Final: Sem. 1 Essentials, Oncogenes + Signal Trans (Incomplete, Ben)

Question 1

What kind of bond do DNA polymerases form and between which atoms?

Answer 1

Phosphodiester between ribose C3 and P grp on next nucleotide

Question 2

What are the prokaryotic DNA polymerases and their actions?

(as in polymerase… exonuclease… repair…gap filling etc.)

Answer 2

• Polymerase I
  
  • ​3>5, 5>3 exonuclease + 5>3 polymerase
  • low proc., gap filling, Okazaki primer removal and repair
• Polymerase II
  
  • ​3>5 exonuclease (proofread/repair only)
• Polymerase III
  
  • ​main prokaryotic 5>3 polymerase, also 3>5 exonuclease
  • highly processive leading/lagging strand synth + proofread
• “DnaG”
  
  • primase only (so not really a polymerase)

Question 3

What are the eukaryotic DNA polymerases and their actions?

Answer 3

• Polymerase α
  
  • ​primase, gap filling + lagging strand synth (low processivity)
• Polymerase β
  
  • 3>5 exonuclease
  • main eukaryotic repair polymerase, base excision
• Polymerase γ
  
  • mitochondrial DNA synth + repair
• Polymerase δ
  
  • ​main eukaryotic 5>3 polymerase, 3>5 exonuclease
  • leading/lagging synth, gap filling + proofreading
• Polymerase Ɛ
  
  • ​can correct delta’s errors, minor role in synth

Question 4

Describe some important components / co-factors for DNA polymerase III and delta in their action of binding DNA.

Answer 4

• DNA polymerase III
  
  • holoenzyme of many subunits, 2 β subunits = sliding DNA clamp
  • with primase + DNA proteins B/C = replisome
• DNA polymerase delta
  
  • 4 subunits POLD1-4
  • uses separate protein PCNA as its sliding clamp
  • Replication Factor C“loads” PCNA onto the polymerase

Question 5

Where does replication initiate in prokaryotes + what characterizes the region?

What are the 7 components of the “replication bubble” there + their functions?

Answer 5

Starts at Ori C rich in A-T…

1. DNA A protein - binds origin + initiates replication
2. DNA B protein - is helicase which unwinds DNA at origin using ATP
3. DNA C protein - w/ helicase + primase, helps make primer
4. SSBPs - bind single straded DNA to prevent re-annealing
5. Primase - creates 4-10 bp RNA primer (+B+C = primosome)
6. Topoisomerase II - w/ ATP creates negative supercoils, prevents tangle
7. DNA polymerase III

Question 6

What histones make up the octamer?

What is the octamer plus DNA called?

And what is this unit plus the stretches of DNA between it?

Answer 6

Octamer = H2A, H2B, H3, and H4

Octamer + DNA = nucleosome

Nucleosome + DNA strand around H1 = Chromatosome

Question 7

How many DNA molecules are in a cell in G2 phase right before cell division?

Answer 7

92

the normal 46 chromosomes duplicated

Question 8

WHat is deaminated cytosine? adenine?

Answer 8

C is uracil, A is hypoxanthine

Question 9

What 3 enzymes perform depurination repair?

Which enzyme starts deamination repair followed by the action of the 3 just mentioned?

Answer 9

• Depurination - endonuclease, polymerase I/Beta,Ligase
• Deamination - starts with an DNA Glycosylase

Question 10

How are “transformed”/cancerous cells different from normal cells?

Answer 10

1. No growth factor requirement
2. No anchorage requirement
3. Telomerase re-activated (“immortal”)
4. No contact inhibition
5. Increased glucose uptake
6. Increased ability to trigger vascular growth
7. Morphology changes (recepters, surface proteins, etc.)

Question 11

What is the most important tumor suppressor gene and what does it do?

Regulation?

Answer 11

P53

• is a transcription factor for genes that encode cell cycle-inhibiting / apoptosis-promoting proteins such as cyclin dependent kinase inhibitors and BAX (respectively)
• P53 is active when phosphorylated by DNA dependent kinases which bind to breaks in DNA, enhance P53 activity and thus arrest cell cycle
• mutations of P53 are very common in tumors + can be caused by viruses