Transcription/Translation Flashcards
What are the different parts to RNA Polymerase?
- B - upper clamp
- B’- lower clamp
- alpha - hinge
- Omega - unknown
- Sigma - sequence specificity
Simple answer - why are sigma factors necessary?
- RNA Pol - is not good at recognizing DNA…needs sigma factors to recognize DNA sequence.
How many domains are in the sigma 70 family? What type of genes are usually encoded using Sigm 70?
- 4 domains
- 2 contacts -10 region
- 4 contacts -35 region
- 1,3 - structural
- Bends DNA but controls expression of housekeeping genes
What are the 4 domains of sigma 54? What expression does it control?
- 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.
When does the RNA Pol being transcprition elongation?
- Undergoes conformational chang after melting at the -10 region
- However, it cannot start until it has a primer (3’ OH)
What are NanoRNAs?
- 2-5 nt RNAs
- Can be used as a primer for RNA Polymerase
- Can be degraded
- Complete function still not known.
Which strand does RNA Pol read- the template strand or the coding strand?
Template strand
Why is transcription slower than replication?
- 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
What helps protect newly synthesized bacterial RNA from being degraded by RNAase?
Triphosphate cap (Euks usually have the 5’ cap).
What are several post-transcriptional regulation mechanisms?
- Noncoding RNAs
- CsrA/ Rsmy & RsmZ
- can bind to RNAs and prevent translation –> degredation
- RNAase will eat any RNA not in use
- rRNA regulations
- 3 types of rRNA coded all at once
- After rRNA synthesis the 3 types will be cut up and sent along their way.
How is Archeael RNA regulated post transcription?
- Cleaved by iteself to remove some introns.
- No spliceosome in Archeae.
- RNA Pol in arch is similar to RNAP in Euks
- No Sigma factors
What are the 2 types of transcription termination?
- Instrinsic
- Uses hairpin loops that are formed from inverted repeats on DNA
- Hairpin followed by Poly U tail
- Held together by NusA
- Extrinsic - Rho dependent
- Rho factor binds to nascent RNA
- Rho is a helicase and it will travel up the DNA breaking shit apart.
What proteins make of the 70s ribosomal unit?
30s and 50s
Which initiation factor prohibits the 30s unit from contacting the RNA?
- Not sure…but the IF 3 prohibits the 50s from binding with the 30s subunit.
What is the Shine Delgarno sequence in E.coli?
AGG AGG
What energetic step is required for the recruitment of the 50s subunit?
GTP Hydrolyzed
What enzyme brings together a tRNA and an amino acid?
aminoacyl-tRNA synthetases
What type of reaction happens during peptide bond formation?
Dehydration
What is the fidelity in translation?
What is the processivity in translatin?
- 1 error in 100,000 amino acids
- 18 amino acids added/second
- 3 aminos per though…so its close to RNA Pol
What are the 3 stop codons intrinsic to RNA?
UGA UAA UAG
What is the function of RF-3?
- RF-3 functions in bacterial translation termination
- catalyzes the release of RF1 and RF2
What is the function of RRF - ribosome release factor?
- EF-G trys to ratchet this protein in
- but itactually causes 50s to leave the 30s
What is tmRNA and what does it do?
- 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.
What are the last few steps in peptide maturation?
- Formyl group from formyl-methionine is cleaved by peptide deformylase
- N-terminal methionine sometimes cleaved off by methione amino peptidase.
What are some advantages to having transcription/translation in the same compartment in prokaryotes?
- Rapid protein synthesis
- Less degradation and more stability of transcripts
Polysome =?
Multiple ribosomes on 1 strand of RNA template
What are translational difference in Archeae compared to Bacteria?
- More complex
- greater number of protiens
- Archaeal mRNAs are capped (like eukaryotes
- Archaea still ahve 50s and 30s –> 70s
What is a leaderless mRNA? Is it found in Bacteria or Archaea?
- 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?!?
What are 3 functions of the chaperone?
- Can help newly synthesized proteins fold
- Can help keep proteins linear if they need to be transported
- Can help misfolded proteins…refold
