are hermaphrodites, producing both sperm and eggs. Most of the time they fertilize themselves, so that any recessive alleles quickly become homozygous and affect the phenotype. On rare occasions, nondisjunction occurs during meiosis with the loss of one X chromosome. Animals with a single X are males and are able to fertilize the eggs of the hermaphrodites (with more success than they have themselves).
C. elegans was the first multicellular eukaryote to have its entire genome sequenced. It contains some 19–20,000 protein-encoding genes incorporated in 100,258,171 base pairs of DNA. In contrast to other eukaryotes, some 13–15% of its genes are grouped in operons containing 2–8 genes each.
C. elegans Fertilization
Like all animals, C. elegans starts life as a fertilized egg (zygote) which then undergoes the mitotic divisions needed to produce the adult. Because the worm is transparent and the pattern of differentiation is so rigid it has been possible to trace the lineage of every single somatic cell in the animal. Just after hatching, the it contains 556 cells and is approximately 0.3 mm long. After reaching maturity, it will contain 959 somatic cells and a variable number of germ cells in its gonad.
The diagrams below show the pathway by which each of the 556 cells in the larva of C. elegans has developed from the zygote. The relative length of the vertical lines indicates the length of the interval before the next mitosis. Some pathways end in the programmed death of the cell (apoptosis) even before the larva is complete.
Several remarkable features have been found from these studies. The pattern of development is invariable from worm to worm. Every one of the 556 cells that make up the newly-hatched larva develops from a rigid pattern of mitotic division leading back to the zygote. 131 cells in the developing embryo die by apoptosis. This cell death is not random; which cells will die and at what stage is completely predictable. Any failures in this programmed cell death can lead to serious abnormalities.
Each organ - skin, nerve, muscle, etc. - is made of cells derived from several different lineages. One might have expected that the earliest cell divisions would produce daughter cells destined to go on to form a single structure in the embryo. But that is not generally the case. Instead, most of the earliest cells will produce descendants that team up with other groups of cells to form the various organs of the animal.
There is less flexibility of cell fate than occurs in mammals (or even amphibians). With a microscopic laser beam, a single cell can be killed in the developing embryo. Often the result is that all the cells that would have descended from that cell fail to form. Neighboring cells may not compensate for the loss as they do so freely in mammals. So it appears that the developmental controls of C. elegans rely more on cell-intrinsic signals rather than inductive signals. But this distinction is relative, not absolute. Cells originally destined to a different fate will in some cases switch their path of differentiation to replace the cells killed by the laser. In these cases, the switch is clearly mediated by inductive signals liberated by nearby cells. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/19%3A_The_Diversity_of_Life/19.01%3A_Eukaryotic_Life/19.1.11%3A_Drosophila_Melanogaster.txt |
Chordata
During their embryonic development, all chordates pass through a stage called the pharyngula with these features:
• The cephalochordates and tunicates never develop a vertebral column. They are thus "invertebrates" and are discussed with the other invertebrates.
• Craniata The vast majority of chordates have a skull enclosing their brain, eyes, inner ear, etc.). All but one group of these (the hagfishes) also convert their notochord into a vertebral column or backbone thus qualifying as vertebrates.
Vertebrata
Although hagfishes, never replace their notochord with a vertebral column, and thus might seem not to qualify as vertebrates, they share a number of other features with other vertebrates and certainly should be classified with them. Still uncertain is whether they represent the most primitive vertebrates or are simply degenerate vertebrates (probably the latter).
All the other members of the craniata convert their notochord into a vertebral column or "backbone" (even though in some it is made of cartilage not bone). They also differ from all other animals in having quadrupled their HOX gene cluster; that is, they have 4 different clusters of HOX genes (on 4 separate chromosomes). Perhaps this acquisition played a key role in the evolutionary diversity that so characterizes the vertebrates.
The vertebrates are subdivided into the
• jawless vertebrates (Agnatha)
• jawed vertebrates (Gnathostomata)
Agnatha
Lampreys and hagfishes are the only jawless vertebrates to survive today. They both have a round mouth and for this reason are often referred to as cyclostomes. They are the most primitive of the vertebrates. By "primitive", a biologist means that they are the least changed from the first vertebrates. Besides lacking jaws,
• They have no paired pectoral (shoulder) or pelvic (hip) fins.
• Their notochord persists for life, never being completely replaced by a backbone even in the lampreys.
• They have no scales.
• The axons of their neurons are unmyelinated (like those of all invertebrates).
• Lampreys have both an innate immune system and an adaptive immune system, but the latter is entirely different from that found in the jawed vertebrates.
The photo (courtesy of the Carolina Biological Supply Company) is of the West Coast lamprey. Note the gill slits and the absence of paired pectoral and pelvic fins.
Gnathostomata
As well as having jaws, all the members of this group have
• Myelin sheaths around the axons of their neurons. This permits much more rapid transmission of nerve impulses - a trait probably as important for active vertebrates as their jaws.
• An adaptive immune system backing up their innate immune system.
Cartilaginous Fishes (Chondrichthyes)
Fossils of cartilaginous fishes become abundant in deposits dating to the Devonian period. They were very much like the sharks of today. The group, which today is made up of some 1,188 species of sharks, skates and rays gets its name from the fact that their skeleton is made of cartilage, not bone.
With their gills exposed to sea water, all marine fishes are faced with the problem of conserving body water in a strongly hypertonic environment. Sea water is about 3.5% salt, over 3 times that of vertebrate blood. The cartilaginous fishes solve the problem by maintaining such a high concentration of urea in their blood (2.5% — far higher than the ~0.02% of other vertebrates) that it is in osmotic balance with - that is, is isotonic to - sea water.
This ability develops late in embryology, so the eggs of these species cannot simply be released in the sea. Two solutions are used:
• Enclose the egg in an impervious case filled with isotonic fluid before depositing it in the sea.
• Retain the eggs and embryos within the mother's body until they are capable of coping with the marine environment.
Both these solutions require internal fertilization, and the cartilaginous fishes were the first vertebrates to develop this. The pelvic fins of the male are modified for depositing sperm in the reproductive tract of the female.
Bony Fishes (Osteichthyes)
As their name indicates, the skeleton in this group is made of bone. The group is subdivided into the
• ray-finned fishes (Actinopterygii)
• lobe-finned fishes (Sarcopterygii)
Ray-finned fishes
• Their fins are thin and supported by spines.
• There are over 30,000 species (representing more than half of all living vertebrates).
• They are an important part of the human diet in many areas of the world and, in affluent nations, support a large sports fishing industry.
Although the earliest bony fishes may have appeared late in the Silurian period, their fossils become abundant in freshwater deposits of the Devonian period. In addition to gills, these fishes had a pair of pouched outgrowths from the pharynx which served as lungs. They were inflated with air taken in through the mouth and may have provided a backup gas exchange organ when the water became too warm and stagnant to carry enough dissolved oxygen. Their kidneys were adapted for the hypotonic environment in which they lived.
These animals diversified through the remainder of the Devonian period (which is often called the "Age of Fishes"). Some migrated to the oceans. In this more stable environment, their lungs became transformed into a swim bladder with which they could alter buoyancy. Their kidneys became transformed as well adapting them to their new - hypertonic - surroundings.
Lobe-finned fishes
The only ones to survive today are:
• two species of coelacanths. Coelacanths were long thought to have become extinct at the end of the Mesozoic era, some 70 million years ago. But in December 1938, a living coelacanth, Latimeria chalumnae, was pulled up from the depths of the ocean off the east coast of Africa. Since then, over 200 additional specimens have been caught.
• several species of lungfish found in Africa, South America, and Australia.
The nostrils of bony fishes open only to the outside and are used for smelling. Some of the lobe-finned fishes developed internal openings to their nostrils. This made it possible to breath air with the mouth closed as modern lungfishes do.
Judging from present-day lungfishes, two other significant adaptations evolved in this group:
• two atria and a partial septum in the ventricle of the heart (similar to the frog heart). This permitted a partial separation of oxygenated blood returning from the lung(s) and the deoxygenated blood returning from the rest of the body.
• an enzyme system to convert ammonia into the less toxic urea. This mechanism is highly-developed in the African and South American lungfishes. While in the water, these fishes excrete their waste nitrogen as ammonia, just as most ray-finned fishes do. In time of drought, these animals burrow in the mud and switch to urea production.
With their bony limbs and lungs inherited from their lobe-finned ancestors, amphibians were so successful during the Carboniferous (Mississippian and Pennsylvanian periods) that these periods are known as the Age of Amphibians.
The Carboniferous was followed by the Permian, when the earth became colder and dryer. The fortunes of the amphibians began to decline until only three groups - totaling about 6500 species - remain today:
• frogs and toads (Anura) (The one pictured is Rana pipiens, the leopard frog.)
• salamanders and newts (Urodela)
• caecilians (Apoda), which are rare, limbless, tropical animals.
As the name suggests, amphibians are only semiterrestrial:
• Their skin is soft and moist so they are at risk of desiccation in dry surroundings.
• Their eggs have no waterproof covering so
• they must be laid in water (which makes them useful animals for studying embryonic development) where they are fertilized or
• placed within the mother's body (some use a pouch in the skin, some use their mouth, some even use their stomach — which stops secreting acid and enzymes for the duration!) after external fertilization.
Amniotes (Amniota)
Some 310 million years ago (in the Pennsylvanian), some amphibians evolved the ability to lay shelled, yolk-filled eggs. The embryo developing within the egg produces 4 extraembryonic membranes:
• amnion, which surrounds the embryo with a fluid as watery as the pond water around a frog's egg (and accounts for the name amniota)
• chorion, which serves for gas exchange
• allantois, which serves both for gas exchange and to store metabolic wastes
• yolk sac, which supplies the embryo with food
With the arrival of the cold, dry Permian, reptiles were well-adapted to survive because of their development of a shelled, yolk-filled egg which could be deposited on land without danger of drying out. The photo (courtesy of the Carolina Biological Supply Company) shows an American chameleon emerging from its egg.
Other adaptations that enabled the reptiles to flourish for the next 220 million years were:
• a dry, water-impermeable skin
• lungs inflated by expansion of the rib cage
• a partial septum in the ventricle reducing the mixing of oxygenated and deoxygenated blood
Beginning late in the Paleozoic era and exploding in the Triassic period, the reptiles underwent a remarkable adaptive radiation producing the diapsids. This group developed the ability to convert their nitrogenous waste into uric acid. Uric acid is almost insoluble in water so its excretion involves little loss of water. (It is the whitish paste that pigeons leave on statues.) This modification largely freed the diapsids and their descendants from a dependence on drinking water; the water in their food is usually sufficient.
Diapsid evolution soon produced:
• lizards and snakes (Squamata - some 6,300 species survive today);
• turtles
• thecodonts.
Thecodonts were able to run fast by rising up on their hind legs, which became larger than their front legs, and using their long tail for balance. The group diversified into:
• crocodiles and alligators (Crocodilia — 22 species survive today)
• an extraordinary array of dinosaurs from some of which evolved today's birds.
Feathers are the feature that most clearly distinguishes the birds from their dinosaur ancestors. These scaly skin outgrowths provide a light, strong surface for the wings;
• heat insulation, making it possible to be small but still warm-blooded.
Other adaptations are:All of these adaptations help birds to fly (to escape predators and find suitable food and nesting sites). Almost 10,000 species are known today. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/19%3A_The_Diversity_of_Life/19.01%3A_Eukaryotic_Life/19.1.13%3A_Vertebrates.txt |
The zebrafish, Danio rerio, has become another popular "model" organism with which to study fundamental biological questions.
The zebrfish is a small (1–1.5 inches)(2.5–3.8 cm) freshwater fish that grows easily in aquaria (it is available at many pet stores). Some of its advantages for biologists:
• It breeds early and often (daily).
• It is a vertebrate, like us, and thus can provide clues to human biology that invertebrates like Drosophila and Caenorhabditis elegans may not.
• Its embryos, like those of most fishes, develop outside the body where they can be easily observed (unlike mice).
• Its embryos are transparent so defects in development can be seen easily.
• Individual cells in the embryo can be labeled with a fluorescent dye and their fate followed.
• Embryonic development is quick (they hatch in two days).
• They can absorb small molecules, such as mutagens, from the aquarium water.
• Individual cells - or clusters of cells - can be transplanted to other locations in the embryo (as Mangold did with newt embryos).
• They can be forced to develop by parthenogenesis to produce at will homozygous animals with either a male-derived or female-derived genome.
• They can be cloned from somatic cells.
• They can be made transgenic (like mice and Drosophila)
• Its genome (1.4 x 109 base pairs) has been sequenced revealing 26,606 protein-coding genes.
Forward and Reverse Genetics
Forward
Since Mendel's time, most genetics has involved
• observing an interesting phenotype
• tracking down the gene responsible for it.
So this "forward" genetics proceeds from phenotype -> genotype.
Some examples:
• Mendel's work
• RFLP analysis of large families
• The one gene - one enzyme theory
These methods have been called "forward" genetics to distinguish them from a more recent approach, which has become an urgent priority with the successes of genome sequencing.
Reverse
Rapid methods of DNA sequencing has generated a vast amount of data. Thousands of suspected genes have been revealed (e.g., finding open reading frames - ORFs), but the function of many of them is still unknown.
But now with a knowledge of the DNA sequence of a gene of unknown function, one can use methods for suppressing that particular gene ("knockdown") and then observe the effect on the phenotype.
So this "reverse" genetics proceeds from genotype -> phenotype.
Reverse genetics has been applied successfully to
• plants
• mice
• C. elegans
• zebrafish
For example, the function of a mysterious gene sequence in Danio can be studied by
• synthesizing a short antisense oligonucleotide complementary to a section of the gene.
• The oligonucleotide is chemically-modified to make it more stable than a fragment of RNA.
• Binding to its complementary sequence on the messenger RNA (mRNA) produced by transcription of the animal's gene, blocks ("knocks down") gene expression by
• preventing translation or
• disrupting normal splicing of the mRNA.
Because we share so many similar gene sequences (orthologous genes) with Danio, if one can discover the function of the gene in Danio, then we have a better idea of the role of its ortholog in humans.
19.1.15: Monotremes
Monotremes are a small but remarkable group of mammals that consists of a single species of duckbill platypus (Ornithorhynchus anatinus) found in Australia and three (perhaps four) species of spiny anteaters (echidnas) found in Australia and New Guinea.
These animals retain several traits of their therapsid ancestors including
• a cloaca - the final segment of the digestive tract into which both the urinary and reproductive tracts empty (monotreme = single hole);
• lay shelled eggs that undergo merobastic cleavage like that of reptiles (and birds) rather than the holoblastic cleavage of all other mammals.
Despite these reptilian features, the monotremes meet all the criteria of true mammals:
• milk secreted from mammary glands (but no nipples)
• hair
• teeth (only in the young; they are lost in adult montremes)
In the May 8 issue of Nature, a consortium of gene sequencers reported the results of sequencing the complete genome of the platypus. They identified 18,527 protein-coding genes distributed on 52 chromosomes.
The mix of mammalian and reptilian phenotypic features turns out to be reflected in the genome as well. Examples:
• The platypus has genes for egg yolk proteins that are also found in birds but not in therians.
• The gene content of their X chromosomes resembles that of the Z chromosome in birds, not the X chromosome of other mammals like us.
Other features of their genome reflect their unique biology:
• The platypus produces a venom with genes which in other mammals encode for antimicrobial peptides called defensins.
• The platypus has some 1000 genes for receptors in its vomeronasal organ — far more than found in other mammals. The platypus hunts for food underwater and probably uses these receptors to detect prey (as well as using its electroreceptors for this purpose). | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/19%3A_The_Diversity_of_Life/19.01%3A_Eukaryotic_Life/19.1.14%3A_Zebrafish.txt |
Bacteria are microscopic organisms whose single cells have neither a membrane-enclosed nucleus nor other membrane-enclosed organelles like mitochondria and chloroplasts. Another group of microbes, the archaea, meet these criteria but are so different from the bacteria in other ways that they must have had a long, independent evolutionary history since close to the dawn of life. In fact, there is considerable evidence that you are more closely related to the archaea than they are to the bacteria!
Properties of Bacteria
• prokaryotic (no membrane-enclosed nucleus)
• no mitochondria or chloroplasts
• a single chromosome
• a closed circle of double-stranded DNA
• with no associated histones
• If flagella are present, they are made of a single filament of the protein flagellin; there are none of the "9+2" tubulin-containing microtubules of the eukaryotes.
• Ribosomes differ in their structure from those of eukaryotes
• Have a rigid cell wall made of peptidoglycan.
• The plasma membrane (in Gram-positive bacteria) and both membranes in Gram-negative bacteria are phospholipid bilayers but contain no cholesterol or other steroids.
• No mitosis
• Mostly asexual reproduction
• Any sexual reproduction very different from that of eukaryotes; no meiosis
• Many bacteria form a single spore when their food supply runs low. Most of the water is removed from the spore and metabolism ceases. Spores are so resistant to adverse conditions of dryness and temperature that they may remain viable even after 50 years of dormancy.
Classification of Bacteria
Until recently classification has done on the basis of such traits as:
• shape
• bacilli: rod-shaped
• cocci: spherical
• spirilla: curved walls
• ability to form spores
• method of energy production (glycolysis for anaerobes, cellular respiration for aerobes)
• nutritional requirements
• reaction to the Gram stain
Figure 19.2.1.1 Gram positive and negative bacteria
Gram-positive bacteria are encased in a plasma membrane covered with a thick wall of peptidoglycan. Gram-negative bacteria are encased in a triple-layer. The outermost layer contains lipopolysaccharide (LPS).
• The bacterial cells are first stained with a purple dye called crystal violet.
• Then the preparation is treated with alcohol or acetone.
• This washes the stain out of Gram-negative cells.
• To see them now requires the use of a counterstain of a different color (e.g., the pink of safranin).
• Bacteria that are not decolorized by the alcohol/acetone wash are Gram-positive.
Although the Gram stain might seem an arbitrary criterion to use in bacterial taxonomy, it does, in fact, distinguish between two fundamentally different kinds of bacterial cell walls and reflects a natural division among the bacteria. More recently, genome sequencing, especially of their 16S ribosomal RNA (rRNA), has provided additional insights into the evolutionary relationships among the bacteria.
Gram-positive Bacteria
Firmicutes
Comparison of their sequenced genomes reveals that all the Gram-positive rods and cocci as well as the mycoplasmas belong to a single clade that has been named the Firmicutes.
Gram-Positive Rods
Aerobic Gram-Positive Rods
• Bacillus anthracis/cereus/thuringiensis. These organisms differ mainly in the plasmids they contain.
• B. anthracis causes anthrax. Currently the biological agent favored by terrorists. Its 2 plasmids contain the genes needed to synthesize
• a capsule which (like those of pneumococci) makes it resistant to phagocytosis
• the three components of the toxin that causes the disease symptoms
• B. thuringiensis — the organism, its toxin, and even the gene (also plasmid-encoded) for the toxin are used as biocontrol agents against a variety of insect pests.
• Bacillus subtilis. A common soil bacterium. Its chromosome contains 4,214,814 bp of DNA encoding 4,100 genes.
• Lactobacillus. Several species are used to convert milk into cheese, butter, and yogurt.
Anaerobic Gram-Positive Rods
• Clostridium tetani. Clostridia are spore-forming obligate anaerobes. The spores of C. tetani are widespread in the soil and often get into the body through wounds. Puncture wounds (e.g., by splinters or nails) are particularly dangerous because they provide the anaerobic conditions needed for germination of the spores and growth of the bacteria.
C. tetani liberates a toxin that blocks transmitter release (by destroying the SNAREs needed) at inhibitory synapses in the spinal cord and brain. This interferes with the reciprocal inhibition of antagonistic pairs of skeletal muscles so the victim suffers violent muscle spasms. Fortunately, the disease - called tetanus - is now rare in developed countries, thanks to almost universal immunization against the toxin. Chemical alteration of the toxin produces a toxoid that still retains the epitopes of the toxin. Incorporated in a vaccine, the toxoid provides a relatively long-lasting (~10 years) immunity against tetanus.
The bacteria in this group grow in characteristic colonies.
• Many cases of "food poisoning" are caused by staphylococci.
• Most Streptococci grow in chains. The electron micrograph (courtesy of the Naval Dental Research Institute, Great Lakes, IL) shows Streptococcus mutans, a common inhabitant of the mouth.
Streptococci cause
• "strep throat"
• impetigo
• middle ear infections
• scarlet fever (a result of a toxin produced by the organism)
• rheumatic fever
• a rare form of toxic shock syndrome
• Pneumococci. The cells of these streptococci grow in pairs. Streptococcus pneumoniae causes bacterial pneumonia. This was once a major killer — especially of the aged and infirm — but today there is an effective vaccine and any infections that do occur usually respond quickly to antibiotics.
Mycoplasmas
Mycoplasmas have the distinction of being the smallest living organisms. They are so small (0.1 µm) that they can be seen only under the electron microscope. Mycoplasmas are obligate parasites; that is, they can live only within the cells of other organisms. They are probably the descendants of Gram-positive bacteria who have lost their peptidoglycan wall as well as much of their genome — now depending on the gene products of their host.
The DNA sequences of the complete genomes of seven mycoplasmas have been determined, including
• Mycoplasma genitalium has 580,073 base pairs of DNA encoding 525 genes (485 for proteins; the rest for RNAs).
• Mycoplasma urealyticum has 751,719 base pairs of DNA encoding 651 genes (613 for proteins; 39 for RNAs).
• Mycoplasma pneumoniae has 816,394 base pairs of DNA encoding 679 genes.
How many genes does it take to make an organism?
The scientists at The Institute for Genomic Research (now known as the J. Craig Venter Institute - JCVI) who determined the Mycoplasma genitalium sequence followed this work by systematically destroying its genes (by mutating them with insertions) to see which ones are essential to life and which are dispensable. Of the 485 protein-encoding genes, they have concluded that only 381 of them are essential to life.
Workers at the JCVI have also succeeded in synthesizing the complete genome of one species of mycoplasma, inserted this into a second species, which converted the second species into the first.
Actinobacteria
Most of these Gram-positive organisms grow as thin filaments - like a mold - rather than as single cells. In fact, they were long thought to be fungi and were called actinomycetes. But fungi are eukaryotes and the actinobacteria are not.
Actinobacteria dominate the microbial life in soil where they play a major role in the decay of dead organic matter. Many of them have turned out to be the source of valuable antibiotics, including streptomycin, erythromycin, and the tetracyclines.
Mycobacteria and Corynebacteria
These Gram-positive organisms are closely related to the actinobacteria and often classified with them. They include three important human pathogens:
• Mycobacterium tuberculosis is the agent of tuberculosis (TB). TB is estimated to have killed 2 million people in 2007. Under ideal conditions, a single bacterium can cause infection. AIDS patients are especially at risk.
Its genome contains 4,411,532 bp of DNA encoding some 3,959 genes.
• Mycobacterium leprae causes leprosy. Its genome contains 3,268,203 bp of DNA encoding only 1,604 genes.
Although a close relative of M. tuberculosis (they share 1,439 genes), much of its DNA encodes pseudogenes, genes that no longer make a functional product. M. leprae is an obligate intracellular parasite; it has never been cultured in vitro. This is probably because it has abandoned many of the genes needed for an independent existence choosing instead to depend on the genes of its host cell.
• Corynebacterium diphtheriae causes diphtheria. As in tetanus, it isn't the growth of the organism (in the throat) that is dangerous but the toxin it liberates. The toxin is the product of a latent bacteriophage in the bacterium. It catalyzes the inactivation of a factor necessary for amino acids to be added to the polypeptide chain being synthesized on the ribosome. Sensibly enough, the toxin has no such effect on the translation machinery of bacteria (or of chloroplasts and mitochondria).
Treatment of the toxin with formaldehyde converts it into a harmless toxoid. Immunization with this toxoid — usually incorporated along with tetanus toxoid and pertussis antigens in a "triple vaccine" (DTP) - protects against the disease.
Gram-negative Bacteria
The Proteobacteria
This large group of bacteria form a clade sharing related rRNA sequences. They are all Gram-negative but come in every shape (rods, cocci, spirilla). They are further subdivided into 5 clades: alpha-, beta-, gamma-, delta-, and epsilon proteobacteria.
Alpha (α) Proteobacteria.
Some examples:
• Rickettsias. These bacteria are too small to be clearly seen under the light microscope. Almost all are obligate intracellular parasites. This means that they can only grow and reproduce while within the living cells of their host - certain arthropods (ticks, mites, lice, fleas) and mammals.
• Rickettsia prowazekii causes typhus fever when it is transmitted to humans by lice.
• Rocky Mountain spotted fever is a rickettsial disease transmitted by ticks.
The mitochondria of eukaryotes probably evolved from endosymbiotic bacteria. Because of the similarities of their genomes, rickettsias may be the closest relatives to the ancestors of mitochondria.
• Rhizobia. These bacteria live in a mutualistic relationship with the roots of legumes where they are able to "fix" nitrogen (N2) in the air into compounds that can be used by living things.
• Magnetospirillum magnetotacticum
• Agrobacterium tumefaciens
Beta (β) Proteobacteria
• Sulfur bacteria.
Certain colorless bacteria share the ability of chlorophyll-containing organisms to manufacture carbohydrates from inorganic raw materials, but they do not use light energy for this. These so-called chemoautotrophic bacteria secure the necessary energy by oxidizing some reduced substance present in their environment. The free energy released by the oxidation is harnessed to the manufacture of food.
For example, some chemoautotrophic sulfur bacteria oxidize H2S in their surroundings (e.g., the water of sulfur springs) to produce energy:
2H2S + O2 → 2S + 2H2O; ΔG = -100 kcal
They then use this energy to reduce carbon dioxide to carbohydrate (like the photosynthetic purple sulfur bacteria)
2H2S + CO2 → (CH2O) + H2O + 2S
• This chemoautotroph oxidizes NH3 (produced from proteins by decay bacteria) to nitrites (NO2). This provides the energy to drive their anabolic reactions. The nitrites are then converted (by other nitrifying bacteria) into nitrates (NO3), which supply the nitrogen needs of plants.
• Three important human pathogens among the β-proteobacteria.
• Neisseria meningitidis.
Causes meningococcal meningitis, an extremely serious infection of the meninges that occasionally occurs in very young children and in military camps. There is a vaccine that is effective against several strains but unfortunately not the most dangerous one.
• Neisseria gonorrhoeae. Causes gonorrhea, one of the most common sexually-transmitted diseases (STDs): over 300,000 cases were reported in the U.S. in 2009. In males, the bacterium invades the urethra causing a discharge of pus and often establishes itself in the prostate gland and epididymis. In females, it spreads from the vagina to the cervix and fallopian tubes. If the infection is untreated (penicillin is usually effective although strains resistant to it are now being encountered), the resulting damage to the fallopian tubes may obstruct the passage of eggs and thus cause sterility.
• Bordetella pertussis; the cause of "whooping cough".
Gamma (γ) Proteobacteria
The largest and most diverse subgroup of the proteobacteria.
Some examples
• Escherichia coli. The most thoroughly-studied of all creatures (possibly excepting ourselves). Its entire genome has been determined down to the last nucleotide: 4,639,221 base pairs of DNA encoding 4,377 genes. Lives in the human colon, usually harmlessly. However, water or undercooked food contaminated with the O157:H7 strain has caused severe - occasionally fatal - infections.
• Salmonella enterica. Two major human pathogens:
• Salmonella enterica var Typhi. Causes typhoid fever, a serious systemic infection occurring only in humans. This microbe is also known as Salmonella typhi.
• Salmonella enterica var Typhimurium. Confined to the intestine, it is a frequent cause of human gastrointestinal upsets but is also found in many other animals (that are often the source of the human infection). Also known as Salmonella typhimurium.
• Vibrio cholerae. Causes cholera, one of the most devastating of the intestinal diseases. The bacteria liberate a toxin that causes massive diarrhea (10–15 liters per day) and loss of salts. Unless the water and salts are replaced quickly, the victim may die (of shock) in a few hours. Like other intestinal diseases, cholera is contracted by ingestion of food or, more often, water that is contaminated with the bacteria.
• Pseudomonas aeruginosa. A common inhabitant of soil and water, it can cause serious illness in humans with
• defective immune systems
• serious burns
• cystic fibrosis
Frequently encountered in hospitals and resistant to most antibiotics and disinfectants.
• Yersinia pestis. This bacillus causes bubonic plague. It is usually transmitted to humans by the bite of an infected flea. As it spreads into the lymph nodes, it causes them to become greatly swollen, hence the name "bubonic" (bubo — swelling of a lymph node) plague. Once in the lungs, however, the bacteria can spread through the air causing the rapidly lethal (2–3 days) "pneumonic" plague. Untreated, ~30% of the cases of bubonic plague are fatal, and the figure for the pneumonic form reaches 100%. The recurrent epidemics of the "black death" in Europe from 1347–1351, which killed off at least 30% of the population, was caused by this organism. DNA sequencing of samples retrieved from the bodies of plague victims of that era confirm this diagnosis. Although no major epidemics have occurred in this century, the threat is not entirely over. Yersinia pestis still flourishes in some rodent populations in the western U. S. and causes a dozen or so cases of human plague - primarily among small game hunters -each year.
• Francisella tularensis causes tularemia. This is primarily a disease of small mammals, but about 100 people become infected each year in the United States. Most cases occur in south-central states (KS, MO, OK, AR). However, the import of infected rabbits by game clubs has introduced the disease to Cape Cod and Martha's Vineyard in Massachusetts. In the summer of 2000, 15 people became ill (one died) on the island. All seem to have acquired their infection as they used lawn mowers and brush cutters that presumably stirred up the organism from the carcasses of infected animals.
• Haemophilus influenzae was once thought to cause influenza. It does not, but it can cause bacterial meningitis and middle ear infections in children and pneumonia in adults — especially those whose resistance is lowered by other diseases (e.g., AIDS). There is now an effective vaccine against the most dangerous strains. The complete genome of Haemophilus influenzae is known: 1,830,138 bp of DNA encoding 1,743 genes.
• Purple Sulfur Bacteria Like green plants, these bacteria are photosynthetic, using the energy of sunlight to reduce carbon dioxide to carbohydrate. Unlike plants, however, they do not use water as a source of electrons.
In the process, they produce elemental sulfur (often - as seen in this photomicrograph of Chromatium - stored as granules within the cell). [Image from H. G. Schlegel and N. Pfennig, Arch. Microbiol. 38[1], 1961.]
Photosynthetic bacteria contain special types of chlorophylls (called bacteriochlorophylls) incorporated into membranes. With this machinery, they can run photosystem I but not photosystem II (which explains their inability to use water as a source of electrons). Most photosynthetic bacteria are obligate anaerobes; they cannot tolerate free oxygen. Thus they are restricted to such habitats as the surface of sediments at the bottom of shallow ponds and estuaries. Here they must make do with whatever radiant energy gets through the green algae and aquatic plants growing above them. However, the absorption spectrum of their bacteriochlorophylls lies mostly in the infrared region of the spectrum so they can trap energy missed by the green plants above them.
Delta (δ) Proteobacteria
This group contains the myxobacteria. They are found in vast numbers in soil and are major players in the decay of organic matter.
Epsilon (ε) Proteobacteria
Two members of this small group that are human pathogens:
• Helicobacter pylori, the main cause of stomach ulcers
• Campylobacter jejuni; the bacterium most frequently implicated in gastrointestinal upsets.
Bacteroidetes
Two notorious examples:
• Treponema pallidum (right), the cause of syphilis, one of the most dangerous of the sexually transmitted diseases (STDs). (Image courtesy of Harry E. Morton.)
• Borrelia burgdorferi is transmitted to humans through the bite of a deer tick causing Lyme disease (over 30,000 cases — the largest number up to then — were reported in the U.S. in 2009).
Both these organisms have had their complete genomes sequenced.
Chlamydiae
Chlamydiae are also obligate intracellular parasites (they cannot make their own ATP).
• Its genome contains 1,042,519 bp of DNA encoding 894 genes. In 2008, over 1.2 million cases were reported in the U. S., and this is probably only half of the true total. The infection is usually spread by sexual intercourse making it the most common sexually-transmitted disease (STD). It is easily cured if diagnosed, but many infections remain untreated and, in females, are a major cause of pelvic inflammatory disease. This causes scarring of the uterus and fallopian tubes and often results in infertility.
Mothers can pass the infection on to their newborn babies causing serious eye disease and pneumonia. To avoid this, pregnant women are usually tested for chlamydia and treated with antibiotics if they are infected.
• Chlamydia psittaci usually infects birds, but can infect their human contacts causing psittacosis (a.k.a. ornithosis).
Cyanobacteria (blue-green algae)
Unlike other photosynthetic bacteria, cyanobacteria
• use chlorophyll a (as do plants)
• use water as the source of electrons to reduce CO2 to carbohydrate (because they have photosystem II as well as photosystem I).
CO2 + 2H2O → (CH2O) + H2O + O2
It is estimated that cyanobacteria are responsible for ~ 25% of the photosynthesis occurring on our planet.
The micrograph is of Oscillatoria, a filamentous cyanobacterium (magnified about 800 times). Each disk in the chains is one cell.
Cyanobacteria also contain two antenna pigments:
• blue phycocyanin (making them "blue-green")
• red phycoerythrin (The Red Sea gets its name from the periodic blooms of red-colored cyanobacteria.)
