Term
| Why does undergoing sexual selection put organisms at a disadvantage if the environment never changes? |
|
Definition
| Because the organism will have to devote time and energy into finding a mate to reproduce with when it is not necessary. An organism that undergoes asexual reproduction just clones itself so it only takes as much time and time and energy as it takes to produce another like itself. Assuming the organism is well adapted to the environment asexual reproduction will increase the population numbers more effectively. |
|
|
Term
| Why is sexual reproduction at a disadvantage in unchanging environments? |
|
Definition
1) it takes more time and energy to find a mate and impress it than it takes to just undergo asexual reproduction.
2) Asexual reproduction will increase an organism's numbers more effectively assuming the organism is adapted to the environment. |
|
|
Term
| Why is sexual reproduction a good thing in most cases? |
|
Definition
| It causes variation and breaks up linkage disequilibrium. |
|
|
Term
| What is linkage disequilibrium. |
|
Definition
| Linkage disequilibrium is when two alleles are linked on the same chromosome. |
|
|
Term
| What is sexual dimorphism? |
|
Definition
| It is where the male and female of a species look different. |
|
|
Term
| In sexual dimorphism what sex will almost always become elaborately decorated? Why? |
|
Definition
| The male will always be more showy than the female because the females are almost always the ones selecting mates. |
|
|
Term
| Why is female selecting males for certain traits selected for by natural selection? |
|
Definition
| Because females select males with large antlers or colorful plumages. The production of these excesses means that the male is fit and will pass on quality genes to the offspring. In the case of antlers and other similar structures, the females might be selecting males that are best at defending their teritory, thus proving their fitness. |
|
|
Term
| Why are females the ones that select their mates? |
|
Definition
| Because there is little metabolic investment involved in producing sperm, but a huge amount of investment involved in producing eggs. the female also has to go through pregnancy and usually raise the offspring in the few cases where the offspring is raised. often times males play no role in care for the offspring. Females can not produce an unlimited number of offspring. All of this means that females only have a couple of chances to produce viable offspring to pass on the mother's genes. |
|
|
Term
| Which gender is MUCH more likely to not produce any offspring at all? |
|
Definition
| Males (majority are unsuccessful in some cases) |
|
|
Term
| Does having multiple partner increase reproductive success more in males or females? |
|
Definition
|
|
Term
| Why do we find that females from the species Sygnaphus typhle (broad nosed pipefish)often die without reproducing where males almost always have reproductive success? |
|
Definition
| Because the males in Sygnathus typhle have to carry the developing embryo in a sac on their ventral side. This means the female only invests an egg, though expensive metabolically, she does not have to bear the offspring. |
|
|
Term
| What is intrasexual selection? What causes it? |
|
Definition
| Intrasexual selection is when members of the same gender with low metabolic investment in sexual reproduction (usually males) compete for the opportunity to mate. It is caused by sexual selection for the most fit individuals by the sex that has the highest metabolic cost in reproduction. |
|
|
Term
| What will be the result of territory defense intrasexual selection? |
|
Definition
| Increased size of the defense structure. (horns for example) |
|
|
Term
| Why dont the horns of a ram grow indefinitely? |
|
Definition
| because the metabolic cost of creating horns that are too big will mean more food will need to be consumed to sustain them. This means the size will be stabilized at some intermediate size. |
|
|
Term
| Why do males often defend a territory from other males? |
|
Definition
| Because they don't have to invest much in reproduction, they adopt strategies to increase their reproductive success (since i males reproductive success is determined by the amount of mates he can sucessfuly breed with) |
|
|
Term
| Where will the most fit males be in populations that have intra-sexual selection? |
|
Definition
| in the highest quality territory. More females visit the higher quality teritory so it is more coveted. |
|
|
Term
| sexual selection leads to.... |
|
Definition
|
|
Term
| How do the coho salmon reproduce? |
|
Definition
| The females deposit eggs on the bottom of the river bed. The older hooknose males fight for a position in line to ejactulate on the eggs. They end up lining up according to size. The smaller Jacks don't stand a chance so they evolved a more sneaky approach to compete. They hide nearby while the female coho salmon is laying her eggs, then quickly swims over and ejaculates on the eggs. |
|
|
Term
| How does the Mediterranean fruit fly deal with the fact that competition for females is fierce? (females mate with multiple males) |
|
Definition
| They deposit 2 times as much sperm in the presence of another male. |
|
|
Term
| What is the correct term for a sperm delivery organ that does not also function as an excretory organ? |
|
Definition
|
|
Term
| What adaptation have damselfly and dragonfly species males developed to deal with competition from other males to mate with females? What is the counter adaptation? |
|
Definition
| The males deposit a cement-like substance after they copulate to plug up the cloaca. Males have counter adapted hooks at the end of their aedeagus to scrape out the plug and at least some of the sperm. |
|
|
Term
| What are the groups called that lions live in? |
|
Definition
|
|
Term
| What gender of lions is born in the pride and stays in the pride, and what gender is unrelated to the pride? |
|
Definition
| The females are born into the pride and stay in the pride. The males come from outside to prevent imbreeding. |
|
|
Term
| What is it like being a male lion in a pride? |
|
Definition
| The male lion leaves the pride he is born into and joins another pride. He must then drive out the male that is currently mating with the females. The female lions can not become pregnant until the cubs are fully weaned. To solve this problem, male lions simply kill off all the cubs from the male that they out-competed. This will bring on fertility faster. |
|
|
Term
| Why are red collared willow birds much larger than the females? Why do they have such enormous tails? |
|
Definition
| Sexual dimorphism = Sexual selection. |
|
|
Term
| Why does the tree frog inflate it's throat? |
|
Definition
| To create a resonance chamber for it's mating call. |
|
|
Term
| Which male tree frog will be chosen by females? |
|
Definition
| The one who has the longest mating call. Other males will also be calling, the males must increase the length of their call to distinguish them from the others. |
|
|
Term
| what is the phototaxis score in the experiment testing female tree frog's response to male calls? |
|
Definition
| The phototaxis score is the ratio of the time it takes a female to approach a control divided by the time it takes a female to approach the experimental. |
|
|
Term
| How did scientists figure out that female tree frogs prefer longer male calls? |
|
Definition
| They set up a control and started measuring the amount of time it takes a female to approach a loudspeaker playing different length calls. They then divided the time it took the control divided by the time it took the experimental to find the phototaxis score for the Y axis of a graph and they placed the length of the call on the X axis. The graph shows that females strongly favor males with longer calls. |
|
|
Term
| Alison welsch wanted to carry out an experiment to test if tree frogs have to wait until they are of reproductive age to reap the benefits of having a father with a long mating call. How did she do this? What were the results? |
