Evolution Exam 1

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What was Essentialism

(400 BC) Greek idea that things are essential and everything has its essence (Dominated Western European thought for 2000 years)

What is the mutation rate in HIV

1 x 10^-3 new nucleotides/nucleotide/replication

What is the mutation rate in eukaryotes

1 x 10^-6 to 1 x 10^-9

What are the 5 steps of the HIV life cycle

1. HIV attached to CD4 and enters cell 2. HIV copies itself to make more virus 3. HIV and CD4 cell fight; HIV damages the cell 4. Young HIV leaves the cell 5. HIV matures and invades other cells

What are the 3 components of clonal selection in HIV

1. Random phenotype variation 2. Differences in fitness 3. Heritability of these phenotypes

What are the 3 criteria for evolution by natural selection

1. Variation 2. Relationship between the trait and fitness in a particular environment 3. Heritability

All humans are about ___% genetically different. HIV generations can be _____% different from the previous oone

2; 30

How old is the Earth estimated to be?

4.6 billion years old

How many times has His evolved into Tyr at amino acid position 83 in HIV envelope protein

7

What did Plato believe

All life is a real, pure, eternal form. Variability is due to imperfection with no meaning.

What is AZT

An HIV drug taken with a drug cocktail

In response to rain, Daphne island birds evolved back to small beaks, what was criterion #2 at the time

Beak size vs. fitness, larger beak size now meant lower fitness

How does AZT work?

Blocks DNA reverse transcriptase by incorporating the wrong base into the virus' DNA so there is no protein synthesis and thus no viral replication.

Is the CD4 T allele or C allele more resistant

CD4 C

What cells does HIV infect?

CD4 helper T cells

What are some traits that can evolve in humans in response to HIV

CD4 receptors CCR 5 receptors Immune response proteins

Who established the principles of geology and rejected the young earth theory in the 1830s

Charles Lyell

Why does a drug-cocktail slow down evolution of resistance

Combination of inhibitors puts replication at approximately 0; 3-5 different mutations would have to arise in a single virus for replication to begin (low probability of mutation origin)

How do we represent heritability

Comparing parental average phenotype to offspring average phenotype

What are the 5 classes of antiretroviral agents that currently exist

Coreceptor inhibitors (CCR5 antagonists) Fusion inhibitors Reverse transcriptase inhibitors Integrase inhibitors Protease inhibitors

What is a pseudogene?

DNA with no promoter - noncoding - no protein made - vestigial trait

How can humans evolve resistance to HIV

Delta 32 CCRF - 35 amino acids that are missing from the proteins surface --Cannot be recognized by the virus --The virus cannot infect individuals with two copies of Delta 32 CCRF

What gene locus controls the armor allele

Eda

Why is HIV's asexual nature advantageous

Exact replication of genotype (no breaking of genes by sexual recombination)

How is evolution both a fact and a theory?

Fact = genetic change has been observed through time Theory = the set of processes by which evolution occurs

T or F: We know the proteins an RNA makes by looking at its sequence

False

T or F: HIV can only evolve within hosts

False, it can evolve across hosts as well

What did Rosemary and Peter Grant do?

Followed every single bird in a population to show evidence of evolution on Daphne Island

What geographic patterns did Darwin take note of

Fossil patterns (Law of Succession) Island patterns (Galapagos birds resembled S. American birds)

What are the groups of HIV-2?

Group A (W. Africa) Group B (W. Africa) Groups C-H

What are the groups of HIV-1

Group M (subtypes A-K) Group N Group O

What are the 2 main types of HIV

HIV-1 HIV-2

What is HAART

Highly Active Anti-Retroviral Therapy (use of a drug cocktail with at least 3 classes of inhibitors)

How is phenotypic variation represented

Histogram X = value of trait Y = number of individuals w/ trait

What are homologous and analogous traits

Homologous: similar because they have common evolutionary origin (synapomorphies) Analogous: traits have the same function, but do not have a common evolutionary origin

What are the two questions to ask ourselves when comparing traits across species

How similar are these two things? Are they the same trait?

Why is resistance to HIV not more prevalent in humans?

Humans = slow evolution HIV = fast evolution

What did Karl Popper say about the scientific method

Hypotheses in the realm of science must be falsifiable, in that it is conceivable that one or more predictions could be refuted by observations.

What is our state fossil (Nevada)

Ichthyosaur (A swimming reptile which acted like the dolphins of today)

Where are the highest levels of human HIV resistance actually found? Why?

In North Western Europe where the virus is relatively new and well-treated; disease outbreaks in the past may have driven a high level of CCR5 causing resistance

Genesis (in the Bible) says what about Earth

It is young

Why is heavy armor a cost in freshwater sticklebacks

It reduces growth rate and thus reproductive success

On Daphne Island, dry environments gave rise to ________ seeds, thus favoring _________

Large; large beak size

How do we represent relationship of phenotype and fitness

Line Graph X=phenotype Y=fitness

Who is resistant to HIV?

Long-term host monkeys

Which have more armor: marine or freshwater stickleback

Marine (thus they have improved fitness in an environment with predators)

What large animal did Darwin find the bones of?