These two pigments also occur in red algae. Their chloroplasts (in fact probably all chloroplasts) evolved from an endosymbiotic cyanobacterium. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/19%3A_The_Diversity_of_Life/19.02%3A_Microbes/19.2A%3A_Bacteria.txt |
When these microscopic organisms were first discovered (in 1977), they were considered bacteria. However, when their ribosomal RNA was sequenced, it became obvious that they bore no close relationship to the bacteria and were, in fact, more closely related to the eukaryotes (including ourselves!) For a time they were referred to as archaebacteria, but now to emphasize their distinctness, we call them Archaea. They have also been called Extremophiles in recognition of the extreme environments in which they have been found:
• thermophiles that live at high temperatures
• hyperthermophiles that live at really high temperatures (present record is 121°C!)
• psychrophiles that like it cold (one in the Antarctic grows best at 4°C)
• halophiles that live in very saline environments (like the Dead Sea)
• acidophiles that live at low pH (as low as pH 1 and who die at pH 7!)
• alkaliphiles that thrive at a high pH.
Most of the >250 named species that have been discovered so far have been placed in two groups: Euryarchaeota and Crenarchaeota
Euryarchaeota
There are three main groups: Methanogens, Halophiles. and Thermoacidophiles.
Methanogens
These are found living in such anaerobic environments as
• the muck of swamps and marshes
• the rumen of cattle (where they live on the hydrogen and $\ce{CO2}$ produced by other microbes living along with them)
• our colon (large intestine)
• sewage sludge
• the gut of termites
They are chemoautotrophs; using hydrogen as a source of electrons for reducing carbon dioxide to food and giving off methane ("marsh gas", $\ce{CH4}$) as a byproduct.
$\ce{4H2 + CO2 -> CH4 + 2H2O} \nonumber$
Two methanogens that have had their complete genomes sequenced:
• Methanocaldococcus jannaschii
• Methanothermobacter thermoautotrophicus
Halophiles
These are found in extremely saline environments such as the Great Salt Lake in the U.S. and the Dead Sea. They maintain osmotic balance with their surroundings by building up the solute concentration within their cells.
Thermoacidophiles
As their name suggests, these like it hot and acid (but not as hot as some of the Crenarchaeota!). They are found in such places as acidic sulfur springs (e.g., in Yellowstone National Park) and undersea vents ("black smokers").
Crenarchaeota
The first members of this group to be discovered like it really hot and so are called hyperthermophiles. One can grow at 121°C (the same temperature in the autoclaves used to sterilize culture media, surgical instruments, etc.). Many like it acid as well as hot and live in acidic sulfur springs at a pH as low as 1 (the equivalent of dilute sulfuric acid). These use hydrogen as a source of electrons to reduce sulfur in order to get the energy they need to synthesize their food (from CO2).
Aeropyrum pernix is one member of the group that has had its genome completely sequenced. Other members of this group seem to make up a large fraction of the plankton in cool, marine waters and the microbes in both soil and the ocean that convert ammonia into nitrites (nitrification).
Evolutionary Position of the Archaea
The archaea have a curious mix of traits characteristic of bacteria as well as traits found in eukaryotes. The table summarizes some of them.
Eukaryotic Traits Bacterial Traits
• DNA replication machinery
• histones
• nucleosome-like structures
• Transcription machinery
• RNA polymerase
• TFIIB
• TATA-binding protein (TBP)
• Translation machinery
• initiation factors
• ribosomal proteins
• elongation factors
• poisoned by diphtheria toxin
• single, circular chromosome
• operons
• no introns
• bacterial-type membrane transport channels
• Many metabolic processes
• energy production
• nitrogen-fixation
• polysaccharide synthesis
What can we conclude from this collection of traits?
Many traits found in the bacteria first appeared in the ancestors of all the present-day groups. The split leading to the archaea and the eukaryotes occurred after the bacteria had gone their own way. However, the acquisition by eukaryotes of mitochondria (probably from an ancestor of today's rickettsias) and chloroplasts (from cyanobacteria) occurred after their line had diverged from the archaea (i.e., the endosymbiosis hypothesis).
As more and more genes are sequenced, it appears that the line that eventually produced eukaryotes split off after the line leading to the euryarchaeota. If that is the case, Archaea is a paraphyletic group, and we shared a common ancestor with the other archaea more recently than they (and we) did with the euryarchaeota.
Economic Importance of the Archaea
Because they have enzymes that can function at high temperatures, considerable effort is being made to exploit the archaea for commercial processes such as providing enzymes to be added to detergents (maintain their activity at high temperatures and pH) and an enzyme to covert corn starch into dextrins. Archaea may also be enlisted to aid in cleaning up contaminated sites, e.g., petroleum spills. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/19%3A_The_Diversity_of_Life/19.02%3A_Microbes/19.2B%3A_Archaea.txt |
Humans, and our domestic animals, can serve as hosts to a wide variety of disease-causing organisms (pathogens) including bacteria, viruses, fungi, protozoans, helminths (worms). This page will examine only those chemical agents that are used to combat bacterial pathogens.
The Problem
There are many chemicals that are lethal to bacteria - cyanide does a good job — but they cannot be used to cure infections because they are lethal to the host as well. The problem, then, is to find substances that attack a metabolic pathway found in the bacterium but not in the host. This is not an insurmountable problem for bacterial pathogens because they differ in many respects from eukaryotes.
The Solution
Natural products. A number of natural products, penicillin for example, have been discovered that are antibiotics suitable for therapy. They were originally discovered as secretions of fungi or soil bacteria. Soils are complex ecosystems, and it is not surprising that its inhabitants have evolved chemical defenses against each other.
The photo (courtesy of Merck & Co., Inc.) shows how the growth of bacteria on the agar in a culture dish has been inhibited by the three circular colonies of the fungus Penicillium notatum. The antibiotic penicillin, diffusing outward from the colonies, is responsible for this effect. Today, penicillin is made from cultures of Penicillium chrysogenum that has been specially adapted for high yields.
• Semi-synthetic products. These are natural products that have been chemically modified in the laboratory (and pharmaceutical facility) to
• improve the efficacy of the natural product
• reduce its side effects
• circumvent developing resistance by the targeted bacteria
• expand the range of bacteria that can be treated with it
• Completely synthetic products. The sulfa drugs are examples.
Sulfa Drugs and Folic Acid Analogs
Sulfa Drugs
Sulfanilamide was the first antibacterial agent. Many other sulfa drugs (such as sulfamethoxazole) have since come into use.
Both bacteria and their human hosts require folic acid for nucleic acid synthesis (it is converted into purines and thymidine) as well as protein synthesis (precursor of the amino acids methionine and glycine). However, bacteria synthesize their folic acid starting with para-aminobenzoic acid (PABA), while we must ingest our folic acid already formed; that is, for us it is a vitamin.
Sulfanilamide, and the other sulfa drugs, are analogs of PABA; they compete with PABA and, when chosen, block the synthesis of folic acid. Mammals ignore PABA and its analogs and thus can tolerate sulfa drugs.
Folic Acid Analogs
These synthetic molecules block the final step in the conversion of PABA to folic acid so they, too, block nucleotide and protein synthesis in bacteria but not in mammals. Trimethoprim is one of several in current use. These folic acid analogs are often used in combination with a sulfa drug.
The Beta-Lactams
The beta-lactams include the
• penicillins such as
• penicillin G (a natural product) produced by the fungus Penicillium chrysogenum
• ampicillin (a semi-synthetic)
• amoxicillin (semi-synthetic)
• cephalosporins There are over two dozen of them in current use. Most are semi-synthetics derived from the secretion of the mold Cephalosporium. Some examples:
• cephalexin (e.g., Keflex®)
• cefaclor (e.g., Ceclor®)
• cefixime (e.g., Suprax®)
• carbapenems such as
• meropenem (Merrem®)
• ertapenem (Invanz®)
The beta-lactams all work by interfering with the synthesis of the bacterial cell wall — a structure that is not found in eukaryotes. The walls of bacteria are made of a complex polymeric material called peptidoglycan.
Peptidoglycan contains both amino acids and amino sugars. The amino sugars are of two kinds
• N-acetylglucosamine (NAG) and its close relative
• N-acetylmuramic acid (NAM).
These two form a linear polymer of NAG alternating with NAM. They are linked by a glycosidic bond between the #1 and #4 carbons (this is the linkage attacked by lysozyme) and are oriented in the same way they are in cellulose. Side chains containing 4 or 5 amino acids are attached to each NAM. These form covalent bonds with amino acids in adjacent chains. The bonds may be direct to the next chain or include additional peptide cross bridges (e.g., 5 glycine residues) which extend to chains in the same plane (shown here) as well as to chains above and below.
This elaborate, covalently cross-linked structure provides the great strength of the cell wall. It also leads to the remarkable conclusion that the bacterial cell wall meets the definition of a single molecule!
The beta-lactam antibiotics bind to and inhibit enzymes needed for the synthesis of the peptidoglycan wall. While they have little effect on resting bacteria, they are lethal to dividing bacteria as defective walls cannot protect the organism form bursting in hypotonic surroundings.
Aminoglycosides
These are products of actinomycetes (soil bacteria) or semi-synthetic derivatives of the natural products.
Examples are:
• streptomycin
• kanamycin
• neomycin
• gentamycin
The 70S bacterial ribosome differs in several ways from the 80S eukaryotic ribosome. The aminoglycosides bind to the 30S subunit of the bacterial ribosome and interfere with the formation of the initiation complex. They also cause misreading of the mRNA. Although the eukaryotic ribosome in the cytosol is relatively unaffected by these drugs, ribosomes in the mitochondria are 70S and sensitive to their effects.
Tetracyclines
These are natural products derived from soil actinomycetes or their semi-synthetic derivatives. Examples:
• chlortetracycline (aureomycin®)
• oxytetracycline (terramycin®)
• doxycycline
• tigecycline (Tygacil®)
Tetracyclines bind to the 30S subunit of the bacterial ribosome. They prevent the transfer of activated amino acids to the ribosome so protein synthesis is halted.
Macrolides, Lincosamides, Streptogramins, and Ketolides
The Chink in the Armor = the bacterial ribosome
These antibiotics bind to the large (50S) subunit of the bacterial ribosome where they block the growing peptide chain from exiting the ribosome thus severely hindering protein synthesis. Because of their similar action, the development of antibiotic resistance to one usually extends to all the others.
Macrolides
Macrolides are also products of actinomycetes (soil bacteria) or semi-synthetic derivatives of them. Erythromycin, azithromycin (Zithromax®), and clarithromycin (Biaxin®) are a commonly-prescribed macrolides.
Lincosamides
The first member of this group was also isolated from a soil actinomycete (found near Lincoln, Nebraska). A semi-synthetic derivative, called clindamycin (Cleocin®), is now widely used against Gram-positive bacteria.
Streptogramins
Quinupristin and dalfopristin are examples. As of 1 October 1999, they will be sold as a mixture under the trade name Synercid. Combined, they show great promise in treating certain infections resistant to vancomycin- currently the antibiotic of last resort for some hospital-acquired infections.
Ketolides
Ketolides are derivatives of macrolides. Telithromycin (Ketek®) is an example. Ketolides also bind to the 50S subunit of the bacterial ribosome. In so doing they cause it to induce frameshifts during translation. Bacteria that have become resistant to macrolides, lincosamides, and streptogramins are still susceptible to ketolides.
Fluoroquinolones
Ciprofloxacin (Cipro®), levofloxacin and norfloxacin are examples. Cipro is the preferred antibiotic for people who have been intentionally exposed to anthrax, although some other antibiotics appear to be equally effective.
The Chink in the Armor = DNA topoisomerases
The fluoroquinolones block the action of two bacterial topoisomerases - enzymes that relieve the coils that form in DNA when the helix is being opened in preparation for replication or transcription or repair. The topoisomerases in eukaryotes are not affected.
Polypeptides
The most common of these is polymixin E (also known as colistin). It behaves as a detergent, increasing the permeability of the membranes that encase bacteria and causing the contents of the bacterial cell to leak out.
Rifampin
This semi-synthetic antibiotic binds to the bacterial RNA polymerase and prevents it from carrying out its role in transcription. Its affinity for the equivalent eukaryotic enzyme is much lower. Rifampin is also known as rifampicin.
Mupirocin
This antibiotic blocks the action of the bacterial isoleucine tRNA synthetase, the enzyme responsible for attaching the amino acid isoleucine (Ile) to its tRNA in preparation for protein synthesis, so protein synthesis is inhibited. It spares the equivalent eukaryotic enzyme.
Cycloserine
Cycloserine inhibits synthesis of the bacterial cell wall but by a different mechanism than the beta-lactam antibiotics discussed above. Cycloserine is an analog of D-alanine and blocks the incorporation of D-alanine into the peptide bridges in the bacterial cell wall. It is derived from an actinomycete.
Aminocyclitols
These products of another actinomycete achieve their effect by interfering with the 30S subunit of the bacterial ribosome. Spectinomycin (trade name = Trobicin®) is an example. It is particularly effective against the gonococcus, the bacterium that causes the sexually-transmitted disease (STD) gonorrhea.
Glycopeptides
Glycopeptides also interfere with the synthesis of the bacterial cell wall but by a different mechanism than the beta-lactams.
Vancomycin is a widely-used glycopeptide in the U.S. It binds to the D-alanines on the precursors of the peptidoglycan cross bridges preventing their cross-linking. It has become the antibiotic of last resort as resistance to the other antibiotics has become more and more common.
Oxazolidinones
The first of these new antibiotics, linezolid (Zyvox®), was approved by the U.S. Food and Drug Administration on 19 April 2000. It is effective against many Gram-positive bacteria that have developed resistance to the older antibiotics.
Linezolid attacks a previously-unexploited chink in the bacterium's armor: the proper assembly of the two ribosomal subunits (30S and 50S). It does not affect eukaryotic ribosomes — and thus translation of mRNAs in the cytosol. However, it does affect the bacterial-like mitochondrial ribosomes and can interfere with the synthesis of those mitochondrial proteins synthesized by them.
Lipopeptides
These are natural compounds derived from a species of Streptomyces. The one now in clinical use is daptomycin (Cubicin®). It is effective against Gram-positive bacteria. It attacks another previously-unexploited chink in the bacterial armor — the integrity of its cell membranes.
So far there is no evidence of bacteria developing resistance against it.
Resistance to Antibiotics
None of the antibiotics discussed above is effective against all bacterial pathogens.
Intrinsic resistance
Some bacteria are intrinsically resistant to certain of the antibiotics. Example: Gram-positive bacteria are much less susceptible to polymixins than Gram-negative bacteria. [The "Gram" designations refer to the behavior of the bacteria when stained with the Gram stain; this behavior is a reflection of the very different organization of their cell walls.]
Acquired resistance
Many bacteria acquire resistance to one or more of the antibiotics to which they were formerly susceptible.
Example: In the U.S. in the decade from 1985–1995, resistance of Shigella (which causes gastrointestinal illness) to ampicillin grew from 32% to 67%. And, while only 7% of these isolates were resistant to the combination of sulfamethoxazole and trimethoprim at the start of the decade, that figure had grown to 35% by the end of the decade.
Bacteria develop resistance by acquiring genes encoding proteins that protect them from the effects of the antibiotic. In some cases the genes arise by mutation; in others, they are acquired from other bacteria that are already resistant to the antibiotic. The genes are often found on plasmids which spread easily from one bacterium to another - even from one species of bacterium to another.
Examples:
• Synthesis of the enzyme penicillinase - or other beta-lactamases - provides protection from the beta-lactam antibiotics. These enzymes break the beta-lactam ring at the position shown with the green arrow in the diagram of penicillin G.
• Likewise synthesis of cephalosporinases defeats the cephalosporins.
• Defeating quinolones:
• Some bacteria do this by modifying their DNA gyrase.
• Others, e.g., Mycobacterium tuberculosis, develop quinolone resistance by synthesizing a protein that resembles a short length of DNA. This protein binds the gyrase so it cannot form the DNA/gyrase complex that is the target of quinolone action.
• Some bacteria synthesize "pumps" in their plasma membrane through which they remove antibiotics like tetracyclines from the interior of the cell.
• Bacteria may methylate their ribosomes obscuring the target of antibiotics (e.g., erythromycin) that ordinarily bind to and inactivate the ribosome — or conversely
• they may enzymatically modify the antibiotic (e.g., kanamycin) so it can no longer "see" its ribosomal target.
• Bacteria may modify the structure of their peptidoglycan wall and thus avoid the inhibitory effects of antibiotics like cycloserine.
An alarming number of human pathogens have acquired genes to combat all the presently-used antibiotics except vancomycin and recently vancomycin-resistant bacteria have appeared. These multidrug-resistant strains are particularly common in hospitals where antibiotic use is heavy, and the patients often have weakened immune systems.
Measuring Antibiotic Resistance
The figure illustrates the simplest method of the several available for measuring antibiotic resistance.
• A suspension of the bacteria to be tested (e.g. cultured from the infected patient) is spread over the surface of a petri dish containing a solid culture medium.
• Disks of several different antibiotics are pressed on the surface of the agar. The concentration of antibiotic in each type of disk is standardized.
• Incubate overnight.
• The bacteria will grown into a "lawn" except where an antibiotic to which they are sensitive has diffused out from its disk.
• Measure the diameter of any zones of inhibition that are formed.
What can you do to delay the spread of antibiotic resistance?
• Don't ask your doctor for an antibiotic to treat a viral disease (e.g., a cold) for which antibiotics are useless. (However, your doctor may prescribe an antibiotic if you are infected by an influenza virus - not to fight the virus but to protect you against a secondary bacterial infection of your damaged lungs.)
• Stay the course. Use all doses prescribed even though you are feeling better. This will minimize the opportunity to select for resistance among the bacteria that remain late in the infection.
• Don't save unused antibiotics for later self-medication.
Farmers can help as well by avoiding the use of antibiotics in their livestock that are similar to those used in humans. Antibiotics are widely used in healthy livestock to improve their growth rate (by an unknown mechanism).
An article in the 20 May 1999 issue of The New England Journal of Medicine documents the recent development of quinolone resistance in Campylobacter jejuni, the most frequent bacterial cause of gastroenteritis in humans. The rise coincides with the approval in 1995 of the use of quinolones by U. S. poultry farmers (chickens also become infected by C. jejuni). Similar recent increases in fluoroquinolone-resistant C. jejuni have been reported in the Netherlands and also in Spain (where as many as 50% of human infections are now caused by bacteria resistant to the antibiotic). In each country, the appearance of resistant strains followed the widespread introduction of quinolone treatment for animals.
Future Prospects
Drug companies - after many years of complacency - are now responding to the threat of antibiotic-resistant bacteria. Over a dozen new antibiotics are being developed and some have already reached clinical trials. Many of these are semi-synthetic modifications of already-existing antibiotics, including new
• beta-lactams
• macrolides
• glycopeptides
• quinolones
• modifications of vancomycin
Others are entirely new, attacking previously-unexploited chinks in the bacterial armor.
• Urea hydroxamates, that block the enzyme (peptide deformylase) that removes fMet from the finished protein so it can begin its work. (Eukaryotes do not begin translation with fMET.)
• Heteroaromatic polycycles (HARP) that bind to bacterial promoters preventing gene transcription. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/19%3A_The_Diversity_of_Life/19.02%3A_Microbes/19.2C%3A_Antibiotics.txt |
Escherichia coli is a bacterium that is a common - but certainly not the most abundant - inhabitant of the human colon. It also lives in the intestine of many other animals, wild as well as domestic.
Normally, E. coli does not cause disease although some strains frequently cause diarrhea in travelers, and it is the most common cause of urinary tract infections. One strain, designated O157:H7, is particularly virulent and has been responsible for several dangerous outbreaks in people eating contaminated food (usually undercooked hamburger).
Drinking water is tested for the presence of E. coli and related bacteria not because these bacteria are particularly dangerous but because they are an indication of contamination by sewage, and sewage may contain organisms (e.g., Salmonella, hepatitis A virus) that are dangerous.
E. coli is one of the most thoroughly studied of all living things. It is a favorite organism for genetic engineering as cultures of it can be made to produce unlimited quantities of the product of an introduced gene. Several important drugs (insulin, for example) are now manufactured in E. coli. However, E. coli cannot attach sugars to proteins so proteins requiring such sugars (e.g., glycoprotein hormones and clotting factors) have to be made in the cells of eukaryotes such as yeast cells and mammalian cells grown in cell culture.
Because E. coli lives in the human intestine, this has raised fears that genetically-engineered versions might escape from the laboratory (or factory) and take up residence in humans, producing a product that might be harmful. For this reason, genetic engineering is done only on strains of E. coli that have been deliberately weakened so that they cannot survive for long in humans.
The complete sequence of the genome of a harmless laboratory strain of E. coli (K-12) was reported in the 5 September 1997 issue of Science. The genome consists of a single molecule of DNA containing 4,639,221 base pairs. These encode 4288 proteins and 89 RNAs. Many of the genes were already known and the function of many others can be deduced from the similarity to known genes.
The complete sequence of the pathogenic strain O157:H7 was reported in the 25 January 2001 issue of Nature. It contains 5416 genes in 5.44 x 106 base pairs of DNA. Remarkably, these include 1,387 genes that are not present in its harmless laboratory relative E. coli K-12 (and K-12 has 528 genes that are not found in O157:H7). So here are two strains of the same species that differ in some 25% of their genes. Compare this with the difference between the genomes of humans and chimpanzees which probably is no more than 1%!)
19.2E: Anthrax
Anthrax is a disease caused by the bacterium Bacillus anthracis. It normally affects cattle, sheep, goats, etc. It is acquired from spores that remain viable in the environment (e.g. soil) for decades always able to germinate into active bacteria if they get into the body of a susceptible host. Humans can be infected by Bacillus anthracis, and if the spores enter by way of the lungs, the disease can be quickly fatal. These properties have made it one of the agents favored by bioterrorists.
Bacillus Anthracis. (CC BY-SA 4.0; BruceBlaus).
It is not the tissue-destructiveness of the active bacteria that is the problem but rather the toxin that they secrete. (This is like the illnesses caused by the bacilli that cause diphtheria, tetanus, and botulism.) The bacteria are susceptible to antibiotics; for example, Ciprofloxacin (Cipro®) is effective as are others such as doxycycline, but they must be given early before the toxin can produce symptoms. Once the toxin is in the system, it can be neutralized by giving antitoxin antibodies (conferring passive immunity). Presently these are harvested from donors who had received anthrax vaccine in the armed forces. But there is hope that monoclonal antibodies can be manufactured that will be able to provide protection.
The anthrax toxin is composed of three different proteins (encoded by genes on one of the two plasmids in the organism):
• PA ("protective antigen") It gets this name because it provides the epitopes that elicit protective antibodies in the anthrax vaccine.
• LF ("lethal factor")
• EF ("edema factor")
Infection
• PA molecules bind to receptors at the cell surface assembling in clusters of 7.
• LF and/or EF molecules then bind to these clusters.
• The complex is engulfed by receptor mediated endocytosis.
• The drop in pH in the endosome (endocytic vesicle) produces a change in the structure of the PA cluster enabling it to release its LF and EF into the cytosol.
• EF is an adenylyl cyclase which raises the intracellular concentration of cAMP inhibiting phagocytosis by neutrophils.
• As it name implies, LF in the cytosol so disturbs the machinery of the cell that it dies.
Future Prospects
In April of 2001, John Collier and his colleagues reported that several mutant versions of PA protected rats from death by the active anthrax toxin. The mutant molecules coassembled with normal PA molecules, and the complex was still able to bind LF and EF. However, the complex could not release LF or EF from the endosome, and the rats remained healthy. Perhaps one of these altered PA molecules can be enlisted in the fight against bioterrorism as both a vaccine to protect people before exposure and a treatment to block the lethal effects of the natural toxin after exposure.
Today's Anthrax Vaccine
The vaccine is made from an extract of a weakened strain of B. anthracis (it makes no surface capsule). The extract contains large amounts of PA, as well as some LF and EF.
Anthrax Strains
Scores of different strains of anthrax have been isolated from many parts of the world. While they share most of their harmful traits, their genomes differ in the number of repeated sequences of noncoding DNA. These are called VNTRs (for variable number of tandem repeats) and are simply longer versions of the short tandem repeats (STRs) now being used by law enforcement agencies for DNA fingerprinting of humans. DNA fingerprinting of any strain of anthrax used by bioterrorists may help track down its source. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/19%3A_The_Diversity_of_Life/19.02%3A_Microbes/19.2D%3A_E._coli.txt |
Bacillus thuringiensis is a bacterium that parasitizes the caterpillars of some harmful moths and butterflies. Spraying or dusting plants with spores of this bacterium appear to be environmentally safe ways to attack such pests as the gypsy moth, the tent caterpillar, and the tobacco hornworm (which also attacks tomatoes). The bacteria kill by a toxin which they secrete. The gene for this toxin has been introduced into some crop plants in an effort to protect them from insect attack without the need for spraying.
On the left is a cotton boll being attacked by a cotton bollworm. The cotton plant that produced the boll on the right contains and expresses the gene for the Bt toxin. The gene was introduced into the plant by genetic engineering. Transgenic cotton and corn (maize) containing the gene for Bt toxin were widely planted for the first time in 1996. By 2009, these crops had been planted on over 334 million acres (135x106 hectares) worldwide. In the United States over 70% of the cotton planted and 63% of the corn planted is now with transgenic varieties. Crops transgenic for Bt toxin have shown improved yields with greatly-reduced need for chemical insecticides. Not only does this reduce costs and possible health effects, but spares the natural enemies of other insect pests.
B. thuringiensis appears to be the same organism as Bacillus cereus, a usually harmless soil organism, and Bacillus anthracis, the cause of anthrax. What gives them their distinctive properties are the genes encoded by the plasmids they contain.
19.2G: The Rapid Identification of Microorganisms
The Need
• diagnosis of infection so that the appropriate treatment (e.g., an antibiotic) can be started.
• testing of food to ensure that it is not contaminated with infectious organisms like E. coli O157:H7 and Salmonella enterica
• to identify the biological agent such as anthrax and smallpox in a possible terrorist attack so that appropriate measures can be taken quickly
Methods
Culturing
• The oldest and still most common.
• For bacteria, spread samples on culture media and examine the resulting colonies for morphology and metabolic traits. For viruses, inoculate cultures of living cells.
• Disadvantage: it make take several days to learn the results.
Polymerase Chain Reaction (PCR)
• Extract DNA from the sample and perform PCR.
• Advantage: rapid (often less than an hour)
• Disadvantage: overly sensitive to presence of contaminants
Immunoassays
Use a method that exploits the specificity and sensitivity of the reaction between antigen and antibodies. Takes 15 minutes or longer.
Biosensors (CANARY)
In the 11 July 2003 issue of Science, a team of scientists at the Lincoln Laboratory in the U. S. reported a new method of rapid identification that exploits living cells. They call their method CANARY (for Cellular Analysis and Notification of Antigen Risks and Yields)
Their "biosensor" is a clone of B lymphocytes (B cells) that have been genetically engineered to express
• a B cell receptor for antigen (BCR) selected to interact with an epitope on the suspected agent. The BCR on their clones is surface IgM.
• aequorin, a protein extracted from the same jellyfish that produces green fluorescent protein.
• Aequorin emits light when it is exposed to calcium ions (Ca2+).
• One of the first events (within seconds) when BCRs bind to antigen is a rise in the level of calcium ions in the cytosol.
Procedure:
• Prepare the sample.
• Mix - in separate wells - with B-cell clones each specific for a different suspected agent.
• Place in a sensitive light detector.
• If a clone has a BCR for an epitope present in the sample, that clone will emit light within a few seconds.
Results:
• highly sensitive: can detect as few as 50 bacteria or 500 virions
• highly specific: can detect the agent even in the presence of related contaminating agents.
• fast: time elapsed from sample preparation to signal from the light detector is often less than 5 minutes. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/19%3A_The_Diversity_of_Life/19.02%3A_Microbes/19.2F%3A_Bacillus_Thuringiensis.txt |
• 19.3A: Viruses
Viruses are obligate intracellular parasites. Probably there are no cells in nature that escape infection by one or more kinds of viruses. Viruses that infect bacteria are called bacteriophages. Outside the cell, they consist of particles called virions.
• 19.3B: Influenza
• 19.3C: φX174
φX174 (phiX174) is a virus that infects the bacterium E. coli. Hence φX174 is a bacteriophage.
• 19.3D: Smallpox
Smallpox certainly qualified as one of the greatest scourges of humanity. It regularly killed 25% and sometimes as many as 50% of its victims. Introduced into Europe around the sixth century A.D., smallpox rivaled plague in its ability to decimate entire populations. Introduced into the New World in the sixteenth century, smallpox devastated the native populations and played a far greater role than weaponry in the Spanish Conquest.
• 19.3E: Retroviruses
The genome of retroviruses consists of RNA not DNA. HIV-1 and HIV-2, the agents that cause AIDS, are retroviruses.
19.03: Viruses
Viruses are obligate intracellular parasites. Probably there are no cells in nature that escape infection by one or more kinds of viruses. Viruses that infect bacteria are called bacteriophages. Outside the cell, they consist of particles called virions.
Virions range in size from as small as the poliovirus shown above magnified some 450,000 times (courtesy of A. R. Taylor), which is 30 nm in diameter (about the size of a ribosome) to as large as Pithovirus sibericum an amoeba-infecting virus which, at 1,500 nm, is larger than many bacteria.
• The virion consists of
• An outer shell, the capsid, made of protein. The capsid is responsible for
• protecting the contents of the core
• establishing what kind of cell the virion can attach to infecting that cell
Some capsids contain other ingredients (e.g., lipids, carbohydrates), but these are derived from their host cells.
• an interior core containing
• the genome; either DNA or RNA The genes are few in number (3–100 depending on the species). They encode those proteins needed for viral reproduction that the host cell will not supply.
• Often, one or more proteins (enzymes) needed to start the process of reproduction within the host cell.
Life Cycle
• The virion attaches to the surface of the host cell - usually binding to a specific cell surface molecule that accounts for the specificity of the infection. Example: HIV-1, the cause of AIDS, binds to the chemokine receptor CCR5 found on human lymphocytes and macrophages.
• Once inside the cell, the virions are uncoated.
• Viral genes begin to be expressed leading to the synthesis of proteins needed for
• replication of the genome
• synthesis of new proteins to make new capsids and cores.
• The details of these processes differ for different types of viruses and are described below for each type.
Viral Genomes
Either DNA or RNA, never both.
DNA viruses can be further divided into
• those that have their genes on a double-stranded DNA molecule (dsDNA). Example: smallpox
• those that have their genes on a molecule of single-stranded DNA (ssDNA). Example: Adeno-Associated Virus (AAV)
RNA viruses occur in four distinct groups:
1. Those with a genome that consists of single-stranded antisense RNA; that is, RNA that is the complement of the message sense. This is also called negative-stranded RNA. Examples: measles, Ebola
2. Those with a genome that consists of single-stranded sense RNA; that is, the RNA has message sense (can act as a messenger RNA - mRNA). This is also called positive-stranded RNA. Examples: poliovirus
3. Those with a genome made of several pieces of double-stranded RNA. Example: reovirus.
4. Retroviruses. Their RNA (also single-stranded) is copied by reverse transcriptase into a DNA genome within the host cell. Example: HIV-1
DNA Viruses
Genome is a molecule of double-stranded DNA
Examples:
• smallpox (variola)
• vaccinia (used to immunize against smallpox until the disease was eliminated from the planet)
• varicella-zoster (causes chicken pox the first time; shingles the second)
• herpesviruses
• herpes simplex viruses
• HSV-1 - usually infects the trigeminal nerves periodically causing "cold sores" on the lips and face
• HSV-2 - usually infects the genitals
• KSHV; causes Kaposi's sarcoma in AIDS patients and other people with suppressed immune systems. Also called human herpesvirus 8 (HHV-8).
• human cytomegalovirus (HCMV); most of us have it; can cause blindness - even death - in people with suppressed immune systems.
• Epstein-Barr virus (EBV); causes mononucleosis and has been implicated in the development of Burkitt's lymphoma (a cancer) and Hodgkin's disease. Its genome has been completely sequenced: 172,282 base pairs of DNA encoding 80 genes.
• adenoviruses; some 50 different strains infect humans; responsible for some cases of the common "cold". Two strains have been modified to serve as vectors in gene therapy trials.
• papilloma viruses; several dozen types infect humans and two of these, HPV-16 and HPV-18, can cause cancer.
• SV40; a virus that infects primate cells and causes tumors in rodent cells.
• Some bacteriophages
• T2 and T4; from which much early information about gene structure and expression was learned.
• lambda; a popular vector
The essential elements of the infective cycle of DNA bacteriophages consist of:
• The virions attach to the surface of their host cell (a).
• The proteins of the capsid inject the DNA core into the cell (b).
• Once within the cell, some of the bacteriophage genes (the "early" genes) are transcribed (by the host's RNA polymerase) and translated (by the host's ribosomes, tRNA, etc.) to produce enzymes that will make many copies of the phage DNA and will turn off (even destroy) the host's DNA.
• As fresh copies of phage DNA accumulate, other genes (the "late" genes) are transcribed and translated to form the proteins of the capsid (c).
• The stockpile of DNA cores and capsid proteins are assembled into complete virions (d).
• Another "late" gene is transcribed and translated into molecules of lysozyme. The lysozyme attacks the peptidoglycan wall (from the inside, of course).
• Eventually the cell ruptures and releases its content of virions ready to spread the infection to new host cells (e).
