Exam 2

Question 1

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

Answer 1

repeats

Question 2

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

Answer 2

deletion

Question 3

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

Answer 3

inversion

Question 4

Who do you score a sequence alignment and dot plots?

Answer 4

matches = +1
anything else = -1

Question 5

Why are 2 examples of indels?

Answer 5

insertion/deletion

Question 6

what is an example of a subsitution?

Answer 6

transversion/transition

Question 7

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

Answer 7

original

Question 8

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

Answer 8

incorrect

Question 9

when dN/dS = 1 is means what?

Answer 9

neutral evolution

Question 10

when dN/dS > 1 it means what?

Answer 10

positive/diverging evolution

Question 11

when dN/dS < 1 means what?

Answer 11

negative/purifying evolution (conserved)

Question 12

how does point mutations affect the coding sequence?

Answer 12

changes the amino acid = change in function

Question 13

how does point mutations affect regulatory sequences?

Answer 13

TF binding site mutations

Question 14

what is polyQ; and what disease does it cause?

Answer 14

polyglutamine mutation; Huntingtons

Question 15

what is the mechanism of polyQ mutation?

Answer 15

emerges from DNA replication slippage causing amino acid repeats

Question 16

What does slippage during replication cause (gene birth)?

Answer 16

repeats at sight of replication that are unstable

Question 17

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

Answer 17

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

Question 18

what is transposible elements (gene birth)?

Answer 18

transient segments of DNA that remove or insert themselves

Question 19

What is fusion (gene birth)?

Answer 19

2 genes are combined to create one gene

Question 20

what is fission (gene birth)?

Answer 20

1 gene breaks into 2

Question 21

What is horizontal gene transfer (gene birth)?

Answer 21

moving genetic info from one organism to another

Question 22

what is de novo gene birth?

Answer 22

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

Question 23

what is whole genome duplication (gene birth)?

Answer 23

when there is 2 copies of each gene after

Question 24

What are the 8 forms of gene birth?

Answer 24

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

Question 25

What is neofunctionalizartion?

Answer 25

gene duplication produces a new gene with a new function

Question 26

what is subfunctionalization?

Answer 26

gene duplication causes function to be split

Question 27

what is pseudofuncationalization?

Answer 27

one gene does not function

Question 28

Orthologs comes about from _____________

Answer 28

speciation event

Question 29

paralogs come about from ____________

Answer 29

duplication event

Question 30

orthologs form a ___________

Answer 30

clade

Question 31

orthology does NOT have to be ____:____

Answer 31

1:1

Question 32

________ usually have similar function

Answer 32

orthologs

Question 33

What are the 4 advantages of multiple copies?

Answer 33

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

Question 34

what is a disadvantage of multiple copies?

Answer 34

lots of energy

Question 35

What is divergent evolution?

Answer 35

a common ancestor 'radiates' out to form sister species

Question 36

what is concerted evolution?

Answer 36

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

Question 37

what is birth and death evolution?

Answer 37

some genes die out

Question 38

Why is E. coli a good model system?

Answer 38

its the model bacteria

Question 39

Why is yeast a good model system?

Answer 39

single celled eukaryote

Question 40

Why is Arbidopsis a good model system?

Answer 40

grows fast (nicotine/tobbaco)

Question 41

Why are flies a good model system?

Answer 41

small genome clear genetic phenotypes

Question 42

Why is C. elegans a good model system?

Answer 42

development

Question 43

Why is sea urchin a good model system?

Answer 43

transparent embryo

Question 44

Why is zebra fish a good model system?

Answer 44

toxicity screens short life span

Question 45

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

Answer 45

development enviornmental toxicity

Question 46

Why is chickens a good model system?

Answer 46

development B/T cells

Question 47

what 3 animals can regenerate?

Answer 47

1. starfish 2. axolotl 3. planana

Question 48

What has the largest neurons?

Answer 48

aplysia (slug)

Question 49

what is organolds?

Answer 49

lab grown organs/ human tissue

Question 50

What 2 things make us human?

Answer 50

1. genome 2. our life

Question 51

what are 2 ways of studying domestication?

Answer 51

1. archeology 2. genome

Question 52

What 2 ways is the genomes of domestication studied?

Answer 52

reference genomes ancient genomes

Question 53

What 3 things can we learn from domesticated genomes?

Answer 53

1. differences in organism 2. when 3. who

Question 54

how does a molecular clock work?

Answer 54

mutation rates are constant; relies on fossil records

Question 55

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

Answer 55

top

Question 56

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

Answer 56

bottom

Question 57

What affect happens when domestication takes place?

Answer 57

bottle necking

Question 58

what is gene flow?

Answer 58

trading of genes across other populations not near them

Question 59

what happens to adrenal function after domestication?

Answer 59

decreased function (neural crest)

Question 60

what does a divergent evolution phylogenetic tree look like?

Answer 60

see picture

Question 61

what does a concerted evolution phylogenetic tree look like?

Answer 61

see picture

Question 62

what is a transversion?

Answer 62

interchanges of purine for pyrimidine bases (DIFFERENT TYPE)

Question 63

what is a transition?

Answer 63

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