Transcription

Question 1

Gene

Answer 1

DNA sequence that’s transcribed

• might not code for protein
• cont controlling transcription

Question 2

RNA composition

Answer 2

Large % rRNA and small mRNA (rapid degradation)

Question 3

RNA P characteristics

Answer 3

1. Catalyses DNA-directed RNA synthesis/transcription

2. Oligomeric protein with 4 different types of sub-units

Question 4

RNA P sub-unit composition

Answer 4

5 make core enzyme

• large beta and beta’ subunits = active site
• > beta = polymerase, beta’ = binding
• alpha = scaffold and assembly

Question 5

Theta sub units

Answer 5

Transcription initiaion

• > bind to core enzymes in w subunit
• > theta 70 in E.coli

Question 6

Outline the chain elongation reaction

Answer 6

1. Growing RNA chain is base-paired to DNA template
2. Incoming ribontriphosphates with correct H-bond
3. Nucleotidyl group transfer reaction
4. ppd linkage + release of pyrophosphate

Question 7

What’s the 5’->3’ reaction equation for chain elongation

Answer 7

RNAn-OH + NTP -> RNA n+1-OH + PPi

Question 8

How is chain elongation thermodynamically favourable?

Answer 8

Delta G decreases because high NTP: RNA

-> assisted by pyrophosphate hydrolysis

Question 9

Which linkages are expended for chain elongation?

Answer 9

2 phosphoanhydride linkages/ nucloetides added to chain

Question 10

What’s the error rate of chain elongation in prokaryotes?

Answer 10

10^-6 because no 3’->5’ exonuclease

Question 11

Growing RNA strand only interacts with template over ___________ forming a ________ product

Answer 11

Short distance, single-stranded

Question 12

Transcripts of _____ length are ______ along genes because ______

Answer 12

Increasing, arrayed, many RNAP transcribe at same time

Question 13

Which two consensus sequences are used in prokaryotes with theta 70 promoters?

Answer 13

TATA -10 bp -> melts within active site

Recognition - 35 bp

Question 14

How is the promoter sequence found?

Answer 14

1D diffusion of RNA P along DNA molecule where enzymes bound non-specifically -> scan 2000 bp for promo sequence

Question 15

Which is the slowest step of initiation events?

Answer 15

RPC -> RPO ( conformational change of RNA and promoter complex)

Question 16

Outline RPO to promotor clearance

Answer 16

1. Temp. strand at polymerisation site
2. Ppd link between 2 ribonucleoside triphosphates
3. H bond with +1 and +2 nucleotides of template
4. Additional nucleotides added to dinucleotide
5. At 10, RNA P -> transition to elongation away from promoter -> release of theta sub-unit with help of accessory proteins

Question 17

Where does transcription termination usually occur?

Answer 17

Near pause site, dyad symmetry, palindromic e.g. G-C rich region (+difficult to melt)

Question 18

Outline hair pin formation

Answer 18

Hairpin formation at transcription destabilises RNA-DNA off part of newly transcribed RNA

• > NusA stabilises hairpin
• > wealky bound to A/V -> easy disruption

Question 19

Rho-independent

Answer 19

Destabilising of structure -> GC bases strong => 8 AT bp

Question 20

Rho

Answer 20

Hexameric ringed protein with potent ATPase activity and affinity for ssRNA
-> acts as RNA. DNA helicase

Question 21

Rho-dependent

Answer 21

80 RNA nucleotides wrap around Rho at rut sites -> dissociate from transcription complex

Question 22

When is ssRNA available?

Answer 22

Only when protein synthesis terminates as translating ribosomes interfere with rho -> minimises wasteful transcription