Lecture 5 - DNA R,R,R pt 1

Question 1

How does cell control mutations in somatic and germline cells during replication? **

Answer 1

Proofreading, 3’ to 5’ exonuclease.

Question 2

How does the cell fix damage that occurs before replication occurs or cell division?

Answer 2

NER, BER, NonHR, HR

Question 3

What are types of spontaneous DNA damage

Answer 3

1. Depurination hydrolysis of N-glycosly inkage b/w guanine and deoxyribose = base removal
2. Deamination - amine froup on cytosine is hydrolzed into ammonia na dleaves carbonyl PRODUING URACIL
3. Uv radiation causeing formation of pyrmidine dimers (TT and CT)
4. all of these lad too deletion or base oarisubitistion

Question 4

What are the differences b.w the types of repair

Answer 4

BER - single nuleotide repair

NER - portion of DNA are repaired

TCR (transcription coupled repair ) - recruits DNA repair to transcribed RNA (ATM)

Question 5

WHat is base excision repair?

Answer 5

1. DNA GLYCOLSYLASES scan for URACIL
2. enzyme mediated flipping of base
3. the glycosyl bond is cleaved no base-sugar bond
   
   1. via AP endonuclease and phosphodiesterase cuts and removed backbone)
4. DNa poly
5. ligase

Question 6

what is Nucleotide excisiton repair?

Answer 6

1. pyrimdine dimer identified w/ multienzyme comlplex
2. excision nuclease makes cut on both sides
3. helicase takes away mutated portion
4. DNA poly and ligase clean up

Question 7

What is transcription coupled repair and whats one diease that results in it?

Answer 7

1. cell mediated
2. RNA poly stalls at lesions and directs repair machinery
3. works with BER,NER,HR,nonHR
4. Results into COCKANYES SYNDROME
   
   1. defective TCR,
   2. RNA poly is permanetly stalled at sites of damage
   3. growth retardation,skeletal abnormalities, sensetitivty to sunlight

Question 8

What is one primary reason why RNA is not used as hereditary information?

Answer 8

If we used RNa as Primary hereditary infor. Deaminiation of cytosine to uracil would be undetecable from right or wrong

Question 9

WHat about DNA modification is problematic?

Answer 9

Methylated cytosine causes it to become thymine

there are 3% of methylated cytosines but they cause 1/3 of all point mutation assocated with inherited diseases

Question 10

What are translesional Polymerases and when are they used?

Answer 10

Used when the cell has sustained extensive damage.

Ex the Jr varsity team to DNA poly high school

Less accutate but they make corrections when a portion of DNA is destroyed eventually DNA poly does come and take over

Lack of endonuclease proofreading activiy

Question 11

know this ish

Answer 11

Question 12

What is DS break repair/

Answer 12

Double strand break in DNA. Repaired via two processes

Non homolougous Cell joining and homologous recombination

Question 13

What are some causes of DS breaks?

Answer 13

ionizing readiation

replication errors (fork falls apart)

Oxidizing agents

other metabolites that cut DNA

Question 14

What do humans use as the prefered fix for a DS break?

Answer 14

nonhomologous end joining

Question 15

WHat is non homolougous end joining?

Answer 15

Cell finds DS break

Ends of break are process and joined together

EFfects:

you dont know what you lose but little of the genome are exonic

Question 16

What are the checks points in the cell cycle?

Answer 16

DNa damage triggers are identified by checkpoints

Checkpoints insure the completeion of the one stage of the cell

1. blocks entry g1 into S
2. slowing down of S phase
3. block transition from g2 into M

Question 17

What is ATM?

Answer 17

a kinase that generates intracellular signals that alert the cell to DNA damage and upregulate expression of DNA repair genes

mutationns lead to ataxia telengiectasia

Question 18

Why do we use homologous recombination

Answer 18

1. fix DNA breaks
   
   1. Stalled or broken replication forks
2. occurs b.w homologous DNA in meiosis
   
   1. genetic variation
3. mechanical role fundamental to all organisms

Question 19

how are heteroduplexes formed?

Answer 19

DNA DS strands look for “similiar DS strand (homology)” via sampling EA. other

DNa double helices hybridize (renature) w/ each other

HOmology is found when 15 nucleotides BP up

Heteroduplex created

Question 20

How many nucleotides to form a heteroduplex or show homoogy?

Answer 20

15

Question 21

What are the steps of homologous recombination?

Answer 21

ds break is process to produced 3’ overhangs via exonuclease

3’ of broken strand invades the other (heteroduplex) VIA RAD51/RECA

DNA polymerase synthesizes finishing off length of invader

invader returns back home

ligase

Question 22

What conducts strand invasion?

Answer 22

• BACTERIA its Rec A + other proteins
  
  • tightly controlled & REQUIRES ATP
• Ieukaryotes its RAD 51
  
  • REQUIRES ATP

Question 23

What happpens when you lose control over regulation of HR

Answer 23

• Loss of heterozygosity
  
  • use of non functioning homologs to repair
• Leads to cancer

Question 24

How is HR regulated?

Answer 24

1. Exonucleases required for creating the 3’ overhang are only active in S and G2
   
   1. allows for cell to know replicated chromosome will be the one targeted for repair
2. Loading of recA and Rad51 is controlled
3. Repair proteins dispersed through cell

Question 25

What are two examples of mutations in recombination?

Answer 25

• BRca1 - regulates the processing of broken ends of chromosomes
  
  • mutation in BRCA1 lead to use of non homologous end joining
• BRCA2 maintains Rad 51 (recA) incactive unit it is at the site of damage
  
  • Mutation causes it not to bind to DNA to form invading strand.

Question 26

KNOW THIS!!!

Answer 26