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z Evolution > Test 1 > Flashcards

Test 1 Flashcards

1
Q

What are the three contents of the HIV virion?

A

Reverse transcriptase, Integrase, Protease

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2
Q

What is the function of HIV’s reverse transcriptase?

A

Uses the virus’s RNA as a template to construct a complementary strand of viral DNA.
Makes the DNA with nucleotides stolen from the host cell (target for drugs)

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3
Q

What is the function of HIV’s integrase enzyme?

A

Splices the HIV DNA genome into the host cell’s genome.

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4
Q

What occurs after the HIV genome is inserted by the integrase enzyme?

A

The host cell’s RNA polymerase transcribes the viral genome into viral mRNA, and the host cell’s ribosomes synthesize viral protein.

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5
Q

What is the function of HIV’s protease enzyme?

A

Cleaves precursors of various viral proteins in a site specific manner into functional forms, allowing the virions to mature.

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6
Q

What are possible targets of HIV drug treatment?

A

HIV’s unique enzymes: Reverse transcriptase, integrase, protease

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7
Q

What was the first target of HIV drug treatment? How did this first treatment occur?

A

The reverse transcriptase enzyme. AZT(azidothymidine) was incorporated by HIV’s reverse transcriptase enzyme, terminating transcription (Lack of a 3’ OH).

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8
Q

How did HIV evolve resistance to AZT?

A

Versions of reverse transcriptase emerged that functioned similar to host reverse transcriptase- having a modified shape.
In 2 years a population evolved that was completely resistant.

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9
Q

What three qualities allow viruses (HIV) to evolve quickly?

A

High fecundity (reproduction), Small generation time (less than days), High mutation rate (coupled with very small genome)

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10
Q

What is the solution to treating HIV if it evolves so quickly?

A

Use a drug cocktail that would require far more unlikely mutations to resist

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11
Q

What is the highest hazard ratio for resistance in terms of % drug usage?

A

80-90% of the drug is taken

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12
Q

What are the three phases of HIV infection?

A

Acute phase, chronic phase, AIDS phase

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13
Q

What is the acute phase of HIV infection?

A

Concentrations of virions climbs quickly while concentration of CD4 T cells plummet.
Ends when viral replication slows and concentration of virions drops. Host’s CD4 T-cell count recover somewhat.
The host may show symptoms of a general infection.

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14
Q

What is the chronic phase of HIV infection?

A

HIV continues to replicate and concentrations stabilize. The concentrations of CD4 T cells fall.

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15
Q

What is the AIDS phase of HIV infection?

A

Concentration of CD4 T cells drops below 200 cells per cubic millimeter, the patients immune system has begun to collapse and no longer can fight off the opportunistic viruses, bacteria, and fungi.

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16
Q

Have humans evolved resistance to HIV?

A

Not really, but there are genetic variations which render some populations more resistant.

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17
Q

Describe the mutation of allele CCR6-delta32

A

32 base pair deletion in the CCR5 gene.
This allele is found most commonly in Northern Europe, about 15%.
Individual with the all are partially to completely resistant to HIV (Only 4 transmembrane domains, not functional or recognizable)

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18
Q

Describe the history of allele CCR6-delta32 mutation

A

The allele is around 700 yrs old (pretty young), however very abundant- it likely occurred through natural selection.

The top hypothesis is that the black plague caused this mutation, since it was a very high selection pressure.

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19
Q

Describe the Allele CD4 substitution variant

A

C868T substation variant (tryptophan for arginine)
Individuals who are heterozygous have lower resistance to HIV.
Occurs in Kenyan female sex workers

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20
Q

How are viral populations transmitted?

A

When an individual is infected there is a small population of virus but the host is naive. Diversity increases with high mutation rate.
A SUBSPECIES of that virus could infect a new host (founder effect/genetic bottleneck). The population of viruses from each host would then be separate clades.
The genetic diversity of the virus in recipient host will represent a subset of diversity found in the donor host.

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21
Q

Describe the Schmidt/Trahan case

A

Uses population genetic to provide reasonable evidence that a doctor infected his nurse with HIV from the doctors HIV infected patient, since they were the same subpopulations of HIV.

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22
Q

Simply, where did HIV come from?

A

Zoonotic virus (came from animals) that switched hosts into humans. Relatively recent pathogen in humans

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23
Q

How many different HIV groups are there? Which one is the significant problem?

A
  1. Group M is the widest spread.
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24
Q

How long ago did group M first infect humans? How do we know this?

A

80 years, we can graph a line on top of the observed mutation rate to the original common ancestor species.

