Study Guide 2012
Living Organisms Reproduce
The Universe, where Life Began
Evolution: How kinds of life
endure and change
1. Living organisms produce offspring of their own kind. (Why? How?)
2. If a population of organisms produces on average one surviving offspring per parent, the population remains the same size over many generations. If more than one offspring per parent survives to reproduce, then the population increases exponentially.
3. In nature, exponential growth can never continue indefinitely. Growth is slowed by: depletion of essential resources; buildup of toxic wastes or poisons; predation or disease.
Decrease of a population (due to the factors listed in point 3) usually
occurs exponentially. The rate of decrease may be faster or slower than
the previous rate of increase.
5. In nature, most populations grow at a rate balanced by death due to disease, waste buildup, resource limitation etc. There are cycles of growth and decline.
6. Reproductive success is increased by dispersal of organisms, or of their gametes (sperm or eggs). Dispersal can be by environmental elements (wind or water); by the organism’s own motility; or by another organism (a “carrier” or “vector”). Dispersal by a vector can be parasitic (harmful) or mutualistic (mutually beneficial).
1. The chromosomes contain the genetic blueprint for the organism to develop and function. Bacteria have one circular chromosome. Plants and animals have several linear chromosomes in the nucleus of each cell.
2. Chromosomes consist of DNA, a code made up of four letters: A, T, C, G. Every individual contains changes in their sequence of these letters, compared to their parents. These changes result from mutation. Therefore, we are all mutants.
3. Humans, like most multicellular animals and plants, have two copies of each chromosome in each of our body cells: one set from the mother, and one from the father.
4. The rate of human mutation is about 2.5 x 10^-8 per "base pair" (that is, per DNA code letter). The human genome is three billion base pairs in length (for one copy). About how many mutations do you have?
5. Most mutations have no effect (we'll find out why later). Only about three of your mutations are deleterious (that is, have a bad effect; make you less fit for your environment than your parents). About what percentage of mutations are deleterious?
6. Most genes are inherited with NO new mutation. You have a 50% chance of inheriting each gene copy (allele) from your mother, and 50% of inheriting each gene copy fromyour father.
7. Some organisms are hermaphrodites; that is, they have both male
and female sex organs, and can fertilize each other. Others reproduce
asexually; that is, they divide and release new cells (or a portion
of their body) without any sexual recombination.
The Universe, where Life Began (Time Machine) Top
Time is a fourth dimension of space, in which we can only travel forward.
Evolution (Time Machine) Top
1. Living organisms produce offspring that look similar to their parents; but also slightly different.
two populations of the same species are separated (prevented from
interbreeding) they eventually will evolve different frequencies of
traits. If separate long enough, they may become different species,
incapable of interbreeding.
4. When environmental conditions favor production of offspring by individuals with certain inherited traits over individuals with different inherited traits, this is called natural selection.
6. Organisms may be classified based on genetic relatedness, or the time since two species diverged from a common ancestor.
8. Traits that confer advantage in natural selection always confer disadvantage as well. If advantage outweighs disadvantage, then the trait will increase in future generations.
10. Environments change, either from external causes, or because the organism changes its own environment.
11. When the environment changes, previously selected traits become deleterious. Many species go extinct. Other species increase in prominence, as the new conditions favor their traits. But in the short term, more species are lost than gained, and diversity decreases.
12. Environmental stability favors evolution of many diverse species occupying specialized niches. Diversity increases.
13. As species diverge through evolution, one species may occupy a niche that an unrelated organism occupies in a distant location. The two species may evolve superficially similar adaptations; hence the term convergent evolution. But despite the apparent similarity, the two species never merge or interbreed.
2. If the two parental copies of a gene differ in function, the function of one copy may mask the function of another. The copy (or "allele") whose function is expressed is said to be dominant. The masked allele is recessive. Often a recessive allele is simply a non-functional copy.
4. In humans, two X chromosomes makes a female; XY makes a male. The Y chromosome actually has degenerated through evolution, and now carries very few genes. Thus for males, most of the genes on the X chromosome (for example, red/green color vision) are inherited only from the mother.
The Biosphere (Dune) Top
1. Life on earth may be considered on various levels of scale. Individual organisms form populations of particular species. Populations of different species participate in ecosystems. All ecosystems are linked within the planetary biosphere.
