Final Content Review

Editor's Notes

• #3: The Lytic Cycle (to break or lyse—host cell is killed shortly after cycle begins)The phage lands on the bacteria and injects DNA into it. The phage has a way to break down the DNA of the host cell; they replicate, translate, and transcribe genetic information and make copies of the phage genome and direct production of phage proteins phage particles are formed and released. (replication occurs until the cell lyses)Virulent phage: lands on bacteria; injects DNA into bacteria. Virus copies its DNA and makes it coat. When bacteria replicates enough, it lyses to release baby viruses.
• #4: The Lysogenic Cycle ( do not immediately lyse the cell)The phage comes and injects the DNA into the cell. DNA is put into the circular DNA of the cell but is not active. Each time the bacterial DNA replicates, the viral DNA is replicatedthis way, all new cells that come from bacteria dividing (binary fission) will have the virus. The virus can be awakened and go into the lytic cycle. ----still don’t know what makes it awaken: like virus that randomly causes cancer and cats and like herpes (outbreaks happen when virus becomes active but you can never get rid of it because it is in your DNA)Temperate phage: (use both modes of reproducing) virus comes and injects DNA and incorporates itself into the bacterial chromosomes (incorporated by crossing over into a specific site on the host cell’s chromosome), not making baby viruses; every time the bacteria replicates, all cells will have virus.
• #5: B. Stabilizing selection
• #6: All viruses have nucleic acid (can have DNA or RNA as genetic material [viral genomes can be either DNA or RNA]) They also have a protein coat made of capsids; capsids are built from a large number of protein subunits called capsomeres. Viral envelopes are derived from the membrane of the host cell.Despite these structural characteristics, all viruses appear different. Viral genes make virus proteins in the ERmembrane, leave cell, or become incorporated into the cell. Most viruses are host specifice.g. may infect humans but not cats. Other viruses are more widespreade.g. rabies or swine flu
• #7: Study of nature to reveal God’s plan
• #9: Mass ExtinctionsA species may become extinct for many reasons: habitat is destroyed, environment may change in an unfavorable direction, or ocean temperatures may fall be a few degrees and species that are well adapted will perish. Stable, biological factors can also change: if more than one species lives in an environment, an evolutionary change in one species is likely to impact others.Adaptive radiation: the emergence of numerous species from a common ancestor introduced into an environment that presents a diversity of new opportunities and challenges. This typically occurs when a few organisms make their way to new, often distant areas or when environmental changes cause numerous extinctions, opening up ecological niches for the survivors. Example: the fossil evidence indicates that mammals underwent a dramatic adaptive radiation after the mass extinctions of dinosaurs 65 million years ago.
• #10: RNADNARNA; viral reverse transcriptase; host RNA polymerase
• #11: C. translocation
• #12: By injecting their DNA into the cell (recall—bacteriophages infect bacteria by injecting DNA into the bacteria)By binding to cells and tricking the cells into taking them in by endocytosis.
• #13: A deme is local population of organisms of one species that actively interbreed with one another and share a distinct gene pool. If there is a species of catfish that lives in AL, then to study it one would find a local population in a pond. These catfish would be morel like each other than when compared to a population in another pond. This is because there is no gene flow between the two ponds. Demes can changeexample: a canal forms between two ponds and all of a sudden we have gene flow between the two ponds. Intraspecific variation: there is variation in the deme itselfInterspecific variation: the deme differs from other populations
• #14: Cuvier was the Father of Paleontology (studied fossils)Fossils are remains or traces of organisms from the past; most fossils are found in sedimentary rocks formed from the sand and mud that settle to the bottom of seas, lakes, and marshes. New layers of sediment cover older ones and compress them into superimposed layers of rock called strata. Fossils in each layer provide a glimpse of some of the organisms that populated Earth at the time that layer formed. this supports evolution. Catastrophism: theory that speculates that each boundary between strata represents a catastrophe, such as a flood or a drought, that destroyed many of the species living at that time.
• #15: A. p2
• #16: Evolution is limited by historical constraints. Each species has a legacy of descent with modification from a long line of ancestral forms---they get what is passed on to them.Adaptations are often compromises. A seal spends part of its time on the rocks; it could probably walk better if it had legs instead of flippers, but then it would not swim nearly as well.Chance and natural selection interact: not all evolution is adaptive because chance plays a role. For example, when a storm blows insects or birds over an ocean to an island, the wind does not necessarily transport the species, or the members of a species, that are best suited to the new environment. Selection can only edit variations that exist, which may not be the ideal traits (do not get new genes on demand).
