WEEK 4

Question 1

Helicase

Answer 1

Two types, but the predominant one moves in 5’ to 3’ direction. Both require AT. Spins along the lagging strand template.

Question 2

SSBs

Answer 2

Single stranded DNA binding proteins, prevents strands from reannealing after helicase has separated them.

Question 3

Primase

Answer 3

Synthesizes RNA primer that polymerase can add onto. DNA primase = RNA primase = Primase (all same thing)

Question 4

Leading strand is synthesized from

Answer 4

a single RNA primer

Question 5

Lagging strand is synthesized from

Answer 5

multiple primers (discontinuously)

Question 6

Okazaki fragments are made of

Answer 6

RNA primer and DNA

Question 7

Blunt ended DNA

Answer 7

Is damaged DNA. Body will try to fuse together.

Question 8

Issues with DNA synthesis/replication

Answer 8

• information is lost during every replication on the lagging strand
• primase is not good at adding primer at very end
• RNA primers must be removed and then theres only a 5’ end which you can’t add to

Question 9

Telomeres

Answer 9

Repetitive DNA sequences at ends of chromosomes that solve problem of information loss. Most eukaryotes have telomeres.

Question 10

Single stranded DNA is

Answer 10

particularly fragile

Question 11

Shortening of the 5’ end is a problem for…

Answer 11

the lagging strand

Question 12

Telomerase

Answer 12

Uses RNA primer adds repeats to make 3’ end long. Adds a G rich sequence.

Question 13

Topoisomerase I and II

Answer 13

• Breaks single strand, does not directly require ATP (DNA can rotate/unwind)
• Uses ATP, cleaves both strands

Question 14

Which has a higher error rate—RNA or DNA polymerases ?

Answer 14

RNA polymerases have more errors

Question 15

Proofreading mechanisms

Answer 15

• 3’ to 5’ exonuclease repair (backspace button of DNA polymerase)
• In eukaryotes, strand directed mismatch repair (occurs before ligase)

Question 16

Proteins associated with strand directed mismatch repair

Answer 16

MutS - recognizes distortion
MutL - scans strands for nicks to see which strand is the new strand because just from distortion alone you can’t tell which one is the mismatch and which is the original strand

Question 17

Prokaryote version of strand directed mismatch repair

Answer 17

Protein looks for unmethylated adenines, doesn’t recognize nicks in the strand

Question 18

Pyrimidine Dimer

Answer 18

Often caused by UV light, consecutive bases on same strand are covalently bonded. Primary cause of melanoma in humans.

Question 19

Types of spontaneous damage to DNA

Answer 19

Depurination and deamination

Question 20

Depurination

Answer 20

Purine nucleosides are hydrolytically cleaved from DNA releasing adenine/guanine. Occurs 500 times a day.

Question 21

Deamination

Answer 21

Cytosine turns to uracil as amine group is replaced with an oxygen (INSTANCE OF URACIL BEING IN DNA). Also occurs 500 times a day.

Question 22

When does a cell have until to recognize and correct an error?

Answer 22

Until next replication event. If it is not resolved, the mutation becomes fixed because polymerase is dumb and just copies template strand.

Question 23

BER

Answer 23

Base Excision Repair
Typically targets one nucleotide. Uracil-DNA glycosylase removes base, AP endonuclease cuts phosphodiester bond, and a specific DNA polymerase removes phosphate group and sugar, adds a new one.

Question 24

NER

Answer 24

Nucleotide Excision Repair

Endonucleases cuts on either side of problem strand, specific helicase removes strand, polymerase fills in, then ligase.