Lecture 11-DNA Recombination and Repair (Nakai)

Question 1

What is the primary purpose of homologous recombination?

Answer 1

to make repair possible!

Question 2

Transition

Answer 2

replacing a purine with a purine or pyrimidine with a pyrimidine

Question 3

transversion

Answer 3

replacing a purine with a pyrimidine or vice versa which results in either 2 single ring structures trying to bp or 2 double ring structures trying to bp
- CANNOT CANNOT result from a simple tautomeric shift

Question 4

What are the main causes for DNA sequence changes? (3)

Answer 4

• cell physiology (O radicals, nucleases making nicks, cytoplasmic conditions causing damage to bases)
• Modification of bases from radiation/chemicals
• polymerase errors

Question 5

Nitrous acid and hydoxylamine

Answer 5

• covalently modify bases leading to incorrect bping and h bonding

Question 6

Why is T used instead of U in DNA?

Answer 6

probably to distinguish when DNA damage has been done because a very common mutation is the deamination of C –> U which happens every day in our cells despite whether or not a damaging agent is present

Question 7

Why is U used in RNA?

Answer 7

its a common way to edit RNA. You can easily deaminate C –> U.
- the liver uses this to introduce premature stop codons and therefore truncated proteins

Question 8

What is the most unstable nucleotide(s)?

Answer 8

• purines, especially guanine

Question 9

What can potentially happen if guanosine has lost its guanine? (2)

Answer 9

• you can either introduce a mutation or cause a collapse at the replication fork.

Question 10

What is the affect of alkylating a base? ex of a base prone to this?

Answer 10

it can change bping of the base

- ex: G

Question 11

Name the 4 potential methylating/alkylating agents

Answer 11

• SAM
• Dimethylnitrosamine
• dimethylsulfate
• nitrogen mustard

Question 12

What is the effect of radiation on bases?

Answer 12

Can shift equilibrium to favor higher energy tautomers (particularly A which will then bp with C)

Question 13

Insertions/deletions are from

Answer 13

• movable genetic elements

Question 14

Name the enzymes involved in BER in order

Answer 14

• DNA glycosylase
• AP endonuclease
• DNA Pol I + NTP
• ligase

Question 15

Dam methylase

Answer 15

Recognizes GATC sequences on newly synthesized DNA strands that occur with statistical frequency and methylates the A!!!

Question 16

MutS/MutL

Answer 16

• MutS recognizes damage in DNA before it has been methylated at its GATC sites by Dam methylase and binds to them using ATP
• MutL associates with MutS and will act as a molecular matchmaker

Question 17

Explain the process of Mismatch repair

Answer 17

• Mut S finds DNA damage and binds (ATP required)
• MutL associates with MutS to act as a molecular matchmaker (ATP required)
• MutS/MutL complex search for nearest GATC site, recruit MutH (ATP required)
• MutH makes nick in the newly synthesized strand near the GATC site
• DNA Helicase II unwinds (ATP?)
• Depending on where the GATC sequence is relative to the error, certain exonucleases will remove a large segment of bps (ATP? either this and/or the helicase require ATP)
• DNA Pol III replaces the DNA since it is a LARGE GAP
• Ligase
• SSB involved

Question 18

Lack of what correctional enzyme would result in a lethal mutation?

Answer 18

• uracil deglycosylase used in BER

Question 19

Cause and effects of Hereditary Nonpolyposis Colorectal Cancer

Answer 19

• mutations in hMLH1 and hMSH2 and therefore ineffective mismatch repair
• cancers often seen in tissues that have rapid cell division: colon, upper urinary tract, stomach, small intestine, uterus, ovaries

Question 20

Causes and effects of XP

Answer 20

• mutation in NER machinery leading to intolerance of sunlight bc of UV damage
• T dimers can’t be fixed and this either leads to cell death or likely cancer if the cell replicates through this
• few cells will replicate through this but some do and live to accumulate mutations

Question 21

Cockaynes Syndrome and Trichothiodystrophy

Answer 21

• both are from a mutation within the NER as well
• mild UV sensitivity
• they lead to developmental issues such as growth retardation (Cockaynes) or mental retardation (Trich.)

Question 22

Explain Transcription coupled repair

Answer 22

• when transcription machinery encounters lesion
• RNA Pol halts
• uncoupling proteins back up the pol without causing it to cease transcription while enzymes repair the lesion
• RNA Pol can then continue
• TFIIH involved

Question 23

Mutations in TFIIH can result in ______

Answer 23

Cockaynes Syndrom or Trichothiodystrophy

Question 24

Homologous recombination definition

Answer 24

exchange of DNA due to homology between sequences

Question 25

Primary and secondary purpose of homolgous recombination

Answer 25

• Primary: restarting DNA replication forks when forks stall, role in meiosis
• Secondary: generation of genetic diversity–reassortment of maternal/paternal alleles

Question 26

What role can homologous recombination play in meiosis?

Answer 26

tells which chromosomes need to be separated during meiosis