• #17: Hutton proposed gradualism (gradual geological change). These changes in rock are not due to catastrophes, but are due to natural processes occurring on the earth.
• #18: One theory: Alvarez found a band of uridium on Earth (an extraterrestrial element rarely found on Earth) that separates sediments form the Mesozoic and Cenozoic eras. Alvarez and his colleagues proposed that this uridium is a fallout from a huge cloud of debris that billowed into the atmosphere when an asteroid or large comet collided with Earth. This cloud would have blocked sunlight and severely disturbed the global climate for several monthsaffecting plant growth, temperature, etc. This was speculated to have happened near the Yucatan peninsula. Other theory: A spike in volcanic activity took place at the time of the Cretaceous mass extinction; this could have spewed lava and ash into the atmosphere and the eruptions may have produced enough carbon dioxide to warm the global climate. Reduced temperature differences between the equator and the poles would have slowed the mixing of ocean water, which would have reduced the amount of oxygen available to marine animals. So, an oxygen deficit in the oceans may have played a role in extinction. (it is also speculated that this spike in volcanic activity was caused by the asteroid/comet that is believed to have hit Earth)
• #19: 250 million years ago (near end of Paleozoic era)plate movements brought all the previously separated landmasses together into a supercontinent that has been named Pangaea (“all land”)tremendous environmental impact that reshaped biological diversity by causing extinctions and providing new opportunities for taxonomic groups that survived the crises. Then they continents drifted apart and each became a separate evolutionary arena with lineages of plants and animals that diverged from those on other continents. This explains why animals in completely opposite parts of the world are somewhat similar, but still significantly different. Pangaea splitLaurasia (north) and Gondwana (south). Australia separated early ononly place in the world where marsupials are so prominent. Marsupials dominate Australia but they cannot compete with placental mammals. The land masses continued to separate; much later: the Himalayas formed when India collided with Eurasia.
• #20: C. Transduction
• #21: Allometric growth: variation in the relative rates of growth of various parts of the body, which helps shape the organism. In humans: the arms and legs lengthen more during growth than the head and trunk. When comparing chimps and humans: the human head grows to accommodate the brain but the chimp’s jaw grows as well as huge brow muscles, leaving the top of the head to be very small.
• #22: Post reduced hybrid fertility
• #23: Lyell (geologist) incorporated Hutton’s idea into uniformitarianism: natural processes that are going on occur in very uniform ways (e.g. erosion, glaciers, etc); these processes have been going on for years and are still going on. Lyell thought such process takes 1000s of years, so the Earth must be VERY old.
• #24: Two main modes of speciation: Allopatric speciation: A population forms a new species while geographically isolated from its parent population. Allopatric means “other homeland.” So we have a pond (deme) and have divided the pond and now have 2 ponds—like founder effect: immediately have different genes in two different ponds. The environment is also different: one pond may have more vegetation around it while the other may be polluted with waste due to a nearby pig farm. Mutations in each pond could be different and adaptation may occur; then the population would be sorted by natural selection. This is divergent speciation/evolution: started out with the same population but it split and then become less and less like each other until they are 2 completely different species. Convergent evolution, on the other hand happens when two species are initially different but start to look like they are coming to be more and more similar. What separates the two populations?A barrier: any physical or ecological feature that prevents a species from moving across it. An example would be a landbridge, water (if you live on land and cannot cross), mountains, canyons (Grand Canyon). The two biggest barriers are oceans and glaciers. These are all extrinsic factors: outside factors that have nothing to do with a species and cause it to be separated from the population. ****SUMMARY: splitdifferent genesdifferent environmentdifferent mutationsdifferent recombination of genesdifferent selection pressuresWe know they are different because they will not breed with one another. Sympatric speciation: A small population becomes a new species with geographic separation—the original pond does not get separated, something happens in the deme. Something happens in the creatures themselveshappens through the genes. So, sympatric speciation is intrinsic—something inside the individuals. This happens through two modes:Autoploidy (much more often in plants than in animals) is when cell division results in more than two chromosome sets, all derived from a single species. For example, a failure of cell division can double a cell’s chromosome number from the diploid number (2n) to the tetraploid number (4n). This happens in nondisjunction happens in all cell. If, with this, the creature has an advantage: the (4n) will stay. This mutation prevents a tetraploid from successfully interbreeding with diploid plants of the original population; if they are viable and fertilea new biological species (plants can do this because they can self-fertilize). An example of this is the huge flowers that smell good and come in brilliant colors at the botanical gardens. Allopolyploidy: (much more common) When two different species interbreed and produce sterile hybrids, these hybrids can change in subsequent generations by various mechanisms into a fertile polyploidy known as an allopolyploid. You will have species A with diploid #4 and species B with diploid #6----with allopolypoloidy, diploid # is always double, so this is how you know if it is autoploidy or allopolyploidy.