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25
Q

Why is it a “good” strategy for HIV to be lethal?

A

HIV has the greatest selection pressure towards reproduction, and for HIV to be effective at transmission, damage to the host is inevitable.

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26
Q

What level of infection should viruses have according to natural selection?

A

The higher the viral load, the shorter the period of AIDS free infection, but the higher the rate of transmission. Therefore viruses should have a median level of infection

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27
Q

Why is the viral load of HIV higher in Zambia than Amsterdam?

A

HIV has a higher opportunity for transmission in Zambia, the loss of host is balanced by the higher transmission rate.

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28
Q

How is HIV protected against the host immune system?

A

Evolution of gp120, one of the surface proteins of the virus that is important for surface binding.
It evolves at a fairly rapid rate, driven by the immune system.
The evolution of gp120 is inversely proportional to the exhaustion of the immune system, no selection pressure after immune system exhaustion

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29
Q

Describe the switching of the virus to a different host cell.

A

Initial viruses require CCR5, sometimes viruses acquire new mutations and can now infect cells with CXCR4.
This is a dead end for the virus (can no longer infect new hosts)
The virus does this because of selection pressure to favor the new, more prevalent CXCR4.

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30
Q

Describe how forms of selection pressure for HIV can be at odds with one another.

A

There is both a selection pressure for efficient replication within a host, and selection for transmission from old host to new host.

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31
Q

Where does the theory of evolution date back to?

A

Before Darwin, theory of a common ancestor for humans and apes dates back towards the 1750s

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32
Q

When did Darwin write On the Origin of Species?

A

1859, around the time of the civil war

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33
Q

What are the fundamental limits for knowledge through science?

A

We can only interrogate the physical world with science

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34
Q

Define science, what is necessary for something to be called science?

A

Science is an endeavor in which falsifiable hypotheses are systematically tested, focused on the natural world
The hypothesis must be falsifiable (ex: supernatural phenomenon cannot be disproven)

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35
Q

What is a theory?

A

A coherent set of well-tested hypothesis that guide scientific research

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36
Q

Compare Special Creation vs Descent with Modification

A
  • Species were created independently vs share a common ancestor
  • Species do not change through time vs change through time
  • Species were created recently vs life on earth is very old
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37
Q

Define Microevolution

A

Microevolution is within a population or species; changes in allele frequencies, relative abundances

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38
Q

Define Macroevolution

A

Macroevolution is changes that occur during the process of speciation (higher level, between species)

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39
Q

What are some examples of microevolution?

A

Soapberry bugs
Ballon Vine
Apple Maggots

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40
Q

Describe Complementation in Mexican Tetra

A

Two individuals that have individually evolved eyelessness when combined have their mutations heterozygous, individuals who are heterozygous now have functional genes for eyes

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41
Q

What is piloerection?

A

Example of change over time in humans (goosebumps)

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42
Q

What was special about Cuvier in 1812

A

He demonstrated that it was possible for species to go extinct with the Irish Elk

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43
Q

What is the law of Succession?

A

A general pattern of correspondence between living and extinct species from the same local
Ex: South America- placental mammals; Australia - marsupials

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44
Q

What is Artificial Selection?

A

Domesticiation, corollary to natural selection

45
Q

What is a fishapod?

A

Transitional species between fish and tetrapods

46
Q

Describe Tiktaalik

A

An ancestor to tetrapods, it was predicted before it was found because we needed a transitional species between fish and tetrapods

47
Q

Describe how the finding of Tiktaalik was an example of hypothesis driven science?

A

They had a hypothesis that there would be a transitional species in a fossil record, specifically in rock that was from that era and could contain an aquatic environment at that era

48
Q

Define Homology

A

Possession by two or more species of a character state derived, with or without modification, from their COMMON ANCESTOR

49
Q

What are some examples of homology?

A

Limb structures across tetrapods

50
Q

Define convergent evolution

A

Individuals that are not closely related to each other share similar phenotypes. Driven by selection pressures

51
Q

What are some examples of convergent evolution?

A

Fish vs aquatic mammals. Seals vs Sea Lions. Anteater vs Pangolin. Eyes in octopus vs other vertebrates

52
Q

Describe examples of Molecular homology

A

All organisms share the same 20 amino acids.
Humans also share virtually all the same genes with other primates.
Fruit flies share similar molecular pathways to humans

53
Q

Describe the significance of PMP-22

A

Peripheral myelin protein-22 has a flanking repeat on human chromosome 17. This allows for misalignment of chromosomes during meiosis, and therefore different neurological diseases can happen in progeny.
This genetic flaw is shared in primates, and therefore powerful evidence for evolution against special creation

54
Q

What are pseudogenes? What two things differentiate pseudogenes from genes?