Megatherium - Giant Ground Sloth found in S. America and would have been found in the Vegas Valley as well

Why is it more difficult to evolve resistance to a drug cocktail

Mutations have to occur at more than one amino acid to overcome each inhibitor; and there is no sexual recombination to share these mutations, one virus has to evolve ALL of the mutations

What do convergent evolution and analogous traits tell us

Natural selection in similar environments is a predictable process

Was the Law of Succession Darwin's idea?

No, he just sees the pattern and asks "Why is there an extinct and living form in the same area? Why does one cease to exist?"

What base is replaced by AZT

OH in Thymidine is replaced by AZT-triphosphate

Is the humerus across species analogous or homologous

Only homologous (highly modified function across species)

What is the epigenetic role of our microbiome

Our microbiome's genetics affects our genetics and functions

What is the idea of special creation

Species are immutable; Species created independently by god; perfect in form and function; no genealogy; species not related to each other

What are the components of descent with modification

Species change over time (microevolution) Lineages split and diverge (speciation) New life forms derive from old ones (macroevolution) All life forms are related (common ancestry) Earth and life are old

What were the ideas behind special creation

Species do not change; lineages do not split; each species is independently created; earth and life are young

What factors contribute to fast evolution

Strong natural selection; Selection not disrupted (asexual reproduction)

Why do patients that take their drugs 80-90% of the time see more viral mutation than those who take their medication only 20% of the time

Strong selection is present, but not strong enough to prevent viral replication, so there is a strong selection for drug-resistant viruses to survive (in the 80-90% group)

What did James Ussher do?

Studied the bible to understand Nature, determined the age of Earth to be 6000 years old (Origin of the age of Young Earth)(1600s)

Christian scholars added what to Essentialism

The Great Chain of Being's addition of God and the incorporation of religion (c. 1200s)

What happens if criterion #3 is not met

There is selection but no evolution

How can we use graphs to prove evolution

Use two histograms from different generations that show a shift in phenotypic frequency; or line graph showing mean phenotype vs time

How does the Law of Parsimony apply to phylogenetic trees

We ask ourselves what tree best explains all of the variation with the least number of mutations

What would happen if we were safer with HIV?

We would be less likely to see the rapid evolution of highly virulent forms (because the virus would die with the infected individual)

Would it be beneficial for a species to become asexual

Yes, because favorable traits would be directly passed on if they have high fitness

Has AZT resistance evolved more than once in HIV

Yes, independent mutations have occurred in different AZT treated individuals. There are also different amino acids that provide different ways to be resistant

What will you find if you take and HIV + patient and keep sampling the HIV over 10 years

You will find that the HIV are becoming more and more genetically diverse

Selection results in __________

a shift in frequency

Why doesn't resistance increase when it becomes resistant to both C and B

because it is still being suppressed by the A in the cocktail

What is the T cell

center of the immune system; the cell that is supposed to hunt and find a virus

What is evolution

change in the frequency of a trait over time

What's another name for natural selection

clonal selection

The 1st AZT resistant virus arose due to mutation, the rest is due to __________

clonal selection (Law of Parsimony)

What is sexual dimorphism?

difference between males and females

What kind of virus is HIV

diploid RNA-based retrovirus

When referring to phylogenetic trees, the base of the tree is _________ in time than the tips

earlier

Glypotodons are _________

extinct giant armadillos

What is the Law of Succession

extinct species resemble extant species in same geographic area

What factors give rise to a higher chance for beneficial mutations

fast mutation rate; large population; short generation time; quick replication

What are some traits that could evolve in HIV virus

gp120 transcription or insertion proteins antiviral drug resistance

What viral protein is associated with the binding to the CD4

gp120 (docking glycoprotein)

A phylogenetic tree is a _________

hypothesis about the evolutionary history of a species

How does HIV kill its host

immune system is weakened --> AIDS --> secondary infections --> death

Where is integrase found in relation to HIV

inside the virus

Why was the finding of the Ichythosaur important

it suggests that swimming with a tail evolved 3 times

Why do we care about gp120

it's something that the virus can evolve to be different

What are CD4+ T cells

mature T helper cells express the surface protein CD4

Non-functional pseudogenes evolve with _______ patterns indicating descent with modification of traits that have no function.

nested

What are vestigial genes

pseudogenes

What are vestigial structures?

remnants of features that served important functions in the organism's ancestors (nonfunctional homologous structures)

What are the essential 3 proteins for HIV

reverse transcriptase, integrase, and protease

Low variance = _____ evolution

slower

Natural selection is not a force/pressure, it is a __________

sorting process

What trait could be extremely advantageous to the virus if they evolved it in the presence of a drug cocktail

the ability to swap genes (like some bacteria)

Where in the world would we expect human resistance to HIV to be the highest

the highest frequency would happen where infections are the greatest and have been happening for the longest period of time

The more nucleotides that give resistance = __________________

the more opportunities for drug resistance to arise

The more we suppress something ________

the more selective pressure and the more advantage the surviving virus has

Why does HIV evolution reach a plateau at some point

the patient's immune system is breaking down and the HIV doesn't have a T cell preventing survival and replication

The phase between DNA synthesis and DNA splicing is called ___________

the transitory phase

Why can't we evolve the loss of a pseudogene

there is no cost or trade off in which natural selection can act upon (no protein therefore no phenotype)

The pattern of independent evolution serves as evidence that _______________

there's a predictable process happening over and over again suggesting the impact of the environment

What is an adaptation

trait that has evolved by natural selection and therefore has a functional match with environment


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