• #25: D. transformation
• #26: Post reduced hybrid viability
• #27: Aristotle: plants and animals are like a laddereach group is better and more complex than the group on the rung before; Species are fixed—don’t change. Linnaeus (1700s): he came up with the binomial system of naming (“bi”=two names). The binomial system made use of the genus and species (Genus is always capitalized, species is lowercase=both are italicized). He started naming and grouping creatures based on certain characteristics. He also believed that these species were fixed and didn’t change.
• #28: The Niche Rule (aka Competitive Exclusion Principle): No two species can occupy the same niche at the same time. A niche is the animal’s role in the community.If 2 species try to compete for resources in a niche, there are 3 outcomes:Extinction: one species is better at doing X than the other one, resulting in the dying out of the “lesser” species. One species leaves and tries another place.Character displacement: the tendency of closely related sympatric species to diverge rapidly in characteristics that reduce the chance of hybridization and/or minimize the competition between them
• #29: Two models for the tempo of speciation:Gradualism model: Species descend from a common ancestor gradually diverge more and more in their morphology as they acquire unique adaptations. Punctuated equilibrium model: (Elredge and Gould) A new species changes most as it buds from a parent species and then changes little for the rest of its existence. (go along and all is the same for a while and then the environment suddenly changesadaptation occurs in a relatively short period of time…and then this process continues) Most allopatric speciation events are geologically instantaneous: they are the results of crisis that punctuates long periods of equilibrium in which the morphology of the species stays the same. They considered gradualism, but thought that this model best supported the fossil records (as there are no “transition” fossils)
• #30: D. Lysogenic phase
• #31: Mutations ( in nonsexual populations this is the only way---raw material of evolution)Gene flowGenetic recombination (coming together of different genes; very important in humans as it is involved in independent assortment of genes during meiosis)
• #32: Genetic drift (“neutral selection”) has only to do with chance—it is random. This refers to unpredictable fluctuations in allele frequencies from one generation to the next because of a population’s finite size. With chance, something happens to the genes----only happens in small populations.The Founder Effect: When a few individuals become isolated from a larger population and this smaller group may establish a new population whose genes pool is not reflective of the source population; the genes of the original population are still in existence. The Bottleneck Effect: When there is a sudden change in the environment (fire, flood, etc) that drastically reduces the size of the population and survivors have passed through a restrictive “bottleneck;” their gene pool may no longer be reflective of the original population’s gene pool. Not all genes survive since a catastrophe hits and wipes out certain creatures. Natural selectionis when genes are exposed and the environment looks at them and decides which genes constitute the best combinations. The environment must see the genesthey must be phenotypically expressed. Somatic mutations (in body cells, not gametes) refer to phenotypic variation that is not the result of genotypic variation---this is not the raw material of evolution. For example, an individual could have an accident and lose a limb or even cut his/her her----all of this is not passed on to the offspring.
• #33: Diploid state: because most eukaryotes are diploid, a considerable amount of genetic variation is hidden from selection in the form of recessive alleles—recessive genes can hide and diversity is maintained Balanced selection/polymorphism: when natural selection maintains stable frequencies of two or more phenotypic forms in a population. This includes heterozygote superiority.Heterozygote superiority: if individuals who are heterozygous at a particular gene locus have greater fitness than the homozygotes; an example of this is that those who are heterozygous for sickle-cell anemia are protected against malaria.Neutral selection: this is when genetic variation in populations has little or no impact on reproductive success and, thus, natural selection does not affect these alleles.
• #34: Pre behavioral isolation
• #35: B. mutation
• #36: Autoploidy (much more often in plants than in animals) is when cell division results in more than two chromosome sets, all derived from a single species. For example, a failure of cell division can double a cell’s chromosome number from the diploid number (2n) to the tetraploid number (4n). This happens in nondisjunction happens in all cell. If, with this, the creature has an advantage: the (4n) will stay. This mutation prevents a tetraploid from successfully interbreeding with diploid plants of the original population; if they are viable and fertilea new biological species (plants can do this because they can self-fertilize). An example of this is the huge flowers that smell good and come in brilliant colors at the botanical gardens. Allopolyploidy: (much more common) When two different species interbreed and produce sterile hybrids, these hybrids can change in subsequent generations by various mechanisms into a fertile polyploidy known as an allopolyploid. You will have species A with diploid #4 and species B with diploid #6----with allopolypoloidy, diploid # is always double, so this is how you know if it is autoploidy or allopolyploidy.