|
Definition
| She took eggs from random females and mated one set with sperm from a short calling frog and one set with sperm from a long calling frog. She then divided the offspring into two groups, one group of LC/SC with ample food, and one group of LC/SC was given a low amount of food. They observed the fitness. They measured time it took to get to metamorphosis, mass of the tadpoles, and the rate of growth after metamorphosis. The results were mixed but always showed that LC were better at surviving. |
|
|
Term
| What does the male rattlebox moth offer the female rattlebox moth for mating? |
|
Definition
| Life insurance. The male deposits a chemical defense on the females after mating that causes spiders to release the moths caught in their web. |
|
|
Term
| what does the male bittacus epicalis (hanging fly) offer the female for mating? What males will be selected for? |
|
Definition
| A blowfly that the male uses to distract her long enough for copulation to take place. She disengages when she is finished eating. Males who bring bigger blowflies will be selected for, up to about 20 minutes. If the female is not done with the blowfly after 20 minutes, the males take the blowfly back and use it on other females. |
|
|
Term
| traits that females prefer in mates will _____ in offspring |
|
Definition
|
|
Term
| Females are more choosey with the mates they choose if ____ |
|
Definition
| There is a high investment in the offspring for the female. |
|
|
Term
| T/F In most case females are the ones who are choosey. |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| They can sense the vibrations that copepods make then they wave there arms around looking for it. |
|
|
Term
|
Definition
| The male can smell the female, but the female might have left, so he must make sure she is still there. He waves his legs at the frequency of a water mite. The female lunges towards him which proves she is there. The male then drops a spermatophore (sperm packet) on the leaf, and vibrates his arms again. This time the female is fertilized. |
|
|
Term
| what are two theories that explain which how the trembling behavior and the netting behavior of water mites arose? |
|
Definition
1) the trembling arm behavior arose, then the feeding behavior arose, then the trembling behavior was lost in one species.
2)the netting behavior arose, then the trembling arose on two seperate occasios. |
|
|
Term
| what is the sexy sons hyothesis? |
|
Definition
| Fathers with a trait that females prefer will pass it on to their offspring who will be more attractive to females like their mother. The trait does not necessarily improve fitness, it is just what the female finds appealing. |
|
|
Term
| why do spotted cucumber beetles adhere to the sexy sons hypothesis? |
|
Definition
| The male that strokes the females antennae fastest are selected by the female for copulation. The only increase in fitness is due to the fact that females like fast stroking cucumber beetles. |
|
|
Term
| What is the sexual dimorphy in diopsids (stalk eyed flies)? |
|
Definition
| Males are much larger than females and have longer eye stalks. |
|
|
Term
| If the male diopsid offspring has long eyestalks, the female offspring will... |
|
Definition
| Prefer longer eyestalks in a mate. |
|
|
Term
| How do they know that diopsids who were born from short eyestalk parents prefer short eyestalk mates? |
|
Definition
| They did an experiment where they raised one group with only short eyestalks, one with only long eyestalks, and a control. They then let each group choose mates from both short and long eyestalked mates and the short eyestalk group chose all short eyestalked mates, the long eyestalked group chose all long eyestalked mates. |
|
|
Term
| are eyestalk length and preferance heritable? |
|
Definition
|
|
Term
| can selection on one trait produce a response in another trait? |
|
Definition
|
|
Term
| Why do diopsids always choose long eye stalked males in nature? |
|
Definition
| Because the long stalked males are more fit only because they have Y-chromosome allele that produces more sons than daughters. Females outnumber males. Females that mate with long eyestalked mates are more likely to produce more sons. |
|
|
Term
|
Definition
|
|
Term
| How do you run a paternity test? |
|
Definition
| DNA from the mother, father, and baby are all collected and placed on an agarose gel. The gel is then placed into radioactive DNA solution, this binds to specific DNA sequences on the agarose gel. they run the samples on the gel and if the baby's dna lines line up with ones seen in the mother and father, they are the parents. If not, the one that the baby does not line up with is not the parent. |
|
|
Term
| Why do female blackbirds nest with one bird but also go out to be fertilized by other birds? |
|
Definition
| She wants to make sure all of her eggs are fertilized. This will increase her reproductive success. |
|
|
Term
| Why do prairie dogs have multiple partners? |
|
Definition
| To increase the success rate of reproduction. They increase the size of their litter this way and make sure they produce offspring. |
|
|
Term
| what do male pipefish choose in females? |
|
Definition
| Larger females with larger skin folds and a lower number of black dots due to parasites. |
|
|
Term
| Can sexual selection select for certain behaviors? |
|
Definition
|
|
Term
| What are phylogenies used for? |
|
Definition
| to create hypotheses for the evolution of a species. |
|
|
Term
| Do plants often show sexual dimorphism? |
|
Definition
|
|
Term
| Do plants often show sexual dimorphism? |
|
Definition
|
|
Term
| In plants, which are usually bigger, male flowers or female flowers? |
|
Definition
|
|
Term
| What is the phenotypic result of sexual selection in male flowers? |
|
Definition
| sexual selection causes more showy flowers. |
|
|
Term
| Explain the culture of the Yanomamo people? |
|
Definition
| They live in the jungles of South America and are very war like. They raid and kill the populations of rival villages. 40% of males have had some involvement in killing someone else. They earn the title "unokai" |
|
|
Term
| Do women favor the Unokai (killers) in the Yanomamo society? |
|
Definition
| Yes, Unokai have more wives and more children on average. |
|
|
Term
| Why is it hard to study sexual selection in humans? |
|
Definition
| Because attractiveness to certain traits varies based on what culture you are raised in. |
|
|
Term
| Why is donald trump like a hanging fly? |
|
Definition
| He gets a lot of women because he has money. Money is a resource just like the blowfly the hanging fly uses to distract while mating. |
|
|
Term
| One study shows that women usually select men who are... |
|
Definition
|
|
Term
| What is usually attractive to the opposite sex in humans? |
|
Definition
| Indicators of good health. |
|
|
Term
| Whales are the cousins of... |
|
Definition
|
|
Term
| What are the two main objectives of evolutionary biology? |
|
Definition
1. to understand the process of evoluion
2. to recover the history of life on earth (systematics) |
|
|
Term
| What is the difference between taxonomy and systematics? |
|
Definition
| Systematics is interested in grouping organisms into groupings based on their evolutionary relationships. Taxonomy assigns organisms into groups usually based on common characteristics. |
|
|
Term
|
Definition
| Two groups that are closely related to eachother through a recent common ancestor. |
|
|
Term
| What is a monophyletic group? |
|
Definition
| A group containing the common ancestor and all it's decendents. |
|
|
Term
| Do paraphyletic groupings reflect evolutionary history? |
|
Definition
|
|
Term
| List an explain the 4 main sources of data for systemic studies. |
|
Definition
Morphology - the physical appearance and physical traits the organism has
Behavioral - the actions of an organism
Ecologial - the place the organism lives, breathes, and feeds.