Hepatitis B
The genome of hepatitis B ("serum hepatitis") is also dsDNA, but its mode of replication is different from the other dsDNA viruses.
• Once inside its host cell (a liver cell), the virion core enters the nucleus.
• The viral DNA is transcribed (by the host's Pol II) into molecules of mRNA.
• These enter the cytoplasm where they are translated (again by host ribosomes, etc.) into the various proteins of the virus, including a viral reverse transcriptase.
• These components are assembled into new viral cores, and in each
• one molecule of mRNA is reverse transcribed into a single strand of DNA, which then serves as the template for the synthesis of the second strand.
Genome is single-stranded DNA
Examples:
• φX174 (phiX174), another famous bacteriophage (infects E. coli) that helped usher in the modern era of molecular genetics. Its single strand of DNA has 5,386 nucleotides and contains 11 protein-encoding genes.
• Adeno-associated virus (AAV). This virus, which can only grow in cells infected with adenovirus, shows great promise as a safe and effective vector for introducing therapeutic genes into human patients.
RNA Viruses
Negative-stranded RNA viruses:
Genome consists of one or more molecules of single-stranded "antisense" RNA.
Examples:
• measles
• mumps
• respiratory syncytial virus (RSV), parainfluenza viruses (PIV), and human metapneumovirus. (In the U.S., these close relatives account for hundreds of thousands of hospital visits each year, mostly by children.)
• rabies
• Ebola
• influenza
Method of replication
• In addition to its antisense RNA genome, the core of the virion contains an RNA replicase, which is an RNA-dependent RNA polymerase.
• Once released in the host cell, this polymerase makes many complementary copies of the genome, which are "sense" and serve as messenger RNAs.
• These are translated into the proteins needed to assemble fresh virions, e.g., capsid proteins and RNA polymerase.
Note that this strategy
• provides many copies of mRNA
• depends on the virion having its own RNA replicase (because the host cell does not) (So, naked RNA molecules of these viruses are not infectious — in contrast to the next group: the positive-stranded RNA viruses)
Positive-stranded RNA
Genome is a molecule of single-stranded "sense" RNA.
Examples:
• polioviruses
• rhinoviruses (frequent cause of the common "cold"; 99 different strains are known)
• noroviruses (frequent cause of outbreaks of gastrointestinal illness — especially in "closed" settings like cruise ships and nursing homes)
• coronaviruses (includes the agent of Severe Acute Respiratory Syndrome (SARS)
• rubella (causes "German" measles)
• yellow fever virus
• West Nile virus
• dengue fever viruses
• equine encephalitis viruses
• hepatitis A ("infectious hepatitis") and hepatitis C viruses
• tobacco mosaic virus (TMV)
Method of replication
• The "sense" RNA encodes an RNA replicase (an RNA-dependent RNA polymerase) that is translated by the host machinery (ribosomes, etc.) into the enzyme, which catalyzes the synthesis of large numbers of "antisense" replicative intermediates.
• These serve as templates for the synthesis of large numbers of mRNA molecules that
• are translated by the host cell machinery into the proteins needed to make fresh virions
• are incorporated into the new virions.
Double-stranded RNA
Examples:
• reovirus
• several plant viruses
Method of replication
The virus particle contains enzymatic machinery that transcribes each of the dsRNA molecules into a mRNA (complete with cap) and exports these into the cytosol of the infected cell.
Retroviruses
These viruses contain a reverse transcriptase that copies their RNA genome into DNA.
Examples:
• The Rous sarcoma virus (RSV)
• HIV-1 and HIV-2, that cause AIDS
• HTLV-1 and HTLV-2. 4–5% of the people infected with HTLV-1 develop adult T-cell leukemia/lymphoma (ATL).
Latent Viruses
Most of the infective cycles described for the various viruses end in the death of the host cell. Bacterial cells literally burst, a process called lysis, and similar infective cycles are called lytic cycles.
Lysogeny
In some cases, though, the events of the lytic cycle are not completed. An E. coli cell infected by a DNA bacteriophage may resume its normal existence, including reproducing itself.
Where has the virus gone?
It is still there and, in fact, is present in the descendants of the bacterium. That these cells still harbor the virus can be demonstrated by irradiating the cells with ultraviolet rays or treating them with certain chemicals. Such treatment restores the normal lytic cycle. The phage is said to have been "rescued" — hardly the case for its host!
The stable relationship between a bacteriophage and its host is called lysogeny. The viral DNA actually becomes replicated when the host's DNA is replicated prior to each cell division. During lysogeny, the phage is called a prophage.
Transduction
In some cases, the prophage DNA becomes inserted into the chromosome of its host. In fact, when the phage is "rescued", the released virions may contain some host genes as well as their own. When these virions infect new hosts, they insert these bacterial genes into them. This process of genetic transfer, a virus-mediated transformation, is called transduction.
What does the prophage do while it is a part of its host genome? It can express certain of its genes. For example, the gene that encodes diphtheria toxin is the property of a prophage in the diphtheria bacillus, not of the bacillus itself.
Some animal viruses can also establish latent infections. Simian virus 40 (SV40) is a DNA virus that produces
• a lytic infection in the kidney cells of the African green monkey (these cells are used to cultivate viruses in the lab)
• but a latent infection in the cells of humans, mice, rats, and hamsters. Like lysogeny in bacteria, the SV40 genome becomes incorporated as a provirus in the DNA of its host (in chromosome 7 in human cells).
Although a human cell with harboring SV40 shows no outward sign of the provirus, its presence can be detected by:
• the appearance of viral-encoded antigens in the host cell
• the ability of these cells to cause a lytic infection in African green monkey cells when fused with them.
Latent infections may also cause the cell to become cancerous. The cell has become transformed. In these cases, the word fulfills both of its biological meanings:
• "transformed" by the incorporation of new DNA
• "transformed" as it becomes cancerous.
In humans,
• lytic infections of plasma cells by the Epstein-Barr virus (EBV) occur in mononucleosis
• latent infections of B cells by EBV predispose the person to lymphoma.
while
• lytic infections by human papilloma virus (HPV) cause genital warts;
• latent infections by some strains of HPV lead to cervical cancer.
and
• while most CD4+ T cells infected by the retrovirus HIV-1 are killed (causing AIDS),
• HIV-1 integrates as a provirus into the DNA of a few memory CD4+ T cells where it can persist for years with the potential of creating active disease in the future. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/19%3A_The_Diversity_of_Life/19.03%3A_Viruses/19.3A%3A_Viruses.txt |
Influenza is a viral infection of the lungs characterized by fever, cough, and severe muscle aches. In the elderly and infirm, it is a major cause of disability and death (often as a result of secondary infection of the lungs by bacteria). Even in the young and healthy, influenza produces a prostrating disease of a few days duration and one not soon forgotten. Influenza is not a case of low fever and sniffles that keeps you home in bed for a day nor a gastrointestinal upset ("stomach flu").
Influenza was responsible for the most devastating plague in human history - the "Spanish" flu that swept around the world in 1918 killing 675,000 people in the U.S. and an estimated 20–50 million people worldwide. (A disease that attacks a large fraction of the population in every region of the world is called a pandemic.) (It is uncertain where the flu first appeared, but it certainly wasn't in Spain.)
No one at the time even knew what disease agent was causing the pandemic. Not until 1930 (in pigs) and 1933 (in humans) was it established that influenza is caused by a virus.
This electron micrograph (courtesy of Dr. K. G. Murti) shows several influenza virus particles (at a magnification of about 265,000x). The surface projections are molecules of hemagglutinin and neuraminidase (see below).
There are three types of influenza:
• Common but seldom causes disease symptoms.
• Often causes sporadic outbreaks of illness, especially in residential communities like nursing homes.
• Responsible for regular outbreaks, including the one of 1918. Influenza A viruses also infect domestic animals (pigs, horses, chickens, ducks) and some wild birds.
The Influenza A Virus
The influenza A virion is
• a globular particle (about 100 nm in diameter)
• sheathed in a lipid bilayer (derived from the plasma membrane of its host)
• Studded in the lipid bilayer are three integral membrane proteins
• some 500 molecules of hemagglutinin ("H")
• some 100 molecules of neuraminidase ("N")
• the M2 membrane protein (not shown).
• Encased by the lipid bilayer are
• some 3000 molecules of matrix protein
• 8 pieces or segments of RNA
Each of the 8 RNA molecules is associated with
• many copies of a nucleoprotein
• the three subunits of its RNA polymerase
• some "non-structural" protein molecules of uncertain function
The Genes of Influenza A
The 8 RNA molecules (the number in brackets is the designated segment number):
• The HA gene [4] encodes the hemagglutinin. 3 distinct hemagglutinins (H1, H2, and H3) are found in human infections; 15 others have been found in animal flu viruses.
• The NA gene [6] encodes the neuraminidase. 2 different neuraminidases (N1 and N2) have been found in human viruses; 9 others in other animals.
• The NP gene [5] encodes the nucleoprotein. Influenza A, B, and C viruses have different nucleoproteins.
• The M gene [7] encodes two proteins (using different reading frames of the RNA): a matrix protein (M1 — shown in blue) and an ion channel (M2) spanning the lipid bilayer (not shown).
• The NS gene [8] encodes two different non-structural proteins (also by using different reading frames). These are found in the cytosol of the infected cell but not within the virion itself.
• One RNA molecule (PA [3], PB1 [2], PB2 [1]) encoding each of the 3 subunits of the RNA polymerase. Occasional frameshifts during translation of PA produce a protein that reduces host gene expression.
The Disease
The influenza virus invades cells of the respiratory passages.
• Its hemagglutinin molecules bind to sialic acid residues on the glycoproteins exposed at the surface of the epithelial cells of the host respiratory system.
• The virus is engulfed by receptor mediated endocytosis.
• The drop in pH in the endosome (endocytic vesicle) produces a change in the structure of the viral hemagglutinin enabling it to
• fuse the viral membrane with the vesicle membrane.
• This exposes the contents of the virus to the cytosol.
• The RNA enter the nucleus of the cell where fresh copies are made.
• These return to the cytosol where some serve as messenger RNA (mRNA) molecules to be translated into the proteins of fresh virus particles.
• Fresh virus buds off from the plasma membrane of the cell (aided by the M2 protein) thus
• spreading the infection to new cells.
The result is a viral pneumonia. It usually does not kill the patient (the 1918 pandemic was an exception; some victims died within hours) but does expose the lungs to infection by various bacterial invaders that can be lethal. Before the discovery of the flu virus, the bacterium Hemophilus influenzae was so often associated with the disease that it gave it its name.
Pandemics and Antigenic Shift
Three pandemics of influenza have swept the world since the "Spanish" flu of 1918.
• The "Asian" flu pandemic of 1957;
• the "Hong Kong" flu pandemic of 1968;
• the "Swine" flu pandemic that began in April of 2009.
The pandemic of 1957 probably made more people sick than the one of 1918. But the availability of antibiotics to treat the secondary infections that are the usual cause of death resulted in a much lower death rate. The hemagglutinin of the 1918 flu virus was H1, its neuraminidase was N1, so it is designated as an H1N1 "subtype". Here are some others.
Some strains of influenza A
Date Strain Subtype Notes
1918 H1N1 pandemic of "Spanish" flu
1957 A/Singapore/57 H2N2 pandemic of "Asian" flu
1962 A/Japan/62 H2N2 epidemic
1964 A/Taiwan/64 H2N2 epidemic
1968 A/Aichi/68 H3N2 pandemic of "Hong Kong" flu
1976 A/New Jersey/76 H1N1 swine flu in recruits
1977 A/USSR/77 H1N1 "Russian" flu
2009 A/California/09 H1N1 pandemic of "swine" flu [now designated A(H1N1)pdm09]
Until 2009, these data suggest that flu pandemics occur when the virus acquires a new hemagglutinin and/or neuraminidase. For this reason, when an H1N1 virus appeared in a few recruits at Fort Dix in New Jersey in 1976, it triggered a massive immunization program (which turned out not to be needed). However, an H1N1 virus appeared the following year (perhaps escaped from a laboratory) causing the "Russian" flu. We now know that this virus was a direct descendant of the 1918 flu. While accumulating mutations that made it less dangerous, it had been infecting humans until it was replaced by the H2N2 "Asian" flu of 1957. Because most people born before the Asian flu pandemic of 1957 had been exposed to the H1N1 viruses circulating before, the Russian flu primarily affected children and young adults. For the same reason, this pattern was also seen in the 2009-10 pandemic of "swine" flu.
Where do the new H or N molecules come from?
Birds appear to be the source. Both the H2 that appeared in 1957 and the H3 that appeared in 1968 came from influenza viruses circulating in birds. The encoding of H and N by separate RNA molecules probably facilitates the reassortment of these genes in animals simultaneously infected by two different subtypes. For example, H3N1 virus has been recovered from pigs simultaneously infected with swine flu virus (H1N1) and the Hong King virus (H3N2). Probably reassortment can also occur in humans with dual infections.
Epidemics and Antigenic Drift
No antigenic shifts occurred between 1957 ("Asian") and 1968 ("Hong Kong"). So what accounts for the epidemics of 1962 and 1964? Missense mutations in the hemagglutinin (H) gene. Flu infections create a strong antibody response. After a pandemic or major epidemic, most people will be immune to the virus strain that caused it. The flu virus has two options:
• wait until a new crop of susceptible young people comes along
• change the epitopes on the hemagglutinin molecule (and, to a lesser degree, the neuraminidase) so that they are no longer recognized by the antibodies circulating in the bodies of previous victims.
• By 1972, the H3 molecules of the circulating strains differed in 18 amino acids from the original "Hong Kong" strain
• By 1975, the difference had increased to 29 amino acids.
The gradual accumulation of new epitopes on the H (and N) molecules of flu viruses is called antigenic drift. Spontaneous mutations in the H (or N) gene give their owners a selective advantage as the host population becomes increasingly immune to the earlier strains.
Flu Vaccines
Although a case of the flu elicits a strong immune response against the strain that caused it, the speed with which new strains arise by antigenic drift soon leaves one susceptible to a new infection. Immunization with flu vaccines has proved moderately helpful in reducing the size and severity of new epidemics.
Some vaccines incorporate inactivated virus particles; others use the purified hemagglutinin and neuraminidase. Both types incorporate antigens from the three major strains in circulation, currently:
• an A strain of the H1N1 subtype
• an A strain of the H3N2 subtype and
• a B strain.
Because of antigenic drift, the strains used must be changed periodically as new strains emerge that are no longer controlled by people's residual immunity.
The process:
• Chicken eggs are infected with the virus expressing the new H and/or N and simultaneously infected with a stock flu virus that grows very well in eggs.
• Genetic reassortment produces some viruses with both the new H and N genes along with the 8 other genes from the stock strain.
• This new virus is then grown in massive amounts and the H and N proteins purified for the new vaccine.
The whole process takes several weeks. A promising way to speed things up is to chemically synthesize the new H and N genes and substitute them for the H and N genes in the stock virus. The new virus can be ready for vaccine production in a few days.
Strains used in vaccines for the flu seasons shown.
Season H1N1 H3N2 Type B
86–87 A/Chile/83* A/Mississippi/85 B/Ann Arbor/86
* As the 86–87 season got underway, it was found that A/Chile/83 no longer gave protection so A/Taiwan/86 was offered as a second shot late in that season.
87–88 A/Taiwan/86 A/Leningrad/86 B/Ann Arbor/86
88–89 A/Taiwan/86 A/Sichuan/87 B/Victoria/87
89–90 A/Taiwan/86 A/Shanghai/87 B/Yamagata/88
90–91 A/Taiwan/86 A/Shanghai/89 B/Yamagata/88
91–92 A/Taiwan/86 A/Beijing/89 B/Panama/90
92–93 A/Texas/91 A/Beijing/89 B/Panama/90
93–94 unchanged unchanged unchanged
94–95 A/Texas/91 A/Shandong/93 B/Panama/90
95–96 A/Texas/91 A/Johannesburg/94 B/Harbin/94
96–97 A/Texas/91 A/Nanchang/95 B/Harbin/94
97–98 A/Johannesburg/96 A/Nanchang/95 B/Harbin/94
98–99 A/Beijing/95 A/Sydney/97 B/Beijing/93
99–00 A/Beijing/95 A/Sydney/97 B/Yamanashi/98
00–01 A/New Caledonia/99 A/Panama/99 B/Yamanashi/98
01–02 A/New Caledonia/99 A/Panama/99 B/Victoria/00 or similar
02–03 A/New Caledonia/99 A/Moscow/99 B/Hong Kong/2001
03–04 A/New Caledonia/99 A/Moscow/99 B/Hong Kong/2001
04–05 A/New Caledonia/99 A/Fujian/2002 B/Shanghai/2002
05–06 A/New Caledonia/99 A/California/2004 B/Shanghai/2002
06–07 A/New Caledonia/99 A/Wisconsin/2005 B/Malaysia/2004
07–08 A/Solomon Islands/06 A/Wisconsin/2005 B/Malaysia/2004
The B/Malasia component of the vaccine provided no protection at all. So all three components of the 08–09 vaccine were changed as shown on the next line.
08–09 A/Brisbane/2007 A/Brisbane/2007 B/Florida/2006
09–10 A/Brisbane/2007 A/Brisbane/2007 B/Brisbane/2008
Because the 2009–2010 pandemic of the newly-emerged "swine flu" virus drove the "seasonal" H1N1 viruses (e.g., A/Brisbane/2007) to near extinction,
the "swine flu" H1N1 – now called A(H1N1)pdm09 – replaced the "seasonal" H1N1 in the 10–11 vaccine.
10–11 A/California/2009 A/Perth/2009 B/Brisbane/2008
11–12 All three components were unchanged from the previous year
12–13 A/California/2009 A/Victoria/2011 B/Wisconsin/2010
13–14 A/California/2009 A/Victoria/2011 B/Massachusetts/2012
14–15 A/California/2009 A/Texas/2012 B/Massachusetts/2012
15–16 A/California/2009 A/Switzerland/2013 B/Phuket/2013
16–17 A/California/2009 A/HongKong/2014 B/Brisbane/2008
Several vaccines for the 2016-17 season will be quadrivalent; that is, contain a fourth component B/Phuket/2013.
FluMist®
On 17 June 2003, the U. S. Food and Drug Administration (FDA) approved FluMist® – a live-virus vaccine that is given as a spray up the nose. The viruses have been weakened so that they do not cause illness, but are able to replicate in the relatively cool tissues of the nasopharynx where they can induce an immune response. Presumably this is tilted towards IgA production, a better defense against infection by inhaled viruses than blood-borne IgG antibodies. In any case, FluMist® induces a more rapid response than inactivated vaccine and there is some evidence that it provides better protection against antigenic drift as well.
All three currently-circulating strains of flu (H1N1, H3N2, and B) are included. As new strains appear, they can be substituted.
At present, this new vaccine (technically known as LAIV "Live Attenuated Influenza Vaccine") is only approved for children older than 24 months and adults younger than 50. People with immunodeficiency (e.g., AIDS) should also be cautious about taking it.
Update: For as yet unknown reasons, the nasal spray did not work during the 2015–2016 season, and it is not recommended for the upcoming season.
Flublok®
On 16 January 2013, the U. S. FDA approved an entirely new type of vaccine. Flublok® is made in cell cultures transformed with recombinant DNA encoding the hemagglutinins of the 3 currently circulating flu strains (H1N1, H3N2, and B). The final concentration of antigens is three times that in the current vaccine. Cultures of insect cells are used so there is no problem with possible egg allergies in those receiving the vaccine.
Other weapons against flu
It takes a while for the flu vaccine to build up a protective level of antibodies. What if you neglected to get your flu shot and now an epidemic has arrived?
Amantadine and Rimantadine
These drugs inhibit the M2 matrix protein needed to get viral RNA into the cytosol. They work against A strains only, and resistance to the drugs evolves quickly. By the 2009-2010 flu season, virtually all strains of both H3N2 and H1N1 had developed resistance.
Zanamivir (Relenza®) and Oseltamivir (Tamiflu®)
These drugs block the neuraminidase and thus inhibit the release and spread of fresh virions. Spraying zanamivir into the nose or inhaling it shortens the duration of disease symptoms by one to three days. Unfortunately, by the 2008-2009 flu season, all H1N1 strains circulating in the U.S. had become resistant to Tamiflu.
Antibiotics
Antibiotics are of absolutely no value against the flu virus. However, they are often given to patients to combat the secondary bacterial infections that occur and that are usually the main cause of serious illness and death.
Why so few drugs?
The mechanisms by which amantadine and zanamivir work provide a clue. There are far fewer anti-viral drugs than antibacterial drugs because so much of the virus life cycle is dependent on the machinery of its host. There are many agents that could kill off the virus, but they would kill off host cell as well. So the goal is to find drugs that target molecular machinery unique to the virus. The more we learn about these molecular details, the better the chance for developing a successful new drug.
The "Spanish" Flu
Jeffery Taubenberger and his colleagues have sequenced the genes of the influenza virus that had been recovered from
• preserved lung tissue of a U.S. soldier who died from influenza in 1918
• lung tissue from a flu victim whose body had remained frozen in the permafrost of Alaska since she died in 1918
But even with all of its genes now completely sequenced, why the 1918 strain was so deadly is not fully understood. But deadly it is. They have even been able to replace the 8 genes of a laboratory strain of flu virus with all 8 genes of the 1918 strain (using strict biosafety containment procedures!). The resulting virus kills mice faster than any other human flu virus tested. (Reported in the 7 October 2005 issue of Science.)
The Swine Flu of 2009
A new H1N1 flu began infecting humans in North America in April 2009 and has now spread throughout much of the world. Sequencing its genome revealed a novel virus - now called A(H1N1)pdm09 - that contained genes previously found in four different strains of swine flu:
• an HA gene (H1) derived from the swine flu of 1930 (and closely-related to the H1 of the great 1918 "Spanish" flu pandemic) along with an NP and NS gene from that virus;
• an NA gene (N1) from a virus that had been circulating in the pigs of Europe and Asia since 1979 along with the M gene from that virus;
• a PA and PB2 gene that entered pigs from birds around 1998;
• a PB1 gene that passed from birds to humans around 1968 and from us to pigs around 1998.
Why this remarkable assortment of genes has enabled he virus to jump so successfully from pigs to humans remains to be determined.
The amino acid sequence around the critical epitopes of its H1 molecules closely resemble those found in the resurrected 1918 flu virus. This would explain why
• Antibodies from elderly survivors of the 1918 pandemic neutralize the new swine flu virus.
• Antibodies (raised in mice) to the new swine flu virus neutralize the resurrected 1918 flu virus.
• The recent pandemic caused serious illness and death mostly in young adults and least in children and the elderly. As for the elderly, this contrast to the usual pattern arose because people over 65, even if not old enough to have been exposed to the 1918 virus, had been exposed to H1 viruses that until 1957 had only drifted from the original 1918 virus, and thus they had developed partial immunity. The antibodies in young adults were specific for seasonal flu strains circulating since 1957. These were unable to protect them against the 2009 virus but may have formed damaging immune complexes with them. Youngsters had no anti-flu antibodies and did not form such immune complexes.
"Bird Flu"
Many influenza A viruses are found in birds, both domestic and wild. Most of these cause little or no illness in these hosts. However, some of their genes can enter viruses able to infect domestic animals, as was the case for the PA and PB2 genes of the swine flu of 2009 (above).
On several occasions, bird flu viruses have also infected humans, often with alarmingly-high fatality rates. In 2003, human cases of an H7N7 bird flu virus infection occurred in the Netherlands, and in the same year an H5N1 bird virus caused human cases in large areas of Asia. Most of the human cases seemed to have been acquired from contact with infected birds rather than from human-to-human transmission.
And now in 2013, a new bird flu virus, H7N9, has appeared in humans in China. By the end of the summer of 2013, it had caused 135 observed cases (no one knows yet whether there may also be infected people who are not sick enough to show up at hospitals). 45 of the observed cases were fatal. The victims appear to have been infected through contact with infected poultry with little or no evidence of human-to-human transmission.
As a glance at the tables above will show, humans have had long experience with infections and vaccines by both H1 and H3 flu viruses. But the human population has absolutely no immunity against any H7 viruses. If this virus develops the capability to spread efficiently from human to human, it could lead to another worldwide pandemic. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/19%3A_The_Diversity_of_Life/19.03%3A_Viruses/19.3B%3A_Influenza.txt |
φX174 (phiX174) is a virus that infects the bacterium E. coli. Hence φX174 is a bacteriophage. Each complete infectious particle (virion) of φX174 consists of a protein coat which envelopes a core that contains both protein and DNA. The coat of the virus contains 60 molecules each of two proteins (F and G) and 12 molecules of another protein (H). The core of the virion contains one molecule of DNA and 60 copies of a fourth protein, the J protein. The DNA molecule is single-stranded (ssDNA) and is in the form of a closed circle. It contains 5386 nucleotides. This tiny genome was the first DNA genome ever to be sequenced (by Fred Sanger in 1976).
When φX174 attaches to its host, its ssDNA molecule is inserted into the cell. Here the DNA strand (+) serves as the template for the synthesis of a complementary (−) strand. The two strands form a double helix which then replicates itself several times. The minus strands of these DNA molecules then serve as templates for the synthesis of:
• mRNA molecules.
• some 200 complementary (+) strands of DNA, each of which will later be packaged into the core of a new virion.
The protein-synthesizing machinery of the host cell translates the viral mRNA molecules into 11 different kinds of proteins. Four of these are the four (F, G, H, and J) that will be incorporated into new virions. As for the other 7 proteins
• A, A*, and C play roles in the replication of viral DNA
• B and D assist in the assembly of the virion proteins into new virions
• E lyses the host cell so the newly-synthesized virions can escape
• K boosts virion production
but none of these proteins become part of the virion.
The 11 proteins encoded by φX174 DNA range in size from the A protein, which contains 513 amino acids, to the J protein, which contains only 38. The 11 proteins together contain a total of 1986 amino acids (the A* protein is simply a shortened version of the A protein). This raises a question. With 3 nucleotides needed to specify one amino acid, φX174 would need 5958 nucleotides to encode 1986 amino acids (5958/3 = 1986). But its DNA molecule contains 5386 nucleotides, only enough to encode 1795 amino acids. Furthermore, it turns out that 217 of the nucleotides do not encode anything, although some of them provide control signals. So there are only 5169 coding nucleotides, and we would expect them to be able to encode only 1723 amino acids. How does φX174 dictate the assembly of the remaining amino acids?
Overlapping Genes
It does so by using some stretches of nucleotides to encode two different sequences of amino acids. The principle is really quite simple. It involves reading the codons it two different "reading frames", that is, grouping the nucleotides in shifted clusters of three.
For example, the sequence
. . . GAGCCGCAACTTC . . .
can be read in three different reading frames:
. . . GAG CCG CAA CTT C . . . which encodes . . Glu-Pro-Gln-Leu . .
or
. . . G AGC CGC AAC TTC . . . which encodes . . Ser-Arg-Asn-Phe . .
or
. . . GA GCC GCA ACT TC . . . which encodes . . Ala-Ala-Thr . .
φX174 actually uses two of these and, as you can see, each encodes a totally different sequence of amino acids.
There is even one spot where a single nucleotide (A) participates in three different codons:
• It is the third nucleotide in the codon (AAA) for the final amino acid (Lys) in protein A;
• the middle nucleotide in the codon AAT, which encodes Asn in the K protein; and
• the first nucleotide in ATG, the codon that places methionine (Met) at the start position of protein C.
Why overlapping genes? φX174 is one of the tiniest viruses. Its use of overlapping genes enables it to increase the amount of information it can store in a given amount of DNA. Not only was the φX174 genome the first to be sequenced, it was also the first to be chemically synthesized in the laboratory. When introduced into E. coli, this synthetic molecule was fully infectious able to produce intact viruses.
Above is an electron micrograph of the double-stranded φX174 DNA extracted from infected E. coli cells. The bar represents 0.5 µm. (Courtesy of David T. Denhardt.) | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/19%3A_The_Diversity_of_Life/19.03%3A_Viruses/19.3C%3A_X174.txt |
The threat of terrorism has raised the spectre of the use of biological agents as weapons. One of the possible agents is the variola virus, the cause of smallpox. On October 26, 1977, Ali Maow Maalin came down with smallpox in the town of Merka in Somalia. Within a few weeks he was fully recovered. Since that time, not a case of smallpox (except as a result of one laboratory accident) has been discovered anywhere in the world. By May of 1980, the World Health Organization (WHO) felt that it could confidently announce that smallpox had been completely eradicated. The WHO also asked that all countries with any stocks of variola virus in their laboratories either destroy them or transfer them to one of two secure laboratories (at the Centers for Disease Control and Prevention (CDC) in Atlanta, Georgia or a state lab in Koltsovo in Russia). Although 74 countries did so, the fear remains that some countries may have retained stocks of the virus. Even before the complete eradication of smallpox, routine vaccination against the disease was halted in most Western countries. So today anyone under 30 years of age is fully susceptible and even those older may have lost protection against the disease.
A Little History
Smallpox certainly qualified as one of the greatest scourges of humanity. It regularly killed 25% and sometimes as many as 50% of its victims. Introduced into Europe around the sixth century A.D., smallpox rivaled plague in its ability to decimate entire populations. Introduced into the New World in the sixteenth century, smallpox devastated the native populations and played a far greater role than weaponry in the Spanish Conquest.
How was such a pestilence eradicated? Four factors were decisive:
1. The variola virus, which causes the disease, attacks only humans; no animal reservoirs have been found (as they have for the yellow fever virus, the rabies virus, and the plague bacillus).
2. If the victim recovers, the virus is completely eliminated from the body. There are no smallpox "carriers" as there are for such diseases as typhoid fever and malaria.
3. An effective vaccine was available. The vaccine could quickly establish a strong (and reasonably long-lasting) immunity. Thus the chain of contagion could be quickly broken by vaccinating all possible contacts associated with a new case.
4. The WHO and the countries involved provided personnel, money, and the determination to do the job. An effective vaccine had, as we shall see, been available since 1796 and had already rendered many parts of the world free of the disease during the first half of the 20th century. But still the disease smoldered in Asia, Indonesia, Brazil, and Africa. Only a heroic public health effort — a campaign that began in 1967 — finally eliminated it worldwide.
Variolation
The first effective attempts to cope with smallpox were made in some of the same regions - Asia, India, Africa - that were the last to be freed of the disease. The technique was deliberately to inoculate susceptible individuals (i.e., those with no pockmarks to indicate that they had survived an earlier epidemic) with material taken from the pustules of people with a mild case of the disease. This practice, called variolation, induced an active case in the recipient, but usually the case was less severe than if the disease had been contracted in the normal way (by inhalation as it turned out).
Variolation was introduced into England and the American colonies early in the 18th century. The practice was often accompanied by violent controversy. It was not entirely safe. The variolated person often became quite ill and the mortality rate, although only a fraction of that for people who contracted the disease in the normal way, was nonetheless appreciable. But far more significant in terms of public acceptance was the fact that variolated people were fully contagious to others during the period of their brief, hopefully mild, illness. Thus a family electing variolation could start a fresh smallpox epidemic. Nonetheless, the practice gradually gained favor until it was replaced by vaccination. This table (from J. B. Blake, Public Health in the Town of Boston, 1630-1832. Harvard University Press, 1959) shows the effect of variolation on the death rate from smallpox during three epidemics in Boston.
Year 1721 1764 1792
Population 10,700 15,500 19,300
Natural Smallpox
Cases 5,759 699 232
Deaths 842 124 69
Deaths/1000 cases 146 177 298
Smallpox Caused by Variolation
Cases 130 4,977 9,152
Deaths 2 46 179
Deaths/1000 cases 15 9 20
Vaccination
Edward Jenner was a Gloucestershire physician who introduced the practice that led to the elimination of smallpox. Jenner's success was grounded on two observations:
1. The regional folk belief that if a milkmaid had ever contracted cowpox, she would never contract smallpox.
2. The inability to variolate successfully those who had an earlier case of cowpox. Cowpox is a disease that produces pustules on the teats and udders of cows. Persons in close contact with cows frequently contracted the disease and suffered a mild and transient infection.
Jenner systematically exploited these observations.
• First he deliberately induced cowpox in his human subjects by inoculating them with material from cowpox pustules.
• Then he showed that these individuals could NOT be variolated.
Jenner's procedure, which we call vaccination, (L. vacca, cow) quickly replaced variolation as a public health measure because:
• Any reaction it induced was far milder than the disease induced by variolation.
• The vaccinated subject was not contagious to others.
Jenner's was the first safe and successful attempt to artificially induce an active immunity. Many successful attempts have followed since Jenner's day, but the principles that guided him are still followed:
• Develop a harmless (or as harmless as possible) preparation that will, upon introduction into the body,
• induce a response that will protect the individual from a harmful pathogen.
Because of Jenner's priority and his success, the term vaccine is used today for all such preparations. The administration of a vaccine is called immunization. The virus used in today's smallpox vaccine is called vaccinia virus. Possibly it is a relative of cowpox virus, but when the switch occurred is lost in the obscurity of the years since Jenner's day.
What's Next?
Jenner himself was so confident of the efficacy of vaccination that he wrote:
"The annihilation of smallpox must be the final result of this practice".
In 1980, his prediction seemed to have been fulfilled. Today we are not so confident. What should we do now? Return to universal vaccination or use the vaccine only for emergency and medical people who might be exposed as they responded to a terrorist attack and those people in a "ring" around any person who comes down with the disease.