A

Derived from a reverse transcriptase process wherein they end up without regulatory elements. Processed pseudogenes lack introns. Can cause genetic diseases.

Lack of introns and regulatory domain

55
Q

What are transposable elements?

A

“selfish” DNA sequences that drive their own replication

56
Q

Define Uniformitarianism

A

The assumption that geological processes taking place now operated similarly in the past- erosion in one small area explained with same process as Grand Canyon

57
Q

Define Catastrophism

A

Todays geological formations resulted from catastrophic events (volcanic eruptions, asteroid) which occurred in the past on a scale never observed today

58
Q

Why are James Hutton and Charles Lyell significant?

A

Late 1700s- credited with studying geological processes such as erosion, mud and sand deposition- demonstrated that the old must be old based on uniformitarian assumptions

59
Q

Which is older, the geological time scale or Darwin’s theory of evolution?

A

The geological time scale. This time scale forms the framework for geological studies today

60
Q

What is radiometric dating?

A

Using radioactive decay to estimate age

61
Q

Describe the life of Charles Darwin

A

Born in 1089, expected to go to medical school but decided to be a naturalist. He spent 5 years on the Beagle traveling all over the world. He then spent 22 years studying his material sand writing before publishing in 1859. First publication example of natural selection- he continued publishing until his death.

62
Q

Describe the life of Russel Wallace

A

Much poorer than Darwin, he began his explorations by apprenticing to a map maker. He explored the Amazon and Southeast Asia. He published Darwinism, a non-technical explanation of natural selection

63
Q

What is important thing aspect of evolution did Darwin and Wallace not know about?

A

They did not have access to Gregor Mendel’s understanding of inheritance. Years after Mendel’s death the “Neo-Darwinian” synthesis occurred (genetics + evolutionary theory

64
Q

What are the 4 postulates of natural selection

A
  1. Individuals vary
  2. This variation is heritable
  3. Some individuals will not survive to reproduce
  4. The survival and reproduction of individuals is not random
65
Q

What is Darwinian Fitness?

A

An individuals ability to survive and reproduce

66
Q

What is an adaptation?

A

A trait that increases an organism’s Darwinian fitness compared to other individuals lacking the trait

67
Q

Describe the evolution of beak shape in Galapagos finches

A

There is a diversity of beak shapes with multiple species but they were all still finches.
Galapagos tortoises have varied phenotypes as well (neck length)

68
Q

Describe Peter and Rosemary Grant and the purpose of their experiment

A

Did research on a very small island of the Galapagos- Daphne Major
They banded every bird and knew parent relationships between all birds
They tested Darwin’s Theories on the group of birds from Daphne Major

69
Q

How did Peter and Rosemary Grant’s experiment line up with Darwin’s postulates?

A

Phenotypic Variation - Yes (body and beak size)
Heritable Variation - Yes (beak depth plotted against offspring beak depth)
Change in ability to survive and reproduce - Yes, drought occurred that shifted selection pressure towards larger beaks

70
Q

What other big explanation could there be for perceived heritability changes?

A

Nutrition

71
Q

Describe the drought that occurred on Daphne Major

A

84% of the population died in 1977 due to drought which limited the amount of seeds.
This was a selection pressure that shifted beak size slightly higher - the only seeds present in 1977 were large and hard seeds. (microevolution example)
Population continued to evolve after 1977 though, evolution is not one dimensional and after the drought smaller beaked birds were favored more highly again

72
Q

Does natural selection act on populations or individuals? What about evolution?

A

Natural selection is acting on individuals, but the populations evolve
Likewise: natural selection acts on phenotypes, but evolution consists of changes in allele frequencies

73
Q

Describe the ability of natural selection to shift particular traits

A

Some traits respond more efficiently to selection pressures.
Although selection acts on existing traits, new traits can evolve as rare allele can become more common (corn oil content)

74
Q

Define Standing Variation

A

The alleles already present in a population.

75
Q

What are exaptations?

A

Phenotypic variation for a trait that could become an adaptation in the FUTURE.
Natural selection can co-opt existing variation to create novel phenotypic structures.

76
Q

What are some examples of exaptations?