Molecular - genetic data in the form of gene order, chromosomal inversions, protein or DNA sequences, etc. |
|
|
Term
| What are the objectives of systematic biology? |
|
Definition
1. to resolve unknown relationships
2. to test previously advanced hypotheses
3. to trace the evolution of a particuar character or set of characters.
4. develop new methods for analyzing data |
|
|
Term
| Taxonomy can result in ______ groups. |
|
Definition
|
|
Term
| can taxonomy answer or ask evolutionary questions? |
|
Definition
|
|
Term
|
Definition
| The science of identification and classification. |
|
|
Term
| what is the problem with the appeal to authority way of approaching evolution? |
|
Definition
| Who is to say who is the most authoritative on the issue? Not all experts agree. The results are not repeatable. |
|
|
Term
| What is another name for numerical taxonomy? |
|
Definition
|
|
Term
| What is Phenetics? What does it not take into account? |
|
Definition
| Phenetics is the grouping of organisms based on their overall similarity. Systemics does not take convergent evolution into account. |
|
|
Term
| What is convergent evolution? |
|
Definition
| The independent acquisition of similar charactersin different evolutionary lineages. |
|
|
Term
| give an example of convergent evolution |
|
Definition
|
|
Term
| What is parallel evolution? Why is it different then convergent evolution? |
|
Definition
| Parallel evolution is the independent acquisition of a similar character in closely related lineages. In convergent evolution, they are not closely related lineages. |
|
|
Term
|
Definition
| A reversal happens when a mutation returns a character to it's ancestral condition. |
|
|
Term
| What is homoplasy? What is it's opposite? |
|
Definition
| Homoplasy is a catchall term for convergent evolution, parallel evolution, and reversals. Opposite is homology. |
|
|
Term
| Why does homoplasy confound systematic studies? |
|
Definition
| Because it incorrectly implies common ancestry. |
|
|
Term
| What is homology? give an example. |
|
Definition
| Homology is similarity in traits due to a common ancestor. An example would be the bones in the arm of every mammal. |
|
|
Term
| Monophyletic groups represent evolutionary history T/F |
|
Definition
|
|
Term
| Paraphyletic groups represent evolutionary history T/F |
|
Definition
|
|
Term
|
Definition
| Evolutionary trees, they reveal the pattern of evolution. |
|
|
Term
| What is phylogenetics concerning? |
|
Definition
| Evolutionary relationships |
|
|
Term
| Phylogenetics seeks to organize classifications into... |
|
Definition
|
|
Term
| Who was the first person to suggest that evolutionary relationships could be organized into a tree-like diagram? |
|
Definition
|
|
Term
| When was the age of numerical taxonomy? |
|
Definition
|
|
Term
|
Definition
| The father of cladistics. A german entomologist |
|
|
Term
| Does cladistics take into account both homology and homoplasy? |
|
Definition
|
|
Term
| What is an ancestral character called? |
|
Definition
|
|
Term
| What are derived characters called? |
|
Definition
|
|
Term
| With respect to the evolution of eukaryotes, is the chloroplast a plesiomorphic or apomorphic character? |
|
Definition
|
|
Term
| With respect to the phylogeny of the plant, is the chloroplast apomorphic or plesiomorphic? Why? |
|
Definition
| Plesiomorphic. The chloroplast was in the ancestor of all plants. We know this because all plants have seeds. |
|
|
Term
| when can you say that seeds are an plesiomorphic character? |
|
Definition
| If you are looking that the phylogeny of seed plants. |
|
|
Term
| When did land plants first evolve? |
|
Definition
|
|
Term
| What are bryophytes? What evolutionary significance do they have? |
|
Definition
| Bryophytes are mosses, they are thought to be the oldest existing lineage of plants. |
|
|
Term
| In what plants does a vascular system first evolve? |
|
Definition
| Pteridiophytes AKA Ferns. |
|
|
Term
| what characters evolve in plants? |
|
Definition
| Mosses - Vascular system - Seeds - Flowers |
|
|
Term
| Using synapomorphies, synplesiomorphies, apomorphies, and plesiomorphies is all part of _______ method. |
|
Definition
|
|
Term
| What is the term for shared ancestral characters? |
|
Definition
|
|
Term
| What is the term for shared derived characters? |
|
Definition
|
|
Term
| Homology is evidence of... |
|
Definition
|
|
Term
| Why is cladistics based on synapomorphies and not synplesiomorphies? |
|
Definition
| Since all members have the synplesiomorphic trait, it does not help us group organisms. |
|
|
Term
| What is Hennig's grouping rule? |
|
Definition
| Synapomorphies are evidence of common ancestry. Synplesiomorphies, convergences, and parallelisms are not evidence of common ancestry. |
|
|
Term
| What is Hennig's Auxillary Principle? |
|
Definition
| Never assume convergent evolution or parallel evolution, always assume homoplasy in the absence of contrary evidence. |
|
|
Term
| How do you create a cladogram? |
|
Definition
| You look at various different orgnisms and figure out whether they have a trait or don't. arange them accordingly assuming homology. |
|
|
Term
| What is the point of making an unrooted phylogenetic tree? |
|
Definition
| They depict relationships but not the order of divergence. They simply group sister taxa. |
|
|
Term
| What animal is thought to be the ancestor of all birds? |
|
Definition
|
|
Term
| Can the outgroup be a member of the group you are studying? |
|
Definition
|
|
Term
| Where on the cladogram is the outgroup? |
|
Definition
|
|
Term
| What do you call the group you are studying? |
|
Definition
|
|
Term
| What charactaristics must your outgroup have? |
|
Definition
| It must have some characteristics similar to your ingroup. |
|
|
Term
| What is the purpose of the outgroup? |
|
Definition
| To help you decide the order that the taxa diverged. The taxa that are most like the outgroup arose first. |
|
|
Term
| What is the term for a derivedcharacter that is not shared? |
|
Definition
|
|
Term
|
Definition
| When a derived species goes reverses to an ancestral characteristic instead of a derived one. |
|
|
Term
|
Definition
| The simplest explanation is always the best. |
|
|
Term
| How can we use the axillary principle to solve a problem where we have to choose between multiple trees? |
|
Definition
| We choose the tree that has the least amount of homoplasy. |
|
|
Term
| What is the principle of parsimony? |
|
Definition
| The answer that requires the fewest changes is preferred to more complex answers. |