The argument against universal vaccination is that present vaccines are not 100% safe. There is a small, but definite, risk of serious complications from the vaccine itself, especially in people who have an immunodeficiency (e.g., from AIDS or taking immunosuppressant drugs). Such problems can be avoided by not giving the vaccine to people at risk. It can also be avoided by having Vaccinia Immune Globulin (VIG) available to treat any cases of a bad response to the vaccine. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/19%3A_The_Diversity_of_Life/19.03%3A_Viruses/19.3D%3A_Smallpox.txt |
The genome of retroviruses consists of RNA not DNA. HIV-1 and HIV-2, the agents that cause AIDS, are retroviruses. In February 1997 it was reported that pig cells contain a retrovirus capable of infecting human cells (at least, in vitro). This is troublesome because of the efforts that are being made to transplant pig tissue into humans (e.g., fetal pig cells into the brains of patients with Parkinson's disease). Transplant recipients must have their immune systems suppressed if the transplant is to avoid rejection. Could immunosuppressed patients be at risk from the retroviruses present in the transplanted cells? The probability that the original hosts for HIV-1 and HIV-2 were some other primate suggests that retroviruses can move from one species to another.
A typical, "minimal" retrovirus consists of:
• an outer envelope which was derived from the plasma membrane of its host
• many copies of an envelope protein embedded in the lipid bilayer of its envelope
• a capsid; a protein shell containing
• two molecules of RNA
• molecules of the enzyme reverse transcriptase
Reverse transcriptase is a DNA polymerase that uses RNA as its template. Thus it is able to make genetic information flow in the reverse (RNA ->DNA) of its normal direction
(DNA -> RNA).
Infection of a host cell requires that the cell have a surface protein that can serve as a receptor for the envelope protein of the retrovirus. The envelope protein of HIV-1 binds to CD4 molecules (this property enables the virus to invade CD4+ T cells and certain other cells that express CD4) and they bind to CCR5 (CC chemokine Receptor 5) - found on Th1 cells and macrophages. All the proteins in the virus particle are encoded by its own genes.
When a retrovirus infects a cell
• Its molecules of reverse transcriptase are carried into the cell attached to the viral RNA molecules.
• The reverse transcriptase synthesizes DNA copies of the RNA.
• These enter the nucleus and are inserted into the DNA of the host.
• These inserts are transcribed by the host's enzymes into fresh RNA molecules which re-enter the cytosol where
• some are translated by host ribosomes
• the gag gene is translated into molecules of the capsid protein
• the pol gene is transcribed into molecules of reverse transcriptase
• the env gene is translated into molecules of the envelope protein
• other RNA molecules become incorporated into fresh virus particles
The genome of retroviruses is flanked at each end by repeated sequences ("R") that enable the DNA copy of the genome to be inserted into the DNA of the host and act as enhancers, causing the host nucleus to transcribe the DNA copies of the retroviral genome at a rapid rate.
The retroviral genome also contains a packaging signal sequence ("P") which is needed for the newly-synthesized RNA molecules to be incorporated in fresh virus particles. Most retroviruses also contain one or more additional genes. Some of these represent RNA copies of genes that earlier were picked up from their eukaryotic host. Several cancers in animals are caused by retroviruses that have, at some earlier time, picked up a proto-oncogene from their mammalian host and converted it into an oncogene. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/19%3A_The_Diversity_of_Life/19.03%3A_Viruses/19.3E%3A_Retroviruses.txt |
• 20.1: Epidemiology
Just because A is often associated with B, does not prove that A causes B. How can one establish that A causes B? In the laboratory you could set up a controlled experiment treating one group of animals with A and having a second control group without A but otherwise treated the same (thus avoiding confounding variables). Such experimentation is rarely possible (or ethical) in humans so we must turn to the methods and criteria of epidemiology.
• 20.2: Types of Clinical Studies
Researchers in human (and veterinary) medicine are always on the lookout for new drugs, medical procedures, and life-style changes that will improve their ability to bring better health to patients. For each one, they must establish whether it truly represents an improvement from what was used before.
• 20.3: Scientific Methods
There is nothing mysterious or even particularly unusual about the things that scientists do. There are many ways to work on scientific problems. They all require common sense. Beyond that, they all display certain features that are especially - but not uniquely - characteristic of science.
• 20.4: Scientific Papers
• 20.5: Statistical Methods
• 20.6: Drugs
Thumbnail: Original map by John Snow showing the clusters of cholera cases in the London epidemic of 1854. (Public Domain).
20: General Science
A statistical correlation between two phenomena is simply that. It does not prove that one phenomenon caused the other. Just because A is often associated with B, does not prove that A causes B. Example: the incidence of cirrhosis of the liver is associated with cigarette smoking. Does smoking cause cirrhosis? Probably not. Excessive consumption of alcohol is a more likely cause. However, as heavy drinkers tend to be heavy smokers, the statistical association is there, but in this case is probably a confounding variable. How can one establish that A causes B? In the laboratory you could set up a controlled experiment treating one group of animals with A and having a second control group without A but otherwise treated the same (thus avoiding confounding variables). Such experimentation is rarely possible (or ethical) in humans so we must turn to the methods and criteria of epidemiology.
John Snow - the First Epidemiologist
During an outbreak of cholera in London in 1854, John Snow plotted on a map the location of all the cases he learned of. Water in that part of London was pumped from wells located in the various neighborhoods. Snow's map revealed a close association between the density of cholera cases and a single well located on Broad Street. The Broad Street well is marked with an X (within the red circle) in the above figure. Removing the pump handle of the Broad Street well put an end to the epidemic. This despite the fact that the infectious agent that causes cholera was not clearly recognized until 1905.
Although an association between two phenomena is no more than that, one can apply several criteria to gauge the strength of the association, and if it is strong, infer that one phenomenon causes the other.
The five criteria to gauge the strength of the association
• a high relative risk
• consistency
• a graded response to a graded dose
• a temporal relationship
• a plausible mechanism
Cigarette Smoking: A Case Study
In Table \(1\), the quotient of observed deaths divided by expected deaths (those in the control group) gives the relative death rate. This value is a measure of risk. Although smoking is associated with many more cases of heart disease than of lung cancer, lung cancer is the disease with the highest relative risk for smokers. The relative death rate from lung cancer is over 10 times greater in smokers than in non-smokers. This is strong evidence that smoking causes lung cancer. Cigarette smoking is estimated to be directly responsible for 80–90% of all lung cancer deaths (which totalled 160,390 in the U.S. in 2007).
This table gives the number of deaths from various causes in a prospective study of cigarette smokers ("observed deaths") compared with the number to be expected among nonsmokers of the same ages ("expected deaths"). The differences between the two represent "excess deaths". The contribution of each disease to the total of excess deaths is given as the "percentage of excess". Note that coronary artery disease accounts for one half of the excess deaths in the smoking group.
Table \(1\): Observed deaths, expected deaths, and relative death rates.
Cause of Death Observed Deaths Expected Deaths Excess Deaths Percentage of Excess Relative Death Rate
Total deaths (all causes) 7316 4651 2665 100.0 1.57
Coronary artery disease 3361 1973 1388 52.1 1.70
Other heart disease 503 425 78 2.9 1.18
Cerebrovascular lesions 556 428 128 4.8 1.30
Aneurysm & Buerger's disease 86 29 57 2.1 2.97
Other circulatory diseases 87 68 19 0.7 1.28
Lung cancer 397 37 360 13.5 10.73
Cancer of mouth, larynx, or esophagus 91 18 73 2.7 5.06
Cancer of the bladder 70 35 35 1.3 2.00
Other cancers 902 651 251 9.4 1.39
Gastric & duodenal ulcer 100 25 75 2.8 4.00
Cirrhosis of the liver 83 43 40 1.5 1.93
Pulmonary disease (except cancer) 231 81 150 5.6 2.85
All other diseases 486 453 33 1.2 1.07
Accident, violence, suicide 363 385 -22 -0.8 0.94
Dividing the number of observed deaths by the number of expected deaths gives the "relative death rate" for each disease. This shows that smokers die of lung cancer 10 times as often (10.73, above) as do nonsmokers, which is a very high relative risk. However, in both groups lung cancer is rarer than coronary artery disease. (Data from E. C. Hammond and D. Dorn, 1966.)
Consistency
Our confidence that A causes B is strengthened when different studies using different populations all show the same association. The earliest studies of smoking were retrospective; that is, after a disease was diagnosed, the patient's smoking habits were determined. Later studies were prospective. A prospective study selects a population in good health and meeting any other desired criteria (smoking habits in this case) and follows it over a period of years to see what happens to its members.
This graph shows essentially the same relationship between smoking and deaths from lung cancer in three different groups (totalling over a million people) studied prospectively. Doll and Hill studied a group of British physicians. Dorn followed the health of a group of U.S. veterans. Horn studied 187,783 U.S. male volunteers. In each case the relative death rates are graphed as a function of number of cigarettes smoked each day (from zero at the left to over a pack at the right).
A Graded Response to a Graded Dose
All three studies graphed above show that the relative death rate from lung cancer increased with an increase in the average number of cigarettes smoked each day. One goal of picking different groups to study is to avoid confounding variables. If, for example, all the groups studied lived in cities, it would be difficult to distinguish between the effects of smoking and the effects of general air pollution.
This graph compares the incidence of lung cancer among male Mormons and non-Mormons living in urban and rural areas of Utah. Male non-Mormons living in the city have a higher risk of developing lung cancer than those living in the country. Is this because of smoking or because of the pollution of urban air? It appears to be the former because Mormons show no such city vs. country difference, and cigarette smoking is prohibited for Mormons. Studies like these help to eliminate the effect of confounding variables. Probably less than 5% of lung cancer is caused by breathing polluted city air.
Temporal Relationship
If A causes B, then exposure to A must have preceded the onset of B. Establishing cause-effect relationships for possible carcinogens has been particularly difficult because for cancers, the latency period between exposure and illness is often many years. Nonetheless, data such as those shown in this graph, provide another strong link in the case against cigarettes.
In recent decades, sales of cigarettes in the U.S. have dropped, both on a per capita basis and in absolute numbers. Whereas half of adult males smoked in the mid-sixties, less than a third do today. This change has already caused the rate of lung cancer in males to level off. Unfortunately, the rate is still rising for women (and in 1987 surpassed breast cancer as the leading cause of cancer deaths in U.S. women).
Plausible Mechanism
Over 40 different chemicals found in cigarette smoke cause an increase in cancer when given over several years to laboratory rats.
So how strong is the case against cigarettes?
Defenders of the tobacco industry frequently claim that no one has proved that cigarette smoking causes lung cancer. In one sense they are right. Proof from epidemiology differs from proof in a laboratory experiment. What we have seen here is that the more closely we can meet the several criteria linking A and B, the more confident we can be that A causes B.
Few epidemiological studies have met these criteria better than those studying the statistical relationship between smoking and health. Smoking is probably the greatest single cause of preventable illness in the United States.
Rules to live by
Hardly a week goes by these days without a report in the press and on TV of another link between an environmental agent and human disease. Does living near nuclear power stations increase one's risk of cancer? living near electric power lines? Does a diet rich in saturated fats predispose U.S. males (but, for some reason, not French males) to early death from coronary artery disease?
I hope that your ability to interpret the avalanche of reported associations - and any adjustments that you make in your life as a result - will benefit from your applying to such reports the five criteria outlined here. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/20%3A_General_Science/20.01%3A_Epidemiology.txt |
Researchers in human (and veterinary) medicine are always on the lookout for new drugs, medical procedures, and life-style changes that will improve their ability to bring better health to patients. For each one, they must establish whether it truly represents an improvement from what was used before.
Retrospective Studies
In a typical retrospective study, the health profiles of the subjects in a particular "case" group (e.g. smokers) are compared with those in a control group that has been selected to be as similar as possible to the "case" group (similar spread of ages, sex, etc.). Retrospective studies are also called "case-control" studies. Retrospective studies run the risk of investigator bias; that is, the investigator picks subjects that are most likely to show the effect that prompted the study in the first place.
Prospective Studies
A prospective study selects a population in good health and meeting any other desired criteria (e.g., smoking habits) and follows it over a period of years to see what happens to its members. Prospective studies are also known as "cohort studies".
Clinical Trials
Where it is possible to do them, clinical trials represent the "gold standard" for evaluation. In performing a clinical trial (e.g. of a new, and possibly better, drug), the investigator
• assembles a group of subjects picked to be as similar as possible in their characteristics (to avoid "confounding variables")
• assigns them randomly to the experimental group and a "control" group
• performs the experiment on the first group. It is best to do this in a "double-blind" fashion; that is neither the subject nor the experimenterknows who is getting the treatment and who is not.
Keeping
• the subjects in the dark avoids the placebo effect; a response (often quite powerful) that is not due to the treatment but to the expectations of the subject;
• the experimenter in the dark avoids bias in the evaluation of the results. So, for example, a microscopist examining a slide of tissue should not know whether it came from an experimental subject or a control.
Analyzing the Data
The data acquired in any type of clinical study must be evaluated to see if any effect seen is significant.
20.03: Scientific Methods
There is nothing mysterious or even particularly unusual about the things that scientists do. There are many ways to work on scientific problems. They all require common sense. Beyond that, they all display certain features that are especially - but not uniquely - characteristic of science.
For example:
• Skepticism. Good scientists use highly-critical standards in the judging of evidence. They approach data, claims, and theories (ideally, even their own!) with healthy doses of skepticism.
• Tolerance of uncertainty. Scientists often work for years - sometimes for an entire career - trying to understand one scientific problem. This often involves finding facts that, for a time, fail to fit into any coherent pattern and that even may support mutually contradictory explanations.
Sometimes, as one listens to scientists vigorously defending their views, their confidence seems absolute. But deep in their hearts, they know that their views are based on probabilities and that a new piece of evidence may turn up at any time and force a major shift in their views.
• Although they certainly have no monopoly on hard work, their willingness to work long hours and years pursuing a problem is the mark of all good scientists. For science is hard work.
• Before undergoing the frustrations - tempered by occasional joys - of wresting more secrets from nature, you must learn the foundations on which your subject is based.
Although scientific methods are as varied as science itself, there is a pattern to the way that scientists go about their work.
Scientific advances begin with observations.
• A census of the members of a species in some habitat is an observation.
• The readings on the display of a laboratory instrument are observations.
But science is more than a catalog of facts. The goal of science is to find an explanation for why the facts are as they are. Such an explanation is a hypothesis.
Testing Hypotheses
A good hypothesis meets several standards:
1. It should provide an adequate explanation of the observed facts.
2. If two or more hypotheses meet this standard, the simpler one is preferred.
3. It should be able to predict new facts.
So if a generalization is valid, then certain specific consequences can be deduced from it. One of the most exciting events in science is to predict the results of an experiment not yet performed if the hypothesis is valid and then to perform the experiment.
The Null Hypothesis
Experimental biology often involves setting up an experimental treatment and — at the same time — a control. Then one compares the results of the experimental treatment with the results in the controls. If there is a difference, what is the probability that it is due to chance alone; that is, the experimental treatment really had no effect?
The hypothesis that the experimental treatment had no effect is called the null hypothesis. Most workers feel that if the probability (designated p) of the observed difference is less than 1 in 20 (p = <0.05), then the null hypothesis is disproved and the observed difference is significant. But significance is not proof. In fact, hypotheses can never be proven to be absolutely "true" is the sense that a theorem in geometry can. The most we can say is that there is a high probability that the hypothesis provides a valid explanation of the phenomenon being studied.
Hypotheses that are supported by many observations come to be called theories. So, in contrast to some areas of human thought, science can never prove that a theory is "true". But it can show that a theory is false. Lest the tentative nature of science cause you to lose confidence in it, think of what science has produced. The many achievements of scientific methods, despite the absence of absolute certainty, has been well-expressed in the sonnet "Paradox" by the late mathematician Clarence Wylie, Jr.
Not truth, nor certainty. These I foreswore
In my novitiate, as young men called
To holy orders must abjure the world.
"If..., then...," this only I assert;
And my successes are but pretty chains
Linking twin doubts, for it is vain to ask
If what I postulate be justified,
Or what I prove possess the stamp of fact.
Yet bridges stand, and men no longer crawl
In two dimensions. And such triumphs stem
In no small measure from the power of this game,
Played with the thrice-attenuated shades
Of things, has over their originals.
How frail the wand, but how profound the spell!
Reproducibility of Scientific Work
The single feature that is most characteristic of science is its reproducibility. If scientists cannot duplicate their first results, they are forced to conclude that these were invalid. This problem occurs often. Its cause is usually some unrecognized, and hence uncontrolled, factor in the experiment (e.g., unrecognized variation in the properties of different batches of the materials used in the experiment). With luck, the inability to reproduce experiments will be discovered by the same scientists who did the first experiments. This is why scientists generally repeat their experiments several times before reporting them in a scientific paper.
On other occasions, workers in another laboratory fail to secure the same results when they repeat experiments that have been published or, more often, perform experiments designed to carry the study into new areas, but these fail because of a flaw in the original experiments. When this happens, all the parties concerned should get together to see if they can find out why their results differ.
• Often it is simply a matter of not using precisely the same materials and methods.
• Sometimes, however, a serious flaw may be discovered in the design and/or execution of the original experiments.
• And sometimes it proves impossible to find out why experiments that once seemed to work no longer do so.
In any of these cases, the failure to confirm the experiments must be reported. Although this is acutely embarrassing for the original investigators, it represent one of the great strengths of science: its built-in system for self-correction.
Scientific Fraud
In the vast majority of cases, irreproducible results in science are caused by honest errors. On rare occasions, however, laboratory reports cannot be confirmed because they are fraudulent. This is distressing to all concerned. If such a fraud becomes widely known, it is also likely to cause a great deal of excitement among the general public. I believe, however, that rather than casting a cloud over the scientific enterprise, these rare aberrations reveal its great strength.
There is probably no other area of human activity where error is detected and corrected more rapidly. I am confident that you can think of a number of other fields of human study and activity where errors have been made that went uncorrected for years and caused widespread harm. Dishonest scientists usually harm only themselves. They are disgraced; their careers often at an end. But the progress of science usually moves forward as fast as (sometimes faster than) before.
Building on the Work of Others
Only rarely does a scientific discovery spring full-blown on the scene. When it does, it is likely to create a revolution in the way scientists perceive the world around them and to open up new areas of scientific investigation. Darwin's theory of evolution and Mendel's rules of inheritance are examples of such revolutionary developments.
Most science, however, consists of adding another brick to an edifice that has been slowly and painstakingly constructed by prior work. In fact, it is possible to construct a genealogical tree that traces the historical development of any scientific discovery (even, to a degree, Darwin's and Mendel's). The way in which science builds on the work of others is another illustration of what a communal activity science is.
The development of a new technique often lays the foundation for rapid advances along many different scientific avenues. Just consider the advances in biology that discovery of the light microscope and, later, the electron microscope have made possible. Throughout these pages, there are many examples of experimental procedures. Each was developed to solve a particular problem. However, each was then taken up by workers in other laboratories and applied to their problems.
In a similar way, the creation of a new explanation (hypothesis) in a scientific field often stimulates workers in related fields to reexamine their own field in the light of the new ideas. Darwin's theory of evolution, for example, has had an enormous impact on virtually every subspecialty in biology (and in other fields as well). To this very day, biologists in specialties as different as biochemistry and animal behavior are guided in their work by evolutionary theory.
Basic Versus Applied Science
The distinction between basic and applied science is more one of goals than of methods. The same rules and standards apply to each. However, the motivation behind the work is somewhat different. Researchers in applied science have before them a practical problem to be solved. Much of the research that goes on in medicine and in agriculture is applied. The researcher in basic science, on the other hand, is primarily driven by curiosity - the desire to find out more about how nature works. Both types of research are not only honorable and demanding professions, but they are mutually dependent as well.
• Applied science repeatedly loses momentum without periodic infusions of fresh ideas and discoveries from basic research. (The light bulb would never have been discovered in the research and development (R and D) department of a candle manufacturer!)
• On the other hand, much basic research has depended on the development of new tools and instruments and, more often than not, these have been developed in laboratories devoted to applied research. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/20%3A_General_Science/20.02%3A_Types_of_Clinical_Studies.txt |
Science is a communal activity. Only as new facts and hypotheses are taken up by the entire community of interested scientists do these facts and hypotheses become part of science. Therefore, one of the major responsibilities of scientists is to see that their work is reported to all those who might be interested.
Often this is done by word of mouth when scientists of similar interests gather together at meetings. But to be assured of a permanent place in the scientific edifice, the work is reported in a paper submitted to a scientific journal. In most cases, the paper will not be accepted for publication until it has been approved by several knowledgeable scientists from other laboratories who serve as referees. Often they will suggest editorial changes in the paper or even additional experiments that should be done before the paper is accepted for publication.
Papers in biology are usually divided into several sections (not necessarily in this order).
Summary or abstract
This section includes only the essence of the other sections. It should be as brief as possible, telling the reader what the goal of the experiment was, what was found, and the significance of the findings. The abstract is often placed at the beginning of the paper rather than at its end.
Introduction
This section of the paper describes the scientific question or problem that was the subject of the investigation. The introduction also includes references to earlier reports of these and other scientists that have served as the foundation for the present work.
Results
Here the authors report what happened in their experiments. This report is usually supplemented with graphs, tables, and photographs.
Discussion
Here the authors point out what they think is the significance of their findings. This is the place to show that the results are compatible with certain hypotheses and less compatible, or even incompatible, with others. If the results contradict the results of similar experiments in other laboratories, the discrepancies are noted here, and an attempt may be made to reconcile the differences.
Materials and Methods
Here are precisely described the materials used (e.g., strains of organism, source of the reagents) and all the methods followed. The goal of this section is to give all the details necessary for workers in other laboratories to be able to repeat the experiments exactly. When many complex procedures are involved, it is acceptable to refer to earlier papers describing these methods in greater detail.
Acknowledgments
In this brief but important section, the authors give credit to those who have assisted them in the work. These usually include technicians (who may have actually performed most of the experiments!) and other scientists who donated materials for the experiments and/or gave advice about them.
20.05: Statistical Methods
What do the data tell us?
There are two kinds of numerical data acquired by biologists:
• counting; e.g. the number of females in a population
• measuring a continuous variable such as length or weight
In the first case, everyone can agree on the "true" value. In the second case, the measured values always reflect a range, the size of which is determined by such factors as
• precision of the measuring instrument and
• individual variability among the objects being measured.
How are such data handled?
Calculating the Standard Deviation
The first step is to calculate a mean (average) for all the members of the set. This is the sum of all the readings divided by the number of readings taken.
But consider the data sets:
46,42,44,45,43 and 52,80,22,30,36
Both give the same mean (44), but I'm sure that you can see intuitively that an experimenter would have much more confidence in a mean derived from the first set of readings than one derived from the second.
One way to quantify the spread of values in a set of data is to calculate a standard deviation (S) using the equation
$s =\sqrt{ \dfrac{\sum (x-\bar{x})^2}{n-1}}$
where ("x minus x-bar)2 is the square of the difference between each individual measurement (x) and the mean ("x-bar") of the measurements. The symbol sigma indicates the sum of these, and n is the number of individual measurements.
Using the first data set, we calculate a standard deviation of 1.6.
The second data set produces a standard deviation of 22.9.
(Many inexpensive hand-held calculators are programmed to do this job for you when you simply enter the values for X.)
Standard Error of the Mean
In our two sets of 5 measurements, both data sets give a mean of 44. But both groups are very small. How confident can we be that if we repeated the measurements thousands of times, both groups would continue to give a mean of 44? To estimate this, we calculate the standard error of the mean (S.E.M. or Sx-bar) using the equation
$S_{\bar{x}} = \dfrac{S}{\sqrt{n}}$
where S is the standard deviation and n is the number of measurements.
In our first data set, the S.E.M. is 0.7.
$S_{\bar{x}} = \dfrac{S}{\sqrt{5}} = \dfrac{1.6}{2.23} = 0.7$
In the second group it is 10.3.
$S_{\bar{x}} = \dfrac{S}{\sqrt{5}} = \dfrac{22.9}{2.23} = 10.3$
95%Confidence Limits
It turns out that there is a 68% probability that the "true" mean value of any effect being measured falls between +1 and −1 standard error (S.E.M.). Since this is not a very strong probability, most workers prefer to extend the range to limits within which they can be 95% confident that the "true" value lies. This range is roughly between −2 and +2 times the standard error.
So
• for our first group, 0.7 x 2 = 1.4
• for our second group, 10.3 x 2 = 20.6
So
• if our first group is representative of the entire population, we are 95% confident that the "true" mean lies somewhere between 42.6 and 45.4 (44 ± 1.4 or 42.6 ≤ 44 ≤ 45.4).
• for our second group, we are 95% confident that the "true" mean lies somewhere between 23.4 and 64.6 (44 ± 20.6 or 23.4 ≤ 44 ≤ 64.6).
Put another way, when the mean is presented along with its 95% confidence limits, the workers are saying that there is only a 1 in 20 chance that the "true" mean value lies outside those limits.
Put still another way: the probability (p) that the mean value lies outside those limits is less than 1 in 20 (p = <0.05 ).
An example:
Assume that
• the first data set ("A") (46,42,44,45,43) represents measurements of five animals that have been given a particular treatment and
• the second data set ("B") (52,80,22,30,36) measurements of five other animals given a different treatment.
• A third set ("C") of five animals was used as controls; they were given no treatment at all, and their measurements were 20,23,24,19,24. The mean of the control group is 22, and the standard error is 2.1.
Did treatment A have a significant effect? Did treatment B?
The graph shows the mean for each data set (red dots). The dark lines represent the 95% confidence limits (± 2 standard errors).
Although both experimental means (A and B) are twice as large as the control mean, only the results in A are significant. The "true" value of B could even be simply that of the untreated animals, the controls (C).
Rejecting the null hypothesis
In principle, a scientist designs an experiment to disprove, or not, that an observed effect is due to chance alone. This is called rejecting the null hypothesis.
The value p is the probability that there is no difference between the experimental and the controls; that is, that the null hypothesis is correct. So if the probability that the experimental mean differs from the control mean is greater than 0.05, then the difference is usually not considered significant. If p = <0.05, the difference is considered significant, and the null hypothesis is rejected.
In our hypothetical example, the difference between the experimental group A and the controls (C) appears to be significant; that between B and the controls does not.
Narrowing the confidence limits
Two approaches can be taken to narrow the confidence limits.
• enlarge the size of the sample being measured (increases n)
• find ways to reduce the fluctuation of measurements about the mean.
The second goal is often much more difficult to achieve; if it proves impossible, perhaps the null hypothesis is right after all!
20.06: Drugs
Testing New Drugs
Thousands of chemicals, both synthetic and extracted from "natural" sources, are being examined in the hope of finding new drugs with which to combat human and veterinary diseases. The first step is to use laboratory tests to find if these substances have a significant effect on, for example:
• cells growing in tissue culture
• laboratory animals such as rats and mice.
If the drug achieves the desired effect in laboratory animals, without killing them in the process, the drug developer applies to the U. S. Food and Drug Administration for an IND, an investigational new drug application. Granting of an IND allows testing in humans to begin. This occurs in three phases.
Phase I
A small group (20–100) of healthy volunteers is given the drug to see
• if it is safe
• how quickly it is absorbed, metabolized, and excreted from the body
Phase II
A group (up to several hundred) of volunteer patients with the disease are given the drug to see
• how effective it is against the signs and symptoms of the disease
• what doses are best
• what side effects may occur
A control group of similar size is given a dummy drug (placebo). Ideally the trials are "blinded" with neither the subjects (nor the investigator) knowing which pill a subject is receiving.
Phase III
Hundreds to thousands of patients with the disease are given the drug to get more reliable data on its
• effectiveness
• safety
• best dose
• rare side effects
all compared with the drug(s) that are currently used for the disease.
If all goes well, the drug manufacturer applies to the Food and Drug Administration for an NDA, a new drug application. If it is granted, the generic name of the drug is replaced by a brand name chosen by the manufacturer. For example, one of the first drugs used against AIDS was azidodideoxythymidine (AZT). When placed on the market, this name was replaced by the brand name Retrovir®. | textbooks/bio/Introductory_and_General_Biology/Biology_(Kimball)/20%3A_General_Science/20.04%3A_Scientific_Papers.txt |
Learning Objectives
• Describe the field of biological science
The Study of Life
Biology is a natural science concerned with the study of life and living organisms. Modern biology is a vast and eclectic field composed of many specialized disciplines that study the structure, function, growth, distribution, evolution, or other features of living organisms. However, despite the broad scope of biology, there are certain general and unifying concepts that govern all study and research:
• the cell is the basic unit of life
• genes (consisting of DNA or RNA) are the basic unit of heredity
• evolution accounts for the unity and diversity seen among living organisms
• all organisms survive by consuming and transforming energy
• all organisms maintain a stable internal environment
Biological research indicates the first forms of life on Earth were microorganisms that existed for billions of years before the evolution of larger organisms. The mammals, birds, and flowers so familiar to us are all relatively recent, originating within the last 200 million years. Modern-appearing humans, Homo sapiens, are a relatively new species, having inhabited this planet for only the last 200,000 years (approximately).
History of Biological Science
Although modern biology is a relatively recent development, sciences related to and included within it have been studied since ancient times. Natural philosophy was studied as early as the ancient civilizations of Mesopotamia, Egypt, the Indian subcontinent, and China. However, the origins of modern biology and its approach to the study of nature are most often traced back to ancient Greece. (Biology is derived from the Greek word “bio” meaning “life” and the suffix “ology” meaning “study of.”)
Advances in microscopy also had a profound impact on biological thinking. In the early 19th century, a number of biologists pointed to the central importance of the cell and in 1838, Schleiden and Schwann began promoting the now universal ideas of the cell theory. Jean-Baptiste Lamarck was the first to present a coherent theory of evolution, although it was the British naturalist Charles Darwin who spread the theory of natural selection throughout the scientific community. In 1953, the discovery of the double helical structure of DNA marked the transition to the era of molecular genetics.
Science and Pseudoscience
Science is a process for learning about the natural world. Most scientific investigations involve the testing of potential answers to important research questions. For example, oncologists ( cancer doctors) are interested in finding out why some cancers respond well to chemotherapy while others are unaffected. Based on their growing knowledge of molecular biology, some doctors suspect a connection between a patient’s genetics and their response to chemotherapy. Many years of research have produced numerous scientific papers documenting the evidence for a connection between cancer, genetics, and treatment response. Once published, scientific information is available for anyone to read, learn from, or even question/dispute. This makes science an iterative, or cumulative, process, where previous research is used as the foundation for new research. Our current understanding of any issue in the sciences is the culmination of all previous work.
Pseudoscience is a belief presented as scientific although it is not a product of scientific investigation. Pseudoscience is often known as fringe or alternative science. It usually lacks the carefully-controlled and thoughtfully-interpreted experiments which provide the foundation of the natural sciences and which contribute to their advancement.
Key Points
• Biology has evolved as a field of science since it was first studied in ancient civilizations, although modern biology is a relatively recent field.
• Science is a process that requires the testing of ideas using evidence gathered from the natural world. Science is iterative in nature and involves critical thinking, careful data collection, rigorous peer review, and the communication of results.
• Science also refers to the body of knowledge produced by scientific investigation.
• Pseudoscience is a belief presented as scientific although it is not a product of scientific investigation.
Key Terms
• pseudoscience: Any belief purported to be scientific or supported by science that is not a product of scientific investigation.
• science: A process for learning about the natural world that tests ideas using evidence gathered from nature.
• Biology: A natural science concerned with the study of life and living organisms. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/01%3A_The_Study_of_Life/1.01%3A_The_Science_of_Biology_-__Introduction_to_the_Study_of_Biology.txt |
Learning Objectives
• Compare and contrast theories and hypotheses
The Process of Science
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. 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 (testable statements) by means of repeatable experiments. 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, paleoanthropology, 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 archaeology: even though one cannot perform repeatable experiments, hypotheses may still be supported. For instance, an archaeologist 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. These hypotheses may be found to be plausible (supported by data) and tentatively accepted, or may be falsified and rejected altogether (due to contradictions from data and other findings). A group of related hypotheses, that have not been disproven, may eventually lead to the development of a verified theory. A theory is a tested and confirmed explanation for observations or phenomena that is supported by a large body of evidence. Science may be better defined as fields of study that attempt to comprehend the nature of the universe.
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 written and tested, and many such predicted changes have been observed, such as the modification of arable areas for agriculture correlated with changes in the average temperatures.
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. Upon 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.
Key Points
• A hypothesis is a statement/prediction that can be tested by experimentation.
• A theory is an explanation for a set of observations or phenomena that is supported by extensive research and that can be used as the basis for further research.
• Inductive reasoning draws on observations to infer logical conclusions based on the evidence.
• Deductive reasoning is hypothesis-based logical reasoning that deduces conclusions from test results.
