EB10

Question 1

Give examples of 6 human point mutations

Answer 1

1. albinism
2. triphalangeal polydactyly
3. Greigs cephalopolynyndactyly.
4. Piebaldism
5. Fibrodysplasia ossifican progressive
6. Hutchinson-Guildford progeria syndrome

Question 2

what is albinism caused by

Answer 2

370 Pro to Ser in FGFR2 gene

Question 3

what is triphalangeal polydactyly caused by

Answer 3

pro to ser GL13 (fingers fused)

Question 4

what is piebaldism caused by

Answer 4

skin patches

796 Arg to Gly in Kit gene

Question 5

what is fibrodysplasia ossifican progressive caused by

Answer 5

206 arg to his
ACVRI
tissues become ossified spontaneously or when damaged

Question 6

what is hutchinson gilford progeria syndrome caused by

Answer 6

lamin A gene

*symptoms resemeble aging

Question 7

Describe the yeast mutation accumulation experiment

Answer 7

4 mutation accumulation lines (MA LINES)
*Initially haploid yeast is isogenic *same genotype
each line is passed through 200 single cell bottlenecks on 3-4 day cycle of clonal growth for a total of ~4800 cell divsions

Question 8

what does bottle necking in MA experiment allow

Answer 8

relaxation of selection through several generations. allows us to see the full spectrum of spontaneous mutations accumulated through tie and measure their fitness effects

Question 9

what did the MA experiment with yeast show

Answer 9

5% average fitness decline at the end and 33 single nt changes

Question 10

what small scale changes occured in the MA yeast experiment

Answer 10

than transversions (A/C, AT, GC, GT)
should be 0.5 with no bias, found at frequency of 0.62.
* rate of G/C-> A/T mutations is 2.9X higher than oppostive
predicts AT bias composition

Question 11

what are gene repeat regions

Answer 11

highly unstable regions with much higher mutation rates than non repetative DNA.
mutation rate increases with rate of microsatellite or polynt repeat.

Question 12

what type of human disease are commonly caused by repeats, give three examples
how does no. of repeats effect disease

Answer 12

neurodegenerative

1. fragile x syndrome
2. Huntington disease
3. Spinocerebellar ataxia

** no of repeats tend to increase with generations, more repeats the more severe the disease

Question 13

what is FXS caused by

Answer 13

CGC repeat on FMR1 gene
normally 6-52, disease 200-2000
leads to loss of FMRP function

Question 14

what is huntingon disease caused by

Answer 14

CAG repeat on HD gene

normal 10-34 disease 40-121

Question 15

what is spinocerebellar ataxia caused by

Answer 15

CAG repeat on SCA6 gene

normal 4-18 disease 21-33

Question 16

what large scale insertions were seen in the yeast MA experiment

Answer 16

11 scale insertions and 4 deletions (5 of these flanked by mobile element insertions which induce chromosomal instabilities
** rate of deletion ususally higher than insertions

Question 17

Describe the second MA yeast experiment with more lines

Answer 17

145 MA instead of 4 lines used. allows observation of large scale events which are much rarer.
** diploidised haploid strain with markers and lines propageted for 2000 generations.
each line passed through a single bottle neck every ~20 generations

Question 18

what were the results of the 145 MA yeast experiment

Answer 18

1. 29 lines had whole chromsome duplication
2. 2 lines had whole chromosome loss: chrom IX (small)
   - — these lines couldnt sporulate (lost sex)
3. 26 small indels occured near simple repeats (stuttering)

Question 19

why is it easier to observe duplication of chromosome than loss

Answer 19

because most loses are lethal

Question 20

what was the rate of mutation per bp per gen for each experiment

Answer 20

1. 0.33x10-9
2. 1.6X10-10

** quite simialr

Question 21

what did they find in single nt mutations in the 145 line yeast MA experiment

Answer 21

equally likely to have S or NS mutations.
as selection was effectively removed by experiment regime
no. of mutations per chromsoome increased with chromosome length.
found no bias towards transitions or transversions

Question 22

what did the 145 MA experiment discover about effect of neighbours

Answer 22

overall there were lower mutation rates at A/T positions and higher at G/C
A/T showed no neighbour effect but C/G did
with cCg and tCg having the highest mutation rate.

Question 23

why would cG have a higher mutation rate in mammals? is this applicable to yeast?