|
|
Term
| How can you apply the principle of parsimony and Occam's razor to a phylogenetic tree? |
|
Definition
| If you have conflicting trees you should choose the one with the least amount of evolutionary steps. |
|
|
Term
| What is a consensus tree? |
|
Definition
| a consensus tree is a tree you make when you have homoplasy and end up with two or more trees that are equally plausable. The idea is that you colapse them intoone tree called a polytomy with all taxa coming from one node. |
|
|
Term
| Which cladogram contains an outgroup: rooted or unrooted? |
|
Definition
|
|
Term
| What rule implies that the cladogram with the least number of steps is prefered? |
|
Definition
| Both the principle of parsimony and Occam's razor. |
|
|
Term
| Both cladistics and Phenetics is preferable to... |
|
Definition
|
|
Term
| The taxa in a phylogeny involve the _____ of different organisms. |
|
Definition
|
|
Term
| Cephalopod mollusks and vertebrate both have a..... this is an example of.... |
|
Definition
Camera eye
Convergent evolution. |
|
|
Term
| Why do systematists use a computer program to erect phylogenetic trees? |
|
Definition
| Because phylogeny actually involve a complex set of mathematical equations called NP completeness problems. There are so many possibilites that it would be impossible to sort through the possibilities. |
|
|
Term
| Is it more of a problem in systematics to add a character or a taxa? |
|
Definition
| A taxa because there are many more possibilities. |
|
|
Term
| The fastest computer programs don't have enough time to check all the possibilities in _______ taxa or more. |
|
Definition
|
|
Term
| Beyond 12 taxa _________ is employed which gives an approximate best result. |
|
Definition
|
|
Term
| How does the computer program that searches different phylogenic trees work? |
|
Definition
| It makes a random tree using the information you gave it then it rolls through the possibilities. Each time it checks the number of changes, and if it's lower than the previous it throws the previous out. |
|
|
Term
| What are the Chiropterans? |
|
Definition
|
|
Term
| What group are the primates most closely related to? |
|
Definition
|
|
Term
|
Definition
| Mammals that have hooves and an odd number of toes such as horses and Rhinos |
|
|
Term
| What are the Artiodactyls? |
|
Definition
| Even toed ungulates. Hippos, pigs, deer, cows. |
|
|
Term
| Where did they used to think the hippo belonged on the cladogram? |
|
Definition
| As a sistergroup to the hippos. |
|
|
Term
| Explain how the Whippo hypothesis came about. |
|
Definition
| John Gatesy sequenced a bunch of milk proteins and used them to build a phylogenetic tree. That tree showed the whale was most closely related to the hippo. |
|
|
Term
| What debate did the whippo hypothesis spark? Between what two groups of evolutionary biologists? |
|
Definition
| It sparked a debate in the scientific community on the imporance of molecular evidence. The morphologists said that morphological differences are based on many different gene interactions, and the molecular systemists said that DNA base pair analysis reduces the amount of homoplasy. |
|
|
Term
| What chalenges did gatesy face with the whippo hypothesis? |
|
Definition
People said that since he used the heuristic search method he may not have got the most parsimonious tree.
People used to astragalus to raise the point that it is not a artiodactyl like astragalus, this would give the tree 2 steps, non-parsimonious. |
|
|
Term
| What evidence led to more acceptance of the whippo hypothesis? |
|
Definition
| Nikaido used LINE's and SINE's to construct a phylogeny that also puts the whale as a sister taxa to the hippo. Finally widespread acceptance came when fossils were found of transition states between the hippo and the whale with the inner ear bones unique to whales, and the astragalus of the artiodactyls. |
|
|
Term
|
Definition
| Long Interspersed Elements. Genome insertions of mRNA reverse transcriptase. |
|
|
Term
|
Definition
| Short Interspersed Elements. They are similar to pseudogenes and they are thought to arise by reverse transcriptase of mRNA. |
|
|
Term
| What are sources for molecular data? |
|
Definition
Presence or absence of genes
Inversions
Gene duplications
Chromosomal inversions or translocations
Microsatellites
Haplotypes
Gene and nucleotide sequences
Protein sequences |
|
|
Term
| What is FOXP and what is the only extant species that has it? |
|
Definition
| FOXP is the gene that gives humans the ability to speak. Only humans have it. Neandertals also had it. |
|
|
Term
| If you find that two species have a chromosomal inversion at the same spot, what does this suggest? |
|
Definition
| The inversion happened in the common ancestor to these two animals. |
|
|
Term
| How do microsattelites help identify synapomorphies among taxa? |
|
Definition
| the presence of microsatellites in the same spot proves linkage between two taxa. |
|
|
Term
| What are the advantages of using gene sequences to create a phylogenic tree? |
|
Definition
| You have use many different characters. This allows you to avoid polytomies and get a more accurate tree becase you have the same number of species and more characters specific to that species. A single gene or protein contains hundreds or even thousands of different characters because every amino acid or nucleotide base is a character. |
|
|
Term
| When do you get polytomies? |
|
Definition
| When you don't have enough variation in your characters to tell which evolved first. |
|
|
Term
| a tree that has no polytomy is ______ compared to a tree that has polytomy |
|
Definition
|
|
Term
| Why is it easier to recognize synapomorphy using molecular analysis with genes and proteins? |
|
Definition
| There ar only 20 different kinds of amino acids and 4 different nucleotides which means there is a limited number of character states. This makes it easier to recognize homology. |
|
|
Term
| What is the disadvantage of gene and protein analysis for systematics? |
|
Definition
| There are only 4 different nucleotides and 20 different amino acids, so it is harder to recognize homeoplasy. Basically, when looking at a gene sequence, many different mutations may have taken place and they both may have converged on nearly identical gene sequences. |
|
|
Term
| How do you compare two gene seqences? |
|
Definition
First you identify homologous sequences
Second you align the sequences with one another so you can see which nucleotides are the same and which differ.