• #37: Hardy-Weinberg Equilibrium: the condition describing a non-evolving population. p + q = 1--------------------allelic frequencyp2 + 2pq + q2 = 1----------genotypic frequency p2 = homozygous dominant stateq2 = homozygous recessive state2pq =heterozygous state
• #38: Continental Drift: refers to the fact that Earth’s continents are not fixed; they drift across our planet’s surface on great plates of crust that float on the hot, underlying mantle. Plate movements rearrange geography slowly, but their cumulative effects are dramatic—they move 2.5 cm/year.
• #39: B. Random mating
• #40: Directional selection: a population’s environment changes drastically or members of a population migrate to a new habituate with different environmental conditions than their former oneshifts frequency curve for some phenotypic character in one direction or he other by favoring individuals that deviate from the average. (the mice on the darker end)Disruptive selection: occurs when conditions favor individuals on both extremes of a phenotypic range over individuals with intermediate phenotypes (favors variants at both ends—very light and very dark fur)Stabilizing selection: acts against extreme phenotypes and favors intermediate variants. This mode of selection reduces variation and maintains the status quo for a particular phenotypic character. (favors the mice with medium-colored fur)
• #41: Pre temporal isolation
• #42: B. Spontaneous mutation must occur to introduce a new allele into the gene pool. When only 1 allele is present in a population, genetic drift cannot alter the allele frequency because it has no place to drift to.
• #43: The habitat is where an individual lives (e.g. forest, pasture, etc). Environmental conditions follow patterns: it is colder in the North than in the South, all of our rains come from Mississippi, etc. There are characteristics within a species that can change with something like altitude---this is geographic variation. Example: yarrow plants get smaller in height as you go up in altitude: they are taller at lower altitudes and shorter at higher altitudes. This is called a cline: a gradual change of a character or feature (phenotype) in a species over a geographical area. 2 biological rules:Bergmann’s rule: The average body size of an individual increases with colder climates (creatures that are similar species get bigger in colder climates). An example is the bears: Tennessee bears are pretty small and vicious but grizzly bears in Montana and, even more so, polar bears in the Arctic are HUGE. Polar bears get bigger to keep warm---surface area in relation to volume, as being bigger helps you overcome heat). Allen’s Rule: The extremities of an animal (tail, ears, length of limbs) decrease when it gets colder.
• #44: A species is a genetically distinctive group of natural populations that share a common gene pool and are reproductively isolated from other such groups. The idea of the “natural population” is important because a horse and a donkey may mate inside a zoo but not in nature.“Gene pool” signifies all genes a population may have and all the different alleles they may have. The “reproductive isolation” refers to the fact that species will mate with each other but not with other species----two animals are of the same species if they produce viable, fertile offspring. A species is the largest unit within a population within which effective gene flow occurs or can occur.
• #45: Comparativeembryology: the comparison of early stages of animal development---reveals additional anatomical homologies not visible in adult organisms. Example: at some point in their development, all vertebrate embryos have a tail posterior to the anus. This is because, with evolution, it is a lot easier to modify things than to start all over againthe “tail” is killed off during development rather than starting from scratch to create an organism without a tail.
• #46: Conditions for Hardy-Weinberg Equilibrium:No mutationsNo gene flowNo natural selectionRandom matingExtremely large population sizeIf one of these conditions is not met, then microevolution occurs (microevolution: evolutionary change on its smallest scale—on the species level)
• #47: Post hybrid breakdown
• #48: HIV (human immunodeficiency viruscauses AIDS (acquired immunodeficiency syndrome); HIV is an RNA virusThis virus is equipped with a special enzyme called reversetranscriptase (this is what makes a retrovirus so different) The HIV virus gets into the cell and releases reverse transcriptasethe reverse transcriptase makes new viral DNA from viral RNA and this DNA is stuck in your original DNA (genome). Every time your DNA is copied, the newly made viral DNA is also copied. The integrated viral DNA, called a provirus, never leaves the host’s genome and remains a permanent resident of the cell. When you get AIDS, this DNA is awakened and the DNA then gets into the helper T cells and starts shutting down the immune system.
• #49: Lamarck’s Theory of EvolutionLamarck published his ideas in 1809. He said that organisms acquire characteristics as environments changewith this, phenotype determines genotype (this is not true because genotype controls phenotype). With his model (both of which are good/true):Things changeAdaptation is very important.EX: Giraffes may have had necks of different lengths but in times when there was little food, only a few could reach the food on the trees and survive to reproduce. The ones that had long necks and thus more food reproduced and gave way to giraffes with longer necks. The other giraffes with shorter necks died because they could get to food.
