Lecture 12

Question 1

Mutations:

Answer 1

• Alterations in DNA structure that can produce permanent changes in genetic information encoded if they are not repaired
• Rarely, mutations serve as a biological advantage – adaption and evolution

Question 2

List 4 mechanisms of DNA damage:

Answer 2

• Spontaneous mutations
• Error during replication
• Chemical mutagens
• Ionizing radiation

Question 3

How often does DNA damage occur in the cell?

Answer 3

• Continually
• 10^12 depurinations occur in your body within the time it takes you to read a sentence
• Deamination and depurination can occur spontaneously

Question 4

What are the consequences of spontaneous mutation

Answer 4

• Depurination can lead to the deletion of one or more nucleotides when DNA replicates
• Deamination can lead to alterations in DNA sequence when DNA replicates
• These mutations are spontaneous

Question 5

Errors during replication:

Answer 5

• Errors during replication are rare, but do occur despite the proof-reading ability of DNA polymerase
• The rate is approx. 1 mistake for every 10^7 correctly added nucleotides

Question 6

Consequences of errors during DNA replication

Answer 6

• If uncorrected, mismatches will lead to permanent mutations in one of the two DNA molecules produced during DNA replication

Question 7

How does nitrous acid function as a chemical mutagen?

Answer 7

• Example: deamination’s can occur at higher frequencies when cells are exposed to nitrous acid
• Nitrous acid is used as a food preservative
• Hypoxanthine pairs with cytosine instead of thymine

Question 8

Ionizing radiation

Answer 8

• UV lights can cause adjacent thymine residues to form covalent bonds with one another
• Which introduces a kink in the DNA that blocks polymerization past this point

Question 9

Xeroderma pigmentosum:

Answer 9

• A rare skin disease where a mutation in a gene necessary for dealing with thymine dimers is not functional (nucleotide excision repair is needed)

Question 10

What are the 5 types of DNA repair?

Answer 10

1. Mismatch repair: used to fix errors that were missed during DNA replication
2. Base excision repair: removes offending base and replaces it
3. Nucleotide excision repair: removes offending nucleotide and replaces it
4. Direct repair: does not remove damaged base, but fixes the damage on spot
5. Homologous recombination: takes advantage of a homologous chromosome to fix double stranded breaks

Question 11

What 3 type of repair are indirect and what mechanism do they use?

Answer 11

1. Mismatch repair
2. Base excision repair
3. Nucleotide excision repair
   Mechanisms:
   - Use an endonuclease to create a nick in the DNA near the damage
   - Remove a section of the damaged DNA with an exonuclease
   - Fill in the gaps with a polymerase and seal it with DNA ligase

Question 12

What are the 3 steps that mismatch repair uses to correct errors during replication?

Answer 12

1. A complex of proteins binds to mismatched base pairs and an endonuclease cuts of damaged strand
2. An exonuclease degrades the DNA from cut site to the mismatch
3. DNA polymerase fills in the missing nucleotides and DNA ligase seals the gap

Question 13

Describe DNA methylation

Answer 13

• DNA is normally methylated
• It takes a few minutes for the newly synthesized DNA strand to become methylated
• Shortly after replication, DNA is hemimethylated… meaning that the template strand is methylated while the newly synthesized strand is not

Question 14

Base excision repair:

Answer 14

• Removes offending base and replaces it
• Multiple nucleotides can be replaced
• Generally, follows the same 3 steps as MMR
  1. Excision of damaged region
  2. Endonuclease cuts DNA
  3. DNA polymerase makes new top strand by using bottom strand as a template
  4. DNA ligase seals the nick (gap)
• Example: deamination of cytosine

Question 15

What are double stranded DNA breaks?

Answer 15

• Both strands are damaged at the same time

Question 16

What is nonhomologous end joining?

Answer 16

• Nucleases remove nucleotides from broken ends and then is ligated together
• Leads to loss of nucleotides
• Can lead to dysfunctional genes

Question 17

Homologous recombination

Answer 17

• Takes advantage of a homologous chromosome to fix double stranded breaks without a loss of nucleotides
• Occurs shortly after DNA replication when there are two copies of the DNA double helix
• Also seen during genetic recombination that occurs during meiosis

Question 18

Outline the process of homologous recombination:

Answer 18

1. DNA double strand break occurs
2. Exonuclease degrades 5’ end of DNA
3. Strand invasion of unbroken homologous chromosome
4. Invading strand is extended by DNA polymerase
5. Invading strand is released
6. DNA polymerase fills in gaps
7. DNA ligase seals the gaps

Question 19

Compare consequences of damage in germ cells vs. somatic cells

Answer 19

• Mutations in germ cells can result in the passing of mutations to future offspring’s
• Mutations in somatic cells over time can lead to abnormalities like cancer

Question 20

Fidelity of DNA replication

Answer 20

• Despite millions of years of divergent evolution, DNA sequences between many species remain very similar
• This is a consequence of the faithfulness of DNA replication and repair