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COB Molecular > Lec 6. Molecular Evolution > Flashcards

Lec 6. Molecular Evolution Flashcards

1
Q

What does Divergent Evolution mean?

A

Homologs are derived from a common ancestor

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2
Q

What are two types of homologs?

A

Paralogs and orthologs

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3
Q

What does paralog mean?

A

Within a species (Gene Duplication)

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4
Q

What does Ortholog mean?

A

Between species

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5
Q

What does Convergent Evolution mean?

A

Same end point, different start point.

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6
Q

Pertaining to convergent evolution, what is similar and not similar?

A

Phenotypes structures similar but nucleotide/amino acid identity not similar

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7
Q

What are four reasons why a phylogenetic Trees can disagree?

A

When comparing phenotypic/molecular info, convergent evolution or horizontal gene transfer has occurred, sequence info has been lost through purifying selection

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8
Q

What is assumption 1 in Zuckerkandl and Linus Pauling’s 1965 hypothesis?

A

Spontaneous DNA mutation is random throughout the genome

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9
Q

What is assumption 2 in Zuckerkandl and Linus Pauling’s 1965 hypothesis?

A

Mutation of each gene is that genome is equally random

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10
Q

What is the observation in Zuckerkandl and Linus Pauling’s 1965 hypothesis?

A

Mutation rates are consistent amongst several mammalian lineages

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11
Q

What is the conclusion in Zuckerkandl and Linus Pauling’s 1965 hypothesis?

A

The rate of molecular evolution is constant over time in all lineages

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12
Q

Was Zuckerkandl and Linus Pauling’s 1965 hypothesis conclusion true or false? why

A

False, within lineages, molecular clocks are roughly constant over time and UNIVERSAL molecular evolutionary clock most definitely does NOT exists.

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13
Q

What are three ways to classify mutations?

A

The cause, phenotypic effects and genotype descriptions

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14
Q

What are the two subtypes of genotype descriptions when pertaining to classifying mutations?

A

Positional and molecular change

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15
Q

What are the three subtypes for molecular change?

A

substitution mutation, Insertions/deletions and transposition.

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16
Q

What are substitution mutations?

A

point mutations

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17
Q

Define substitution mutations

A

A single base pair changed indentity

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18
Q

What causes substitution mutations?

A

Pol error that was not proofread and error-prone DNA damage repair

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19
Q

During substitution mutations what changes occur?

A

Transition and transversion

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20
Q

What is transition?

A

Purine to purine or pyrimidine to pyrimidine

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21
Q

What is transversion?

A

purine to pyrimidine and vice versa

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22
Q

What are the effects of substitution mutations?

A

silent mutations, Missense mutations, Neutral mutation and Nonsense mutation

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23
Q

Define a silent mutation

A

No change in amino acid

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24
Q

Define Missense mutation

A

Change in amino acid

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25
Q

Define Neutral mutation

A

Change to a chemically similar amino acid

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26
Q

Define Nonsense mutation

A

change to a stop codon

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27
Q

Neutral mutation falls under what other mutation?

A

Missense mutation

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28
Q

Which of the three mutations pertaining to substitution mutation are synonymous?

A

Silent mutation

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29
Q

Which of the three mutations pertaining to substitution mutation are nonsynonymous?

A

Missense and nonsense

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30
Q

With Codon degeneracy, what two rules do you need to keep in mind?

A

Changes in the 1st and 2nd codon position are usually nonsynonymous. Transitions in the 3rd codon position are usually silent

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31
Q

Consider every position of every codon, and mutate each to ever other possible nucleotide. What NS:S ratio would we see?

A

3:1:1

32
Q

In the absense of selection, what NS:S ratio do we expect?

A

3:1:1

33
Q

If positive selection (mutations are good) is present, what do we expect from the NS:S ratio?

A

To be larger

34
Q

If purifying selection is present (mutation is bad), what do we expect from the NS:S ratio?

A

to be smaller

35
Q

What is the definition for insertion or deletion?