2. For life to exist in a biosphere, a planet needs sufficient gravity to hold essential gases in its atmosphere, such as oxygen (O2), water (H2O), and nitrogen (N2).
3. The average temperature and atmospheric pressure must be high enough (but not too high) to permit existence of liquid water.
4. Water dissolves in the atmosphere as water vapor. As the air cools, the saturation limit decreases. If the saturation limit decreases below the level of water vapor, the water condenses as fog, dew, or rain.
"Relative humidity is the ratio of the current absolute humidity to the highest possible absolute humidity (which depends on the current air temperature). A reading of 100 percent relative humidity means that the air is totally saturated with water vapor and cannot hold any more, creating the possibility of rain. This doesn't mean that the relative humidity must be 100 percent in order for it to rain -- it must be 100 percent where the clouds are forming, but the relative humidity near the ground could be much less." (from Howstuffworks)
6. The initial outgassing (release of gases by volcanoes) of an Earth-sized planet produces an atmosphere composed mainly of carbon dioxide (CO2).
7. Photosynthesis by microbes (and later by plants) produced all the oxygen in Earth’s atmosphere, and fixed most of the carbon dioxide as complex organic components of living organisms. Other kinds of microbes produce nitrogen gass (N2) and "fix" nitrogen into forms that plants and animals can use.
Energetics in Ecology (Dune) Top
1. Overall, energy cannot be created or destroyed. Energy can be transformed among different forms: electromagnetic radiation, chemical bonds, mechanical movement. (Nuclear reactions can transform mass into energy; this happens only within stars and within nuclear reactors, NOT within pre-human ecosystems.)
2. As energy is transformed, a certain portion always escapes as heat, and therefore unavailable for any future living organism. Thus, energy cannot be recycled. Energy does pass between organisms along the food chain, but ultimately all energy is lost as heat radiated off the planet.
3. Primary producers build CO2 into complex biological molecules. They require a constant supply of (1) light energy for photosynthesis (most ecosystems) or (2) reduced minerals for lithotrophy, upwelling from volcanoes (small ecosystems, very limited contribution to biosphere.)
4. Consumers eat producers or other consumers, using respiration (combining with oxygen, or oxidized minerals) or fermentation (food breakdown without oxidation).
5. Natural selection favors survival of those organisms who use energy most efficiently, dissipating the least waste heat while producing the most offspring. For example, photosynthesis and respiration both are processes that transform 95% of the chemical energy theoretically available for cellular processes.
6. Despite strong selection for efficiency, about 90% of available energy is lost by every consumer up the food chain. That is why eating meat is more "expensive" ecologically than eating vegetables.
Material Cycles in Ecology (Dune) Top
1. Water is an essential part of every ecosystem. All habitats, from ocean to desert, include some water that evaporates into the atmosphere, driven by solar energy (heat). Evaporation of water is the first part of the hydrological cycle.
2. When changes in atmospheric temperature and pressure decrease its physical ability to hold water, the water vapor condenses as clouds, which ultimately precipitate as rain. On the oceans, more water evaporates than falls as rain. On dry land, the reverse is true. Rainwater returns to the ocean through rivers and wetlands, an exceptionally productive habitat for life.
3. One source of rainfall is that air currents reach mountains and rise, cooling, so that the water condenses, forming clouds and rain. As the air current continues across the mountain, it is dry and tends to dry out the land below; this region is likely to be a desert. Deserts can also exist in regions where winds from the equator descend, warming and picking up moisture (about 30o north and south of the equator.)
4. Below land, water exists in underground lakes called aquifers. Many aquifers in the United States are being pumped out by humans faster than rain refills them. Water from aquifers always contains trace salts; these tend to build up during irrigation of crop lands (salinization). Aquifers can be contaminated permanently by industrial or agricultural pollution.
5. Carbon cycles between CO2 in the atmosphere, the body parts of plants and animals, and carbonates in the oceans. Human industrial pollution has produced more CO2 than plants can assimilate, resulting in increased retention of heat by our atmosphere; this is called the greenhouse effect.
6. Decomposers are needed to decrease buildup of dead plant and animal bodies and recycle their minerals in the ecosystem. In some ecosystems, fire plays the role of decomposer.