• #50: Coevolution is the mutual evolutionary influence between two different species interacting with each other and reciprocally influencing each other’s adaptations. Example: a hummingbird and the tubular flowers with which it interacts coevolve because they reciprocally influence each other’s adaptations.
• #51: Preadaptation: something evolved for one organism was changed for another organism; something simplistic has modifications to become more advanced for another animal. Structures that evolve in one context but become co-opted for another function are sometimes called exaptations to distinguish them from the adaptive origin of the original structure. Example: the honeycombed bones of bird are homologous to the bones of birds’ earthbound ancestors. Long ago, small, fast dinosaurs with lightweight bonesreptiles with lightweight bonesbirds with lightweight bones…can fly easily.
• #52: Prions are infectious proteins. (prion diseases=neurodegenerative diseases)Scrapie: in ship—the skin itches so badly that they peel their skin off; can’t walk.Kuru: in population of humans—mothers and children contracted this, but not the adult males. This was because the general practice of a culture as eating the brains of the dead as a way to preserve their souls. The women and children were contracting this by eating bits of the brain. They couldn’t walk either. Creutzfeldt-Jakobdisease: very rareMadcowdisease: spongiform encephalopathy; humans get this by eating hamburgers that are not cooked well. The scrapie virus was transmitted to the cow because cows were given ground up sheep insides to eat. In prion diseases, the protein is not replicating: the protein does not copy itself over and over again but, rather, changes the proteins that are already there. Prions are misfolded versions of normal brain proteins. When a prion contacts a normal “twin,” it may induce the normal protein to assume the abnormal shape. The resulting chain reaction may continue until prions accumulate in aggregates to dangerous levels, causing cellular malfunction and eventual degeneration of the brain.
• #53: Heterochrony: an evolutionary change in the rate or timing of developmental events. Example: an organism’s shape depends on the relative growth rates of different body parts during development---in salamanders (ground-dwelling versus tree-dwelling), foot growth in tree-dwelling salamanders ends sooner and leaves them with short, more webbed digits that enable it to climb tree branches. The difference in webbing between the two salamanders is due to programmed cell death during development: the skin cells between the digits die and are cut out. Heterochronoy can also alter the timing of reproductive development relative to the development of somatic organs. If reproductive development accelerates compared to somatic development, the sexually mature state of a species may retain body features that were juvenile structures in an ancestral species---this is paedomorphosis (“baby shape”). This is seen in humans: humans keep juvenile characteristics, such as the “baby” head, but acquire the ability to reproduce.
• #54: The Origin of Species: plants and animals change gradually (idea of gradualism) over time due to natural selection. Descent with Modification (all organisms are related through descent form an ancestor that lived in the remote past; for Darwin, this had two parts)Species haven’t always been as they are now, but have evolved from ancestral species.This happens through the process of natural selection (differential reproduction in nature leading to an increase in the frequency of some genes or gene combinations and a decrease in others), so one of the reasons that species have this going on is adaptation.
• #55: A. 2 cm
• #56: C greater than 2 cm AND less than 2 cm
• #57: B. Greater than 2 cm OR less than 2 cm
• #58: E. Heterozygotes
• #59: Homologous structures are structures that have similarities in function that come from a common ancestor. Example: Whales use their forelimbs to swim while bats use them to fly.Analogous structures have the same function but different origins—did not arise due to a common ancestor. Example: Bird wings and insect wings.Vestigial structures are structures of marginal, if any, importance to the organism that are the remnants of structures that served important functions in the organism’s ancestors. See these as underdeveloped and useless in one species but these are being used in a second similar species. (turn off regulatory genechange the structure) Examples of vestigial structures in humans: wisdom teeth, tail bone, appendix, muscles to move ears and nose, the little hairs on the body with muscles (dogs can make themselves fluffy when they are cold but we can’t)
• #60: Summary of Natural Selection (must have…)Variation (mutations; genetic recombinations—share genes but also have different genes)Competition among individuals for limited resources (food, shelter, mate)Survive to reproduce (must get old enough to pass on genes)Population: each species has an amount of individuals, all of which will not survive.
• #61: The “Cambrian Explosion”: Most of the major phyla of animals appear suddenly in the fossil record that was laid down during the first 20 million years of the Cambrian period, a phenomenon referred to as the “Cambrian explosion.” This was nearly 542 million years agomany new animals were formed, especially invertebrates, and already divergent phyla (many phyla re thought to have originated much earlier) expanded in diversity relatively suddenly and simultaneously. The “explosion” included many large animals with hard shells.
• #62: B. MIGRATION