Key Terms
• theory: a well-substantiated explanation of some aspect of the natural world based on knowledge that has been repeatedly confirmed through observation and experimentation
• hypothesis: a tentative conjecture explaining an observation, phenomenon, or scientific problem that can be tested by further observation, investigation, and/or experimentation | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/01%3A_The_Study_of_Life/1.02%3A__The_Science_of_Biology_-_Scientific_Reasoning.txt |
Learning Objectives
• Discuss hypotheses and the components of a scientific experiment as part of the scientific method
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) who set up inductive methods for scientific inquiry. The scientific method 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. A teenager notices that his friend is really tall and wonders why. So his question might be, “Why is my friend so tall? ”
Proposing a Hypothesis
Recall that a hypothesis is an educated guess that can be tested. Hypotheses often also include an explanation for the educated guess. To solve one problem, several hypotheses may be proposed. For example, the student might believe that his friend is tall because he drinks a lot of milk. So his hypothesis might be “If a person drinks a lot of milk, then they will grow to be very tall because milk is good for your bones.” Generally, hypotheses have the format “If…then…” Keep in mind that there could be other responses to the question; therefore, other hypotheses may be proposed. A second hypothesis might be, “If a person has tall parents, then they will also be tall, because they have the genes to be tall. ”
Once a hypothesis has been selected, the student can make a prediction. A prediction is similar to a hypothesis but it is truly a guess. For instance, they might predict that their friend is tall because he drinks a lot of milk.
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. For example, a control group could be a group of varied teenagers that did not drink milk and they could be compared to the experimental group, a group of varied teenagers that did drink milk. Thus, 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. To test the first hypothesis, the student would find out if drinking milk affects height. If drinking milk has no affect on height, then there must be another reason for the height of the friend. To test the second hypothesis, the student could check whether or not his friend has tall parents. 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. Using the scientific method, the hypotheses that are inconsistent with experimental data are rejected.
While this “tallness” 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 hypothesis to explain this occurrence might be, “If I eat breakfast before class, then I am better able to pay attention.” The student could then design an experiment with a control to test this hypothesis.
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. 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.
Key Points
• In the scientific method, observations lead to questions that require answers.
• In the scientific method, the hypothesis is a testable statement proposed to answer a question.
• In the scientific method, experiments (often with controls and variables) are devised to test hypotheses.
• In the scientific method, analysis of the results of an experiment will lead to the hypothesis being accepted or rejected.
Key Terms
• scientific method: a way of discovering knowledge based on making falsifiable predictions (hypotheses), testing them, and developing theories based on collected data
• hypothesis: an educated guess that usually is found in an “if…then…” format
• control group: a group that contains every feature of the experimental group except it is not given the manipulation that is hypothesized | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/01%3A_The_Study_of_Life/1.03%3A__The_Science_of_Biology_-_The_Scientific_Method.txt |
Learning Objectives
• Differentiate between basic and applied science
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 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 such as improving crop yields, finding a cure for a particular disease, or saving animals threatened by a natural disaster. 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 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 to seek 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.
Key Points
• The only goal of basic science research is to increase the knowledge base of a particular field of study.
• Applied science uses the knowledge base supplied by basic science to devise solutions, often technological, to specific problems.
• The basic science involved in mapping the human genome is leading to applied science techniques that will diagnose and treat genetic diseases.
Key Terms
• basic science: research done solely to expand the knowledge base
• applied science: The discipline dealing with the art or science of applying scientific knowledge to practical problems. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/01%3A_The_Study_of_Life/1.04%3A__The_Science_of_Biology_-_Basic_and_Applied_Science.txt |
Learning Objectives
• Describe the role played by peer-reviewed scientific articles
Reporting Scientific Work
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, a major aspect of a scientist’s work is 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. Scientific writing must be brief, concise, and accurate. It 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 and justification for the work. 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 and the techniques used by the researchers to gather data. The description should be thorough, yet concise, while providing enough information to allow another researcher to repeat the experiment and obtain similar results. 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.
Journals may require separate results and discussion sections, or it may combine them in one section. 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. A well-written 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. They typically include extensive reference sections.
Key Points
• The body of scientific knowledge is recorded in peer-reviewed science journals which allow other scientists to determine what has been done previously and where their own research fits in the larger field of study.
• A scientific article generally follows the steps of the scientific method: introduction (background, observations, question), materials and methods (hypothesis and experimental plan), results (analysis of collected data), and discussion (conclusions drawn from analysis).
• Peer reviewers are other researchers in that field of study who carefully dissect, analyze, and critique a research article submitted for publication.
• Review articles (summaries and commentaries on prior research in a field of study) also go through the peer-review process.
Key Terms
• peer review: The scholarly process whereby manuscripts intended to be published in an academic journal are reviewed by independent researchers to evaluate the contribution, importance, and accuracy of the manuscript’s contents. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/01%3A_The_Study_of_Life/1.05%3A__The_Science_of_Biology_-_Publishing_Scientific_Work.txt |
Learning Objectives
• Recognize the various subfields of biology; e.g. microbiology, genetics, evolutionary, etc.
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. The biological branches are divided according to the focus of the discipline and can even be divided based on the types of techniques and tools used to study that specific focus. However, with the increasing amount of basic biological information growing due to advances in technology and databases, there is often cross-discipline and collaboration between branches. For instance, molecular biology and biochemistry study biological processes at the molecular and chemical level, respectively, 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.
Biological Disciplines and Careers
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.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, including the processing of DNA found in many different environments and materials associated with the crime scenes.
Another field of biological study, neurobiology, is the study 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 focuses on different functions of the nervous system using molecular, cellular, developmental, medical, and computational approaches.
Additional branches of biology include paleontology, which uses fossils to study life’s history; zoology, which studies animals; and botany, which studies plants. Biologists can also specialize as biotechnologists, ecologists, or physiologists. 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.
Key Points
• Biology is broad and focuses on the study of life from various perspectives.
• The branches and subdisciplines of biology, which are highly focused areas, have resulted in the development of careers that are specific to these branches and subdisciplines.
• Branches of biological study include microbiology, physiology, ecology and genetics; subdisciplines within these branches can include: microbial physiology, microbial ecology and microbial genetics.
Key Terms
• genetic engineering: the deliberate modification of the genetic structure of an organism
• forensic: Relating to the use of science and technology in the investigation and establishment of facts or evidence in a court of law. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/01%3A_The_Study_of_Life/1.06%3A__The_Science_of_Biology_-_Branches_and_Subdisciplines_of_Biology.txt |
Learning Objectives
• Describe the properties of life
All living organisms share several key characteristics or functions: order, sensitivity or response to the environment, reproduction, growth and development, regulation, homeostasis, and energy processing. When viewed together, these eight 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, 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 can respond to diverse stimuli. For example, plants can grow toward a source of light, climb on fences and walls, or respond to touch. 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.
Reproduction
Single-celled organisms reproduce by first duplicating their DNA. They then divide 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
All 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 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, 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.
Evolution
As a population of organisms interacts with the environment, individuals with traits that contribute to reproduction and survival in that particular environment will leave more offspring. Over time those advantageous traits (called adaptations ) will become more common in the population. This process, change over time, is called evolution, and it is one of the processes that explain the diverse species seen in biology. Adaptations help organisms survive in their ecological niches, and adaptive traits may be structural, behavioral, or physiological; as such, adaptations frequently involve other properties of organisms such as homeostasis, reproduction, and growth and development.
Key Points
• Order can include highly organized structures such as cells, tissues, organs, and organ systems.
• Interaction with the environment is shown by response to stimuli.
• The ability to reproduce, grow and develop are defining features of life.
• The concepts of biological regulation and maintenance of homeostasis are key to survival and define major properties of life.
• Organisms use energy to maintain their metabolic processes.
• Populations of organisms evolve to produce individuals that are adapted to their specific environment.
Key Terms
• phototaxis: The movement of an organism either towards or away from a source of light
• gene: a unit of heredity; the functional units of chromosomes that determine specific characteristics by coding for specific proteins
• chemotaxis: the movement of a cell or an organism in response to a chemical stimulant | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/01%3A_The_Study_of_Life/1.07%3A_Themes_and_Concepts_of_Biology_-_Properties_of_Life.txt |
Learning Objectives
• Describe the biological levels of organization from the smallest to highest level
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 which are chemical structures 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), which contains the instructions for the structure and functioning of all living organisms.
From Organelles to Biospheres
Macromolecules can form aggregates within a cell that are surrounded by membranes; these are called organelles. Organelles are small structures that exist within cells. Examples of these 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, and 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. Furthermore, 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, 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. Taken together, all of these levels comprise the biological levels of organization, which range from organelles to the biosphere.
Key Points
• The atom is the smallest and most fundamental unit of matter. The bonding of at least two atoms or more form molecules.
• The simplest level of organization for living things is a single organelle, which is composed of aggregates of macromolecules.
• The highest level of organization for living things is the biosphere; it encompasses all other levels.
• The biological levels of organization of living things arranged from the simplest to most complex are: organelle, cells, tissues, organs, organ systems, organisms, populations, communities, ecosystem, and biosphere.
Key Terms
• molecule: The smallest particle of a specific compound that retains the chemical properties of that compound; two or more atoms held together by chemical bonds.
• macromolecule: a very large molecule, especially used in reference to large biological polymers (e.g. nucleic acids and proteins)
• polymerization: The chemical process, normally with the aid of a catalyst, to form a polymer by bonding together multiple identical units (monomers). | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/01%3A_The_Study_of_Life/1.08%3A__Themes_and_Concepts_of_Biology_-_Levels_of_Organization_of_Living_Things.txt |
Learning Objectives
• Recognize the three major domains used for classification
The fact that biology has such a broad scope as a science 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 using phylogeny. 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.
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. 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. 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. DNA, the universal genetic material, contains the instructions for the structure and function of all living organisms and can be divided into genes whose expression varies between organisms. The RNA, which is transcribed from DNA, varies between organisms as well based on the expression of specific genes. Thus, to examine differences at this molecular level provides a more accurate depiction of the diversity which exists.
Key Points
• The three major Domains of Life include: Domain Bacteria, Domain Eukarya and Domain Archaea.
• Domain Bacteria and Domain Archaea include prokaryotic cells that lack membrane-enclosed nuclei and organelles.
• Domain Eukarya include eukaryotes and more complex organisms that contain membrane-bound nuclei and organelles.
• Carl Woese defined Archaea as a new domain and constructed the phylogentic tree of life which shows separation of all living organisms.
• The phylogenetic tree of life was constructed by Carl Woese using sequencing data of ribosomal RNA genes. Therefore, genetics classification surpassed morphological cataloguing, which was the traditional way of organizing living beings.
Key Terms
• phylogeny: the evolutionary history of an organism
• extremophile: an organism that lives under extreme conditions of temperature, salinity, etc; commercially important as a source of enzymes that operate under similar conditions
• DNA: a biopolymer of deoxyribonucleic acids (a type of nucleic acid) that has four different chemical groups, called bases: adenine, guanine, cytosine, and thymine | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/01%3A_The_Study_of_Life/1.09%3A__Themes_and_Concepts_of_Biology_-_The_Diversity_of_Life.txt |
Learning Objectives
• Discuss the electronic and structural properties of an atom
An atom is the smallest unit of matter that retains all of the chemical properties of an element. Atoms combine to form molecules, which then interact to form solids, gases, or liquids. For example, water is composed of hydrogen and oxygen atoms that have combined to form water molecules. Many biological processes are devoted to breaking down molecules into their component atoms so they can be reassembled into a more useful molecule.
Atomic Particles
Atoms consist of three basic particles: protons, electrons, and neutrons. The nucleus (center) of the atom contains the protons (positively charged) and the neutrons (no charge). The outermost regions of the atom are called electron shells and contain the electrons (negatively charged). Atoms have different properties based on the arrangement and number of their basic particles.
The hydrogen atom (H) contains only one proton, one electron, and no neutrons. This can be determined using the atomic number and the mass number of the element (see the concept on atomic numbers and mass numbers).
Atomic Mass
Protons and neutrons have approximately the same mass, about 1.67 × 10-24 grams. Scientists define this amount of mass as one atomic mass unit (amu) or one Dalton. Although similar in mass, protons are positively charged, while neutrons have no charge. 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. Therefore, they do not contribute much to an element’s overall atomic mass. 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.
Electrons contribute greatly to the atom’s charge, as each electron has a negative charge equal to the positive charge of a proton. Scientists define these charges as “+1” and “-1. ” In an uncharged, neutral atom, 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.
Table \(1\): Protons, neutrons, and electrons: Both protons and neutrons have a mass of 1 amu and are found in the nucleus. However, protons have a charge of +1, and neutrons are uncharged. Electrons have a mass of approximately 0 amu, orbit the nucleus, and have a charge of -1.
Charge Mass (amu) Location
proton +1 1 nucleus
neutron 0 1 nucles
electron -1 0 orbitals
Exploring Electron Properties: Compare the behavior of electrons to that of other charged particles to discover properties of electrons such as charge and mass.
Volume of Atoms
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. Despite all this empty space, solid objects do not just pass through one another. The electrons that surround all atoms are negatively charged and cause atoms to repel one another, preventing atoms from occupying the same space. These intermolecular forces prevent you from falling through an object like your chair.
Interactive Element
Interactive: Build an Atom: Build an atom out of protons, neutrons, and electrons, and see how the element, charge, and mass change. Then play a game to test your ideas!
Key Points
• An atom is composed of two regions: the nucleus, which is in the center of the atom and contains protons and neutrons, and the outer region of the atom, which holds its electrons in orbit around the nucleus.
• Protons and neutrons have approximately the same mass, about 1.67 × 10-24 grams, which scientists define as one atomic mass unit (amu) or one Dalton.
• Each electron has a negative charge (-1) equal to the positive charge of a proton (+1).
• Neutrons are uncharged particles found within the nucleus.
Key Terms
• atom: The smallest possible amount of matter which still retains its identity as a chemical element, consisting of a nucleus surrounded by electrons.
• proton: Positively charged subatomic particle forming part of the nucleus of an atom and determining the atomic number of an element. It weighs 1 amu.
• neutron: A subatomic particle forming part of the nucleus of an atom. It has no charge. It is equal in mass to a proton or it weighs 1 amu.
2.02: Atoms Isotopes Ions and Molecules - Atomic Number and Mass Number
Learning Objectives
• Determine the relationship between the mass number of an atom, its atomic number, its atomic mass, and its number of subatomic particles
Atomic Number
Neutral atoms of an element contain an equal number of protons and electrons. The number of protons determines an element’s atomic number (Z) and distinguishes one element from another. For example, carbon’s atomic number (Z) is 6 because it has 6 protons. The number of neutrons can vary to produce isotopes, which are atoms of the same element that have different numbers of neutrons. The number of electrons can also be different in atoms of the same element, thus producing ions (charged atoms). For instance, iron, Fe, can exist in its neutral state, or in the +2 and +3 ionic states.
Mass Number
An element’s mass number (A) is the sum of the number of protons and the number of neutrons. 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. Protons and neutrons both weigh about one atomic mass unit or amu. Isotopes of the same element will have the same atomic number but different mass numbers.
Scientists determine the atomic mass by calculating the mean of the mass numbers for its naturally-occurring isotopes. Often, the resulting number contains a decimal. For example, the atomic mass of chlorine (Cl) is 35.45 amu because chlorine is composed of several isotopes, some (the majority) with an atomic mass of 35 amu (17 protons and 18 neutrons) and some with an atomic mass of 37 amu (17 protons and 20 neutrons).
Given an atomic number (Z) and mass number (A), you can find the number of protons, neutrons, and electrons in a neutral atom. For example, a lithium atom (Z=3, A=7 amu) contains three protons (found from Z), three electrons (as the number of protons is equal to the number of electrons in an atom), and four neutrons (7 – 3 = 4).
Key Points
• Neutral atoms of each element contain an equal 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.
• Since an element’s isotopes have slightly different mass numbers, the atomic mass is calculated by obtaining the mean of the mass numbers for its isotopes.
Key Terms
• mass number: The sum of the number of protons and the number of neutrons in an atom.
• atomic number: The number of protons in an atom.
• atomic mass: The average mass of an atom, taking into account all its naturally occurring isotopes. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/02%3A_The_Chemical_Foundation_of_Life/2.01%3A_Atoms_Isotopes_Ions_and_Molecules_-_Overview_of_Atomic_Structure.txt |
Learning Objectives
• Discuss the properties of isotopes and their use in radiometric dating
What is an Isotope?
Isotopes are various 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 multiple naturally-occurring isotopes. Isotopes are defined first by their element and then by the sum of the protons and neutrons present.
• Carbon-12 (or 12C) contains six protons, six neutrons, and six electrons; therefore, it has a mass number of 12 amu (six protons and six neutrons).
• Carbon-14 (or 14C) contains six protons, eight neutrons, and six electrons; its atomic mass is 14 amu (six protons and eight neutrons).
While the mass of individual isotopes is different, their physical and chemical properties remain mostly unchanged.
Isotopes do differ in their stability. Carbon-12 (12C) is the most abundant of the carbon isotopes, accounting for 98.89% of carbon on Earth. Carbon-14 (14C) is unstable and only occurs in trace amounts. Unstable isotopes most commonly emit alpha particles (He2+) and electrons. Neutrons, protons, and positrons can also be emitted and electrons can be captured to attain a more stable atomic configuration (lower level of potential energy ) through a process called radioactive decay. The new atoms created may be in a high energy state and emit gamma rays which lowers the energy but alone does not change the atom into another isotope. These atoms are called radioactive isotopes or radioisotopes.
Radiocarbon Dating
Carbon is normally present in the atmosphere in the form of gaseous compounds like carbon dioxide and methane. Carbon-14 (14C) is a naturally-occurring radioisotope that is created from atmospheric 14N (nitrogen) by the addition of a neutron and the loss of a proton, which is caused by cosmic rays. This is a continuous process so more 14C is always being created in the atmosphere. Once produced, the 14C often combines with the oxygen in the atmosphere to form carbon dioxide. Carbon dioxide produced in this way diffuses in the atmosphere, is dissolved in the ocean, and is incorporated by plants via photosynthesis. Animals eat the plants and, ultimately, the radiocarbon is distributed throughout the biosphere.
In living organisms, the relative amount of 14C in their body is approximately equal to the concentration of 14C in the atmosphere. When an organism dies, it is no longer ingesting 14C, so the ratio between 14C and 12C will decline as 14C gradually decays back to 14N. This slow process, which is called beta decay, releases energy through the emission of electrons from the nucleus or positrons.
After approximately 5,730 years, half of the starting concentration of 14C will have been converted back to 14N. This is referred to as its half-life, or the time it takes for half of the original concentration of an isotope to decay back to its more stable form. Because the half-life of 14C is long, it is used to date formerly-living objects such as old bones or wood. Comparing the ratio of the 14C concentration found in an object to the amount of 14C 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 can be accurately calculated, as long as the material is believed to be less than 50,000 years old. This technique is called radiocarbon dating, or carbon dating for short.
Other elements have isotopes with different half lives. For example, 40K (potassium-40) has a half-life of 1.25 billion years, and 235U (uranium-235) has a half-life of about 700 million years. Scientists often use these other radioactive elements to date objects that are older than 50,000 years (the limit of carbon dating). Through the use of radiometric dating, scientists can study the age of fossils or other remains of extinct organisms.
Key Points
• Isotopes are atoms of the same element that contain an identical number of protons, but a different number of neutrons.
• Despite having different numbers of neutrons, isotopes of the same element have very similar physical properties.
• Some isotopes are unstable and will undergo radioactive decay to become other elements.
• The predictable half-life of different decaying isotopes allows scientists to date material based on its isotopic composition, such as with Carbon-14 dating.
Key Terms
• isotope: Any of two or more forms of an element where the atoms have the same number of protons, but a different number of neutrons within their nuclei.
• half-life: The time it takes for half of the original concentration of an isotope to decay back to its more stable form.
• radioactive isotopes: an atom with an unstable nucleus, characterized by excess energy available that undergoes radioactive decay and creates most commonly gamma rays, alpha or beta particles.
• radiocarbon dating: Determining the age of an object by comparing the ratio of the 14C concentration found in it to the amount of 14C in the atmosphere. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/02%3A_The_Chemical_Foundation_of_Life/2.03%3A__Atoms_Isotopes_Ions_and_Molecules_-_Isotopes.txt |
Learning Objectives
• Discuss the organization of the periodic table
Matter and Elements
Matter comprises all of the physical objects in the universe, those that take up space and have mass. All matter is composed of atoms of one or more elements, pure substances with specific chemical and physical properties. There are 98 elements that naturally occur on earth, yet living systems use a relatively small number of these. Living creatures are composed mainly of just four elements: carbon, hydrogen, oxygen, and nitrogen (often remembered by the acronym CHON). As elements are bonded together they form compounds that often have new emergent properties that are different from the properties of the individual elements. Life is an example of an emergent property that arises from the specific collection of molecules found in cells.
Elements of the human body arranged by percent of total mass: There are 25 elements believed to play an active role in human health. Carbon, hydrogen, oxygen, and nitrogen make up approximately 96% of the mass in a human body.
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. In the periodic table the elements are organized and displayed according to their atomic number and are arranged in a series of rows (periods) and columns (groups) based on shared chemical and physical properties. If you look at a periodic table, you will see the groups numbered at the top of each column from left to right starting with 1 and ending with 18. 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 arrangement of the periodic table allows the elements to be grouped according to their chemical properties. Within the main group elements ( Groups 1-2, 13-18), there are some general trends that we can observe. The further down a given group, the elements have an increased metallic character: they are good conductors of both heat and electricity, solids at room temperature, and shiny in appearance. Moving from left to right across a period, the elements have greater non-metallic character. These elements are insulators, poor heat conductors, and can exist in different phases at room temperature (brittle solid, liquid, or gas). The elements at the boundary between the metallic elements (grey elements) and nonmetal elements (green elements) are metalloid in character (pink elements). They have low electrical conductivity that increases with temperature. They also share properties with both the metals and the nonmetals.
Today, the periodic table continues to expand as heavier and heavier elements are synthesized in laboratories. These large elements are extremely unstable and, as such, are very difficult to detect; but their continued creation is an ongoing challenge undertaken by scientists around the world.
Key Points
• All matter is made from atoms of one or more elements. Living creatures consist mainly of carbon, hydrogen, oxygen, and nitrogen (CHON).
• Combining elements creates compounds that may have emergent properties.
• The periodic table is a listing of the elements according to increasing atomic number that is further organized into columns based on similar physical and chemical properties and electron configuration.
• As one moves down a column or across a row, there are some general trends for the properties of the elements.
• The periodic table continues to expand today as heavier and heavier elements are created in laboratories around the world.
Key Terms
• element: Pure chemical substances consisting of only one type of atom with a defined set of chemical and physical properties.
• emergent properties: Properties found in compound structures that are different from those of the individual components and would not be predicted based on the properties of the individual components.
• periodic table: A tabular chart of the chemical elements according to their atomic numbers so that elements with similar properties are in the same column. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/02%3A_The_Chemical_Foundation_of_Life/2.04%3A__Atoms_Isotopes_Ions_and_Molecules_-_The_Periodic_Table.txt |
Learning Objectives
• Construct an atom according to the Bohr model
Electron Shells and the Bohr Model
As previously discussed, 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. Each element, when electrically neutral, has a 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. These orbits form electron shells or energy levels, which are a way of visualizing the number of electrons in the various 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 orbit shells in a consistent order. Under standard conditions, atoms fill the inner shells (closer to the nucleus) 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 that, with the exception of the innermost shell, 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. As shown, 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 electrons in their outer shells, respectively. Theoretically, they would be more energetically stable if they followed the octet rule and had eight.
An atom may gain or lose electrons to achieve a full valence shell, the most stable electron configuration. The periodic table is arranged in columns and rows based on the number of electrons and where these electrons are located, providing a tool to understand how electrons are distributed in the outer shell of an atom. As shown in, the group 18 atoms helium (He), neon (Ne), and argon (Ar) all have filled outer electron shells, making it unnecessary for them to gain or lose electrons 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). In comparison, the group 1 elements, including hydrogen (H), lithium (Li), and sodium (Na), all have one electron in their outermost shells. This means that they can achieve a stable configuration and a filled outer shell by donating or losing an electron. As a result of losing a negatively-charged electron, they become positively-charged ions. When an atom loses an electron to become a positively-charged ion, this is indicated by a plus sign after the element symbol; for example, Na+. Group 17 elements, including fluorine and chlorine, have seven electrons in their outermost shells; they tend to fill this shell by gaining an electron from other atoms, making them negatively-charged ions. When an atom gains an electron to become a negatively-charged ion this is indicated by a minus sign after the element symbol; for example, F-. 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.
Key Points
• In the Bohr model of the atom, the nucleus contains the majority of the mass of the atom in its protons and neutrons.
• Orbiting the positively-charged core are the negatively charged electrons, which contribute little in terms of mass, but are electrically equivalent to the protons in the nucleus.
• In most cases, electrons fill the lower- energy orbitals first, followed by the next higher energy orbital until it is full, and so on until all electrons have been placed.
• Atoms tend to be most stable with a full outer shell (one which, after the first, contains 8 electrons), leading to what is commonly called the ” octet rule “.
• The properties of an element are determined by its outermost electrons, or those in the highest energy orbital.
• Atoms that do not have full outer shells will tend to gain or lose electrons, resulting in a full outer shell and, therefore, stability.
Key Terms
• octet rule: A rule stating that atoms lose, gain, or share electrons in order to have a full valence shell of 8 electrons. (Hydrogen is excluded because it can hold a maximum of 2 electrons in its valence shell. )
• electron shell: The collective states of all electrons in an atom having the same principal quantum number (visualized as an orbit in which the electrons move). | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/02%3A_The_Chemical_Foundation_of_Life/2.05%3A__Atoms_Isotopes_Ions_and_Molecules_-_Electron_Shells_and_the_Bohr_Model.txt |
Learning Objectives
• Distinguish between electron orbitals in the Bohr model versus the quantum mechanical 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 rather 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.
First Electron Shell
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 always filled before any other orbital. 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, hydrogen and helium are the only two elements in the first row (period); this is because they are the sole elements to have electrons only in their first shell, the 1s orbital.
Second Electron Shell
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. 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: it rarely forms a chemical bond with other atoms.
Third Electron Shell
Larger elements have additional orbitals, making up the third electron shell. Subshells d and f have more complex shapes and contain five and seven orbitals, respectively. 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. 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.
Key Points
• The Bohr model of the atom does not accurately reflect how electrons are spatially distributed around the nucleus as they do not circle the nucleus like the earth orbits the sun.
• The electron orbitals are the result of mathematical equations from quantum mechanics known as wave functions and can predict within a certain level of probability where an electron might be at any given time.
• The number and type of orbitals increases with increasing atomic number, filling in various electron shells.
• The area where an electron is most likely to be found is called its orbital.
Key Terms
• electron shell: The collective states of all electrons in an atom having the same principal quantum number (visualized as an orbit in which the electrons move).
• orbital: A specification of the energy and probability density of an electron at any point in an atom or molecule. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/02%3A_The_Chemical_Foundation_of_Life/2.06%3A__Atoms_Isotopes_Ions_and_Molecules_-_Electron_Orbitals.txt |
Learning Objectives
• Describe the properties of chemical reactions and compounds
According to the octet rule, elements are most stable when their outermost shell is filled with electrons. This is because it is energetically favorable for atoms to be in that configuration. However, since not all elements have enough electrons to fill their outermost shells, atoms form chemical bonds with other atoms, which helps them obtain 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, which bond together to form water. 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. For the creation of the water molecule shown above, the chemical equation would be:
\[\ce{2H2+O2→2H2O}\]
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 (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.
\[\ce{2H2O2→2H2O+O2}\]
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 representative of a subclass of molecules known as compounds: they contain atoms of more than one type of element. Molecular oxygen, on the other hand, consists of two doubly bonded oxygen atoms and is not classified as a compound but as an element.
Irreversible and Reversible Reactions
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, 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.
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.
Interactive Element
Interactive: What is a Chemical Reaction?: Explore reactions in which chemical bonds are formed and broken with this model. Press run, then try heating and cooling the atoms to see how temperature affects the balance between bond formation and breaking.
Key Points
• Atoms form chemical bonds with other atoms thereby obtaining the electrons they need to attain a stable electron configuration.
• The substances used in the beginning of a chemical reaction are called the reactants and the substances found at the end of the reaction are known as the products.
• Some reactions are reversible and will reach a relative balance between reactants and products: a state called equilibrium.
• An arrow is typically drawn between the reactants and products to indicate the direction of the chemical reaction.
Key Terms
• reactant: Any of the participants present at the start of a chemical reaction.
• molecule: The smallest particle of a specific compound that retains the chemical properties of that compound; two or more atoms held together by chemical bonds.
• reaction: A transformation in which one or more substances is converted into another by combination or decomposition | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/02%3A_The_Chemical_Foundation_of_Life/2.07%3A__Atoms_Isotopes_Ions_and_Molecules_-_Chemical_Reactions_and_Molecules.txt |
Learning Objectives
• Predict whether a given element will more likely form a cation or an anion
Ions and Ionic Bonds
Some atoms are more stable when they gain or lose an electron (or possibly two) and form ions. This results in a full outermost electron shell and makes them energetically more stable. Now, 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 (as the number of protons is now greater than the number of electrons). Negative ions are formed by gaining electrons and are called anions (wherein there are more electrons than protons in a molecule ). Anions are designated by their elemental name being altered to end in “-ide”. For example, the anion of chlorine is called chloride, and the anion of sulfur is called sulfide.
This movement of electrons from one element to another is referred to as electron transfer. As illustrated, 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. When sodium loses an electron, it will have 11 protons, 11 neutrons, and only 10 electrons. This leaves it with an overall charge of +1 since there are now more protons than electrons. 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. This gives it a net charge of -1 since there are now more electrons than protons. 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 outer shells. 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 form sodium chloride, or table salt, a crystalline molecule with zero net charge. The attractive force holding the two atoms together is called the electromagnetic force and is responsible for the attraction between oppositely charged ions.
Certain salts are referred to in physiology as electrolytes (including sodium, potassium, and calcium). Electrolytes are 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.
Key Points
• Ions form from elements when they gain or lose an electron causing the number of protons to be unequal to the number of electrons, resulting in a net charge.
• If there are more electrons than protons (from an element gaining one or more electrons), the ion is negatively charged and called an anion.
• If there are more protons than electrons (via loss of electrons), the ion is positively charged and is called a cation.
• Ionic bonds result from the interaction between a positively charged cation and a negatively charged anion.
Key Terms
• ion: An atom, or group of atoms, bearing an electrical charge, such as the sodium and chlorine atoms in a salt solution.
• ionic bond: A strong chemical bond caused by the electrostatic attraction between two oppositely charged ions. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/02%3A_The_Chemical_Foundation_of_Life/2.08%3A__Atoms_Isotopes_Ions_and_Molecules_-_Ions_and_Ionic_Bonds.txt |
Learning Objectives
• Compare the relative strength of different types of bonding interactions
The octet rule can be satisfied by the sharing of electrons between atoms to form covalent bonds. These bonds are stronger and much more common than are ionic bonds in the molecules of living organisms. Covalent bonds are commonly found in carbon-based organic molecules, such as DNA and proteins. Covalent bonds are also found in inorganic molecules such as H2O, CO2, and O2. One, two, or three pairs of electrons may be shared between two atoms, 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 nitrogenous 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. The resulting strong triple bond makes it difficult for living systems to break apart this nitrogen in order to use it as constituents of biomolecules, such as proteins, DNA, and RNA.
The formation of water molecules is an example of covalent bonding. The hydrogen and oxygen atoms that combine to form water molecules are bound together by covalent bonds. The electron from the hydrogen splits its time between the incomplete outer shell of the hydrogen atom and the incomplete outer shell of the oxygen atom. In return, the oxygen atom shares one of its electrons with the hydrogen atom, creating a two-electron single covalent bond. To completely fill the outer shell of oxygen, which has six electrons in its outer shell, two electrons (one from each hydrogen atom) are needed. Each hydrogen atom needs only a single electron to fill its outer shell, hence the well-known formula H2O. The electrons that are shared between the two elements fill the outer shell of each, making both elements more stable.
Polar Covalent Bonds
There are two types of covalent bonds: polar and nonpolar. In a polar covalent bond, the electrons are unequally shared by the atoms because they are more attracted to one nucleus than the other. The relative attraction of an atom to an electron is known as its electronegativity: atoms that are more attracted to an electron are considered to be more electronegative. 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 known as a dipole; this is an important property of water and accounts for many of its characteristics. The dipole in water occurs because oxygen has a higher electronegativity than hydrogen, which means that the shared electrons spend more time in the vicinity of the oxygen nucleus than they do near the nucleus of the hydrogen atoms.
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. The four bonds of methane are also considered to be nonpolar because the electronegativies of carbon and hydrogen are nearly identical.
Hydrogen Bonds and Van Der Waals Interactions
Not all bonds are ionic or covalent; weaker bonds can also form between molecules. Two types of weak bonds that frequently occur 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 are formed, the hydrogen atom in that bond has a slightly positive charge (δ+) because the shared electrons are pulled more strongly toward the other element and away from the hydrogen atom. Because the hydrogen has a slightly positive charge, it’s attracted to neighboring negative charges. The weak interaction between the δ+ charge of a hydrogen atom from one molecule and the δ- charge of a more electronegative atom is called a hydrogen bond. Individual hydrogen bonds are weak and easily broken; however, they occur in very large numbers in water and in organic polymers, and the additive force can be very strong. For example, hydrogen bonds are responsible for zipping together the DNA double helix.
Like hydrogen bonds, van der Waals interactions are weak 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 can lead to slight temporary dipoles around a molecule. For these attractions to happen, the molecules need to be very close to one another. These bonds, along with hydrogen bonds, help form the three-dimensional structures of the proteins in our cells that are required for their proper function.
Interactive Element
Interactions between different types of molecules: In this interactive, you can explore how different types of molecules interact with each other based on their bonds.