(Door into Ocean) Top
8. Animals breathe by exchanging CO2 in their lungs for O2. The CO2 in the blood combines with water (H2O) to form carbonic acid: H2CO3 . H2CO3 serves as an important pH buffer:
+ HCO3- <-> 2H+
Sex and Reproduction (Door into Ocean) Top
1. The chromosomes contain the genetic blueprint for the organism to develop and function. Bacteria have one circular chromosome. Plants and animals have several linear chromosomes in the nucleus of each cell. Most multicellular organisms have two copies of each chromosome, one from the mother and one from the father.
Sex determination occurs differently in different species
-- Egg incubation temperature determines sex (alligators).
-- Two X chromosomes makes a female; XY makes a male (in mammals). The Y chromosome actually has degenerated through evolution, and now carries very few genes. Thus for males, most of the genes on the X chromosome (for example, red/green color vision) are inherited only from the mother.
-- Two Z chromosomes makes a male; WZ makes a female (in birds).
-- Males arise from non-fertilized eggs, inheriting all genes from the mother (in bees, ants, termites). Only one female (queen) passes on genes; other females are workers. Males (drones) are discarded after sex.
-- Young individuals are female, but mature into males (some fish species).
Young individuals are male, but mature into females. Females recruit
young males (clown fish).
4. The cytoplasm of sperm develops into a specialized structure for swimming and delivery. It contributes no cytoplasm to the offspring. The egg, however, provides greatly expanded cytoplasm, including RNA expressed from maternal-effect genes. The egg also contributes mitochondria, which use oxygen to metabolize food for the cell.
5. Mitochondria have their own circular chromosomes, with a small number of genes. Genetic traits carried on the mitochondrial chromosome—including some defects leading to disease—are passed on only by mothers, to all of the mother=s children.
6. In some species (fish, amphibians, reptiles, insects) the egg can maintain two copies of its chromosomes and produce offspring without sperm (parthenogenesis). This does not work in humans, because of "imprinting".
7. In humans, nuclear chromosomes carry many molecular modifications, such as methyl groups. The sperm and egg carry different patterns of modifications. This is called imprinting. Both male and female patterns of imprinting are needed for the fertilized egg to develop successfully as an embryo.
8. Fertilization can be performed "in the test tube" (in vitro) to make a "test-tube baby." This in vitro fertilization (IVF) is routine today, though expensive and it doesn't always work.
9. Traits that originated for sex have evolved non-reproductive functions that enhance survival, such as social cooperation and conflict reduction. These functions enhance survival, especially in birds and mammals. A common example is the sexual pairing of two male birds to provide enough food for a female to lay eggs. Another common example in apes is sexual contact between males, or between females, to prevent fighting.
Population Interactions (Avatar and Door into Ocean) Top
1. A species evolves to fill a certain niche in the ecosystem. The niche is defined by habitat, choice of food, and other environmental needs. Usually two species in an ecosystem cannot occupy exactly the same niche, although they may compete for aspects of it.
2. If one species of organism exists, chances are that related species exist in the ecosystem. The species must have evolved to occupy slightly (or extremely) different niches.
3. Other species in the ecosystem (not related genetically) form part of the habitat of any given species. Change in the population size of Species A may cause change in the population size of Species B. A "ripple" effect can occur throughout the ecosystem, with results hard to predict.
4. About 90% of available energy is lost by every consumer up the food chain. That is why eating meat is more "expensive" ecologically than eating vegetables. In any ecosystem, the "biomass" of organisms will be lower on the higher (consumer) levels of the food chain.
5. Because producers and consumers evolve simultaneously (coevolution) it turns out that consumers can actually have beneficial effects on the producers they consume; not "on purpose," but simply because the producer has adapted to an environment that includes the consumer.
6. Parasitism is an interaction between two species in which Species A (parasite) benefits at the expense of Species B (host) without immediately killing the host. The host may die eventually as a result of negative effects.
7. A commensal enjoys benefits from a host, while neither harming nor benefiting the host. Commensals are usually more common than parasites, and possibly more highly evolved, because they best maintain a high-quality habitat (a healthy host.)
8. Cooperation may occur between two species who provide things for each other that neither could obtain as effectively on its own. Some species may cooperate or cheat, depending on the environmental conditions.
