G24

Question 1

What kind of nt change occurs more frequencty?

Answer 1

transition mutation

Question 2

what is a transition mutation

Answer 2

purine to purine A G

pyrimidine to pyrimidine T ->C

Question 3

what is a transversion mutation

Answer 3

Purine to pyrmidine vv
A - T
A - C
G - T
G -C

Question 4

what is genetic saturation waht can this be seen in

Answer 4

Genetic saturation is the reduced appearance, which occurs over time, of sequence divergence rate that results from reverse mutations, homoplasmies and other multiple changes occurring at single sites along two genetic lineages.
can be seen in transition mutations but not transversion

Question 5

What do we need to correct for when measuring sequence divergence

Answer 5

changes we dont see

Question 6

What kind of changes can be seen and what changes cannot be seen

Answer 6

seen: single substituion, multiple substitution, coincidental subsitution
not seen: parrallel, convergent or back

Question 7

what is the acctual no. of substitutions when sequence diveregence is low

Answer 7

is very close to the observed no.

Question 8

what is the equation for the jukes cantor model

what is it

Answer 8

d(distance) = -3/4ln(1-4/3p)
where p = proportion of nt differences
multiple hit correction equation produces maximum liklihood estimate of the no. of nt subs between two species

Question 9

what are the assumptions for the jukes cantor model?

Answer 9

rate of nt sub is the same for all pairs of the 4 nts,
equality of substitution rates among sites, equal nt frequences
doesnt correct for higher rate of transitional substitutions as compared to transversional substitutions.

Question 10

how does the Kimura 2 model differ from the Jukes Cantor model

Answer 10

it takes into accounts transversions as well as transitions

Question 11

give an example of the failings of the molecualr clock in virology

Answer 11

HIV-1 and HIV-2
rather than take fossil, isolate A and then later take B from same patient, use this to show changer per year.
this showed dthat HIV 1 and 2 are about 50% divergent
wanted to discover when they diverged from each other, figure was 50 years or so using molecular clock
however later evidence showed them to be 200,000 years diverged, although more likekly to be millions of fyears

Question 12

what do comparisons of paralogous globin genes in different species show?

Answer 12

that different globin species seem to be evolving at the same rate as envisioned by amount of change between them,
despite differences in breeding geernation time etc, between shark humans and carp beta globins
- shown that globins seem to be on absolute time, independent of generation time.

Question 13

What effect does the generation time effect have on evoltuion

Answer 13

The shorter the generation time, the more generations can be seen in a fixed period of time. Since mutations occur at gamete formation and fertilisation, this would mean that the rate of evolution is faster.

Question 14

what kind of effect do silent substitutions show

Answer 14

generation time effect

Question 15

what are motherless genss

Answer 15

geness that appear out of non coding DNA but then have high mutation rates

Question 16

How can you measure how fast a gene will evolve

Answer 16

using dN/dS ratios
N = non synonmous substitutions
dN = proportion of non synonmous (change in aa protein)
dS = synonmous - doesnt change AA = assumed to be neutral as doesnt change AA so sam sub rate across sequence

Question 17

give an example of a greatly constrained gene

Answer 17

carboxyl peptidase, any AA sub will kill the organism

Question 18

what does it mean if dN/dS =1

Answer 18

neutral so no selection at all - pesudo gene,

de novo motherless are close to 1

Question 19

what does it mean if dN/dS >1

Answer 19

evolutionary arms race, not whole gene bits of gene typically large.

Question 20

How can genome size change

Answer 20

polyploidy - gene dosage stops effects
aneuploidy - non disjunction gives abnormal chromosome no.
chromsomal duplication/fussion - fusion more frequent than duplication
transposition
replication slippage
unequal crossing over - relatively infrequent

Question 21

give an example of codon usage bias

Answer 21

despite the fact that CUG and CUA both code for leucine and change is considered silent, evidence shows mutations are under low level of selection to mainatian codon bias. - perhaps for house keeping genes

Question 22

when is the molecular clock linear

Answer 22

over absolute time irrespective of the number of generations that have passed

Question 23

why do globin genes show absolute time effect

Answer 23

because they have a specific purpose they are functionally constrained

Question 24

what show a linear trend over generation time?

Answer 24

silent mutation

not selected