A

Pandas and their radial sesamoid bone.
Evolution of placental mammals- fetus develops to an advanced state inside the womb (Inflammatory response was co-oped as an exaptation to allow for embryo implantation)

77
Q

Explain why natural selection does not lead to perfection

A

It is constrained by existing variation

Ex: Vertebrate eye blind spot, Larynx and esophagus pass over each other

78
Q

Describe evolutionary trade-offs and examples

A

Natural selection leads to an optimal phenotype that may strike a balance between alternative evolutionary forces.
Examples: mosquitofish gonopodia size, the fragile bones of cheetahs

79
Q

Define Blending inheritance. Why is it flawed?

A

The old favored view of how traits were passed from parents to offspring, you are an average of your parents (flawed).
If this were true, rare advantageous alleles would have no hope of spreading, but they do through natural selection

80
Q

Describe Modern Synthesis

A

Fusion of genetics with darwinian evolution.
Gradual evolution (microevolution) results from small genetic changes that are acted upon by natural selection.
Microevolution explains macroevolution.

81
Q

What is a taxa in a phylogenetic tree?

A

Tips of branches- sometimes species, genera, populations

82
Q

What is an operational taxonomic unit

A

An operational definition used to classify groups of closely related individuals. Can simply be the group of organisms currently being studied

83
Q

What is a characteristic we can create a universal phylogenetic tree from?

A

16S Ribosomal RNA subunit

84
Q

What is a node in a phylogenetic tree?

A

Internal points where branches split, shared ancestor

85
Q

What is a character is a phylogenetic tree?

A

Heritable traits that can be compared across organisms

86
Q

How are relationships inferred from a phylogenetic tree?

A

Horizontal distances. Look at common ancestors to determine relationships

87
Q

How often do changes in evolution trees occur?

A

All the time. Evolutionary trees are hypothesis, even if they are well supported.

88
Q

What is a clade?

A

A group of a taxa that share one or more derived traits

89
Q

What is a cladogram?

A

A phylogenetic tree based on derived traits

90
Q

What is a monophyletic group?

A

A set of species descended from a single common ancestor

91
Q

What is a paraphyletic group?

A

includes a common ancestor and some, but not all, of its descendants

92
Q

What is a synapomorphy?

A

A shared, derived character

93
Q

What is an autapomorphy?

A

A derived character redistricted to a single lineage

94
Q

What is homoplasy?

A

Character shared by a set of species but not present in their common ancestor

95
Q

What are the two ways in which homoplasy can arise?

A

Reversal or convergent evolution

96
Q

What is a reversal?

A

A derived character reverts to an ancestral character through mutation or selection

97
Q

Differentiate between transition and transvehrsion mutations

A

(purine-purine is transition), (purine-pyrimidine is transversion)
Transition mutations are far more common

98
Q

What is the challenge with using DNA sequence data to determine phylogenetic tree?

A

Need to use lots of genes, requires good computer

99
Q

How does Maximum Parsimony method work?

A

1) Consider all possible phylogenetic relationships
2) Calculate the number of transition state/mutational steps necessary for the data to explain that particular tree
3) Identify the tree that minimizes the number of character state changes

100
Q

Describe the qualities of the Maximum Parsimony method

A

The simplest explanation is often right, but not always

Not as accurate but fairly easy

101
Q

How does Maximum Likelihood method work?

A

Uses a model of evolution that does not assume all morphological changes are equal.

102
Q

Describe the qualities of the Maximum Likelihood method

A

Clearly superior to maximum parsimony.
Requires a lot of math and has a complicated formula
Often very similar to Parsimony, but has to consider every tree

103
Q

How does the Bayesian Influence method work?

A

Evaluates each tree to calculate the probability of the tree given the data
- The answer to this is the posterior probability for each tree, which should all add up to 1. We look for the single tree that has the highest posterior probability

104
Q

How does the Neighbor-Joining method work?

A

A distance method (not cladistic- dependent on derived traits). Counts up the number of DNA differences between each pair, and then calculates the sequence divergence.

105
Q

Describe the qualities of the Neighbor-Joining method

A

Exists because it is fast and easy

Usually works but often fails

106
Q

What is Bootstrapping?

A

A statistical method of resampling the data and calculating the proportion of times a solution is supported.

  • Creating new DNA sequence replicant and seeing which that sequence reports
  • Measures how robust the data is, tend to get smaller values with less data
107
Q

Describe heuristics

A

Any approach to problem solving or self-discovery that employs a practical method not perfect but sufficient for reaching an immediate goal.
(A shortcut- in terms of maximum likelihood we can eliminate groups once we know that one group is better

108
Q

What is similar between the maximum likelihood, maximum parsimony, and bayesian influence methods?

A

All are cladistic methods that consider ancestral and derived traits
All three evaluate every single possible tree (although heuristic methods can be used)

z Evolution (2 decks)

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