Cycle 3 - DNA Repair, Mutations

Question 1

Explain proofreading and its mechanism

Answer 1

Proofreading: a mechanism for correcting errors made by DNA polymerase during replication (ex., it puts in the wrong base creating DNA damage which buldges)

• If this is detected, it removes the offending base and then restarts
  
  • But it may replace the opposite base that was correct –> mutation
• 3’ –> 5’ exonuclease activity is used

Question 2

Explain mismatch repair/excision repair and its mechanism

Answer 2

Sometimes proofreading does not catch an error and the DNA damage remains

• However, the bulge is still detectable and can be removed and repaired post-replication
• Again, the opposite base could be replaced leading to mutation

Question 3

What are thymine dimers and how are they repaired?

Answer 3

• In the presence of photons of UV light, DNA absorbs that energy
• This can accidentally covalently attach thymines that are side by side

Many life forms have the photolyase enzyme that breaks these bonds. Blue light is required to activate photolyase.

However, mammals have lost this ability over evolutionary time, so we are forced to use _excision repai_r to correct this.

Question 4

Explain non-homologous end joining

Answer 4

Non-homologous end-joining

• When a double stranded break in a chromosome can occur, cells “slam” these ends back together via non-homologous end-joining
• Some bases, nucleotides are lost –> thus, despite “repair” there is a double-stranded change, thus mutation persists

Question 5

Explain the contents of the human genome

Answer 5

• 25% unknown (junk)
• 10% essential (2% actually codes for proteins)
• 10% introns (junk)
• 55% transposons, dead genes, viruses (junk)

This is exactly what we would predict after 4 billion years of evolution.

Question 6

Explain the differences between human genomes

Answer 6

There is about a 0.2% difference in DNA between any two individuals.

Question 7

Explain SNPs

Answer 7

SNPs are single nucleotide (pair) polymorphism; ie a mutation involving one nucleotide pair. There are 2 types:

• Mutations of the single pair variety (ex., mismatch not fixed properly or at all)
• Spontaneous tautomeric (isomeric) shifts (ex., thymine asks for 3 and pairs with guanine accidentally)

Question 8

Explain mobile elements

Answer 8

These are DNA element that move around in the DNA. (ex., streaked corns and flower colour is caused by mobile elements moving into and out of pigmentation genes.) 2 types:

1. Transposons/jumping genes: these transposons move around by copy paste or cut and paste with the help of transposase (cut/paste)
2. Retrotransposons: move via reverse transcription (copy/paste)

These increasing genome size over time.

Question 9

Define mutagen

Provide an example

Answer 9

An agent that causes genetic mutation

Mobile elements are mutagens, because they are biological elements that can spontaneously create severe mutations

Question 10

Define endogenous viruses

Answer 10

Endogenous viruses: these viruses entered our cells but suffered a mutation and trapped themselves. All they do is copy their genome and insert it elsewhere. These make up a majority of the Y chromosome LOL!

Question 11

Explain and draw insertions and deletions caused by slippage

Answer 11

• Slippage can occur in a repeated sequence of nucleotide. This is when one nucleotide pops out, causing an additional nucleotide to be required
• Initially, this is damage, but when it replicates, a double stranded change will occur thus a mutation.

Question 12

Explain radiation damage

Answer 12

• When radiation blasts though the water in our body, it creates ROS: reactive oxygen species –> it rips electrons away from oxygen.
• These species of reactive oxygen damage other molecules by stealing electrons, creating double stranded breaks

Question 13

Explain copy number variations

Answer 13

Copy Number Variations (CNV): deviation from the norm in terms of the number of copies of genes

• Can originate from unequal recombination when they do not line up perfectly (ex., 4 loci on one, 4 loci on the other. They pair up and cross over unequally resulting in 6 loci on one and 2 on the other)
• Not always bad: having multiple copies of genes can enable evolution

Question 14

Why do African populations have more unique SNPs than other populations?

Answer 14

1. This would be predicted if humans originated in Africa (founder effect - folks who migrated out took some of the variation as they left, but of course not all of it. And repopulated with less variation available.)
2. Additionally, African populations are original, so they are older, and thus have had more time to accumulate random SNPs.

Question 15

Expain in/del, duplication, inversion, translocation mutations

Answer 15

All of these can arise from non-homologous end joining

A deletion/insertion of a sequence

• Slippage

A duplication: sequence is doubled

• Can arise during recombination in meiosis if crossing-over occurs unequally (like CNV)

A translocation occurs if a broken segment is attached to a different chromosome.

An inversion occurs if a broken segment reattaches to the same chromosome from which it was lost, but in reversed orientation.