DNA Structure and Replication

Question 1

Base pairing. Which is stronger?

Answer 1

G-C and A-T. G-C stronger due to extra H-bond.

Question 2

DNA replicates ____. Each round of replication results in ___.

Answer 2

Semiconservatively. Each replication results in a daughter strand with a parent strand. Meselson-Stahn experiment with Nitrogen-15.

Question 3

Replication forks

Answer 3

Active zones of DNA replication

Question 4

Leading strand replication occurs in ___ direction _____. While lagging strand is made in _____.

Answer 4

Leading strand replication occurs in 5’–> 3’ direction continuously while lagging strand is made in Okazaki fragments.

Question 5

RNase H does what?
DNA Pol I?
DNA ligase?

Answer 5

RNase H removes the RNA primer fragments in the lagging strand during replication.

DNA Pol I replaces gaps with DNA. Also has 5’–>3’ exonuclease activity that removes RNA primer.

DNA ligase seals backbone

Question 6

DNA helicase does what?

Answer 6

Unwinds DNA at replication fork

Question 7

Single strand DNA binding proteins

Answer 7

Prevents DNA from folding back on itself during replication

Question 8

Sliding clamp

Answer 8

Supports DNA and DNA pol, making replication a processive process

Question 9

Contents of replisome and what they do

Answer 9

Replisome = set of proteins and enzymes required for DNA replication. Include:

(1) Helicase: unwinds DNA
(2) Topoisomerase: removes DNA supercoild
(3) single-stranded binding proteins: stabilize ssDNA
(4) Primase: lay down RNA primers on lagging strand
(5) DNA ligase: ligates Okazaki fragments on logging strand

Question 10

Exonuclease domain

Answer 10

Domain in all DNA pols 3’–>5’ that allows DNA pol to backspace removing most incorrectly inserted bases

Question 11

Main DNA pol is ___. It is a ___.

Answer 11

DNA pol III. It is a dimer. One domain binds leading strand, the other the lagging strand.

Question 12

Replication initiates at ___ and ends at ___.

Answer 12

Origins of replication (ori) and ends at termination points.

Question 13

Main sources of DNA damage (3)

Answer 13

(1) Reactive oxygen species
(2) Ionizing radiation
(3) Chemical exposure

Question 14

Oncogenes

Tumor-suppressor genes

Answer 14

Oncogenes are genes that can lead to cell cycle disregulation if they experience a gain-of-function mutation.

Tumor-suppressor genes can lead to cell cycle disregulation if they experience a loss-of-function mutation.

Question 15

Types of DNA damage repair

Answer 15

(1) Direct repair
(2) Excision repair (a) base excision (b) mismatch repair (c) nucleotide excision repair
(3) Recombination repair

Question 16

Base excision repair

• Timing of repair?
• Does what? Steps?
• Failure could lead to?

Answer 16

• Repairs DNA damage throughout cell cycle
• Removes small, non-helix distorting base lesions (e.g. oxidized/alkylated bases, uracil incorporation
  (1) Glycosylase removes base
  (2) Endonuclease and phosphodiesterase removes sugar phosphate
  (3) DNA polymerase adds new nucleotide and ligase seals
• Failure could lead to breaks in DNA

Question 17

Mismatch repair

• Does what? Mistake corrected where?
• Can be detected in prokaryotes via?
• Steps

Answer 17

• Corrects errors of DNA replication that result in mispaired nucleotides.
• Strand specific –> corrects mistake on new daughter strand
• Look for unmethylated DNA in prokaryotes
  (1) MutS binds mismatched DNA and MutL scans DNA for nick
  (2) MutL removes DNA in mismatched strand
  (3) DNA polymerase synthesizes new DNA

Question 18

Nucleotide excision repair

• Does what?
• Steps?

Answer 18

• Removes bulky DNA lesions due to UV, tobacco smoke, etc.
  (1) Exonuclease binds to DNA at side of lesion and cleaves damaged DNA around lesion
  (2) DNA strand removed by helicase
  (3) Gap filled by DNA polymerase and nick filled by ligase

Question 19

Nonhomologous end-joining

• Does what?
• Occurs when?
• Can lead to?
• What is used to recognize and process broken ends?

Answer 19

• Repairs double stranded DNA break by altering DNA sequence at break to join ends together
• Occurs before cells duplicate DNA
• Can lead to deletions and translocations
• Ku protein used to recognize and process broken chromosome ends

Question 20

Homologous recombination

• Does what?
• Can be used when?

Answer 20

• Repairs double stranded DNA breaks by using duplicated sister chromatids as template to repair sequence lost in break
• Restores original DNA sequence but can only be used after DNA duplication (S/G2 phases)