Genome Sequence Variation

Question 1

Substitution

Answer 1

SNPs
Transition (purine –> purine) (pyrimidine–> pyrimidine)
Transversion (purine –> pyrimidine)

Question 2

Indels

Answer 2

Insertion

Deletions

Question 3

Inversion

Answer 3

create complement to genome

rotate 180°

Question 4

Translocation

Answer 4

movement btwn diff chromosomes

Question 5

Mutation Rate

Answer 5

gene mutation rate > DNA sequence mutation rate

- genes more nucleotides

Question 6

Tautomeric Shifts

Answer 6

Alternate Base Pairing

• G now binds regular T
• C now binds regular A

Question 7

Wobble

Answer 7

Alternate Base Pairing

- line up differently

Question 8

Strand Slippage

Answer 8

Insertions + Deletions

- low sequence complexity

Question 9

Unequal Crossing Over

Answer 9

Insertion + Deletions

- homologous pair don’t align properly

Question 10

Deamination

Answer 10

Transition

C –> T/U (bp with A now)

Question 11

Depurination

Answer 11

Transversion

- remove purine base

Question 12

Base Analogs

Answer 12

Transition

T –> 5-Bromouracil (bp with G now)

Question 13

Alkylating Agents

Answer 13

Transition

• ethylates G and T
• G –> ethylguanine (bp with T now)

Question 14

Hydroylamine

Answer 14

Transition

C –> hydroxylamine-cytosine (bp with A now)

Question 15

Oxidative Radicals

Answer 15

Transversion

G –> oxy-guanine (bp with A now)

Question 16

Intercalating Agents

Answer 16

Insertions + Deletions

- molecules slide btwn bp

Question 17

UV light

Answer 17

• bonds btwn adjacent thymine bases = thymine dimers

Question 18

Mismatch Repair

Answer 18

• Search for methylation
• Nick and degrade
• Synthesize and ligate

Question 19

Direct Repair

Answer 19

• specific enzymes to specific base modification

Question 20

Base-Excision Repair

Answer 20

• Remove base

- Nick, Synthesize, Ligate

Question 21

Nucleotide-Excision Repair

Answer 21

• Separate strands
• 2 nicks
• Synthesize and ligate

Question 22

Transposons

Answer 22

• mobile elements in genome

1) Increase Genome size (noncoding DNA)
2) Disrupt Genes (insert in active)
3) Altered Expression (on regulatory sequence)
4) Genome Rearrangement
- direct orientation – deletion + duplication (same) translocation (diff)
- inverted orientation – inversion (same)

Question 23

Duplicate Target Sequence

Answer 23

• transposase = staggered break
• insert TE
• gaps filled (terminal inverted sequence + flanking direct repeats)

Question 24

Type II transposons

Answer 24

• DNA intermediates
• short inverted repeats at end
• replicative
• cut + paste

Question 25

Type I retrotransposition

Answer 25

• RNA intermediates
• long terminal direct repeats
• transcribed to mRNA –> DNA copy –> insert new site

Question 26

SNPs

Answer 26

• genetic markers

- close together = rarely separated at recombination

Question 27

Manhattan Plot

Answer 27

Low = SNPs randomly associate with phenotype
High = SNPs associated with phenotype

Question 28

Human Evolution

Answer 28

• migrate out of Africa
• Neanderthals –> Europe
• Denisovans –> Asia
• Homo Sapiens = interbreed