9. A highly intimate, necessary association between two species is called mutualism or symbiosis. When one partner actually lives inside the other, this is called endosymbiosis.
10. Within a species, individuals may cooperate as a group in order to compete successfully against other groups, if the net result is increased reproduction of genes for all group members.
11. Individuals always share some degree of genetic inheritance. Two siblings inherit 50% of the same genes. Two cousins inherit 25% of the same genes.
12. Altruism occurs only when an organism can increase propagation of its own genes by sacrificing itself or its resources for another organism. (This is still a controversial theory, especially its application to humans.)
13. Some individuals reproduce their genes by helping relatives instead of (or in addition to) producing their own offspring. This is known as kin selection. How organisms "know" who their relatives are is a fascinating question in behavioral biology.
selection may operate among humans; this question is studied by anthropologists.
Some scientists believe that "cultural evolution" takes precedence
over genetic evolution; that human behaviors tend to propagate reproduction
of cultural processes and beliefs, rather than (or in addition to)
Genes and Cloning (Jurassic Park) Top
1. DNA is composed of nucleotides with bases: Adenine, Thymine, Cytosine, and Guanine. All genetic information is encoded in pairs of complementary nucleotide bases: A-T, T-A, C-G, G-C. The ladder of base pairs is twisted into a helix. The DNA molecule replicates itself by "unzipping"down the middle, while each strand progressively fills in its new complementary strand. This process is performed by polymerase enzymes.
2. The replication of DNA is extraordinarily accurate; less than one mistake in a billion base pairs. But over a large number of base pairs, and many generations, errors (mutations) are bound to occur. Mutations are increased by mutagens, such as oxidative reactions or ultraviolet light absorption.
3. On average, the mutation rate for most species is constant over time. Therefore, one can measure the time of evolution by counting the number of base-pair differences between the genes of two species. These data tell us, for example, that humans diverged from gorillas more recently than we diverged from organgutans. If we had enough dinosaur DNA, we could tell whether in fact dinosaurs diverged from birds more recently than from reptiles.
4. We can purify DNA from unknown samples, and a polymerase enzyme from a standard source (a thermophilic bacterium is used, whose polymerase can withstand boiling temperature). The polymerase can perform cycles of unzipping DNA and replicating it. This process is called polymerase chain reaction (PCR). It can amplify tiny traces of DNA a million-fold.
5. The pieces of amplified DNA are very short (100-1,000 base pairs). A vertebrate chromosome may contain billions of base pairs. Thus, to reconstruct an entire chromosome of an extinct organism would require "piecing together" many short overlapping sequences.
6. Genes and chromosomes evolved along with the organisms in which they reside. Many genes have duplicated themselves within the organism; then the duplicates evolved into distinct functions. Members of these gene families still contain sequences that are very similar. This poses problems when trying to place overlapping segments accurately.
11. Some naturally occuring viruses contain DNA that can be spliced into the chromosome of a host cell, by enzymes that the virus encodes and expresses. A plasmid is a circular loop of DNA that needs a host cell to replicate (like viruses) but does not destroy the host. Some plasmids can splice DNA into a host chromosome.
In the laboratory, we can create an artificial splicing reaction using
enzymes purified from bacteria, and DNA purified from any source. Pieces
of DNA from anywhere, including a human, can be spliced into a plasmid
or a viral chromosome. This is popularly called "recombinant DNA."
11. DNA spliced into a vector (plasmid or viral chromosome) can be put into a host cell, where it replicates and is expressed as part of the host. This is called genetic engineering.
Cloning a Dinosaur
12. To clone a dinosaur would require: purifying DNA; amplifying all the sequences and piecing into chromosomes; putting all the chromosomes into the nucleus of an egg of a closely related species; precise development of the egg into a dinosaur.
13. Development is a program in which a three-dimensional collection of cells shapes itself over time. Each step of the program requires control by specific genes and proteins. One mistake can lead to malformation or death of the embryo.
14. When the egg forms, in most cases a number of genes are transcribed to RNA before fertilization. These RNA copies in the cytoplasm give the developing egg a "jump start" before the nuclear genes are expressed. Therefore, the egg cytoplasm contains genetic information from the mother. The genes involved are called maternal effect genes.