Third you identify substitutions, deletions, and insertions
Fourth you add gaps where insertions/deletions shifted the genome. |
|
|
Term
| Why do you add gaps to the gene sequences you are comparing? |
|
Definition
| Deletions and insertions shift the whole genome. Adding gaps shows the deletion but also realigns the genome to show similarities again. |
|
|
Term
|
Definition
| Sometimes you are left with more than one possibility and you can't be sure which one is accurate. |
|
|
Term
| How do computer algorythms solve the problem of when to add gaps to the gene sequence? |
|
Definition
| It uses program settings such as the gap to change cost - basically it is programmed to only put a gap in if there is more than two nucleotides misaligned in a row. |
|
|
Term
| What do you do once you have properly aligned the gene sequences? |
|
Definition
| You put it into a phylogenic tree program to try to find the best fit in the tree. |
|
|
Term
| What are the advantages of parsimony? |
|
Definition
All characters are considered independently - there is no loss of character information.
It is the best method for combining different sources of data.
It makes the fewest assumptions. |
|
|
Term
| What are some objections to the parsimony method? |
|
Definition
| It can ignore the idea that DNA similarities in base pairs are due to convergent evolution. They assume that everything is due to homology as long as there's no evidence to the contrary. The "long branch" problem. Basically, organisms that split from a common ancestor a long time ago are more likely to undergo convergent evolution. Cladistics does not have any statistical values that allow scientists to compare it to other hypotheses. "the best tree is the shortest tree" means that if you get a short tree with some very suprising relationships, and a slightly longer tree will have more traditional relationships, it's hard to argue that the shorter one is better. |
|
|
Term
| What is a long branch attraction probelem? |
|
Definition
| The more distantly related 2 species are the more likely they are to undergo convergent evolution. This tricks cladists into thinking species distantly related are actually very closely related. |
|
|
Term
| Some systemetists do not like using cladistics, what do they use instead? Which method is most commonly used as an alternative? |
|
Definition
Distance methods.
Statistical methods like maximum likelihood.
Maximum likelihood is more popular. |
|
|
Term
| What are primary homology statements |
|
Definition
| The alignment of the Gene sequences. |
|
|
Term
| What is the distance method? |
|
Definition
| Basically it is phenetics applied to molecular data. Similar sequences are placed together as sister taxa on a tree. The amount of difference in the nucleotides are used to estimate how distantly related two organisms are. |
|
|
Term
| What are some benefits to the distance method? |
|
Definition
| It is the fastest method of analysis and it always produces a fully resolved tree. |
|
|
Term
| do most systemists use distance methods? are they skeptical about distance method results? |
|
Definition
|
|
Term
| what is bad about the distance method? |
|
Definition
| an entire gene sequence of information is reduced to one number. There is no character by character analysis like in other methods. |
|
|
Term
| Why is maximum likelihood used more today than it was 10 year ago? |
|
Definition
| Computing power has increased enough to allow us to perform the complecated calculations involved. |
|
|
Term
| What happens in the Maximum likelihood method (statistical methods)? |
|
Definition
| You enter your data into the computer then the computer will analyze it and tell you what program you should use. It assembles the data into phylogenetic trees by doing something similar to the heuristic method - searching for shorter and shorter trees. Then it calculates the likelihood ratio of each tree, the lowest likelihood ratio is selected as the one that best fits the data. |
|
|
Term
| What are some advantages of maximum likelihood? |
|
Definition
It uses each individual character. There is no loss of character info.
Can determine if a specific hypothesis is better than another because it caculates likelihood. |
|
|
Term
| What are some problems with the maximum likelihood method? |
|
Definition
Your results depend on your model. If you do not choose the right model paralleling how evolution took place in this case, your results will be meaningless. However, the models are estimated from the data.
You can't combine models. If you want to combine molecular and morphological data, you will have to come up with a model for how the morphological characters evolved.
Maximum likelihood is computationally intensive. |
|
|
Term
| What are the three molecular evolution models? |
|
Definition
1) Jukes Cantor - all mutations are equally likely
2)Kimura 2 peramiter model - unequal rates of trasitions and transversions
3)General Time Reversable model (GTR) - a different rate for each possible change. |
|
|
Term
| What is good about the Jukes Cantor model? |
|
Definition
| It doesn't make any assumptions there's no evidence for. |
|
|
Term
|
Definition
| A purine (A or G) is turned into another purine. Or when a Pyrimidine is turned into another Pyrimidine (C T) |
|
|
Term
|
Definition
| A pyrimidine (C or T) is turned into another pyrimidine. |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| What did Kimura find out about molecular biology? |
|
Definition
| Transitions occur more frequently than inversions. |
|
|
Term
| What are the specifics of Kimura's model? |
|
Definition
| Transitions are given a value of 1 and transversions are given a value of .5 |
|
|
Term
| Why do they think the reason is that transitions happen more than transversions? |
|
Definition
| The shapes of bases prefer to be replaced by similarly shaped bases. |
|
|
Term
| Why is the General time reversible model sometimes used? |
|
Definition
| Because sometimes the rate is different for each type of transition/transversion. |
|
|
Term
| Is the most complex model always the best model to use? |
|
Definition
| No. The best model to use will be calculated by the Maximum Likelihood program. |
|
|
Term
| Which will be more variable in a gamma distribution: More variable sites or less? |
|
Definition
|
|
Term
| What is the difference between bootstrapping and jacknifing? |
|
Definition
| Bootstraping means the machine will pull out a random sample of your characters, replace it, and repeat pulling out samples and testing then replacing them. Jacknifing, on the other hand, does not replace the characters it tests. |
|
|
Term
| What is a bremer support value? |
|
Definition
| The amount of homoplasy that would be necessary to colapse your set of relationships into a polytomy |
|
|
Term
| What is horizontal transfer? |
|
Definition
| When bacteria exchange DNA with each other. |
|
|
Term
| Which two types of organisms can transfer dna from themselves to another organism? |
|
Definition