Answer 23

as tend to be methylated which increases change of mutation
yeast was thought to have no mutation however recent study found 0.36% methylation at cytosines in yeast. calcualted that 1/22 of the CCg and TCG sites may be methylated

Question 24

what did the experiment showing mutation accumualtion in human sperm show

Answer 24

no. of mutations tend to double from 40-80 over 20 years.

also found gene effects, different genotypes are more or less likely to respond strongly with age.

Question 25

what is the mutation rate for primordial germ cells and post PGCs for males and females

Answer 25

simialr for both

Question 26

what affect does puberty have on fathers mutation rate of germ cells

Answer 26

drops much lower than pre/post PGC.

Question 27

how is sperm produced

Answer 27

constantly via assymetric division of self-renewing spermatogonial SCs ar a rate of 23 divisions/yeaer

Question 28

why might sperm be more likely to get mutations

Answer 28

as sperm divide more and more divisions could lead to mutations and as mutations tend to be deleterious a mutation improving fidelity of replication would be selected for.

Question 29

what is mutational bias

Answer 29

mutation has a bias towards creating more ATS

*rate of mutation to AT is 2.9X higher than oppostive, prediciting high AT biased composition.

Question 30

what is the predicted proportion of AT in yeast genome

Answer 30

 A/T -> G/C u=1, G/C -> A/T v = 2.9
 Equilibrium G/C composition predicted u/v
 v/u = 2.9
 p/1-p = 2.9, p = 2.9(1-p), p = 2.9 -2.9p
 p + 2.9p = 2.9, 3.9p =2.9, P = 2.9/3.9
 P = 0.74
Yeast genome predicted to be 74% AT
** assumes no selection, genome composition is only determined by rate of mutation in two directions.

Question 31

What was the observed AT proportion in yeast genome what does this tell us

Answer 31

59% AT composition in yeast
therefore reject null hypothesis
there must be selection against high AT composition or selection favouring G/C

Question 32

where else can AT bias be found

Answer 32

mitochondria mutation rate is 37X higher than nucleus and AT observed composition is 83%

Question 33

how do mutations vary across species, why?

Answer 33

mutation rate seems to vary across species

variation in fidelity of replicating and repair enzymes etc.

Question 34

what have the highest mutation rates

Answer 34

RNA viruses
no proof reading difficult to repair ss breaks e.g. HIV has high genetic variability during course of human infection of single strain of virus.

Question 35

what is the mutation rate in humans and HIV

Answer 35

human: 1 x10-10 per bp
HIV-1 = 5x10-4 per bp

**HIV-1 mutation rate is a million times higher than humans

Question 36

how does genome size correlate with mutation rate

why

Answer 36

increase in genome size lads to decrease in mutation rate.
* rna virus = smallest genome and highest mutation rate.
DNA viruses have slightly higher mutation rate than RNA and tend to be larger
*** larger you are the higher fidelity is required for replication.

Question 37

How do mutation rates vary in different tissues?

Answer 37

1. germline has the lowest mutation rate *makes sense
2. whereas retina, fibroblasts and lymphocytes have much higher mutation rates
3. mammalian mt has a higher mutation rate then nuclear.

Question 38

why might there be a reduced efficiency of selection power for mitochondria compared to nuclear

Answer 38

as mt is maternally inherited so only 1/2 nuclear so perhaps reduced efficiency of selection power due to lower Ne.

Question 39

what mechanisms have evolved to reduce mutation rate

Answer 39

proof reading mismatch repair etc.
*in sexual species if a mutationreduces fitness by x every generation then an allele whcih stopped all mutations would have a selective advantage of x.

Question 40

why is there an additional selection to reduce mutation rates in somatic cells of multicellular organisms

Answer 40

to prevent cancer,

*germ line rates may evolve as a correlated response.

Question 41

what may limits to selection for lower mutation rates come from?

Answer 41

pleiotropic costs

- e.g. slower replication.

Question 42

what happens in KO MMR system?

in yeast, C. elegans and humans

Answer 42

increases mutation by 27X in yeast
42X in C. elegans
54 X in humans

Question 43

what is the percentage repair by MMR in yeast, c. elegans and humans

Answer 43

yeast = 96.3%
c. elegans = 97.6%
humasn 98.1%