Transcription/Translation

Question 1

What are the different parts to RNA Polymerase?

Answer 1

1. B - upper clamp
2. B’- lower clamp
3. alpha - hinge
4. Omega - unknown
5. Sigma - sequence specificity

Question 2

Simple answer - why are sigma factors necessary?

Answer 2

• RNA Pol - is not good at recognizing DNA…needs sigma factors to recognize DNA sequence.

Question 3

How many domains are in the sigma 70 family? What type of genes are usually encoded using Sigm 70?

Answer 3

• 4 domains
  
  • 2 contacts -10 region
  • 4 contacts -35 region
  • 1,3 - structural
• Bends DNA but controls expression of housekeeping genes

Question 4

What are the 4 domains of sigma 54? What expression does it control?

Answer 4

• Domains
  
  • Activator Binding site
  • Core Binding Domain
  • -12 binding domain
  • -24 binding domain
• Requires upstreamt transcprition factor and a protein that will bend the DNA so as to recruit the sigma 54.

Question 5

When does the RNA Pol being transcprition elongation?

Answer 5

• Undergoes conformational chang after melting at the -10 region
• However, it cannot start until it has a primer (3’ OH)

Question 6

What are NanoRNAs?

Answer 6

• 2-5 nt RNAs
• Can be used as a primer for RNA Polymerase
• Can be degraded
• Complete function still not known.

Question 7

Which strand does RNA Pol read- the template strand or the coding strand?

Answer 7

Template strand

Question 8

Why is transcription slower than replication?

Answer 8

• helicase activity is less efficient (no helicase or gyrase preceeding)
• Lots of pausing and backtracking
• RNA Poly complex = 3000 complex/cell
• DNA Pol complex = 10. complex/cell

Question 9

What helps protect newly synthesized bacterial RNA from being degraded by RNAase?

Answer 9

Triphosphate cap (Euks usually have the 5’ cap).

Question 10

What are several post-transcriptional regulation mechanisms?

Answer 10

1. Noncoding RNAs
   
   1. CsrA/ Rsmy & RsmZ
   2. can bind to RNAs and prevent translation –> degredation
2. RNAase will eat any RNA not in use
3. rRNA regulations
   
   1. 3 types of rRNA coded all at once
   2. After rRNA synthesis the 3 types will be cut up and sent along their way.

Question 11

How is Archeael RNA regulated post transcription?

Answer 11

• Cleaved by iteself to remove some introns.
• No spliceosome in Archeae.
• RNA Pol in arch is similar to RNAP in Euks
• No Sigma factors

Question 12

What are the 2 types of transcription termination?

Answer 12

1. Instrinsic
   
   1. Uses hairpin loops that are formed from inverted repeats on DNA
   2. Hairpin followed by Poly U tail
   3. Held together by NusA
2. Extrinsic - Rho dependent
   
   1. Rho factor binds to nascent RNA
   2. Rho is a helicase and it will travel up the DNA breaking shit apart.

Question 13

What proteins make of the 70s ribosomal unit?

Answer 13

30s and 50s

Question 14

Which initiation factor prohibits the 30s unit from contacting the RNA?

Answer 14

• Not sure…but the IF 3 prohibits the 50s from binding with the 30s subunit.

Question 15

What is the Shine Delgarno sequence in E.coli?

Answer 15

AGG AGG

Question 16

What energetic step is required for the recruitment of the 50s subunit?

Answer 16

GTP Hydrolyzed

Question 17

What enzyme brings together a tRNA and an amino acid?

Answer 17

aminoacyl-tRNA synthetases

Question 18

What type of reaction happens during peptide bond formation?

Answer 18

Dehydration

Question 19

What is the fidelity in translation?

What is the processivity in translatin?

Answer 19

1. 1 error in 100,000 amino acids
2. 18 amino acids added/second
   
   1. 3 aminos per though…so its close to RNA Pol

Question 20

What are the 3 stop codons intrinsic to RNA?

Answer 20

UGA UAA UAG

Question 21

What is the function of RF-3?

Answer 21

• RF-3 functions in bacterial translation termination
  
  • catalyzes the release of RF1 and RF2

Question 22

What is the function of RRF - ribosome release factor?

Answer 22

• EF-G trys to ratchet this protein in
  
  • but itactually causes 50s to leave the 30s

Question 23

What is tmRNA and what does it do?

Answer 23

• Bacteria have made this to help with stalled RNA
• Function
  
  • charged with amino acid - alanine
  • In reading frame it has a stop codon within it
    
    • displaces the lower template.

Question 24

What are the last few steps in peptide maturation?

Answer 24

1. Formyl group from formyl-methionine is cleaved by peptide deformylase
2. N-terminal methionine sometimes cleaved off by methione amino peptidase.

Question 25

What are some advantages to having transcription/translation in the same compartment in prokaryotes?

Answer 25

1. Rapid protein synthesis
2. Less degradation and more stability of transcripts

Question 26

Polysome =?

Answer 26

Multiple ribosomes on 1 strand of RNA template

Question 27

What are translational difference in Archeae compared to Bacteria?

Answer 27

• More complex
  
  • greater number of protiens
  • Archaeal mRNAs are capped (like eukaryotes
• Archaea still ahve 50s and 30s –> 70s

Question 28

What is a leaderless mRNA? Is it found in Bacteria or Archaea?

Answer 28

• Found in both bacteria and archaea
• Have a promoter - but no 5’ untranslated region
• No ribosome binding site
  
  • ribosome starts at same start site of RNA Pol
  • Any ribosome can translate this.
• Primitive translation?!?

Question 29

What are 3 functions of the chaperone?

Answer 29

1. Can help newly synthesized proteins fold
2. Can help keep proteins linear if they need to be transported
3. Can help misfolded proteins…refold