Key Points
• A polar covalent bond arises when two atoms of different electronegativity share two electrons unequally.
• A non-polar covalent bond is one in which the electrons are shared equally between two atoms.
• Hydrogen bonds and Van Der Waals are responsible for the folding of proteins, the binding of ligands to proteins, and many other processes between molecules.
Key Terms
• hydrogen bond: A weak bond in which a hydrogen atom in one molecule is attracted to an electronegative atom (usually nitrogen or oxygen) in the same or different molecule.
• covalent bond: A type of chemical bond where two atoms are connected to each other by the sharing of two or more electrons.
• dipole: Any object (such as a magnet, polar molecule or antenna), that is oppositely charged at two points (or poles). | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/02%3A_The_Chemical_Foundation_of_Life/2.09%3A__Atoms_Isotopes_Ions_and_Molecules_-_Covalent_Bonds_and_Other_Bonds_and_Interactions.txt |
Learning Objectives
• Describe how hydrogen bonds and van der Waals interactions occur
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.
Hydrogen Bonding
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 one 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, an 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.
Applications for Hydrogen Bonds
Hydrogen bonds occur in inorganic molecules, such as water, and organic molecules, such as DNA and proteins. The two complementary strands of DNA are held together by hydrogen bonds between complementary nucleotides (A&T, C&G). Hydrogen bonding in water contributes to its unique properties, including its high boiling point (100 °C) and surface tension.
In biology, intramolecular hydrogen bonding is partly responsible for the secondary, tertiary, and quaternary structures of proteins and nucleic acids. The hydrogen bonds help the proteins and nucleic acids form and maintain specific shapes.
Van der Waals Interactions
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 proteins that is necessary for their proper function.
Interactive Element
Van der Waals attraction: Explore how Van der Waals attractions and temperature affect intermolecular interactions.
Key Points
• 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.
• Hydrogen bonds occur in inorganic molecules, such as water, and organic molecules, such as DNA and proteins.
• Van der Waals attractions can occur between any two or more molecules and are dependent on slight fluctuations of the electron densities.
• While hydrogen bonds and van der Waals interactions are weak individually, they are strong combined in vast numbers.
Key Terms
• van der Waals interactions: A weak force of attraction between electrically neutral molecules that collide with or pass very close to each other. The van der Waals force is caused by temporary attractions between electron-rich regions of one molecule and electron-poor regions of another.
• electronegativity: The tendency of an atom or molecule to draw electrons towards itself, form dipoles, and thus form bonds.
• hydrogen bond: The attraction between a partially positively-charged hydrogen atom attached to a highly electronegative atom (such as nitrogen, oxygen, or fluorine) and another nearby electronegative atom. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/02%3A_The_Chemical_Foundation_of_Life/2.10%3A__Atoms_Isotopes_Ions_and_Molecules_-_Hydrogen_Bonding_and_Van_der_Waals_Forces.txt |
Learning Objectives
• Describe the actions that occur due to water’s polarity
One of water’s important properties is that it is composed of polar molecules. The two hydrogen atoms and one oxygen atom 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, or electron loving, than hydrogen. Thus, it is more likely that a shared electron would be found near the oxygen nucleus than the hydrogen nucleus. Since water is a nonlinear, or bent, molecule, the difference in electronegativities between the oxygen and hydrogen atoms generates the partial negative charge near the oxygen and partial positive charges near both hydrogens.
As a result of water’s polarity, each water molecule attracts other water molecules because of the opposite charges between them, forming hydrogen bonds. Water also attracts, or is attracted to, other polar molecules and ions, including many biomolecules, such as sugars, nucleic acids, and some amino acids. A polar substance that interacts readily with or dissolves in water is referred to as hydrophilic (hydro- = “water”; -philic = “loving”). In contrast, nonpolar molecules, such as oils and fats, do not interact well with water, as shown in. These molecules 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”).
Interactive Element
Hydrogen bonds: This interactive shows the interaction of the hydrogen bonds among water molecules.
Key Points
• The difference in electronegativities between oxygen and hydrogen atoms creates partial negative and positive charges, respectively, on the atoms.
• Water molecules attract or are attracted to other polar molecules.
• Molecules that do not dissolve in water are known as hydrophobic (water fearing) molecules.
Key Terms
• hydrophilic: having an affinity for water; able to absorb, or be wetted by water
• hydrophobic: lacking an affinity for water; unable to absorb, or be wetted by water
• polarity: The intermolecular forces between the slightly positively-charged end of one molecule to the negative end of another or the same molecule.
2.12: Water - Gas Liquid and Solid Water
Learning Objectives
• Explain the biological significance of ice’s ability to float on water
Water’s States: Gas, Liquid, and Solid
The formation of hydrogen bonds is an important quality of 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). This makes ice less dense than liquid water, a phenomenon not seen in the solidification of other liquids.
Interactive Element
Phases of matter: See what happens to intermolecular bonds during phase changes in this interactive.
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 low density of ice, an anomaly, causes it to float at the surface of liquid water, such as an iceberg or the ice cubes in a glass of water. In lakes and ponds, ice forms 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.
Key Points
• As water is boiled, kinetic energy causes the hydrogen bonds to break completely and allows water molecules to escape into the air as gas (steam or water vapor).
• When water freezes, water molecules form a crystalline structure maintained by hydrogen bonding.
• Solid water, or ice, is less dense than liquid water.
• Ice is less dense than water because the orientation of hydrogen bonds causes molecules to push farther apart, which lowers the density.
• For other liquids, solidification when the temperature drops includes the lowering of kinetic energy, which allows molecules to pack more tightly and makes the solid denser than its liquid form.
• Because ice is less dense than water, it is able to float at the surface of water.
Key Terms
• density: A measure of the amount of matter contained by a given volume. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/02%3A_The_Chemical_Foundation_of_Life/2.11%3A_Water_-_Waters_Polarity.txt |
Learning Objectives
• Explain how heat of vaporization is related to the boiling point of water
Water in its liquid form has an unusually high boiling point temperature, a value close to 100°C. As a result of the network of hydrogen bonding present between water molecules, a high input of energy is required to transform one gram of liquid water into water vapor, an energy requirement called the heat of vaporization. Water has a heat of vaporization value of 40.65 kJ/mol. A considerable amount of heat energy (586 calories) 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 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 each other 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 humans, the evaporation of sweat, which is 90 percent water, allows the organism to cool so that homeostasis of body temperature can be maintained.
Key Points
• The dissociation of liquid water molecules, which changes the substance to a gas, requires a lot of energy.
• The boiling point of water is the temperature in which there is enough energy to break the hydrogen bonds between water molecules.
• Water is converted from its liquid form to its gaseous form (steam) when the heat of vaporization is reached.
• Evaporation of sweat (mostly water) removes heat from the surface of skin, cooling the body.
Key Terms
• heat of vaporization: The energy required to transform a given quantity of a substance from a liquid into a gas at a given pressure (often atmospheric pressure).
2.14: Water - High Heat Capacity
Learning Objectives
• Explain the biological significance of water’s high specific heat
Water’s High Heat Capacity
The capability for a molecule to absorb heat energy is called heat capacity, which can be calculated by the equation shown in the figure. Water’s high heat capacity is a property caused by hydrogen bonding among water molecules. When heat is absorbed, hydrogen bonds are broken and water molecules can move freely. When the temperature of water decreases, the hydrogen bonds are formed and release a considerable amount of energy. Water has the highest specific heat capacity of any liquid. 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, or 4.184 Joules. As a result, it takes water a long time to heat and a 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.
C=QΔT.C=QΔT.
The resistance to sudden temperature changes makes water an excellent habitat, allowing organisms to survive without experiencing wide temperature fluctuation. Furthermore, because many organisms are mainly composed of water, the property of high heat capacity allows highly regulated internal body temperatures. For example, the temperature of your body does not drastically drop to the same temperature as the outside temperature while you are skiing or playing in the snow. 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.
Key Points
• Water has the highest heat capacity of all liquids.
• Oceans cool slower than the land due to the high heat capacity of water.
• To change the temperature of 1 gram of water by 1 degree Celsius, it takes 1.00 calorie.
Key Terms
• heat capacity: The capability of a substance to absorb heat energy
• specific heat: the amount of heat, in calories, needed to raise the temperature of 1 gram of water by 1 degree Celsius
2.15: Water - Waters Solvent Properties
Learning Objectives
• Explain why some molecules do not dissolve in water.
Water’s Solvent Properties
Water, which not only dissolves many compounds but also dissolves more substances than any other liquid, is considered the universal solvent. A polar molecule with partially-positive and negative charges, it readily dissolves ions and polar molecules. Water is therefore referred to as a solvent: a substance capable of dissolving other polar molecules and ionic compounds. The charges associated with these molecules form hydrogen bonds with water, surrounding the particle with water molecules. This is referred to as a sphere of hydration, or a hydration shell, and serves to keep the particles separated or dispersed in the water.
When ionic compounds are added to water, individual ions interact with the polar regions of the water molecules during the dissociation process, disrupting their ionic bonds. 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 Clions, and spheres of hydration form around the ions. 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 in the water molecule.
Since many biomolecules are either polar or charged, water readily dissolves these hydrophilic compounds. Water is a poor solvent, however, for hydrophobic molecules such as lipids. Nonpolar molecules experience hydrophobic interactions in water: the water changes its hydrogen bonding patterns around the hydrophobic molecules to produce a cage-like structure called a clathrate. This change in the hydrogen-bonding pattern of the water solvent causes the system’s overall entropy to greatly decrease, as the molecules become more ordered than in liquid water. Thermodynamically, such a large decrease in entropy is not spontaneous, and the hydrophobic molecule will not dissolve.
Key Points
• Water dissociates salts by separating the cations and anions and forming new interactions between the water and ions.
• Water dissolves many biomolecules, because they are polar and therefore hydrophilic.
Key Terms
• dissociation: The process by which a compound or complex body breaks up into simpler constituents such as atoms or ions, usually reversibly.
• hydration shell: The term given to a solvation shell (a structure composed of a chemical that acts as a solvent and surrounds a solute species) with a water solvent; also referred to as a hydration sphere. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/02%3A_The_Chemical_Foundation_of_Life/2.13%3A_Water_-_Heat_of_Vaporization.txt |
Learning Objectives
• Describe the cohesive and adhesive properties of water.
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 (the mass per unit volume) 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.
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.
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 use the surface tension of water to stay afloat on the surface layer of water and even mate there.
Key Points
• Cohesion holds hydrogen bonds together to create surface tension on water.
• Since water is attracted to other molecules, adhesive forces pull the water toward other molecules.
• Water is transported in plants through both cohesive and adhesive forces; these forces pull water and the dissolved minerals from the roots to the leaves and other parts of the plant.
Key Terms
• adhesion: The ability of a substance to stick to an unlike substance; attraction between unlike molecules
• cohesion: Various intermolecular forces that hold solids and liquids together; attraction between like molecules | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/02%3A_The_Chemical_Foundation_of_Life/2.16%3A_Water_-_Cohesive_and_Adhesive_Properties.txt |
Learning Objectives
• Explain the composition of buffer solutions and how they maintain a steady pH
Self-Ionization of Water
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. The hydroxide ions remain in solution because of their hydrogen bonds with other water molecules; the hydrogen ions, consisting of naked protons, are immediately attracted to un-ionized water molecules and form hydronium ions (\(\ce{H3O^{+}}\)). By convention, scientists refer to hydrogen ions and their concentration as if they were free in this state in liquid water.
\[\ce{2H2O⇋H3O^{+} + OH^{−}}\]
The concentration of hydrogen ions dissociating from pure water is 1 × 10-7 moles H+ ions per liter of water. The pH is calculated as the negative of the base 10 logarithm of this concentration:
\[pH = -\log_{10}[\ce{H^{+}}]\]
The negative log of 1 × 10-7 is equal to 7.0, which is also known as neutral pH. Human cells and blood each maintain near-neutral pH.
pH Scale
The pH of a solution indicates its acidity or basicity (alkalinity). The pH scale is an inverse logarithm that ranges from 0 to 14: 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 basic (or alkaline ). Extremes in pH in either direction from 7.0 are usually considered inhospitable to life. The pH in cells (6.8) and the blood (7.4) are both very close to neutral, whereas the environment in the stomach is highly acidic, with a pH of 1 to 2.
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, and low concentrations a high pH.
An acid is a substance that increases the concentration of hydrogen ions (H+) in a solution, usually by dissociating one of its hydrogen atoms. A base provides either hydroxide ions (OH) or other negatively-charged ions that react with hydrogen ions in solution, thereby reducing the concentration of H+ and raising the pH.
Strong Acids and Strong Bases
The stronger the acid, the more readily it donates H+. For example, hydrochloric acid (HCl) is highly acidic and completely dissociates into hydrogen and chloride ions, whereas the acids in tomato juice or vinegar do not completely dissociate and are considered weak acids; conversely, strong bases readily donate OH and/or react with hydrogen ions. Sodium hydroxide (NaOH) and many household cleaners are highly basic and give up OH rapidly when placed in water; the OHions react with H+ in solution, creating new water molecules and lowering the amount of free H+ in the system, thereby raising the overall pH. An example of a weak basic solution is seawater, which has a pH near 8.0, close enough to neutral that well-adapted marine organisms thrive in this alkaline environment.
Buffers
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 usually consist of a weak acid and its conjugate base; this enables them to readily absorb excess H+ or OH, keeping the system’s pH within a narrow range.
Maintaining a constant blood pH is critical to a person’s well-being. The buffer that maintains 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, excess carbonic acid can be converted into carbon dioxide gas and exhaled through the lungs; this prevents too many free hydrogen ions from building up in the blood and dangerously reducing its 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 jeopardize survival.
Antacids, which combat excess stomach acid, are another example of buffers. Many over-the-counter medications work similarly to blood buffers, often with at least one ion (usually carbonate) capable of absorbing hydrogen and moderating pH, bringing relief to those that suffer “heartburn” from stomach acid after eating.
Key Points
• A basic solution will have a pH above 7.0, while an acidic solution will have a pH below 7.0.
• Buffers are solutions that contain a weak acid and its a conjugate base; as such, they can absorb excess H+ ions or OHions, thereby maintaining an overall steady pH in the solution.
• pH is equal to the negative logarithm of the concentration of H+ ions in solution: pH = – log[H+].
Key Terms
• alkaline: having a pH greater than 7; basic
• acidic: having a pH less than 7
• buffer: a solution composed of a weak acid and its conjugate base that can be used to stabilize the pH of a solution | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/02%3A_The_Chemical_Foundation_of_Life/2.17%3A_Water_-_pH_Buffers_Acids_and_Bases.txt |
Learning Objectives
• Explain the properties of carbon that allow it to serve as a building block for biomolecules
Carbon is the fourth most abundant element in the universe and is the building block of life on earth. On earth, carbon circulates through the land, ocean, and atmosphere, creating what is known as the Carbon Cycle. This global carbon cycle can be divided further into two separate cycles: the geological carbon cycles takes place over millions of years, whereas the biological or physical carbon cycle takes place from days to thousands of years. In a nonliving environment, carbon can exist as carbon dioxide (CO2), carbonate rocks, coal, petroleum, natural gas, and dead organic matter. Plants and algae convert carbon dioxide to organic matter through the process of photosynthesis, the energy of light.
Carbon is Important to Life
In its metabolism of food and respiration, an animal consumes glucose (C6H12O6), which combines with oxygen (O2) to produce carbon dioxide (CO2), water (H2O), and energy, which is given off as heat. The animal has no need for the carbon dioxide and releases it into the atmosphere. A plant, on the other hand, uses the opposite reaction of an animal through photosynthesis. It intakes carbon dioxide, water, and energy from sunlight to make its own glucose and oxygen gas. The glucose is used for chemical energy, which the plant metabolizes in a similar way to an animal. The plant then emits the remaining oxygen into the environment.
Cells are made of many complex molecules called macromolecules, which include 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.
Structure of Carbon
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 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.
Key Points
• All living things contain carbon in some form.
• Carbon is the primary component of macromolecules, including proteins, lipids, nucleic acids, and carbohydrates.
• Carbon’s molecular structure allows it to bond in many different ways and with many different elements.
• The carbon cycle shows how carbon moves through the living and non-living parts of the environment.
Key Terms
• octet rule: A rule stating that atoms lose, gain, or share electrons in order to have a full valence shell of 8 electrons (has some exceptions).
• carbon cycle: the physical cycle of carbon through the earth’s biosphere, geosphere, hydrosphere, and atmosphere; includes such processes as photosynthesis, decomposition, respiration and carbonification
• macromolecule: a very large molecule, especially used in reference to large biological polymers (e.g., nucleic acids and proteins) | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/02%3A_The_Chemical_Foundation_of_Life/2.18%3A_Carbon_-_The_Chemical_Basis_for_Life.txt |
Learning Objectives
• Discuss the role of hydrocarbons in biomacromolecules
Hydrocarbons
Hydrocarbons are organic molecules consisting entirely of carbon and hydrogen, such as methane (CH4). Hydrocarbons are often used as fuels: 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. The geometry of the methane molecule, where the atoms reside in three dimensions, is determined by the shape of its electron orbitals. The carbon 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; 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. The overall geometry of the molecule is altered by the different geometries of single, double, and triple covalent bonds. 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, butene, 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
The hydrocarbons discussed so far 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. The benzene ring is present in many biological molecules including some amino acids and most steroids, which includes cholesterol and 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.
Key Points
• Hydrocarbons are molecules that contain only carbon and hydrogen.
• Due to carbon’s unique bonding patterns, hydrocarbons can have single, double, or triple bonds between the carbon atoms.
• The names of hydrocarbons with single bonds end in “-ane,” those with double bonds end in “-ene,” and those with triple bonds end in “-yne”.
• The bonding of hydrocarbons allows them to form rings or chains.
Key Terms
• covalent bond: A type of chemical bond where two atoms are connected to each other by the sharing of two or more electrons.
• aliphatic: Of a class of organic compounds in which the carbon atoms are arranged in an open chain.
• aromatic: Having a closed ring of alternate single and double bonds with delocalized electrons. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/02%3A_The_Chemical_Foundation_of_Life/2.19%3A__Carbon_-_Hydrocarbons.txt |
Learning Objectives
• Give examples of 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
Structural isomers (such as butane and isobutane ) 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 isobutane is suited for use as a refrigerant and a propellant in spray cans.
Geometric Isomers
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. 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.
Cis or Trans Configurations
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. 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.
Key Points
• Isomers are molecules with the same chemical formula but have different structures.
• Isomers differ in how their bonds are positioned to surrounding atoms.
• 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.
• Triglycerides, which show both cis and trans configurations, can occur as either saturated or unsaturated, depending upon how many hydrogen atoms they have attached to them.
Key Terms
• fatty acid: Any of a class of aliphatic carboxylic acids, of general formula CnH2n+1COOH, that occur combined with glycerol as animal or vegetable oils and fats.
• isomer: Any of two or more compounds with the same molecular formula but with different structure. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/02%3A_The_Chemical_Foundation_of_Life/2.20%3A__Carbon_-_Organic_Isomers.txt |
Learning Objectives
• Give examples of enantiomers
Stereoisomers are a type of isomer where the order of the atoms in the two molecules is the same but their arrangement in space is different. The two main types of stereoisomerism are diastereomerism (including ‘cis-trans isomerism’) and optical isomerism (also known as ‘enantiomerism’ and ‘chirality’). Optical isomers are stereoisomers formed when asymmetric centers are present; for example, a carbon with four different groups bonded to it. Enantiomers are two optical isomers (i.e. isomers that are reflections of each other). Every stereocenter in one isomer has the opposite configuration in the other. They share the same chemical structure and chemical bonds, but differ in the three-dimensional placement of atoms so that they are mirror images, much as a person’s left and right hands are. Compounds that are enantiomers of each other have the same physical properties except for the direction in which they rotate polarized light and how they interact with different optical isomers of other compounds.
The amino acid alanine is example of an entantiomer. The two structures, D-alanine and L-alanine, 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.
Organic compounds that contain a chiral carbon usually have two non-superposable structures. These two structures are mirror images of each other and are, thus, commonly called enantiomorphs; hence, this structural property is now commonly referred to as enantiomerism. Enantiopure compounds refer to samples having, within the limits of detection, molecules of only one chirality.
Enantiomers of each other often show different chemical reactions with other substances that are also enantiomers. Since many molecules in the bodies of living beings are enantiomers themselves, there is sometimes a marked difference in the effects of two enantiomers on living beings. In drugs, for example, often only one of a drug’s enantiomers is responsible for the desired physiologic effects, while the other enantiomer is less active, inactive, or sometimes even responsible for adverse effects. Owing to this discovery, drugs composed of only one enantiomer (“enantiopure”) can be developed to enhance the pharmacological efficacy and sometimes do away with some side effects.
Key Points
• Enantiomers are stereoisomers, a type of isomer where the order of the atoms in the two molecules is the same but their arrangement in space is different.
• Many molecules in the bodies of living beings are enantiomers; there is sometimes a large difference in the effects of two enantiomers on organisms.
• Enantiopure compounds refer to samples having, within the limits of detection, molecules of only one chirality.
• Compounds that are enantiomers of each other have the same physical properties except for the direction in which they rotate polarized light and how they interact with different optical isomers of other compounds.
Key Terms
• enantiomer: One of a pair of stereoisomers that is the mirror image of the other, but may not be superimposed on this other stereoisomer.
• chirality: The phenomenon in chemistry, physics, and mathematics in which objects are mirror images of each other, but are not identical.
• stereoisomer: one of a set of the isomers of a compound in which atoms are arranged differently about a chiral center; they exhibit optical activity
2.22: Carbon - Organic Molecules and Functional Groups
Learning Objectives
• Describe the importance of functional groups to organic molecules
Location of Functional Groups
Functional groups are groups of atoms that occur within organic molecules and confer specific chemical properties to those molecules. When functional groups are shown, the organic molecule is sometimes denoted as “R.” Functional groups are found along the “carbon backbone” of macromolecules which 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. 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.
Properties of Functional Groups
A functional group can participate in specific chemical reactions. Some of the important functional groups in biological molecules include: hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl groups. These groups play an important role in the formation of molecules like DNA, proteins, carbohydrates, and lipids.
Classifying Functional Groups
Functional groups are usually classified as hydrophobic or hydrophilic depending on their charge or polarity. 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 acid heads that form triglycerides and phospholipids. This carboxyl group ionizes to release hydrogen ions (H+) from the COOH group resulting in the negatively charged COOgroup; 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
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 and maintain the appropriate shape needed to function correctly. Hydrogen bonds are also involved in various recognition processes, such as DNA complementary base pairing and the binding of an enzyme to its substrate.
Key Points
• Functional groups are collections of atoms that attach the carbon skeleton of an organic molecule and confer specific properties.
• Each type of organic molecule has its own specific type of functional group.
• Functional groups in biological molecules play an important role in the formation of molecules like DNA, proteins, carbohydrates, and lipids.
• Functional groups include: hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl.
Key Terms
• hydrophobic: lacking an affinity for water; unable to absorb, or be wetted by water
• hydrophilic: having an affinity for water; able to absorb, or be wetted by water | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/02%3A_The_Chemical_Foundation_of_Life/2.21%3A__Carbon_-_Organic_Enantiomers.txt |
Learning Objectives
• Identify the four major classes of biological macromolecules
Nutrients are the molecules that living organisms require for survival and growth but that animals and plants cannot synthesize themselves. Animals obtain nutrients by consuming food, while plants pull nutrients from soil.
Many critical nutrients are biological macromolecules. The term “macromolecule” was first coined in the 1920s by Nobel laureate Hermann Staudinger. Staudinger was the first to propose that many large biological molecules are built by covalently linking smaller biological molecules together.
Monomers and Polymers
Biological macromolecules play a critical role in cell structure and function. Most (but not all) biological macromolecules are polymers, which are any molecules constructed by linking together many smaller molecules, called monomers. Typically all the monomers in a polymer tend to be the same, or at least very similar to each other, linked over and over again to build up the larger macromolecule. These simple monomers can be linked in many different combinations to produce complex biological polymers, just as a few types of Lego blocks can build anything from a house to a car.
Examples of these monomers and polymers can be found in the sugar you might put in your coffee or tea. Regular table sugar is the disaccharide sucrose (a polymer), which is composed of the monosaccharides fructose and glucose (which are monomers). If we were to string many carbohydrate monomers together we could make a polysaccharide like starch. The prefixes “mono-” (one), “di-” (two),and “poly-” (many) will tell you how many of the monomers have been joined together in a molecule.
Biological macromolecules all contain carbon in ring or chain form, which means they are classified as organic molecules. They usually also contain hydrogen and oxygen, as well as nitrogen and additional minor elements.
Four Classes of Biological Macromolecules
There are four major classes of biological macromolecules:
1. carbohydrates
2. lipids
3. proteins
4. nucleic acids
Each of these types of macromolecules performs a wide array of important functions within the cell; a cell cannot perform its role within the body without many different types of these crucial molecules. In combination, these biological macromolecules make up the majority of a cell’s dry mass. (Water molecules make up the majority of a cell’s total mass.) All the molecules both inside and outside of cells are situated in a water-based (i.e., aqueous) environment, and all the reactions of biological systems are occurring in that same environment.
Interactive: Monomers and Polymers
Carbohydrates, proteins, and nucleic acids are built from small molecular units that are connected to each other by strong covalent bonds. The small molecular units are called monomers (mono means one, or single), and they are linked together into long chains called polymers (poly means many, or multiple). Each different type of macromolecule, except lipids, is built from a different set of monomers that resemble each other in composition and size. Lipids are not polymers, because they are not built from monomers (units with similar composition).
Key Points
• Biological macromolecules are important cellular components and perform a wide array of functions necessary for the survival and growth of living organisms.
• The four major classes of biological macromolecules are carbohydrates, lipids, proteins, and nucleic acids.
Key Terms
• polymer: A relatively large molecule consisting of a chain or network of many identical or similar monomers chemically bonded to each other.
• monomer: A relatively small molecule that can form covalent bonds with other molecules of this type to form a polymer. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/02%3A_The_Chemical_Foundation_of_Life/2.23%3A_Synthesis_of_Biological_Macromolecules_-_Types_of_Biological_Macromolecules.txt |
Learning Objectives
• Explain dehydration (or condensation) reactions
Dehydration Synthesis
Most macromolecules are made from single subunits, or building blocks, called monomers. The monomers combine with each other via 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. ” It is also considered to be a condensation reaction since two molecules are condensed into one larger molecule with the loss of a smaller molecule (the water.)
In a dehydration synthesis reaction between two un-ionized monomers, such as monosaccharide sugars, the hydrogen of one monomer combines with the hydroxyl group of another monomer, releasing a molecule of water in the process. The removal of a hydrogen from one monomer and the removal of a hydroxyl group from the other monomer allows the monomers to share electrons and form a covalent bond. Thus, the monomers that are joined together are being dehydrated to allow for synthesis of a larger molecule.
When the monomers are ionized, such as is the case with amino acids in an aqueous environment like cytoplasm, two hydrogens from the positively-charged end of one monomer are combined with an oxygen from the negatively-charged end of another monomer, again forming water, which is released as a side-product, and again joining the two monomers with a covalent bond.
As additional monomers join via multiple dehydration synthesis reactions, the chain of repeating monomers begins to form a polymer. Different types of monomers can combine in many configurations, giving rise to a diverse group of macromolecules. Three of the four major classes of biological macromolecules (complex carbohydrates, nucleic acids, and proteins), are composed of monomers that join together via dehydration synthesis reactions. Complex carbohydrates are formed from monosaccharides, nucleic acids are formed from mononucleotides, and proteins are formed from amino acids.
There is great diversity in the manner by which monomers can combine to form polymers. For example, glucose monomers are the constituents of starch, glycogen, and cellulose. These three are polysaccharides, classified as carbohydrates, that have formed as a result of multiple dehydration synthesis reactions between glucose monomers. However, the manner by which glucose monomers join together, specifically locations of the covalent bonds between connected monomers and the orientation (stereochemistry) of the covalent bonds, results in these three different polysaccharides with varying properties and functions. In nucleic acids and proteins, the location and stereochemistry of the covalent linkages connecting the monomers do not vary from molecule to molecule, but instead the multiple kinds of monomers (five different monomers in nucleic acids, A, G, C, T, and U mononucleotides; 21 different amino acids monomers in proteins) are combined in a huge variety of sequences. Each protein or nucleic acid with a different sequence is a different molecule with different properties.
Key Points
• During dehydration synthesis, either the hydrogen of one monomer combines with the hydroxyl group of another monomer releasing a molecule of water, or two hydrogens from one monomer combine with one oxygen from the other monomer releasing a molecule of water.
• The monomers that are joined via dehydration synthesis reactions share electrons and form covalent bonds with each other.
• As additional monomers join via multiple dehydration synthesis reactions, this chain of repeating monomers begins to form a polymer.
• Complex carbohydrates, nucleic acids, and proteins are all examples of polymers that are formed by dehydration synthesis.
• Monomers like glucose can join together in different ways and produce a variety of polymers. Monomers like mononucleotides and amino acids join together in different sequences to produce a variety of polymers.
Key Terms
• covalent bond: A type of chemical bond where two atoms are connected to each other by the sharing of two or more electrons.
• monomer: A relatively small molecule which can be covalently bonded to other monomers to form a polymer. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/02%3A_The_Chemical_Foundation_of_Life/2.24%3A_Synthesis_of_Biological_Macromolecules_-_Dehydration_Synthesis.txt |
Learning Objectives
• Explain hydrolysis reactions
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. During these reactions, the polymer is broken into two components. If the components are un-ionized, one part gains a hydrogen atom (H-) and the other gains a hydroxyl group (OH–) from a split water molecule. This is what happens when monosaccharides are released from complex carbohydrates via hydrolysis.
If the components are ionized after the split, one part gains two hydrogen atoms and a positive charge, the other part gains an oxygen atom and a negative charge. This is what happens when amino acids are released from protein chains via hydrolysis.
These reactions are in contrast to dehydration synthesis (also known as condensation) reactions. In dehydration synthesis reactions, a water molecule is formed as a result of generating a covalent bond between two monomeric components in a larger polymer. In hydrolysis reactions, a water molecule is consumed as a result of breaking the covalent bond holding together two components of a polymer.
Dehydration and hydrolysis reactions are chemical reactions that 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.
In our bodies, food is first hydrolyzed, or broken down, into smaller molecules by catalytic enzymes in the digestive tract. 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 trypsin, pepsin, peptidase and others. Lipids are broken down by lipases. Once the smaller metabolites that result from these hydrolytic enzymezes are absorbed by cells in the body, they are further broken down by other enzymes. The breakdown of these macromolecules is an overall energy-releasing process and provides energy for cellular activities.
Key Points
• Hydrolysis reactions use water to breakdown polymers into monomers and is the opposite of dehydration synthesis, which forms water when synthesizing a polymer from monomers.
• Hydrolysis reactions break bonds and release energy.
• Biological macromolecules are ingested and hydrolyzed in the digestive tract to form smaller molecules that can be absorbed by cells and then further broken down to release energy.
Key Terms
• enzyme: a globular protein that catalyses a biological chemical reaction
• hydrolysis: A chemical process of decomposition involving the splitting of a bond by the addition of water.
Exercise \(1\)
1. What are biological macromolecules? Name the four major classes.
2. Biological macromolecules are organic. What does that mean?
3. What are monomers? What are polymer?
4. Explain the process “dehydration synthesis.” Is there another name for this process? Explain.
5. Explain Figure 1 in your own words.
6. Give an example of how condensation can form different carbohydrates.
7. Explain the process of Hydrolysis.
8. Explain Figure 2 in your own words.
9. What role do enzymes play in hydrolysis and condensation? Explain.
10. In our bodies, food is hydrolyzed, or broken down into smaller molecules. Explain why.
11. The breakdown of macromolecules provides...
12. Create a comparison chart to indicate the enzymes that break down carbohydrates, proteins, and lipids. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/02%3A_The_Chemical_Foundation_of_Life/2.25%3A_Synthesis_of_Biological_Macromolecules_-_Hydrolysis.txt |
Learning Objectives
• Describe the structure of mono-, di-, and poly-saccharides
Carbohydrates can be represented by the stoichiometric formula (CH2O)n, where n is the number of carbons in the molecule. Therefore, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. The origin of the term “carbohydrate” is based on its components: carbon (“carbo”) and water (“hydrate”). Carbohydrates are classified into three subtypes: monosaccharides, disaccharides, and polysaccharides.
Monosaccharides
Monosaccharides (mono- = “one”; sacchar- = “sweet”) are simple sugars. In monosaccharides, the number of carbons usually ranges from three to seven. 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). Monosaccharides can exist as a linear chain or as ring-shaped molecules; in aqueous solutions they are usually found in ring forms.
Common Monosaccharides
Glucose (C6H12O6) is a common monosaccharide and 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.
Galactose (a milk sugar) and fructose (found in fruit) are other common monosaccharides. Although glucose, galactose, and fructose all have the same chemical formula (C6H12O6), they differ structurally and stereochemically. This makes them different molecules despite sharing the same atoms in the same proportions, and they are all isomers of one another, or isomeric monosaccharides. Glucose and galactose are aldoses, and fructose is a ketose.
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. Glycosidic bonds (also called glycosidic linkages) can be of the alpha or the beta type.
Common Disaccharides
Common disaccharides include lactose, maltose, and sucrose. 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. Starch, glycogen, cellulose, and chitin are primary examples of polysaccharides.
