lecture 6 - transcription

Question 1

where does protein synthesis occur in prokaryotes

Answer 1

on the ribosome

Question 2

how is transcription different to dna rep in prokaryotes

Answer 2

only one dna template strand is transcribed, small fraction of DNA is transcribed, no primer required

Question 3

what makes up RNA polymerase for e coli

Answer 3

alpha unit (assembly, chain initiation)
beta (binds nucleoside triphosphates, initiation and elongation)
beta’ (binds dna)
sigma (recognizes specific sequences)

Question 4

where does transcription begin

Answer 4

promoter sequence

Question 5

what is the bacterial promoter sequence comprised of

Answer 5

purine at the start point, TATA box at -10 and hexamer at -35

Question 6

what is the protein necessary for transcription

Answer 6

RNA polymerase

Question 7

which way does the transcription bubble move in DNA rep

Answer 7

5’-3’

Question 8

when is the sigma unit released in transcription

Answer 8

at the end of initiation, once about ~10 nucleotides have been added

Question 9

what is the sigma subunit necessary for

Answer 9

initiation

Question 10

what does the sigma factor do

Answer 10

changed DNA binding properties of RNA pol so its affinity for general DNA is reduced while affinity for promoters is increased

Question 11

how long is the transcription bubble in prokaryotes

Answer 11

~12-14 bp

Question 12

how long is RNA-DNA hybrid in transcription in prokaryotes

Answer 12

~8-9 bp

Question 13

what are the names of the stands in transcription

Answer 13

template and non-template (coding)

Question 14

how fast does elongation move

Answer 14

20-50 nucleotides/second but slower in G/C rich regions

Question 15

what is the error rate in transcription in prokaryotes

Answer 15

1/10^4

Question 16

how does factor-indepent termination occur

Answer 16

there is a G-C rich hairpin in RNA product followed by U-rich region that termination occurs in

Question 17

how does rho-dependent termination occur

Answer 17

rho is a helicase that binds to C-rich, G-poor sequence of rut site in Rna and then tracks along RNA to reach RNA pol where RNA is released

Question 18

what are positive strand RNA viruses

Answer 18

viruses that function as a genome and the mRNA can be directly translated to viral proteins. some proteins are required to copy mRNA to make dsRNA which is used as template to make more RNA copies

Question 19

how do negative strand RNA viruses work

Answer 19

work as complementary strands from which mRNA is synthezise by RdRp. the mRNA can be translated or used as teplate to make more copies of viral genome

Question 20

what are examples of positive strand RNA viruses

Answer 20

covid

Question 21

what are examples of negative strand RNA viruses

Answer 21

ebold, influenze, rabies

Question 22

how do double-stranded RNA viruses work

Answer 22

genome is used as template to generate positive RNA strand (usind RdRp) which can be translated or replicated

Question 23

what are examples of double stranded RNA viruses

Answer 23

rotavirus, blue tongue virus

Question 24

what is RdRp? what does it lack?

Answer 24

rna-dependent rna polymerase (lacks proof-reading)

Question 25

what are retroviruses

Answer 25

RNA viruses that use DNA intermediate to integrate into host. the genome is reverse transcribed to DS DNA which is integrated into host renome

Question 26

what does RdDp and whats another name for it

Answer 26

rna dependent dna polymerase and also called reverse transcriptase

Question 27

how does reverse transcription work

Answer 27

use host tRNA as primer which binds to Primer Bindng Site on Rna genome. RT copies part of one strand of RNA to make DNA and then becuase there are repeat regions at end of RNA genome, the new DNA can prime the other end of the genome. most of the RNA strand is degraded by RNaseH activity of RT but the remaining regions of RNA are used to prime syntheisis of second dna strand