transcription 1

Question 1

what is the coding strand

Answer 1

strand of DNA that has the same sequence as the mRNA

Question 2

how many RNA polymerases in prokaryotes and eukaryotes

Answer 2

1 RNA polymerase in prokaryotes and 3 RNA polymerases in eukaryotes

Question 3

what does a sigma factor do

Answer 3

confers specifity to bind to a promoter on DNA in Prokaryotes

Question 4

what confers specifity in eukaryotes?

Answer 4

transcription factors

Question 5

can an RNA polymerase assemble from an αNTD domain

Answer 5

yes

Question 6

what domain is involved in activation?

Answer 6

the αCTD domain

Question 7

what is the name of the specific DNA sequence that sigma factor confers on RNA polymerase to bind to

Answer 7

the promoter

Question 8

what is the primary sigma factor in E.coli

Answer 8

sig70

Question 9

what is the primary sigma factor in bacillus subtilis

Answer 9

sigA

Question 10

how many domains does σ70/σ4 have

Answer 10

4 main domains

Question 11

what does region 1 domain of σ70/σ4 do?

Answer 11

it is self inhibitory

Question 12

what does region 2 of σ70/σ4 do?

Answer 12

2 has 4 sub domains some unassigned others melt DNA and recognise and interacts with the -10 region (TATAAT) of the promoter

Question 13

what does region 3 of the σ70/σ4 do?

Answer 13

interacts with DNA upstream of the -10 region of promoter

Question 14

what does region 4 of σ70/σ4 do ?

Answer 14

has 2 sub domains 4.1 has no specific function. 4.2 interacts with the -35 region of the promoter

Question 15

what is suppressor analysis

Answer 15

Suppressor analysis is a technique used in genetics and molecular biology to identify genes or mutations that can restore the function of a mutant protein or RNA molecule.

Question 16

what do you need to identify in terms of suppressor analysis methodology?

Answer 16

you need to identify the DNA operational sites (the promoters)

Question 17

what are the steps following on for the suppressor analysis methodology?

Answer 17

1. promoter probes plasmids 2. suppressor analysis 3. primer extension analysis 4. footprinting 5. bioinformatic information

Question 18

where and how is the transcriptor fired?

Answer 18

it is fired bythe promoter onto a piece of DNA and all of its copies.

Question 19

what is transcriptional fusion?

Answer 19

Transcriptional fusion is a molecular biology technique used to study gene expression by joining the regulatory regions of one gene with the coding sequence of another gene, resulting in a single mRNA transcript that can be used to measure gene expression levels.

Question 20

where does fusion occur

Answer 20

just at the level of transcription

Question 21

where do you find the promoter?

Answer 21

Promoter is the sequence usually at 5’ end of operons that RNA pol binds to specifically to initiate transcription

Question 22

what spacing portion is critical for the promoter?

Answer 22

the spacing between -10 and -35

Question 23

what does the addition of bases do ?

Answer 23

it doesnt elongate the helix, it just moves the helix around itself.

Question 24

what happens when 5 bases are added to the -10 and -35 spacing?

Answer 24

it can completely alter the positioning of further base pairs.

Question 25

what is the consensus promoter sequence?

Answer 25

it presents the bases most commonly found at each position of the promoter for a particular promoter family

Question 26

what happens to promoters that deviate from the consensus sequence?

Answer 26

usually weaker

Question 27

what is the series of stages that initiation of prokaryotic transcription occurs at?

Answer 27

R + P ->RPc <–>RP1 <–> RP0, where RPc is closed complex, RP1 is intermediate complex, RP0 is open complex.

Question 28

what is the formation of RP0 required for?

Answer 28

to initiate transcription.

Question 29

give two statements regarding consensus promoters

Answer 29

1 they are very strong since cell needs to balance promoter strength (limited amount of RNA pol) 2 their activity is fully on, so can only be controlled by turning them off.

Question 30

do most promoters deviate from the consensus

Answer 30

yes

Question 31

what happens when these promoters are activated and repressed

Answer 31

activated: transcription can be increased
repressed: transcription can be turned off

Question 32

what happens when there is an increase in RPc formation ?

Answer 32

affinity increased of DNA promoter for RNA polymerase

Question 33

what happens when RPo is increased?

Answer 33

increases conversion of RPc into RPo.

Question 34

what do activator proteins do

Answer 34

bind to RNA polymerase and to promoter DNA, also provide contact between RNA polymerase and DNA therefore increase affinity between them. they also increase rate of RP0 formation

Question 35

how many interactions has RNA polymerase when bound to the promoter?

Answer 35

two interactions: -35 DNA sequence and region 4.2 of sig70, and -10 DNA sequence and region 2.4 of sig70

Question 36

what is an UP element

Answer 36

a DNA sequence which alpha CTD domain of RNA polymerase can bind to, making it three interactions

Question 37

what indirectly happens due to the UP element

Answer 37

affinity increased between RNA pol and DNA and increased RPc formation / increased transcription

Question 38

how is transcription increased ?

Answer 38

by increased clearance of promoter and by increased affinity between RNA polymerase and the promoter.