|
|
Term
| What is an example of a way that there can be no ancestor to decendent relationship in the genes? |
|
Definition
|
|
Term
| How can you avoid the problem of possibly tracing a gene which may have undergone gene transfer instead of tracing the organism? |
|
Definition
|
|
Term
| Why do systemetists analyze multiple genes? |
|
Definition
| Because one gene may have undergone horizontal gene transfer, you want a large sample of genes that give the same results. |
|
|
Term
| What must you choose carefully when running a gene analysis to erect a phylogeny? |
|
Definition
| The gene regions you use. You don't want to use an ancestral gene region because that would be useless. No variation. This would be like using a chloroplast to erect the plant phylogeny. |
|
|
Term
| do different gene regions acquire mutations at the same or different rates? |
|
Definition
| Gene regions acquire mutations at different rates. |
|
|
Term
| What mutation rate do you want in a gene? |
|
Definition
| You want a mutation rate that is fast enough that you can recognize variation across species, but slow enough that you wont mistake homoplasy for homology. |
|
|
Term
| Why does a high mutation rate cause you to mistake homoplasy for homology? |
|
Definition
| Because when analyzing DNA if the nucleotide undergoes 2 mutations it is going to look the same as a gene that didn't mutate at all... Also long time since common descent with high rates of evolution means higher likelihod of convergent evolution. |
|
|
Term
| Which areas acquire mutations more rapidly: coding or noncoding regions? WHy? |
|
Definition
| Noncoding. Because natural selection has no effect on them which means mutations are neutral and can accumulate. |
|
|
Term
| Why are mutation rates in the 3rd position of the codon moore likely? |
|
Definition
| Because the third nucleotide in a codon usually does not change the amino acid that is produced. |
|
|
Term
| Why would a gene aquire mutations very slowly? |
|
Definition
| Because they perform a vital function: the histone genes are a good example. |
|
|
Term
| Is the rate of mutation higher in mitochondrial DNA? |
|
Definition
|
|
Term
| hat are the three reasons why rates of mutations are higher in mitochondrial DNA? |
|
Definition
1) the DNA polymerase has no proofreeding function.
2) There are higher rates of free radicals in the mitochondria causing more mutationos.
3) there is less selective pressure on mitochondria because there are multiple mitochondria in the cell. |
|
|
Term
| Why are antioxidants good? |
|
Definition
| Because they take the free oxygen out of our bodies before it has a chance to affect our genomes. |
|
|
Term
| When would looking at the mitochondrial genome of two organisms be appropriate? |
|
Definition
| If the two organisms are thought to have evolved pretty recently. |
|
|
Term
| Is it better to run multiple small data sets and compare the results to choose the answer many converge on, or to run a large data set to create a tree? |
|
Definition
| Get a large data set and one tree. |
|
|
Term
| Why might you end up with a polytomy in a gene analysis? |
|
Definition
| Becase the species diverged so recently there had not been enough time for the relationship to resolve because there isn't enough variation. |
|
|
Term
|
Definition
| The smallest evolutionary unit. |
|
|
Term
| What is mitochondrial analysis bad at? |
|
Definition
| Determinging evolutionar relationships far back in evolutionary history |
|
|
Term
| Why is it easy to age hawaii? |
|
Definition
| Because the islands are the tips of volcanoes. |
|
|
Term
| Nuclear dna can give the evolutionary history between these time frames ... |
|
Definition
|
|
Term
| Mt. DNA can give evolutionary history up to ... and resolve divergence from... |
|
Definition
|
|
Term
| T/F combining mdna and dna data sets gives the best tree |
|
Definition
|
|
Term
| What has evolution showed us about the migration of drosophala flies on the hawaiian islands? |
|
Definition
| Kaua'i -> O'ahu -> 3 seperate migrations to maui -> big island. at the same time one migration from kaua'a to big island. |
|
|
Term
| is there an absolutely true tree? |
|
Definition
| No, they are all hypotheses. |
|
|
Term
| What good are phylogenetic trees? |
|
Definition
They tell us the history of life on earth.
They help us understand the processs of evolution. |
|
|
Term
| can phylogenies be used to study co-evolution? |
|
Definition
|
|
Term
| What is the biological species theory? |
|
Definition
| A species is a group of organisms that can produce viable offspring. |
|
|
Term
| What is the main problems with the biological species theory? |
|
Definition
1)You must know the mating habits of the organisms in question. You can't do this with extinct organisms!
2) some species don't undergo sexual reproduction.
3) many obvious species DO hybridize and produce viable offspring. Usually these are plants. |
|
|
Term
| What mechanisms do species use to make sure they only mate with members of their own species? |
|
Definition
Lock and key genetalia.
Geographical isolation
Mating rituals
different mating seasons. |
|
|
Term
| How do worm sperm and eggs of species like the palolo worm who put there gametes at the surface of the sea stop other species from fertilizing them? |
|
Definition
| the gametes have chemical barriers |
|
|
Term
| What is hybrid breakdown? |
|
Definition
| The hydbrids offspring have reduced viability or fertility. |
|
|
Term
| what are the three bariers to interspecies fertilization? |
|
Definition
Prezygotic barriers
Mating barriers
Fertitization barriers |
|
|
Term
| What is the morphologicial species concept? |
|
Definition
| defines species based on their physical appearance. |
|
|
Term
| What is the problem with the morphological species concept? |
|
Definition
only usueful for some species. protists and bacteria might look alike but are completely different.
It is often wrong
Some snails have different shells but are the same species. |
|
|
Term
| What is the ecological species concept? |
|
Definition
| Defines species based on where they live. |
|
|
Term
| What is the pleuralistic species concept? |
|
Definition
| Defines species using many different concepts: Ecological, morphological, biological... |
|
|
Term
| What is currently the best definition of a species? |
|
Definition
| The phylogenetic (genealogical) species concept. A species has a unique evolutionary history. |
|
|
Term
| what is the downside to the phylogenetic species concept? |
|
Definition
| You have to create a phylogenetic tree to define a species. |
|
|
Term
| when is a character said to be fixed in the population? |
|
Definition
| When ever member of the population has the exact same character. |
|
|
Term
| what do fixed character indicate? |
|
Definition
| reproductive isolation has occured |
|
|
Term
| what is population aggregation analysis? |
|
Definition
when you examine individuals in a population to figure out if some character is fixed in the population.
