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Genomic Biology > Exam 2 > Flashcards

Exam 2 Flashcards

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1
Q

What kind of mutation has multiple slashes through it on a dot plot?

A

repeats

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2
Q

what kind of mutation has a missing portion of the line on a dot plot?

A

deletion

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3
Q

What kind of mutation makes an X on a dot plot?

A

inversion

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4
Q

Who do you score a sequence alignment and dot plots?

A

matches = +1
anything else = -1

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5
Q

Why are 2 examples of indels?

A

insertion/deletion

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6
Q

what is an example of a subsitution?

A

transversion/transition

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7
Q

synonymous (dS) mutations means the __________ amino acid is coded for

A

original

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8
Q

non-synonymous (dN) mutations mean the _________ amino acid is coded for

A

incorrect

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9
Q

when dN/dS = 1 is means what?

A

neutral evolution

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10
Q

when dN/dS > 1 it means what?

A

positive/diverging evolution

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11
Q

when dN/dS < 1 means what?

A

negative/purifying evolution (conserved)

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12
Q

how does point mutations affect the coding sequence?

A

changes the amino acid = change in function

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13
Q

how does point mutations affect regulatory sequences?

A

TF binding site mutations

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14
Q

what is polyQ; and what disease does it cause?

A

polyglutamine mutation; Huntingtons

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15
Q

what is the mechanism of polyQ mutation?

A

emerges from DNA replication slippage causing amino acid repeats

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16
Q

What does slippage during replication cause (gene birth)?

A

repeats at sight of replication that are unstable

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17
Q

what is unequal cross over during meiosis (gene birth)?

A

when loci replicate and there are duplicates or portions of gene missing

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18
Q

what is transposible elements (gene birth)?

A

transient segments of DNA that remove or insert themselves

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19
Q

What is fusion (gene birth)?

A

2 genes are combined to create one gene

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20
Q

what is fission (gene birth)?

A

1 gene breaks into 2

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21
Q

What is horizontal gene transfer (gene birth)?

A

moving genetic info from one organism to another

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22
Q

what is de novo gene birth?

A

new gene comes from a DNA sequence that used to not code for a protein

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23
Q

what is whole genome duplication (gene birth)?

A

when there is 2 copies of each gene after

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24
Q

What are the 8 forms of gene birth?

A
  1. slippage during replication
  2. unequal cross over
  3. transposable elements
  4. Fision
  5. fussion
  6. horizontal gene transfer
  7. de novo gene birth
  8. whole gene duplication
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25
Q

What is neofunctionalizartion?

A

gene duplication produces a new gene with a new function

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26
Q

what is subfunctionalization?

A

gene duplication causes function to be split

27
Q

what is pseudofuncationalization?

A

one gene does not function

28
Q

Orthologs comes about from _____________

A

speciation event

29
Q

paralogs come about from ____________

A

duplication event

30
Q

orthologs form a ___________

A

clade

31
Q

orthology does NOT have to be ____:____

A

1:1

32
Q

________ usually have similar function

A

orthologs

33
Q

What are the 4 advantages of multiple copies?

A
  1. back ups
  2. many functions
  3. increased diversity
  4. regulatory flexability
34
Q

what is a disadvantage of multiple copies?

A

lots of energy

35
Q

What is divergent evolution?

A

a common ancestor ‘radiates’ out to form sister species

36
Q

what is concerted evolution?

A

related genes within a species undergo genetic exchange, causing their sequence evolution to be concerted over some period of time.

37
Q

what is birth and death evolution?

A

some genes die out

38
Q

Why is E. coli a good model system?

A

its the model bacteria

39
Q

Why is yeast a good model system?

A

single celled eukaryote

40
Q

Why is Arbidopsis a good model system?

A

grows fast (nicotine/tobbaco)

41
Q

Why are flies a good model system?

A

small genome
clear genetic phenotypes

42
Q

Why is C. elegans a good model system?

A

development

43
Q

Why is sea urchin a good model system?

A

transparent embryo

44
Q

Why is zebra fish a good model system?

A

toxicity screens
short life span

45
Q

Why is xenopus laeu (frog) a good model system?

A

development
enviornmental toxicity

46
Q

Why is chickens a good model system?

A

development
B/T cells

47
Q

what 3 animals can regenerate?

A
  1. starfish
  2. axolotl
  3. planana
48
Q

What has the largest neurons?

A

aplysia (slug)

49
Q

what is organolds?

A

lab grown organs/ human tissue

50
Q

What 2 things make us human?

A
  1. genome
  2. our life
51
Q

what are 2 ways of studying domestication?

A
  1. archeology
  2. genome
52
Q

What 2 ways is the genomes of domestication studied?

A

reference genomes
ancient genomes

53
Q

What 3 things can we learn from domesticated genomes?

A
  1. differences in organism
  2. when
  3. who
54
Q

how does a molecular clock work?

A

mutation rates are constant; relies on fossil records

55
Q

on a graph of time v. mutation rate, is positive selection on the top or bottom?

A

top

56
Q

on a graph of time v. mutation rate, is negative selection on the top or bottom?

A

bottom

57
Q

What affect happens when domestication takes place?

A

bottle necking

58
Q

what is gene flow?

A

trading of genes across other populations not near them

59
Q

what happens to adrenal function after domestication?

A

decreased function (neural crest)

60
Q

what does a divergent evolution phylogenetic tree look like?

A

see picture

61
Q

what does a concerted evolution phylogenetic tree look like?

A

see picture

62
Q

what is a transversion?

A

interchanges of purine for pyrimidine bases
(DIFFERENT TYPE)

63
Q

what is a transition?

A

interchanges of two-ring purines (A G), or of one-ring pyrimidines (C T)
(SAME TYPE)

Genomic Biology (6 decks)

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