Lectures 8-14

Question 1

At what point in human development do mutations occur the most?

Answer 1

Gametogenesis, mainly from the sperm

Question 2

Define polar effects in genetics

Answer 2

When mutation in a gene negatively impacts downstream genes

Question 3

What are the different types of mutations?

Answer 3

SNPs
Indels
Inversions

Question 4

Are bacteria always haploid?

Answer 4

No, genes around origin/replication genes are duplicated

Question 5

Why are RNA viruses so mutagenic?

Answer 5

Lack proofreading
Short and replicate quickly but fail most of the time. It takes a lot of energy to reduce mutation rates

Question 6

Persistence in populations depends on

Answer 6

Natural selection - select advantages
Artificial selection - We choose
Genetic drift - random

Question 7

Define evolution

Answer 7

The inevitable change of organisms (and non-living replicators) overtime due to non-perfect replication

Question 8

Define natural selection

Answer 8

How the natural world selects winners and culls losers from populations, thus shifting gene pools and sculpting species

Question 9

Define a transition mutation

Answer 9

Switch between purines or switch between pyrimidines
(A <–> G) or (T <–> C)

Question 10

Define a transversion mutation

Answer 10

Switch between purines to pyrimidines and vice versa
(A or G <–> C or T)

Question 11

Explain the Ames test

Answer 11

Tests carcinogenic effects of chemicals.
Involves placing a salmonella auxotroph (needs histidine to survive) with a potential mutagen. If growth = mutagenic substance (reversion to wild type). If no growth = not mutagenic.

Question 12

How does mutS know which strand is the parent strand of DNA and which strand contains the mutation?

Answer 12

The old strand will have methyl groups attached to GATC cites. Methylation takes a while to fully implement which allows mutS to determine which strand is old and which contains the mutation. This means that MutS has a limited time to find replication errors.

Question 13

What enzyme methylates DNA?

Answer 13

Dam methylase (5’ GATC)

Question 14

What does a loss of mutS function mean?

Answer 14

Increased mutation rate
Increased loss of genes

Question 15

Evolution of the Cit+ train involved 3 successive processes:

Answer 15

Potentiation
Actualization
Refinement

Question 16

Define historical contingency

Answer 16

The concept that preparatory mutations lay the work for some mutation to occur = significant change

Question 17

Define potentiation

Answer 17

Evolution of a genetic background in which a particular function became accessible through eventual mutation

Question 18

Define actualization

Answer 18

An extremely weak mutation with a particular function emerges

Question 19

Define refinement

Answer 19

Allows the rise of a particular mutation in a population to numerical dominance

Question 20

Why do humans have more transposable elements than chimpanzies?

Answer 20

Humans have more TE than chimps because TE’s gave us the evolutionary advantage over them. Allowed humans to become what we are today.

Question 21

As twisting of DNA increases growth (increases/decreases)?

Answer 21

Increases!

Question 22

What enzyme/gene causes DNA relaxing? What does this mean for the cell?

Answer 22

TopA. An increase in TopA means more relaxed DNA = slower growth/replication.

Question 23

Is it beneficial or not to have a mutation in TopA and why

Answer 23

Beneficial. TopA function decreases, DNA replication speed increases = fitter cells

Question 24

What regions of DNA are more likely to “breathe”? Why?

Answer 24

AT rich regions. AT regions melt spontaneously more frequently

Question 25

A supercoiling increase means an (increases/decreases) ____________ the likelihood of melting

Answer 25

increases

Question 26

What are two ways to evade CRISPR-cas?

Answer 26

mutate protospacer or mutate PAM

Question 27

Explain how Homology directed repair works

Answer 27

HDR works by first creating 3' tails using RecB, RecC, RecD. RecB and D move both 3' and 5' end along while cutting them up until a chi site is recognized by RecC. Things keep moving along until the 3' end is bunched up a lot. Then the RecBCD complex lets go and a 3' overhang is created. The 3' end of the broken DNA strand invades another strand, a homologous sequence, and DNA strands are copied and replicated until complete. DSB is then fixed!

Question 28

What would happen if Chi sites didn't exist in cells DNA?

Answer 28

DNA would continue to be degraded after a DSB and the RecBCD complex would not stop = loss of all DNA if one DSB occurs.

Question 29

What causes thymine dimers? What do thymine dimers mean for DNA replication.

Answer 29

UVB rays. Thymine dimers prevent polymerase from proceeding

Question 30

What happens if there is a mutation (like a thymine dimer) that DNA polymerase cannot fix or replicate over?

Answer 30

SOS polymerases are deployed and copy over the dimer "recklessly" by shoving whatever bases it can in there. Once over the lesion, it leaves and normal polymerase comes back to finish the job.