A

1-1000s of base pairs are added or removed

36
Q

What causes insertions or deletions?

A

Transposon cut/paste, pol slippage, unequal crossing over.

37
Q

What are the effects of insertions or deletions in a coding region?

A

No much if the number of base pairs was a multiple of 3 but FRAMESHIFT mutation if not a multiple of 3

38
Q

What are the effects of insertions or deletions in a noncoding region?

A

Can alter regulation, deposition of a new/duplicate exon or gene

39
Q

What is another effect of insertions or deletions?

A

Creation of a fragile site on the chromosome

40
Q

What is the definition of Transposition?

A

Movement of a transposon within the genome

41
Q

What are two characteristics of Transposition?

A

Excision is not precise, so host sequences go along for the ride to the next destination. Removal leaves behind a scar

42
Q

What are the effects of Transposition?

A

In general the same as insertions and deletions.

43
Q

What is one thing to note about Transposition?

A

This is the second way to make a gene duplication

44
Q

What are two ways to duplicate all/part of the gene?

A

Transposition or crossing over

45
Q

Duplicate all/part of the chromosome

A

aneuploidy

46
Q

Duplicate the whole genome

A

polyploidy

47
Q

What are two outcomes after gene duplication occurs?

A

Gene inactivation or change of gene function

48
Q

True or False? Mutations are more likely to be advantageous than detrimental

A

False. Are more likely to be detrimental

49
Q

Why do most duplicate genes become inactive?

A

Mutations are more likely to be detrimental

50
Q

What are pseudogenes?

A

Non-functional genes

51
Q

What is a pseudoexon?

A

Non-functional exon

52
Q

True or False? Some genes that become active can become active once more

A

True

53
Q

Do single-copy genes become pseudogenes?

A

Rarely

54
Q

What is one single-copy gene that became a pseudogene in vertebrates?

A

L-gulono-γ-lactone oxidase

55
Q

How did we lose L-gulono-γ-lactone oxidase?

A

Via diet. Not having enough vitamin C

56
Q

What are two reasons for a duplicate gene to be retained?

A

Extra expression is needed or a new function is created

57
Q

What are two ways the function of a gene can change?

A

Addition of function by protein elongation or mutation accumulation tinkers with protein function

58
Q

What are 4 ways of adding function by protein elongation?

A

duplicate a protein domain, remove the stop codon, remove a splice site, and transposon/viral insertion into an exon

59
Q

What are gene terms?

A

Exon, intron

60
Q

What are protein terms?

A

Domain

61
Q

Can domain boundaries by different than exons?

A

Yes. Moving an exon does not mean moving a domain

62
Q

What is an example of domain repeats?

A

Immunoglobulins

63
Q

What are three ways mutation accumulation tinkers with protein function

A

Subfunctionalization, Neofunctionalization and gene rearrangements

64
Q

Define subfunctionalization

A

Fine-tuning the exsisting function

65
Q

Define Neofunctionalization

A

A brand new function emerges

66
Q

Define gene rearrangements

A

Shuffle of the deck

67
Q

What are three ways to exon shuffle?

A

Exon duplication (protein elongation, Exon deletion (protein shortening) and exon Insertion (protein domain swapping)

68
Q

What are the 5 types of gene rearrangements?

A

Exon shuffling, alternative splicing, overlapping genes, intron sliding, genes within introns

69
Q

What are mosaic/chimeric proteins?

A

Pieces of one protein mixed with another protein usually resulting from Exon insertion.

70
Q

What is a good example of mosaic/chimeric proteins?

A

Blood clotting agents

71
Q

What is alternative splicing?

A

Temporary domain swapping

72
Q

Define overlapping genes

A

Constrains mutation

73
Q

What is an example of how overlapping genes can occur?

A

Frameshift mutation

74
Q

What does intron sliding do?

A

Expose/cover protein coding regions

75
Q

What are Intron-encoded protein genes?

A

Translated gene within excised intron

76
Q

What is a nested gene?

A

gene in antisense strand of an intron

COB Molecular (36 decks)

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