Plants are able to synthesize glucose, and the excess glucose is stored as starch in different plant parts, including roots and seeds. Starch is the stored form of sugars in plants and is made up of glucose monomers that are joined by α1-4 or 1-6 glycosidic bonds. The starch in the seeds provides food for the embryo as it germinates while the starch that is consumed by humans is broken down by enzymes into smaller molecules, such as maltose and glucose. The cells can then absorb the glucose.
Common Polysaccharides
Glycogen is the storage form of glucose in humans and other vertebrates. It 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 and provides structural support to the cell. Cellulose is made up of glucose monomers that are linked by β 1-4 glycosidic bonds. 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.
Carbohydrate Function
Carbohydrates serve various functions in different animals. Arthropods have an outer skeleton, the exoskeleton, which protects their internal body parts. This exoskeleton is made of 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.
Key Points
• Monosaccharides are simple sugars made up of three to seven carbons, and they can exist as a linear chain or as ring-shaped molecules.
• Glucose, galactose, and fructose are monosaccharide isomers, which means they all have the same chemical formula but differ structurally and chemically.
• Disaccharides form when two monosaccharides undergo a dehydration reaction (a condensation reaction); they are held together by a covalent bond.
• Sucrose (table sugar) is the most common disaccharide, which is composed of the monomers glucose and fructose.
• A polysaccharide is a long chain of monosaccharides linked by glycosidic bonds; the chain may be branched or unbranched and can contain many types of monosaccharides.
Key Terms
• isomer: Any of two or more compounds with the same molecular formula but with different structure.
• dehydration reaction: A chemical reaction in which two molecules are covalently linked in a reaction that generates H2O as a second product.
• biopolymer: Any macromolecule of a living organism that is formed from the polymerization of smaller entities; a polymer that occurs in a living organism or results from life. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/03%3A_Biological_Macromolecules/3.01%3A__Carbohydrates_-_Carbohydrate_Molecules.txt |
Learning Objectives
• Describe the benefits provided to organisms by carbohydrates
Benefits of Carbohydrates
Biological macromolecules are large molecules that are necessary for life and are built from smaller organic molecules. One major class of biological macromolecules are carbohydrates, which are further divided into three subtypes: monosaccharides, disaccharides, and polysaccharides. Carbohydrates are, in fact, an essential part of our diet; grains, fruits, and vegetables are all natural sources of carbohydrates. Importantly, carbohydrates provide energy to the body, particularly through glucose, a simple sugar that is a component of starch and an ingredient in many basic foods.
Carbohydrates in Nutrition
Carbohydrates have been a controversial topic within the diet world. People trying to lose weight often avoid carbs, and some diets completely forbid carbohydrate consumption, claiming that a low-carb 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. In 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 and attaches to the cholesterol in the small intestine and prevents the cholesterol particles from entering the bloodstream. 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 adenosine triphosphate (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.
Key Points
• Carbohydrates provide energy to the body, particularly through glucose, a simple sugar that is found in many basic foods.
• Carbohydrates contain soluble and insoluble elements; the insoluble part is known as fiber, which promotes regular bowel movement, regulates the rate of consumption of blood glucose, and also helps to remove excess cholesterol from the body.
• 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.
• Since carbohydrates are an important part of the human nutrition, eliminating them from the diet is not the best way to lose weight.
Key Terms
• carbohydrate: A sugar, starch, or cellulose that is a food source of energy for an animal or plant; a saccharide.
• glucose: a simple monosaccharide (sugar) with a molecular formula of C6H12O6; it is a principal source of energy for cellular metabolism
• ATP: A nucleotide that occurs in muscle tissue, and is used as a source of energy in cellular reactions, and in the synthesis of nucleic acids. ATP is the abbreviation for adenosine triphosphate. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/03%3A_Biological_Macromolecules/3.02%3A__Carbohydrates_-_Importance_of_Carbohydrates.txt |
Learning Objectives
• Differentiate between saturated and unsaturated fatty acids
Glycerol and Fatty Acids
A fat molecule consists of two main components: glycerol and fatty acids. Glycerol is an alcohol with three carbons, five hydrogens, and three hydroxyl (OH) groups. Fatty acids have a long chain of hydrocarbons with a carboxyl group attached and may have 4-36 carbons; however, most of them have 12-18. In a fat molecule, the fatty acids are attached to each of the three carbons of the glycerol molecule with an ester bond through the oxygen atom. During the ester bond formation, three molecules are released. Since fats consist of three fatty acids and a glycerol, they are also called triacylglycerols or triglycerides.
Saturated vs. Unsaturated Fatty Acids
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 since single bonds increase the number of hydrogens on each carbon. Stearic acid and palmitic acid, which are commonly found in meat, are examples of saturated fats.
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. Most unsaturated fats are liquid at room temperature and are called oils. If there is only one double bond in the molecule, then it is known as a monounsaturated fat; e.g. olive oil. If there is more than one double bond, then it is known as a polyunsaturated fat; e.g. canola oil. Unsaturated fats help to lower blood cholesterol levels whereas saturated fats contribute to plaque formation in the arteries.
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.
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. During this hydrogenation process, gas is bubbled through oils to solidify them, and the 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.
Essential Fatty Acids
Essential fatty acids are fatty acids required for biological processes, but not synthesized by the human body. Consequently, they have to be supplemented through ingestion via the diet and are nutritionally very important. Omega-3 fatty acid, or alpha-linoleic acid (ALA), falls into this category and is one of only two fatty acids known to be essential for humans (the other being omega-6 fatty acid, or linoleic acid). These polyunsaturated fatty acids 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. 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.
Key Points
• Fats provide energy, insulation, and storage of fatty acids for many organisms.
• Fats may be saturated (having single bonds) or unsaturated (having double bonds).
• Unsaturated fats may be cis (hydrogens in same plane) or trans (hydrogens in two different planes).
• Olive oil, a monounsaturated fat, has a single double bond whereas canola oil, a polyunsaturated fat, has more than one double bond.
• Omega-3 fatty acid and omega-6 fatty acid are essential for human biological processes, but they must be ingested in the diet because they cannot be synthesized.
Key Terms
• hydrogenation: The chemical reaction of hydrogen with another substance, especially with an unsaturated organic compound, and usually under the influence of temperature, pressure and catalysts.
• ester: Compound most often formed by the condensation of an alcohol and an acid, by removing water. It contains the functional group carbon-oxygen double bond joined via carbon to another oxygen atom.
• carboxyl: A univalent functional group consisting of a carbonyl and a hydroxyl functional group (-CO.OH); characteristic of carboxylic acids.
Fats have important functions, and many vitamins are fat soluble. Fats serve as a long-term storage form of fatty acids and act as a source of energy. They also provide insulation for the body. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/03%3A_Biological_Macromolecules/3.03%3A_Lipid_Molecules_-_Introduction.txt |
Learning Objectives
• Describe the roles played by waxes
Waxes
Waxes are a type of long chain nonpolar lipid. Natural waxes are typically esters of fatty acids and long chain alcohols. Waxes are synthesized by many animals and plants. Animal wax esters are typically derived from a variety of carboxylic acids and fatty alcohols. The composition of a wax depends not only on the species, but also on the geographic location of the organism. The best known animal wax is beeswax, but other insects secrete waxes as well. A major component of beeswax is the ester myricyl palmitate, which bees use for constructing honeycombs. Spermaceti is also a wax that occurs in large amounts in the oil of a sperm whale’s head. One of its main constituents is cetyl palmitate, an ester of a fatty acid and fatty alcohol. Plant waxes are derived from mixtures of long-chain hydrocarbons containing functional groups such as alkanes, fatty acids, alcohols, diols, ketones, and aldehydes. Plants also use waxes as a protective coating to control evaporation and hydration and to prevent them from drying out. Waxes are valuable to both plants and animals because of their hydrophobic nature. This makes them water resistant, which prevents water from sticking on surfaces.
Unlike most natural waxes, which are esters, synthetic waxes consist of long-chain hydrocarbons lacking functional groups. Paraffin wax is a type of synthetic wax derived from petroleum and refined by vacuum distillation. Synthetic waxes may also be obtained from polyethylene. Millions of of these waxes are produced annually, and they are used in adhesives, cosmetics, sealants and lubricants, insecticides, and UV protection. They are also used in foods like chewing gum.
Key Points
• Natural waxes are typically esters of fatty acids and long chain alcohols.
• Animal wax esters are derived from a variety of carboxylic acids and fatty alcohols.
• Plant waxes are derived from mixtures of long-chain hydrocarbons containing functional groups.
• Because of their hydrophobic nature, waxes prevent water from sticking on plants and animals.
• Synthetic waxes are derived from petroleum or polyethylene and consist of long-chain hydrocarbons that lack functional groups.
• Synthetic and waxes are used in adhesives, cosmetics, food, and many other commercial products.
Key Terms
• paraffin wax: A waxy white solid hydrocarbon mixture used to make candles, wax paper, lubricants, and sealing materials.
• polyethylene: A polymer consisting of many ethylene monomers bonded together; used for kitchenware, containers etc.
3.05: Lipid Molecules - Phospholipids
Learning Objectives
• Describe phospholipids and their role in cells
Defining Characteristics of Phospholipids
Phospholipids are major components of the plasma membrane, the outermost layer of animal cells. Like fats, they are composed of fatty acid chains attached to a glycerol backbone. Unlike triglycerides, which have three fatty acids, phospholipids have two fatty acids that help form a diacylglycerol. The third carbon of the glycerol backbone is also occupied by a modified phosphate group. However, just a phosphate group attached to a diacylglycerol does not qualify as a phospholipid. This would be considered a phosphatidate (diacylglycerol 3-phosphate), the precursor to phospholipids. To qualify as a phospholipid, the phosphate group should be modified by an alcohol. Phosphatidylcholine and phosphatidylserine are examples of two important phospholipids that are found in plasma membranes.
Structure of a Phospholipid Molecule
A phospholipid is an amphipathic molecule which means it has both a hydrophobic and a hydrophilic component. A single phospholipid molecule has a phosphate group on one end, called the “head,” and two side-by-side chains of fatty acids that make up the lipid “tails. ” The phosphate group is negatively charged, making the head polar and hydrophilic, or “water loving.” The phosphate heads are thus attracted to the water molecules in their environment.
The lipid tails, on the other hand, are uncharged, nonpolar, and hydrophobic, or “water fearing.” A hydrophobic molecule repels and is repelled by water. Some lipid tails consist of saturated fatty acids and some contain unsaturated fatty acids. This combination adds to the fluidity of the tails that are constantly in motion.
Phospholipids and Biological Membranes
The cell membrane consists of two adjacent layers of phospholipids, which form a bilayer. The fatty acid tails of phospholipids face inside, away from water, whereas the phosphate heads face the outward aqueous side. Since the heads face outward, one layer is exposed to the interior of the cell and one layer is exposed to the exterior. As the phosphate groups are polar and hydrophilic, they are attracted to water in the intracellular fluid.
Because of the phospholipds’ chemical and physical characteristics, the lipid bilayer acts as a semipermeable membrane; only lipophilic solutes can easily pass the phospholipd bilayer. As a result, there are two distinct aqueous compartments on each side of the membrane. This separation is essential for many biological functions, including cell communication and metabolism.
Membrane Fluidity
A cell’s plasma membrane contain proteins and other lipids (such as cholesterol) within the phospholipid bilayer. Biological membranes remain fluid because of the unsaturated hydrophobic tails, which prevent phospholipid molecules from packing together and forming a solid.
If a drop of phospholipids is placed in water, the phospholipids spontaneously form a structure known as a micelle, with their hydrophilic heads oriented toward the water. Micelles are lipid molecules that arrange themselves in a spherical form in aqueous solution. The formation of a micelle is a response to the amphipathic nature of fatty acids, meaning that they contain both hydrophilic and hydrophobic regions.
Key Points
• Phospholipids consist of a glycerol molecule, two fatty acids, and a phosphate group that is modified by an alcohol.
• The phosphate group is the negatively-charged polar head, which is hydrophilic.
• The fatty acid chains are the uncharged, nonpolar tails, which are hydrophobic.
• Since the tails are hydrophobic, they face the inside, away from the water and meet in the inner region of the membrane.
• Since the heads are hydrophilic, they face outward and are attracted to the intracellular and extracellular fluid.
• If phospholipids are placed in water, they form into micelles, which are lipid molecules that arrange themselves in a spherical form in aqueous solutions.
Key Terms
• micelle: Lipid molecules that arrange themselves in a spherical form in aqueous solutions.
• amphipathic: Describing a molecule, such as a detergent, which has both hydrophobic and hydrophilic groups. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/03%3A_Biological_Macromolecules/3.04%3A_Lipid_Molecules_-_Waxes.txt |
Learning Objectives
• Describe some functions of steroids
Structure of Steroid Molecules
Unlike phospholipids and fats, steroids have a fused ring structure. Although they do not resemble the other lipids, they are grouped with them because they are also hydrophobic and insoluble in water. All steroids have four linked carbon rings, and many of them, like cholesterol, have a short tail. Many steroids also have the –OH functional group, and these steroids are classified as alcohols called sterols.
Cholesterol
Cholesterol is the most common steroid and is mainly synthesized in the liver; it is the precursor to vitamin D. Cholesterol is also a precursor to many important steroid hormones like estrogen, testosterone, and progesterone, which are secreted by the gonads and endocrine glands. Therefore, steroids play very important roles in the body’s reproductive system. Cholesterol also plays a role in synthesizing the steroid hormones aldosterone, which is used for osmoregulation, and cortisol, which plays a role in metabolism.
Cholesterol is also the precursor to bile salts, which help in the emulsification of fats and their absorption by cells. It is a component of the plasma membrane of animal cells and 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. Thus, steroids also play an important role in the structure and function of membranes.
It has also been discovered that steroids can be active in the brain where they affect the nervous system, These neurosteroids alter electrical activity in the brain. They can either activate or tone down receptors that communicate messages from neurotransmitters. Since these neurosteroids can tone down receptors and decrease brain activity, steroids are often used in anesthetic medicines.
Key Points
• Steroids are lipids because they are hydrophobic and insoluble in water, but they do not resemble lipids since they have a structure composed of four fused rings.
• Cholesterol is the most common steroid and is the precursor to vitamin D, testosterone, estrogen, progesterone, aldosterone, cortisol, and bile salts.
• Cholesterol is a component of the phospholipid bilayer and plays a role in the structure and function of membranes.
• Steroids are found in the brain and alter electrical activity in the brain.
• Because they can tone down receptors that communicate messages from neurotransmitters, steroids are often used in anesthetic medicines.
Key Terms
• neurotransmitter: any substance, such as acetylcholine or dopamine, responsible for sending nerve signals across a synapse between two neurons
• osmoregulation: the homeostatic regulation of osmotic pressure in the body in order to maintain a constant water content
• hormone: any substance produced by one tissue and conveyed by the bloodstream to another to affect physiological activity
3.07: Proteins - Types and Functions of Proteins
Learning Objectives
• Differentiate among the types and functions of proteins
Types and Functions of Proteins
Proteins perform essential functions throughout the systems of the human body. These long chains of amino acids are critically important for:
• catalyzing chemical reactions
• synthesizing and repairing DNA
• transporting materials across the cell
• receiving and sending chemical signals
• responding to stimuli
• providing structural support
Proteins (a polymer) are macromolecules composed of amino acid subunits (the monomers ). These amino acids are covalently attached to one another to form long linear chains called polypeptides, which then fold into a specific three-dimensional shape. Sometimes these folded polypeptide chains are functional by themselves. Other times they combine with additional polypeptide chains to form the final protein structure. Sometimes non-polypeptide groups are also required in the final protein. For instance, the blood protein hemogobin is made up of four polypeptide chains, each of which also contains a heme molecule, which is ring structure with an iron atom in its center.
Proteins have different shapes and molecular weights, depending on the amino acid sequence. For example, hemoglobin is a globular protein, which means it folds into a compact globe-like structure, but collagen, found in our skin, is a fibrous protein, which means it folds into a long extended fiber-like chain. You probably look similar to your family members because you share similar proteins, but you look different from strangers because the proteins in your eyes, hair, and the rest of your body are different.
Because form determines function, any slight change to a protein’s shape may cause the protein to become dysfunctional. Small changes in the amino acid sequence of a protein can cause devastating genetic diseases such as Huntington’s disease or sickle cell anemia.
Enzymes
Enzymes are proteins that catalyze biochemical reactions, which otherwise would not take place. These enzymes are essential for chemical processes like digestion and cellular metabolism. Without enzymes, most physiological processes would proceed so slowly (or not at all) that life could not exist.
Because form determines function, each enzyme is specific to its substrates. The substrates are the reactants that undergo the chemical reaction catalyzed by the enzyme. The location where substrates bind to or interact with the enzyme is known as the active site, because that is the site where the chemistry occurs. When the substrate binds to its active site at the enzyme, the enzyme may help in its breakdown, rearrangement, or synthesis. By placing the substrate into a specific shape and microenvironment in the active site, the enzyme encourages the chemical reaction to occur. There are two basic classes of enzymes:
• Catabolic enzymes: enzymes that break down their substrate
• Anabolic enzymes: enzymes that build more complex molecules from their substrates
Enzymes are essential for digestion: the process of breaking larger food molecules down into subunits small enough to diffuse through a cell membrane and to be used by the cell. These enzymes include amylase, which catalyzes the digestion carbohydrates in the mouth and small intestine; pepsin, which catalyzes the digestion of proteins in the stomach; lipase, which catalyzes reactions need to emulsify fats in the small intestine; and trypsin, which catalyzes the further digestion of proteins in the small intestine.
Enzymes are also essential for biosynthesis: the process of making new, complex molecules from the smaller subunits that are provided to or generated by the cell. These biosynthetic enzymes include DNA Polymerase, which catalyzes the synthesis of new strands of the genetic material before cell division; fatty acid synthetase, which the synthesis of new fatty acids for fat or membrane lipid formation; and components of the ribosome, which catalyzes the formation of new polypeptides from amino acid monomers.
Hormones
Some proteins function as chemical-signaling molecules called hormones. These proteins are secreted by endocrine cells that act to control or regulate specific physiological processes, which include growth, development, metabolism, and reproduction. For example, insulin is a protein hormone that helps to regulate blood glucose levels. Other proteins act as receptors to detect the concentrations of chemicals and send signals to respond. Some types of hormones, such as estrogen and testosterone, are lipid steroids, not proteins.
Other Protein Functions
Proteins perform essential functions throughout the systems of the human body. In the respiratory system, hemoglobin (composed of four protein subunits) transports oxygen for use in cellular metabolism. Additional proteins in the blood plasma and lymph carry nutrients and metabolic waste products throughout the body. The proteins actin and tubulin form cellular structures, while keratin forms the structural support for the dead cells that become fingernails and hair. Antibodies, also called immunoglobins, help recognize and destroy foreign pathogens in the immune system. Actin and myosin allow muscles to contract, while albumin nourishes the early development of an embryo or a seedling.
Key Points
• Proteins are essential for the main physiological processes of life and perform functions in every system of the human body.
• A protein’s shape determines its function.
• Proteins are composed of amino acid subunits that form polypeptide chains.
• Enzymes catalyze biochemical reactions by speeding up chemical reactions, and can either break down their substrate or build larger molecules from their substrate.
• The shape of an enzyme’s active site matches the shape of the substrate.
• Hormones are a type of protein used for cell signaling and communication.
Key Terms
• amino acid: Any of 20 naturally occurring α-amino acids (having the amino, and carboxylic acid groups on the same carbon atom), and a variety of side chains, that combine, via peptide bonds, to form proteins.
• polypeptide: Any polymer of (same or different) amino acids joined via peptide bonds.
• catalyze: To accelerate a process. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/03%3A_Biological_Macromolecules/3.06%3A_Lipid_Molecules_-_Steroids.txt |
Learning Objectives
• Describe the structure of an amino acid and the features that confer its specific properties
Structure of an Amino Acid
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. In the aqueous environment of the cell, the both the amino group and the carboxyl group are ionized under physiological conditions, and so have the structures -NH3+ and -COO, respectively. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group. This R group, or side chain, gives each amino acid proteins specific characteristics, including size, polarity, and pH.
Types of Amino Acids
The name “amino acid” is derived from the amino group and carboxyl-acid-group in their basic structure. There are 21 amino acids present in proteins, each with a specific R group or side chain. Ten of these are considered essential amino acids in humans because the human body cannot produce them and they must be obtained from the diet. All organisms have different essential amino acids based on their physiology.
Characteristics of Amino Acids
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 composition of the side chain determines the characteristics of the amino acid. Amino acids such as valine, methionine, and alanine are nonpolar (hydrophobic), while amino acids such as serine, threonine, and cysteine are polar (hydrophilic). The side chains of lysine and arginine are positively charged so these amino acids are also known as basic (high pH) amino acids. Proline is an exception to the standard structure of an amino acid because its R group is linked to the amino group, forming a ring-like structure.
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.
Peptide Bonds
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. When two amino acids are covalently attached by a peptide bond, the carboxyl group of one amino acid and the amino group of the incoming amino acid combine and release a molecule of water. Any reaction that combines two monomers in a reaction that generates H2O as one of the products is known as a dehydration reaction, so peptide bond formation is an example of a dehydration reaction.
Polypeptide Chains
The resulting chain of amino acids is called a polypeptide chain. 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. When reading or reporting the amino acid sequence of a protein or polypeptide, the convention is to use the N-to-C direction. That is, the first amino acid in the sequence is assumed to the be one at the N terminal and the last amino acid is assumed to be the one at the C terminal.
Although the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically any polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have folded properly, combined with any additional components needed for proper functioning, and is now functional.
Key Points
• Each amino acid contains a central C atom, an amino group (NH2), a carboxyl group (COOH), and a specific R group.
• The R group determines the characteristics (size, polarity, and pH) for each type of amino acid.
• Peptide bonds form between the carboxyl group of one amino acid and the amino group of another through dehydration synthesis.
• A chain of amino acids is a polypeptide.
Key Terms
• amino acid: Any of 20 naturally occurring α-amino acids (having the amino, and carboxylic acid groups on the same carbon atom), and a variety of side chains, that combine, via peptide bonds, to form proteins.
• R group: The R group is a side chain specific to each amino acid that confers particular chemical properties to that amino acid.
• polypeptide: Any polymer of (same or different) amino acids joined via peptide bonds. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/03%3A_Biological_Macromolecules/3.08%3A_Proteins_-_Amino_Acids.txt |
Learning Objectives
• Summarize the four levels of protein structure
The shape of a protein is critical to its function because it determines whether the protein can interact with other molecules. Protein structures are very complex, and researchers have only very recently been able to easily and quickly determine the structure of complete proteins down to the atomic level. (The techniques used date back to the 1950s, but until recently they were very slow and laborious to use, so complete protein structures were very slow to be solved.) Early structural biochemists conceptually divided protein structures into four “levels” to make it easier to get a handle on the complexity of the overall structures. To determine how the protein gets its final shape or conformation, we need to understand these four levels of protein structure: primary, secondary, tertiary, and quaternary.
Primary Structure
A protein’s primary structure is the unique sequence of amino acids in each polypeptide chain that makes up the protein. Really, this is just a list of which amino acids appear in which order in a polypeptide chain, not really a structure. But, because the final protein structure ultimately depends on this sequence, this was called the primary structure of the polypeptide chain. For example, the pancreatic hormone insulin has two polypeptide chains, A and B.
The gene, or sequence of DNA, ultimately determines the unique sequence of amino acids in each peptide chain. 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 therefore function.
The oxygen-transport protein hemoglobin consists of four polypeptide chains, two identical α chains and two identical β chains. In sickle cell anemia, a single amino substitution in the hemoglobin β chain causes a change the structure of the entire protein. When the amino acid glutamic acid is replaced by valine in the β chain, the polypeptide folds into an slightly-different shape that creates a dysfunctional hemoglobin protein. So, just one amino acid substitution can cause dramatic changes. These dysfunctional hemoglobin proteins, under low-oxygen conditions, start associating with one another, forming long fibers made from millions of aggregated hemoglobins that distort the red blood cells into crescent or “sickle” shapes, which clog arteries. People affected by the disease often experience breathlessness, dizziness, headaches, and abdominal pain.
Secondary Structure
A protein’s secondary structure is whatever regular structures arise from interactions between neighboring or near-by amino acids as the polypeptide starts to fold into its functional three-dimensional form. Secondary structures arise as H bonds form between local groups of amino acids in a region of the polypeptide chain. Rarely does a single secondary structure extend throughout the polypeptide chain. It is usually just in a section of the chain. The most common forms of secondary structure are the α-helix and β-pleated sheet structures and they play an important structural role in most globular and fibrous proteins.
In the α-helix chain, the hydrogen bond forms between the oxygen atom in the polypeptide backbone carbonyl group in one amino acid and the hydrogen atom in the polypeptide backbone amino group of another amino acid that is four amino acids farther along the chain. This holds the stretch of amino acids in a right-handed coil. Every helical turn in an alpha helix has 3.6 amino acid residues. The R groups (the side chains) of the polypeptide protrude out from the α-helix chain and are not involved in the H bonds that maintain the α-helix structure.
In β-pleated sheets, stretches of amino acids are held in an almost fully-extended conformation that “pleats” or zig-zags due to the non-linear nature of single C-C and C-N covalent bonds. β-pleated sheets never occur alone. They have to held in place by other β-pleated sheets. The stretches of amino acids in β-pleated sheets are held in their pleated sheet structure because hydrogen bonds form between the oxygen atom in a polypeptide backbone carbonyl group of one β-pleated sheet and the hydrogen atom in a polypeptide backbone amino group of another β-pleated sheet. The β-pleated sheets which hold each other together align parallel or antiparallel to each other. The R groups of the amino acids in a β-pleated sheet point out perpendicular to the hydrogen bonds holding the β-pleated sheets together, and are not involved in maintaining the β-pleated sheet structure.
Tertiary Structure
The tertiary structure of a polypeptide chain is its overall three-dimensional shape, once all the secondary structure elements have folded together among each other. Interactions between polar, nonpolar, acidic, and basic R group within the polypeptide chain create the complex three-dimensional tertiary structure of a protein. When protein folding takes place in the aqueous environment of the body, the hydrophobic R groups of nonpolar amino acids mostly lie in the interior of the protein, while the hydrophilic R groups lie mostly on the outside. Cysteine side chains form 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 will no longer be functional.
Quaternary Structure
The quaternary structure of a protein is how its subunits are oriented and arranged with respect to one another. As a result, quaternary structure only applies to multi-subunit proteins; that is, proteins made from more than one polypeptide chain. Proteins made from a single polypeptide will not have a quaternary structure.
In proteins with more than one subunit, weak interactions between the subunits help to stabilize the overall structure. Enzymes often play key roles in bonding subunits to form the final, functioning protein.
For example, insulin is a ball-shaped, globular protein that contains both hydrogen bonds and disulfide bonds that hold its two polypeptide chains together. Silk is a fibrous protein that results from hydrogen bonding between different β-pleated chains.
Key Points
• Protein structure depends on its amino acid sequence and local, low-energy chemical bonds between atoms in both the polypeptide backbone and in amino acid side chains.
• Protein structure plays a key role in its function; if a protein loses its shape at any structural level, it may no longer be functional.
• Primary structure is the amino acid sequence.
• Secondary structure is local interactions between stretches of a polypeptide chain and includes α-helix and β-pleated sheet structures.
• Tertiary structure is the overall the three-dimension folding driven largely by interactions between R groups.
• Quarternary structures is the orientation and arrangement of subunits in a multi-subunit protein.
Key Terms
• antiparallel: The nature of the opposite orientations of the two strands of DNA or two beta strands that comprise a protein’s secondary structure
• disulfide bond: A bond, consisting of a covalent bond between two sulfur atoms, formed by the reaction of two thiol groups, especially between the thiol groups of two proteins
• β-pleated sheet: secondary structure of proteins where N-H groups in the backbone of one fully-extended strand establish hydrogen bonds with C=O groups in the backbone of an adjacent fully-extended strand
• α-helix: secondary structure of proteins where every backbone N-H creates a hydrogen bond with the C=O group of the amino acid four residues earlier in the same helix. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/03%3A_Biological_Macromolecules/3.09%3A_Proteins_-_Protein_Structure.txt |
Learning Objectives
• Discuss the process of protein denaturation
Each protein has its own unique sequence of amino acids and the interactions between these amino acids create a specify shape. This shape determines the protein’s function, from digesting protein in the stomach to carrying oxygen in the blood.
Changing the Shape of a Protein
If the protein is subject to changes in temperature, pH, or exposure to chemicals, the internal interactions between the protein’s amino acids can be altered, which in turn may alter the shape of the protein. Although the amino acid sequence (also known as the protein’s primary structure) does not change, the protein’s shape may change so much that it becomes dysfunctional, in which case the protein is considered denatured. Pepsin, the enzyme that breaks down protein in the stomach, only operates at a very low pH. At higher pHs pepsin’s conformation, the way its polypeptide chain is folded up in three dimensions, begins to change. The stomach maintains a very low pH to ensure that pepsin continues to digest protein and does not denature.
Because almost all biochemical reactions require enzymes, and because almost all enzymes only work optimally within relatively narrow temperature and pH ranges, many homeostatic mechanisms regulate appropriate temperatures and pH so that the enzymes can maintain the shape of their active site.
Reversing Denaturation
It is often possible to reverse denaturation because the primary structure of the polypeptide, the covalent bonds holding the amino acids in their correct sequence, is intact. Once the denaturing agent is removed, the original interactions between amino acids return the protein to its original conformation and it can resume its function. However, denaturation can be irreversible in extreme situations, like frying an egg. The heat from a pan denatures the albumin protein in the liquid egg white and it becomes insoluble. The protein in meat also denatures and becomes firm when cooked.
Chaperone proteins (or chaperonins ) are helper proteins that provide favorable conditions for protein folding to take place. The chaperonins clump around the forming protein and prevent other polypeptide chains from aggregating. Once the target protein folds, the chaperonins disassociate.
Key Points
• Proteins change their shape when exposed to different pH or temperatures.
• The body strictly regulates pH and temperature to prevent proteins such as enzymes from denaturing.
• Some proteins can refold after denaturation while others cannot.
• Chaperone proteins help some proteins fold into the correct shape.
Key Terms
• chaperonin: proteins that provide favorable conditions for the correct folding of other proteins, thus preventing aggregation
• denaturation: the change of folding structure of a protein (and thus of physical properties) caused by heating, changes in pH, or exposure to certain chemicals
3.11: Nucleic Acids - DNA and RNA
Learning Objectives
• Describe the structure of nucleic acids and the types of molecules that contain them
Types of Nucleic Acids
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 chloroplasts and mitochondria. In prokaryotes, the DNA is not enclosed in a membranous envelope, but rather free-floating within the cytoplasm.
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. In eukaryotes, 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.
Nucleotides
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:
1. a nitrogenous base
2. a pentose (five-carbon) sugar
3. a phosphate group
Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to one or more phosphate groups.
Nitrogenous Base
The nitrogenous bases are organic molecules and are so named because they contain carbon and nitrogen. They are bases because they contain an amino group that has the potential of binding an extra hydrogen, and thus, decreasing the hydrogen ion concentration in its environment, making it more basic. Each nucleotide in DNA contains one of four possible nitrogenous bases: adenine (A), guanine (G) cytosine (C), and thymine (T).
Adenine and guanine are classified as purines. The primary structure of a purine consists of two carbon-nitrogen rings. Cytosine, thymine, and uracil are classified as pyrimidines which have a single carbon-nitrogen ring as their primary structure. 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.
Five-Carbon Sugar
The pentose sugar in DNA is deoxyribose and in RNA it is ribose. 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”).
Phosphate Group
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.
Key Points
• The two main types of nucleic acids are DNA and RNA.
• Both DNA and RNA are made from nucleotides, each containing a five-carbon sugar backbone, a phosphate group, and a nitrogen base.
• DNA provides the code for the cell ‘s activities, while RNA converts that code into proteins to carry out cellular functions.
• The sequence of nitrogen bases (A, T, C, G) in DNA is what forms an organism’s traits.
• The nitrogen bases A and T (or U in RNA) always go together and C and G always go together, forming the 5′-3′ phosphodiester linkage found in the nucleic acid molecules.
Key Terms
• nucleotide: the monomer comprising DNA or RNA molecules; consists of a nitrogenous heterocyclic base that can be a purine or pyrimidine, a five-carbon pentose sugar, and a phosphate group
• genome: the cell’s complete genetic information packaged as a double-stranded DNA molecule
• monomer: A relatively small molecule which can be covalently bonded to other monomers to form a polymer. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/03%3A_Biological_Macromolecules/3.10%3A_Proteins_-_Denaturation_and_Protein_Folding.txt |
Learning Objectives
• Describe the structure of DNA
A Double-Helix Structure
DNA has a double-helix structure, with sugar and phosphate on the outside of the helix, forming the sugar-phosphate backbone of the DNA. The nitrogenous bases are stacked in the interior in pairs, like the steps of a staircase; the pairs are bound to each other by hydrogen bonds. The two strands of the helix run in opposite directions. This antiparallel orientation is important to DNA replication and in many nucleic acid interactions.
Base Pairs
Only certain types of base pairing are allowed. This means Adenine pairs with Thymine, and Guanine pairs with Cytosine. This is known as the base complementary rule because the DNA strands are complementary to each other. If the sequence of one strand is AATTGGCC, the complementary strand would have the sequence TTAACCGG.