It uses species identification as a criteria. |
|
|
Term
| what is genetic barcoding? |
|
Definition
| using a genetic sequence to identify the species. |
|
|
Term
| How do they do genetic barcoding? |
|
Definition
they use the CO1 region on the mitochondrial dna
compare it to a database of CO1 sequences of barcoding studies. |
|
|
Term
|
Definition
| When a bridge prevent speciation narrows until there is geographical isolation leading to speciation |
|
|
Term
|
Definition
| changes in allele frequency in a population |
|
|
Term
|
Definition
| creation of new genera or families |
|
|
Term
| where does speciation sit? |
|
Definition
| On the boundary between microevolution and macroevolution |
|
|
Term
| What is the founder event? |
|
Definition
|
|
Term
| WHat is sympatric speciation? |
|
Definition
| When speciation occurs in a population due to different mating habits, etc |
|
|
Term
| what is probably the main cause of alopatric speciation? |
|
Definition
|
|
Term
| What is alopatric speciation? |
|
Definition
| When speciation occurs due to some physical barrier |
|
|
Term
| What are the three stages of speciation? |
|
Definition
1. populations have to become isolated from one another
2. traits have to diverge
3. teh divergence of traits reenforces reproductive isolation. |
|
|
Term
| what are the three factors that cause speciation? |
|
Definition
Genetic drift
natural selection
sexual selection |
|
|
Term
| what two things can happen with allopatric speciation? |
|
Definition
| they can either remeet ancd can interbreed or they cant and speciation occcurs |
|
|
Term
| What is it called why hybrids are produced with reduced viability? |
|
Definition
| Reenforcement. it reenforces to barriers to gene flow. |
|
|
Term
| SOme hybrid lines work well together and become selected for |
|
Definition
|
|
Term
|
Definition
| Areas where species overlap and hybridization is increased |
|
|
Term
| what habitat do viable hybrid species occupy? |
|
Definition
| the habitats between the two species they were made from |
|
|
Term
| What is reticulate evolution? |
|
Definition
| When hybrids have greater fitness |
|
|
Term
| When do the hybrid zones stabilize? |
|
Definition
| When hybrids are more fit thatn the parent species |
|
|
Term
| Can resluts found to be true in one specie be extrapolated to other species? |
|
Definition
|
|
Term
| Who created the biological species concept? |
|
Definition
|
|
Term
| Why is the popular misconception that "we used to be monkeys" wrong? |
|
Definition
| Because we only share a common ancestor with monkeys. Our closest living great ape relative is the pan troglodytes, the chimpanzee |
|
|
Term
| When and where did Homo Sapiens first originate? |
|
Definition
| 100,000 years ago on the grassy plains of east Africa. |
|
|
Term
| Why is the misconception that man is the pinnacle of creation wrong? |
|
Definition
| Because evolution is no more slanted to give rise to humans than it is to give rise to any other animal. We are not the most recently evolved animal. |
|
|
Term
| What did Anaximander think man descended from in 600 BC? |
|
Definition
|
|
Term
| What is the biological junkyard hypothesis? |
|
Definition
| Animals were formed from randomly assembled arms and legs, the best combinations survived. |
|
|
Term
| Who thought of the biological junkyard hypothesis? When? |
|
Definition
|
|
Term
| Why is the biological junkyard hypothesis significant? |
|
Definition
| Because it was selection. |
|
|
Term
| Did Carol Von Linnae Believe in evolution? |
|
Definition
| No, he believed in creationism. |
|
|
Term
| What did Carol Von Linnae do? |
|
Definition
| Cataloged living things. Created the idea of a species. |
|
|
Term
| What did Bonnet believe about the origin of life? |
|
Definition
| All living things arose from germs that the planet was seeded with. These germs develop when conditions are right. |
|
|
Term
| What did Comte de Buffon believe about life? |
|
Definition
| There is a mold that the particles of living things were assembled in. |
|
|
Term
| What is spontaneous generation? What evidence supported this? |
|
Definition
| Spontaneous generation means life came into existence out of thin air. The evidence of this was that soup left for a week would be full of microorganisms. Also they thought mice spontaneously generated in bags of grain. |
|
|
Term
| What did Linnaeus create? |
|
Definition
|
|
Term
| What information does the name Drosophila melanogaster give you? |
|
Definition
Genus: Drosophila
Species: Melanogaster |
|
|
Term
| The scopes monkey trial was held when and where? |
|
Definition
|
|
Term
| "All scientific hypothesis must be _____" -Karl Popper |
|
Definition
|
|
Term
| What is methodological naturalism? |
|
Definition
| Only natural causes can be invoked to explain natural phenomenon. |
|
|
Term
| What is ontological naturalism? |
|
Definition
| There are no supernatural causes, only natural causes are real. |
|
|
Term
| Explain intelligent design's argument using the bacterial flagella. |
|
Definition
| The bacterial flagella requires 23 separated proteins to function, the odds of evolving 23 proteins simultaneously is astronomical. |
|
|
Term
| In 2005 Intelligent design was deemed to be the same as ______ by the US district court in Pennsylvania. |
|
Definition
|
|
Term
| What are the four great blows to humanity? |
|
Definition
1. Copernicus' discovery that the earth is not the center of the universe.
2. Freud's discovery that we have an unconscious that makes us unaware of what we are doing or why we are doing sometimes.
3. The holocaust showed that man is not generally a good and kind creature.
4. Darwin showed that humans are not special, but just one of many species of animals. |
|
|
Term
| George Lyell (1797-1875) is called the ______ and created the theory of _______ which states ______. |
|
Definition
Father of geology
Uniformatarianism
Geological processes taking place today are the same that took place in the distant past. |
|
|
Term
| Uniformitarianism leads us to the conclusion that ______ |
|
Definition
| The earth is much older than previously thought. |
|
|
Term
| Thomas Malthus introduced the idea of overpopulation due to _____. |
|
Definition
|
|
Term
| Darwin (1809-1882), a wealthy aristocrat, dropped out of ______ and couldn't find a real job. He decided to get a job on the Beagle doing what? |
|
Definition
Medical school
He joined the Beagle in 1831, his job was to keep the captain of the Beagle company since he was also an aristocrat and there were only sailors around. |