15. Correct development of an embryo requires precise regulation and timing of gene expression. The regulation of gene expression is tremendously subtle. A small sequence of base pairs to one side of a gene will bind to a specific regulatory protein, which recognizes the precise shape of the cleft of DNA helix at that particular sequence. If one or two base pairs are changed (mutated), the embryo will fail to develop properly.
Genes Make Products (Jurassic Park) Top
1. DNA information can be copied into RNA, a disposable copy of the "permanent" information in DNA. Some RNA molecules perform tasks of their own in the cell. But most RNA molecules are messenger RNA, each of which directs ribosomes to make a particular protein.
The sequence of information in the DNA constitutes genes. Each
gene specifies one functional product. Each
protein, determined by a particular gene, has a particular function
in the cell; for instance hemoglobin carries oxygen.
The two different copies of a gene provided by the two different parents
can differ slightly in information. These slight differences
arise rarely, from mutation of the DNA sequence; but once they occur,
they are inherited indefinitely by Mendelian rules.
4. After a messenger RNA molecule is transcribed from DNA, its sequence of bases (A, C, G, U—uracil replacing thymine) is translated by ribosomes into protein code: three DNA bases per amino acid of the protein. There are twenty essential amino acids.
5. Each kind of amino acid has to be synthesized within the cells of the organism, or consumed in food. Amino acids are synthesized by specific enzymes, encoded by specific genes. If a strain of organism is mutant for a enzyme needed to make an amino acid, it must consume food containing the amino acid. This kind of strain is called an auxotroph.
Genetic engineering can be used to construct bacteria that will make
a valuable product, such as human growth hormone or insulin. The protein
product is then applied as a medical therapy.
Genetic engineering can be used to splice a DNA gene directly into a
chromosome of a host, such as in human body cells. A functional gene
copy may replace a non-functional copy, curing a defect. This is somatic
gene surgery or gene therapy.
8. If a gene were to be spliced directly into the sex cells of a host, and "cure" the defect in the eggs or sperm, the transmission of the "defective" gene to future generations would be prevented. This is called germ-line gene surgery.
1. Most microbes do not interact with humans. However, some species have evolved to live in a human host.
2. Microbes adapted to a different species may behave very differently in humans, because of differences in the molecular environment. For example, viruses that are harmless in monkeys may kill a human. The HIV virus evolved from a harmless virus in apes.
3. A virulent microbe (pathogen) has evolved a strategy of maximizing (1) production of offspring at the expense of the host, (2) rate of transmission to a new host.
4. A beneficial microbe (commensal flora or probiotic) balances its production of offspring with benefits to the host, in order to prolong a high-quality host environment. Since hosts are mortal, transmission to new hosts is still needed.
5. Conditions that limit transmission and enhance host survival select for evolution of beneficial or less-harmful microbes.
6. Conditions that favor transmission and decrease host survival
select for evolution of virulent microbes.
Neuroscience and AI (Brain Plague) Top
1. All sensory pathways involve adaptation to the stimulus level. The more the stimulus is applied, the greater the level needed for the next effect. This applies to the five senses, as well to pleasure-reward pathways.
2. Sensation and perception are mediated by the brain. Neuroscientists are figuring out the molecular basis of brain perception. Direct brain stimulation, and direct "mental" effects of the brain on the outside world, can be achieved through technology.
3. Some designers of computer software are now following logic analogous to "artificial selection" to develop new kinds of software. Programs are "mutated" in various ways, then allowed to run, and the "most fit" programs are selected for further mutation.
4. New computer structures are being designed to mimic biological processes, replacing "yes-or-no" logic with probabilistic circuits that allow the potential for "mistakes;" the circuit then "learns" from its mistakes. Such a circuit, called a neural net, achieves only approximate solutions to problems, but may come up with unexpectedly creative results.
5. Will computers eventually be built with so many connections that they "wake up" as self-aware or sentient? The answer is unknown, but two different arguments are made:
-- Computers will soon have more connections than the number of neurons in the human brain. Already, we have computers that approach the behavioral complexity of an insect. Achieving self-awareness is just a matter of time.
-- Neuroscience is discovering much greater levels of complexity in the brain than we were aware of. A much larger computer system may actually be needed to approach human complexity. Self-awareness may require types of training that we do not yet understand.