DNA Replication
During DNA replication, each strand is copied, resulting in a daughter DNA double helix containing one parental DNA strand and a newly synthesized strand. At this time it is possible a mutation may occur. A mutation is a change in the sequence of the nitrogen bases. For example, in the sequence AATTGGCC, a mutation may cause the second T to change to a G. Most of the time when this happens the DNA is able to fix itself and return the original base to the sequence. However, sometimes the repair is unsuccessful, resulting in different proteins being created.
Key Points
• The structure of DNA is called a double helix, which looks like a twisted staircase.
• The sugar and phosphate make up the backbone, while the nitrogen bases are found in the center and hold the two strands together.
• The nitrogen bases can only pair in a certain way: A pairing with T and C pairing with G. This is called base pairing.
• Due to the base pairing, the DNA strands are complementary to each other, run in opposite directions, and are called antiparallel strands.
Key Terms
• mutation: any error in base pairing during the replication of DNA
• sugar-phosphate backbone: The outer support of the ladder, forming strong covalent bonds between monomers of DNA.
• base pairing: The specific way in which bases of DNA line up and bond to one another; A always with T and G always with C.
3.13: Nucleic Acids - DNA Packaging
Learning Objectives
• Describe how DNA is packaged differently in prokaryotes and eukaryotes
A eukaryote contains a well-defined nucleus, whereas in prokaryotes the chromosome lies in the cytoplasm in an area called the nucleoid. In eukaryotic cells, DNA and RNA synthesis occur in a separate compartment from protein synthesis. In prokaryotic cells, both processes occur together. What advantages might there be to separating the processes? What advantages might there be to having them occur together?
The size of the genome in one of the most well-studied prokaryotes, E.coli, is 4.6 million base pairs (approximately 1.1 mm, if cut and stretched out). So how does this fit inside a small bacterial cell? The DNA is twisted by what is known as supercoiling. Supercoiling means that DNA is either under-wound (less than one turn of the helix per 10 base pairs) or over-wound (more than 1 turn per 10 base pairs) from its normal relaxed state. Some proteins are known to be involved in the supercoiling; other proteins and enzymes such as DNA gyrase help in maintaining the supercoiled structure.
Eukaryotes, whose chromosomes each consist of a linear DNA molecule, employ a different type of packing strategy to fit their DNA inside the nucleus. At the most basic level, DNA is wrapped around proteins known as histones to form structures called nucleosomes. The histones are evolutionarily conserved proteins that are rich in basic amino acids and form an octamer. The DNA (which is negatively charged because of the phosphate groups) is wrapped tightly around the histone core. This nucleosome is linked to the next one with the help of a linker DNA. This is also known as the “beads on a string” structure. This is further compacted into a 30 nm fiber, which is the diameter of the structure. At the metaphase stage the chromosomes are at their most compact, approximately 700 nm in width, and are found in association with scaffold proteins.
In interphase, eukaryotic chromosomes have two distinct regions that can be distinguished by staining. The tightly packaged region is known as heterochromatin, and the less dense region is known as euchromatin.
Heterochromatin usually contains genes that are not expressed, and is found in the regions of the centromere and telomeres. The euchromatin usually contains genes that are transcribed, with DNA packaged around nucleosomes but not further compacted.
Key Points
• In eukaryotic cells, DNA and RNA synthesis occur in a different location than protein synthesis; in prokaryotic cells, both these processes occur together.
• DNA is “supercoiled” in prokaryotic cells, meaning that the DNA is either under-wound or over-wound from its normal relaxed state.
• In eukaryotic cells, DNA is wrapped around proteins known as histones to form structures called nucleosomes.
Key Terms
• nucleosomes: The fundamental subunit of chromatin, composed of a little less than two turns of DNA wrapped around a set of eight proteins called histones.
• histones: The chief protein components of chromatin, which act as spools around which DNA winds. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/03%3A_Biological_Macromolecules/3.12%3A_Nucleic_Acids_-__The_DNA_Double_Helix.txt |
Learning Objectives
• Describe the structure and function of RNA
RNA Structure and Function
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 and is found in the nucleus of eukaryotes and in the chloroplasts and mitochondria. In prokaryotes, the DNA is not enclosed in a membranous envelope.
The other type of nucleic acid, RNA, is mostly involved in protein synthesis. Just like in DNA, RNA is made of monomers called nucleotides. Each nucleotide is made up of three components: a nitrogenous base, a pentose (five-carbon) sugar called ribose, and a phosphate group. Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to one or more phosphate groups.
In RNA, the nitrogenous bases vary slightly from those of DNA. Adenine (A), guanine (G), and cytosine (C) are present, but instead of thymine (T), a pyrimidine called uracil (U) pairs with adenine. RNA is a single stranded molecule, compared to the double helix of DNA.
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). When proteins need to be made, the mRNA enters the nucleus and attaches itself to one of the DNA strands. Being complementary, the sequence of nitrogen bases of the RNA is opposite that of the DNA. This is called transcription. For example, if the DNA strand reads TCCAAGTC, then the mRNA strand would read AGGUUCAG. The mRNA then carries the code out of the nucleus to organelles called ribosomes for the assembly of proteins.
Once the mRNA has reached the ribosomes, they do not read the instructions directly. Instead, another type of RNA called transfer RNA (tRNA) needs to translate the information from the mRNA into a usable form. The tRNA attaches to the mRNA, but with the opposite base pairings. It then reads the sequence in sets of three bases called codons. Each possible three letter arrangement of A,C,U,G (e.g., AAA, AAU, GGC, etc) is a specific instruction, and the correspondence of these instructions and the amino acids is known as the “genetic code.” Though exceptions to or variations on the code exist, the standard genetic code holds true in most organisms.
The ribosome acts like a giant clamp, holding all of the players in position, and facilitating both the pairing of bases between the messenger and transfer RNAs, and the chemical bonding between the amino acids. The ribosome has special subunits known as ribosomal RNAs (rRNA) because they function in the ribosome. These subunits do not carry instructions for making a specific proteins (i.e., they are not messenger RNAs) but instead are an integral part of the ribosome machinery that is used to make proteins from mRNAs. The making of proteins by reading instructions in mRNA is generally known as ” translation.”
Key Points
• The nitrogen bases in RNA include adenine (A), guanine (G), cytosine (C), and uracil (U).
• Messenger RNA (mRNA) carries the code from the DNA to the ribosomes, while transfer RNA (tRNA) converts that code into a usable form.
• Ribosomes are the sites where tRNA and rRNA assemble proteins.
• RNA differs from DNA in that it is single stranded, has uracil instead of thymine, carries the code for making proteins instead of directing all of the cell ‘s functions, and has ribose as its five-carbon sugar instead of deoxyribose.
Key Terms
• codon: a sequence of three adjacent nucleotides, which encode for a specific amino acid during protein synthesis or translation
• transcription: the synthesis of RNA under the direction of DNA | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/03%3A_Biological_Macromolecules/3.14%3A_Nucleic_Acids_-__Types_of_RNA.txt |
Learning Objectives
• State the general characteristics of a cell
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.
Cells as Building Blocks
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). 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.
Types of Specialized 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.
Key Points
• A living thing can be composed of either one cell or many cells.
• There are two broad categories of cells: prokaryotic and eukaryotic cells.
• Cells can be highly specialized with specific functions and characteristics.
Key Terms
• prokaryotic: Small cells in the domains Bacteria and Archaea that do not contain a membrane-bound nucleus or other membrane-bound organelles.
• eukaryotic: Having complex cells in which the genetic material is contained within membrane-bound nuclei.
• cell: The basic unit of a living organism, consisting of a quantity of protoplasm surrounded by a cell membrane, which is able to synthesize proteins and replicate itself.
4.02: Studying Cells - Microscopy
Learning Objectives
• Compare and contrast light and electron microscopy.
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; 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 they 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. 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 undergraduate college laboratories, 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 use a beam of electrons instead of a beam of light. Not only does this allow for higher magnification and, thus, more detail, 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.
Key Points
• Light microscopes allow for magnification of an object approximately up to 400-1000 times depending on whether the high power or oil immersion objective is used.
• Light microscopes use visible light which passes and bends through the lens system.
• Electron microscopes use a beam of electrons, opposed to visible light, for magnification.
• Electron microscopes allow for higher magnification in comparison to a light microscope thus, allowing for visualization of cell internal structures.
Key Terms
• resolution: The degree of fineness with which an image can be recorded or produced, often expressed as the number of pixels per unit of length (typically an inch).
• electron: The subatomic particle having a negative charge and orbiting the nucleus; the flow of electrons in a conductor constitutes electricity. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/04%3A_Cell_Structure/4.01%3A_Studying_Cells_-_Cells_as_the_Basic_Unit_of_Life.txt |
Learning Objectives
• Identify the components of cell theory
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. The unified cell theory 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.
Schleiden and Schwann proposed spontaneous generation as the method for cell origination, but spontaneous generation (also called abiogenesis) was later disproven. Rudolf Virchow famously stated “Omnis cellula e cellula”… “All cells only arise from pre-existing cells. “The parts of the theory that did not have to do with the origin of cells, however, held up to scientific scrutiny and are widely agreed upon by the scientific community today. The generally accepted portions of the modern Cell Theory are as follows:
1. The cell is the fundamental unit of structure and function in living things.
2. All organisms are made up of one or more cells.
3. Cells arise from other cells through cellular division.
The expanded version of the cell theory can also include:
• Cells carry genetic material passed to daughter cells during cellular division
• All cells are essentially the same in chemical composition
• Energy flow (metabolism and biochemistry) occurs within cells
Key Points
• The cell theory describes the basic properties of all cells.
• The three scientists that contributed to the development of cell theory are Matthias Schleiden, Theodor Schwann, and Rudolf Virchow.
• A component of the cell theory is that all living things are composed of one or more cells.
• A component of the cell theory is that the cell is the basic unit of life.
• A component of the cell theory is that all new cells arise from existing cells.
Key Terms
• cell theory: The scientific theory that all living organisms are made of cells as the smallest functional unit.
4.04: Studying Cells - Cell Size
Learning Objectives
• Describe the factors limiting cell size and the adaptations cells make to overcome the surface area to volume issue
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. 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.
In general, small size is necessary for all cells, whether prokaryotic or eukaryotic. Consider the area and volume of a typical cell. Not all cells are spherical in shape, but most tend to approximate a sphere. The formula for the surface area of a sphere is 4πr2, while the formula for its volume is 4πr3/3. 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 (below). 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.
Smaller single-celled organisms have a high surface area to volume ratio, which allows them to rely on oxygen and material diffusing into the cell (and wastes diffusing out) in order to survive. The higher the surface area to volume ratio they have, the more effective this process can be. Larger animals require specialized organs (lungs, kidneys, intestines, etc.) that effectively increase the surface area available for exchange processes, and a circulatory system to move material and heat energy between the surface and the core of the organism.
Increased volume can lead to biological problems. King Kong, the fictional giant gorilla, would have insufficient lung surface area to meet his oxygen needs, and could not survive. For small organisms with their high surface area to volume ratio, friction and fluid dynamics (wind, water flow) are relatively much more important, and gravity much less important, than for large animals.
However, increased surface area can cause problems as well. More contact with the environment through the surface of a cell or an organ (relative to its volume) increases loss of water and dissolved substances. High surface area to volume ratios also present problems of temperature control in unfavorable environments.
Key Points
• As a cell grows, its volume increases much more rapidly than its surface area. Since the surface of the cell is what allows the entry of oxygen, large cells cannot get as much oxygen as they would need to support themselves.
• As animals increase in size they require specialized organs that effectively increase the surface area available for exchange processes.
Key Terms
• surface area: The total area on the surface of an object. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/04%3A_Cell_Structure/4.03%3A_Studying_Cells_-_Cell_Theory.txt |
Learning Objectives
• Describe the structure of prokaryotic 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: a jelly-like cytosol within the cell in which other cellular components are found
3. DNA: the genetic material of the cell
4. ribosomes: where protein synthesis occurs
However, prokaryotes differ from eukaryotic cells in several ways.
A prokaryote is a simple, single-celled (unicellular) organism that lacks an organized 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.
Most prokaryotes have a peptidoglycan cell wall and many have a polysaccharide capsule. 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.
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. 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 4πr2, while the formula for its volume is 4/3πr3. 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. 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 led to the development of more sophisticated cells called eukaryotic cells.
Key Points
• Prokaryotes lack an organized nucleus and other membrane-bound organelles.
• Prokaryotic DNA is found in a central part of the cell called the nucleoid.
• The cell wall of a prokaryote acts as an extra layer of protection, helps maintain cell shape, and prevents dehydration.
• Prokaryotic cell size ranges from 0.1 to 5.0 μm in diameter.
• The small size of prokaryotes allows quick entry and diffusion of ions and molecules to other parts of the cell while also allowing fast removal of waste products out of the cell.
Key Terms
• eukaryotic: Having complex cells in which the genetic material is organized into membrane-bound nuclei.
• prokaryotic: Of cells, lacking a nucleus.
• nucleoid: the irregularly-shaped region within a prokaryote cell where the genetic material is localized | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/04%3A_Cell_Structure/4.05%3A_Prokaryotic_Cells_-_Characteristics_of_Prokaryotic_Cells.txt |
Learning Objectives
• Describe the structure of eukaryotic cells
Eukaryotic Cell Structure
Like a prokaryotic cell, a eukaryotic cell has a plasma membrane, cytoplasm, and ribosomes. However, unlike prokaryotic cells, eukaryotic cells have:
1. a membrane-bound nucleus
2. numerous membrane-bound organelles (including the endoplasmic reticulum, Golgi apparatus, chloroplasts, and mitochondria)
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. ” Organelles (meaning “little organ”) have specialized cellular roles, just as the organs of your body have specialized roles. They allow different functions to be compartmentalized in different areas of the cell.
The Nucleus & Its Structures
Typically, the nucleus is the most prominent organelle in a cell. Eukaryotic cells have a true nucleus, which means the cell’s DNA is surrounded by a membrane. Therefore, the nucleus houses the cell’s DNA and directs the synthesis of proteins and ribosomes, the cellular organelles responsible for protein synthesis. The nuclear envelope is a double-membrane structure that constitutes the outermost portion of the nucleus. 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. Furthermore, chromosomes are structures within the nucleus that are made up of DNA, the genetic material. In prokaryotes, DNA is organized into a single circular chromosome. In eukaryotes, chromosomes are linear structures.
Other Membrane-Bound Organelles
Mitochondria are oval-shaped, double membrane organelles that have their own ribosomes and DNA. These organelles are often called the “energy factories” of a cell because they are responsible for making adenosine triphosphate (ATP), the cell’s main energy-carrying molecule, by conducting cellular respiration. The endoplasmic reticulum modifies proteins and synthesizes lipids, while the golgi apparatus is where the sorting, tagging, packaging, and distribution of lipids and proteins takes place. Peroxisomes are small, round organelles enclosed by single membranes; they carry out oxidation reactions that break down fatty acids and amino acids. Peroxisomes also detoxify many poisons that may enter the body. 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. All of these organelles are found in each and every eukaryotic cell.
Animal Cells Versus Plant Cells
While all eukaryotic cells contain the aforementioned organelles and structures, there are some striking differences between animal and plant cells. Animal cells have a centrosome and lysosomes, whereas plant cells do not. The centrosome is a microtubule-organizing center found near the nuclei of animal cells while lysosomes take care of the cell’s digestive process.
In addition, plant cells have a cell wall, a large central vacuole, chloroplasts, and other specialized plastids, whereas animal cells do not. The cell wall protects the cell, provides structural support, and gives shape to the cell while the central vacuole plays a key role in regulating the cell’s concentration of water in changing environmental conditions. Chloroplasts are the organelles that carry out photosynthesis.
Key Points
• Eukaryotic cells are larger than prokaryotic cells and have a “true” nucleus, membrane-bound organelles, and rod-shaped chromosomes.
• The nucleus houses the cell’s DNA and directs the synthesis of proteins and ribosomes.
• Mitochondria are responsible for ATP production; the endoplasmic reticulum modifies proteins and synthesizes lipids; and the golgi apparatus is where the sorting of lipids and proteins takes place.
• Peroxisomes carry out oxidation reactions that break down fatty acids and amino acids and detoxify poisons; vesicles and vacuoles function in storage and transport.
• Animal cells have a centrosome and lysosomes while plant cells do not.
• Plant cells have a cell wall, a large central vacuole, chloroplasts, and other specialized plastids, whereas animal cells do not.
Key Terms
• eukaryotic: Having complex cells in which the genetic material is organized into membrane-bound nuclei.
• organelle: A specialized structure found inside cells that carries out a specific life process (e.g. ribosomes, vacuoles).
• photosynthesis: the process by which plants and other photoautotrophs generate carbohydrates and oxygen from carbon dioxide, water, and light energy in chloroplasts | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/04%3A_Cell_Structure/4.06%3A_Eukaryotic_Cells_-_Characteristics_of_Eukaryotic_Cells.txt |
Learning Objectives
• Explain the structure and purpose of the plasma membrane of a cell
The Plasma Membrane
Despite differences in structure and function, all living cells in multicellular organisms have a surrounding plasma membrane (also known as the cell membrane). As the outer layer of your skin separates your body from its environment, the plasma membrane separates the inner contents of a cell from its exterior environment. The plasma membrane can be described as a phospholipid bilayer with embedded proteins that 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 membrane.
The cell membrane is an extremely pliable structure composed primarily of two adjacent sheets of phospholipids. Cholesterol, also present, contributes to the fluidity of the membrane. A single phospholipid molecule consists of a polar phosphate “head,” which is hydrophilic, and a non-polar lipid “tail,” which is hydrophobic. Unsaturated fatty acids result in kinks in the hydrophobic tails. The phospholipid bilayer consists of two phospholipids arranged tail to tail. The hydrophobic tails associate with one another, forming the interior of the membrane. The polar heads contact the fluid inside and outside of the cell.
The plasma membrane’s main function is to regulate the concentration of substances inside the cell. These substances include ions such as Ca++, Na+, K+, and Cl; nutrients including sugars, fatty acids, and amino acids; and waste products, particularly carbon dioxide (CO2), which must leave the cell.
The membrane’s lipid bilayer structure provides the cell with access control through permeability. The phospholipids are tightly packed together, while the membrane has a hydrophobic interior. This structure causes the membrane to be selectively permeable. A membrane that has selective permeability allows only substances meeting certain criteria to pass through it unaided. In the case of the plasma membrane, only relatively small, non-polar materials can move through the lipid bilayer (remember, the lipid tails of the membrane are nonpolar). Some examples of these materials are other lipids, oxygen and carbon dioxide gases, and alcohol. However, water-soluble materials—such as glucose, amino acids, and electrolytes—need some assistance to cross the membrane because they are repelled by the hydrophobic tails of the phospholipid bilayer.
Transport Across the Membrane
All substances that move through the membrane do so by one of two general methods, which are categorized based on whether or not energy is required. Passive (non-energy requiring) transport is the movement of substances across the membrane without the expenditure of cellular energy. During this type of transport, materials move by simple diffusion or by facilitated diffusion through the membrane, down their concentration gradient. Water passes through the membrane in a diffusion process called osmosis. Osmosis is the diffusion of water through a semi-permeable membrane down its concentration gradient. It occurs when there is an imbalance of solutes outside of a cell versus inside the cell. The solution that has the higher concentration of solutes is said to be hypertonic and the solution that has the lower concentration of solutes is said to be hypotonic. Water molecules will diffuse out of the hypotonic solution and into the hypertonic solution (unless acted upon by hydrostatic forces).
In contrast to passive transport, active (energy-requiring) transport is the movement of substances across the membrane using energy from adenosine triphosphate (ATP). The energy is expended to assist material movement across the membrane in a direction against their concentration gradient. Active transport may take place with the help of protein pumps or through the use of vesicles. Another form of this type of transport is endocytosis, where a cell envelopes extracellular materials using its cell membrane. The opposite process is known as exocytosis. This is where a cell exports material using vesicular transport.
Cytoplasm
The cell’s plasma membrane also helps contain the cell’s cytoplasm, which provides a gel-like environment for the cell’s organelles. The cytoplasm is the location for most cellular processes, including metabolism, protein folding, and internal transportation.
Key Points
• All eukaryotic cells have a surrounding plasma membrane, which is also known as the cell membrane.
• The plasma membrane is made up by a phospholipid bilayer with embedded proteins that separates the internal contents of the cell from its surrounding environment.
• Only relatively small, non- polar materials can easily move through the lipid bilayer of the plasma membrane.
• Passive transport is the movement of substances across the membrane that does not require the use of energy while active transport is the movement of substances across the membrane using energy.
• Osmosis is the diffusion of water through a semi- permeable membrane down its concentration gradient; this occurs when there is an imbalance of solutes outside of a cell compared to the inside the cell.
Key Terms
• phospholipid: Any lipid consisting of a diglyceride combined with a phosphate group and a simple organic molecule such as choline or ethanolamine; they are important constituents of biological membranes
• hypertonic: having a greater osmotic pressure than another
• hypotonic: Having a lower osmotic pressure than another; a cell in this environment causes water to enter the cell, causing it to swell. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/04%3A_Cell_Structure/4.07%3A_Eukaryotic_Cells_-_The_Plasma_Membrane_and_the_Cytoplasm.txt |
Learning Objectives
• Explain the purpose of the nucleus in eukaryotic cells
The Nucleus
One of the main differences between prokaryotic and eukaryotic cells is the nucleus. As previously discussed, prokaryotic cells lack an organized nucleus while eukaryotic cells contain membrane-bound nuclei (and organelles ) that house the cell’s DNA and direct the synthesis of ribosomes and proteins.
The nucleus stores chromatin (DNA plus proteins) in a gel-like substance called the nucleoplasm. To understand chromatin, it is helpful to first consider chromosomes. Chromatin describes the material that makes up chromosomes, which 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. In order to organize the large amount of DNA within the nucleus, proteins called histones are attached to chromosomes; the DNA is wrapped around these histones to form a structure resembling beads on a string. These protein-chromosome complexes are called chromatin.
The nucleoplasm is also where we find the nucleolus. The nucleolus is a condensed region of chromatin where ribosome synthesis occurs. Ribosomes, large complexes of protein and ribonucleic acid (RNA), are the cellular organelles responsible for protein synthesis. They receive their “orders” for protein synthesis from the nucleus where the DNA is transcribed into messenger RNA (mRNA). This 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.
Lastly, the boundary of the nucleus is called the nuclear envelope. It consists of two phospholipid bilayers: an outer membrane and an inner membrane. The nuclear membrane is continuous with the endoplasmic reticulum, while nuclear pores allow substances to enter and exit the nucleus.
Key Points
• The nucleus contains the cell ‘s DNA and directs the synthesis of ribosomes and proteins.
• Found within the nucleoplasm, the nucleolus is a condensed region of chromatin where ribosome synthesis occurs.
• Chromatin consists of DNA wrapped around histone proteins and is stored within the nucleoplasm.
• Ribosomes are large complexes of protein and ribonucleic acid (RNA) responsible for protein synthesis when DNA from the nucleus is transcribed.
Key Terms
• histone: any of various simple water-soluble proteins that are rich in the basic amino acids lysine and arginine and are complexed with DNA in the nucleosomes of eukaryotic chromatin
• nucleolus: a conspicuous, rounded, non-membrane bound body within the nucleus of a cell
• chromatin: a complex of DNA, RNA, and proteins within the cell nucleus out of which chromosomes condense during cell division
4.09: Eukaryotic Cells - Mitochondria
Learning Objectives
• Explain the role of the mitochondria.
One of the major features distinguishing prokaryotes from eukaryotes is the presence of mitochondria. Mitochondria are double-membraned organelles that contain their own ribosomes and DNA. Each membrane is a phospholipid bilayer embedded with proteins. Eukaryotic cells may contain anywhere from one to several thousand mitochondria, depending on the cell’s level of energy consumption. Each mitochondrion measures 1 to 10 micrometers (or greater) in length and exists in the cell as an organelle that can be ovoid to worm-shaped to intricately branched.
Mitochondria Structure
Most mitochondria are surrounded by two membranes, which would result when one membrane-bound organism was engulfed into a vacuole by another membrane-bound organism. The mitochondrial inner membrane is extensive and involves substantial infoldings called cristae that resemble the textured, outer surface of alpha-proteobacteria. The matrix and inner membrane are rich with the enzymes necessary for aerobic respiration.
Mitochondria have their own (usually) circular DNA chromosome that is stabilized by attachments to the inner membrane and carries genes similar to genes expressed by alpha-proteobacteria. Mitochondria also have special ribosomes and transfer RNAs that resemble these components in prokaryotes. These features all support the hypothesis that mitochondria were once free-living prokaryotes.
Mitochondria Function
Mitochondria 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 by-product.
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.
In addition to the aerobic generation of ATP, mitochondria have several other metabolic functions. One of these functions is to generate clusters of iron and sulfur that are important cofactors of many enzymes. Such functions are often associated with the reduced mitochondrion-derived organelles of anaerobic eukaryotes.
Origins of Mitochondria
There are two hypotheses about the origin of mitochondria: endosymbiotic and autogenous, but the most accredited theory at present is endosymbiosis. The endosymbiotic hypothesis suggests mitochondria were originally prokaryotic cells, capable of implementing oxidative mechanisms. These prokaryotic cells may have been engulfed by a eukaryote and became endosymbionts living inside the eukaryote.
Key Points
• Mitochondria contain their own ribosomes and DNA; combined with their double membrane, these features suggest that they might have once been free-living prokaryotes that were engulfed by a larger cell.
• Mitochondria have an important role in cellular respiration through the production of ATP, using chemical energy found in glucose and other nutrients.
• Mitochondria are also responsible for generating clusters of iron and sulfur, which are important cofactors of many enzymes.
Key Terms
• alpha-proteobacteria: A taxonomic class within the phylum Proteobacteria — the phototropic proteobacteria.
• adenosine triphosphate: a multifunctional nucleoside triphosphate used in cells as a coenzyme, often called the “molecular unit of energy currency” in intracellular energy transfer
• cofactor: an inorganic molecule that is necessary for an enzyme to function | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/04%3A_Cell_Structure/4.08%3A_Eukaryotic_Cells_-_The_Nucleus_and_Ribosomes.txt |
Learning Objectives
• Differentiate between the structures found in animal and plant cells
Animal Cells versus Plant Cells
Each eukaryotic cell has a plasma membrane, cytoplasm, a nucleus, ribosomes, mitochondria, peroxisomes, and in some, vacuoles; however, 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. 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 the advantage of compartmentalizing the eukaryotic cell into organelles is apparent.
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, a polysaccharide comprised of glucose units. 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 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. 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.
The Central Vacuole
The central vacuole plays a key role in regulating the cell’s concentration of water in changing environmental conditions. When 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.
Key Points
• Centrosomes and lysosomes are found in animal cells, but do not exist within plant cells.
• The lysosomes are the animal cell’s “garbage disposal”, while in plant cells the same function takes place in vacuoles.
• Plant cells have a cell wall, chloroplasts and other specialized plastids, and a large central vacuole, which are not found within animal cells.
• The cell wall is a rigid covering that protects the cell, provides structural support, and gives shape to the cell.
• The chloroplasts, found in plant cells, contain a green pigment called chlorophyll, which captures the light energy that drives the reactions of plant photosynthesis.
• The central vacuole plays a key role in regulating a plant cell’s concentration of water in changing environmental conditions.
Key Terms
• protist: Any of the eukaryotic unicellular organisms including protozoans, slime molds and some algae; historically grouped into the kingdom Protoctista.
• 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)/04%3A_Cell_Structure/4.10%3A_Eukaryotic_Cells_-_Comparing_Plant_and_Animal_Cells.txt |
Learning Objectives
• Summarize the functions of vesicles and vacuoles in cells
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. The membrane of a vacuole does not fuse with the membranes of other cellular components. Additionally, some agents within plant vacuoles, such as enzymes, break down macromolecules.
Vesicles
A vesicle is a small structure within a cell, consisting of fluid enclosed by a lipid bilayer. Vesicles form naturally during the processes of secretion (exocytosis), uptake (phagocytosis) and transport of materials within the cytoplasm. Alternatively, they may be prepared artificially, in which case they are called liposomes. Vesicles can fuse with the plasma membrane to release their contents outside the cell. Vesicles can also fuse with other organelles within the cell.
Vesicles perform a variety of functions. Because they are separated from the cytosol, the inside of a vesicle can be different from the cytosolic environment. For this reason, vesicles are a basic tool used by the cell for organizing cellular substances. Vesicles are involved in metabolism, transport, buoyancy control, and enzyme storage. They can also act as chemical reaction chambers.
Lysosomes
Animal cells have a set of organelles not found in plant cells: lysosomes. Lysosomes are a cell’s “garbage disposal.” Enzymes within the lysosomes aid the breakdown of proteins, polysaccharides, lipids, nucleic acids, and 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.
Vacuoles
Vacuoles are an essential component of plant cells. If you look at the figure below, 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, and houses the digestive processes.
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.
Contractile vacuoles are found in certain protists, especially those in Phylum Ciliophora. These vacuoles take water from the cytoplasm and excrete it from the cell to avoid bursting due to osmotic pressure.
Key Points
• Vesicles are small structures within a cell, consisting of fluid enclosed by a lipid bilayer involved in transport, buoyancy control, and enzyme storage.
• Lysosomes, which are found in animal cells, are the cell’s “garbage disposal.” The digestive processes take place in these, and enzymes within them aid in the breakdown of proteins, polysaccharides, lipids, nucleic acids, and worn-out organelles.
• Central vacuoles, which are found in plants, play a key role in regulating the cell’s concentration of water in changing environmental conditions. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/04%3A_Cell_Structure/4.11%3A_The_Endomembrane_System_and_Proteins_-_Vesicles_and_Vacuoles.txt |
Learning Objectives
• Describe the structure of the endoplasmic reticulum and its role in synthesis and metabolism
The Endoplasmic Reticulum
The endoplasmic reticulum (ER) 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. 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. 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. Since the RER is engaged in modifying proteins (such as enzymes, for example) that will be secreted from the cell, 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. 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.
Key Points
• If the endoplasmic reticulum (ER) has ribosomes attached to it, it is called rough ER; if it does not, then it is called smooth ER.
• The proteins made by the rough endoplasmic reticulum are for use outside of the cell.
• Functions of the smooth endoplasmic reticulum include synthesis of carbohydrates, lipids, and steroid hormones; detoxification of medications and poisons; and storage of calcium ions.
Key Terms
• lumen: The cavity or channel within a tube or tubular organ.
• reticulum: A network
4.13: The Endomembrane System and Proteins - The Golgi Apparatus
Learning Objectives
• Describe the structure of the Golgi apparatus and its role in protein modification and secretion
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.
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.
Key Points
• The Golgi apparatus is a series of flattened sacs that sort and package cellular materials.
• The Golgi apparatus has a cis face on the ER side and a trans face opposite of the ER.
• The trans face secretes the materials into vesicles, which then fuse with the cell membrane for release from the cell.
Key Terms
• vesicle: A membrane-bound compartment found in a cell. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/04%3A_Cell_Structure/4.12%3A_The_Endomembrane_System_and_Proteins_-_The_Endoplasmic_Reticulum.txt |
Learning Objectives
• Describe how lysosomes function as the cell’s waste disposal system
A lysosome has three main functions: the breakdown/digestion of macromolecules (carbohydrates, lipids, proteins, and nucleic acids), cell membrane repairs, and responses against foreign substances such as bacteria, viruses and other antigens. When food is eaten or absorbed by the cell, the lysosome releases its enzymes to break down complex molecules including sugars and proteins into usable energy needed by the cell to survive. If no food is provided, the lysosome’s enzymes digest other organelles within the cell in order to obtain the necessary nutrients.
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.
A lysosome is composed of lipids, which make up the membrane, and proteins, which make up the enzymes within the membrane. Usually, lysosomes are between 0.1 to 1.2μm, but the size varies based on the cell type. The general structure of a lysosome consists of a collection of enzymes surrounded by a single-layer membrane. The membrane is a crucial aspect of its structure because without it the enzymes within the lysosome that are used to breakdown foreign substances would leak out and digest the entire cell, causing it to die.
Lysosomes are found in nearly every animal-like eukaryotic cell. They are so common in animal cells because, when animal cells take in or absorb food, they need the enzymes found in lysosomes in order to digest and use the food for energy. On the other hand, lysosomes are not commonly-found in plant cells. Lysosomes are not needed in plant cells because they have cell walls that are tough enough to keep the large/foreign substances that lysosomes would usually digest out of the cell.
Key Points
• Lysosomes breakdown/digest macromolecules (carbohydrates, lipids, proteins, and nucleic acids), repair cell membranes, and respond against foreign substances such as bacteria, viruses and other antigens.
• Lysosomes contain enzymes that break down the macromolecules and foreign invaders.
• Lysosomes are composed of lipids and proteins, with a single membrane covering the internal enzymes to prevent the lysosome from digesting the cell itself.
• Lysosomes are found in all animal cells, but are rarely found within plant cells due to the tough cell wall surrounding a plant cell that keeps out foreign substances.
Key Terms
• enzyme: a globular protein that catalyses a biological chemical reaction
• lysosome: An organelle found in all types of animal cells which contains a large range of digestive enzymes capable of splitting most biological macromolecules. | textbooks/bio/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/04%3A_Cell_Structure/4.14%3A_The_Endomembrane_System_and_Proteins_-_Lysosomes.txt |
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