|
|
Term
| What 6 factors did Darwin use to figure out evolution by natural selection |
|
Definition
1. Old earth (Lyell)
2. Fossil record of changing organisms.
3. Species have variation.
4. Organisms seem adapted to their environment.
5. With limited resources, only some organisms will survive. (Malthus)
6. Linnaean system shows similarities between some organisms. |
|
|
Term
| Alfred Russel Wallace (1823-1913) did a lot of ______. |
|
Definition
|
|
Term
| in 1852 Alfred Russel Wallace was ______. |
|
Definition
| Shipwreaked and survived 10 days on a life raft. |
|
|
Term
| What is the name of the famous paper written by Alfred Russel Wallace while he had malaria in 1854? Why was it significant? |
|
Definition
| On the Tendency of Varieties to Depart Indefinitely from the Original Type. It described evolution before Darwin released "On the Origin of Species." |
|
|
Term
| Darwin published "On the Origin of Species" in..... |
|
Definition
|
|
Term
| Natural selection is competition between _______ for food. |
|
Definition
| members of the same species |
|
|
Term
| The _______ acts on variation in populations to produce organisms that are best adapted. |
|
Definition
|
|
Term
| Many biologists think that the first molecule to arise on earth were the ___. |
|
Definition
| Ribozymes (RNA molecules) |
|
|
Term
| an RNA enzyme molecule called a ribozyme was probably the first molecule because it can ____ and ____. |
|
Definition
Catalyze certain reactions
Store genetic material |
|
|
Term
| Two chiral molecules are ______ of each other. |
|
Definition
|
|
Term
| Two achiral molecules are ______ of each other. |
|
Definition
|
|
Term
| D-dopa is the enantiomer of L-dopa, does D-dopa treat parkinson's disease like L-dopa does? |
|
Definition
|
|
Term
| a mixture of equal parts of two chiral molecules is called a ______ |
|
Definition
|
|
Term
| What is the evidence that the amino acids in the Murchison meteorite are not from earth or an organism? |
|
Definition
| If they were from earth there would be a racemic mixture of both enantiomers. If they were from an organism there would be just one enantiomer. There is an uneven mixture of amino acid enantiomers. |
|
|
Term
| Meteorites that originated on mars have been found on earth containing what kind of life? |
|
Definition
|
|
Term
| All of the biological macromolecules that are polymers can be readily synthesized in water by ____ and broken down by _____. |
|
Definition
dehydration synthesis
Hydrolysis |
|
|
Term
| Do polymer chains break down easily? |
|
Definition
|
|
Term
| How can you prevent the breakdown of polymer chains such as nucleotides? |
|
Definition
| Immobilize them on a clay-like substance. In many experiments Montmorillonite is used because many things stick to it. (it is adsorbent) |
|
|
Term
| Once nucleotides are adsorbed to the montmorillonite, how to you create nucleic acid polymers? |
|
Definition
| You wash the montmorillonite repeatedly with activated nucleotides |
|
|
Term
| How do we think protein synthesis took place in the beginning? |
|
Definition
| RNA nucleotides attached to a clay substrate bound to specific amino acids which connect together into a polymer. This polymer facilitates copying of the RNA causing the RNA to increase in number. |
|
|
Term
|
Definition
| Aggregations of molecules |
|
|
Term
|
Definition
| A protobiont - an aggregation of lipid molecules that forms a bubble like cell membrane. |
|
|
Term
|
Definition
| When a tectonic plates slides under another tectonic plate |
|
|
Term
| Is graphite produced biotically or abiotically? |
|
Definition
| Abiotically and biotically. |
|
|
Term
| How can we tell if graphite has been produced abiotically or biotically? |
|
Definition
| the ratio of isotopes of graphite tell us whether it is abiotic graphite or biotic graphite. |
|
|
Term
| The oldest fossils of cells are how old? |
|
Definition
|
|
Term
| on the tree of life you will see many fusing branches between early organisms. This is due to _____. |
|
Definition
|
|
Term
| When you look at a sedimentary rock what are the red layers? What is their significance? |
|
Definition
| Iron oxide (rust). Formed when iron and oxygen come in contact. It means there was some organism undergoing photosynthesis and pumping oxygen into the water. |
|
|
Term
| What happens to the oxygen produced by photosynthesis in the water? |
|
Definition
| The oxygen is taken up by the iron dissolved in the water first. This iron oxide falls to the bottom of the ocean. After all of the Iron has been used up the oxygen bubbles out of the water and enters the environment. |
|
|
Term
| what is oxidative phosphorylation? |
|
Definition
| the use of the electron transport chain to produce energy in eukaryotes. |
|
|
Term
| give examples of protists. |
|
Definition
|
|
Term
| what were probably the source of plastids? |
|
Definition
|
|
Term
| What were probably the source of mitochondria? |
|
Definition
|
|
Term
|
Definition
| They are RNA molecules folded into certain shapes. They have a limited ability to do catalyze reactions. |
|
|
Term
| Cech and Altman found the first ribozyme in the genome of a ________. |
|
Definition
| Ciliated protist similar to the paramecium |
|
|
Term
| what is special about the RNA intron between the regions that code for rRNA genes in the Tetrahymena? |
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Definition
| The RNA in these regions can splice itself out by folding itself into a tertiary structure. |
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Term
| ____ and ____ are the source of energy for almost all cellular processes |
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Definition
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Term
| Two types of RNA are used in protein synthesis _____ and ____. |
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Definition
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Term
| The tetrahymena ribozyme can also _____ after it has cut itself out of the genome. |
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Definition
| Bind to other RNA molecules and cut them out by breaking the phosphodiester bond that holds adjacent nucleotides together. It then attaches this sequence to it's 3' end |
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Term
| phosphodiester bonds _____. |
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Definition
| hold adjacent nucleotides together |
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Term
| What do experiments simulating conditions of an early earth show? |
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Definition
| That Nucleotide monomers and then RNA polymers could arise outside of the cell. |
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Term
| No experiment has shown that RNA can replicate itself, however it has been shown that RNA molecules can ______. |
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Definition
| Replicate other RNA molecules |
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Term
| What did the experiment using Q beta RNA and RNA replicase show? |
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Definition
| RNA evolution. after the 74th test tube incubation *with replicase* there was a 5% difference from the original sequence. |
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Term
| why can't proteins have been the first molecules to arise on earth? |
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Definition
| They can't replicate themselves |
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Term
| Why couldn't DNA have been the first molecule to arise on earth? |
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Definition
| Because DNA needs DNA polymerase to reproduce itself. |
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Term
| What are most enzymes made out of? |
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Definition
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