lecture 4

Question 1

what are the steps in transcription?

Answer 1

• initiation
• elongation
• termination

Question 2

what supports transcription?

Answer 2

• transcription regulators
• transcription factors

Question 3

what is transcription?

Answer 3

copy the DNA into RNA

Question 4

how many RNA polymerases do eukaryotes have?

Answer 4

3

Question 5

how many RNA polymerases fo bacteria have?

Answer 5

1

Question 6

what is the structure of bacteria RNA polymerase?

Answer 6

5 subunits
- 400-450 kDa

Question 7

what is the function of RNA polymerases?

Answer 7

reading and transcribing a gene sequence into an RNA product

Question 8

is RNApol a conserved structure?

Answer 8

RNA polymerase general architacture and catalytic function is conserved across the three domains of life

Question 9

what is the action of bacterial RNA pol?

Answer 9

• bacterial RNAP has a crab-cpaw appearance that opens and closes during transcription
• the incoming dsDNA goes into the cleft, becomes unwound and is transcribed into a strand of RNA
• the exiting DNA comes out in a perpendicular direction

Question 10

what is the structure of the core of RNA polymerase?

Answer 10

parts of the beta and beta’ and the two alpha subunits

Question 11

what is the structure of the jaw-lobe of RNA polymerase?

Answer 11

parts of the beta subunit

Question 12

what is the role of sigma in bacterial RNA polymerase?

Answer 12

participates in recognizing the promoter and initiate transcription

Question 13

where does the sigma factor bind on bacterial RNA polymerase?

Answer 13

to the cleft

Question 14

what happens in the initiation stage of transcription?

Answer 14

RNAP binds to the promoter, near the beginning of a gene transcription bubble

Question 15

what happens in the elongation stage of transcription?

Answer 15

RNAP reads the template strand one base at a time
RNAP buikds a complementary RNA molecule

Question 16

what happens in the termination stage of transcription?

Answer 16

Terminators signal that the RNA transcript is complete RNAP is released

Question 17

what is the bacterial promoter region in a gene?

Answer 17

specific dsDNA region where the RNAPol binds

promoter regions have very conserved structure

Question 18

what are the regions of the promoter of a bacterial gene?

Answer 18

UP element: -37 to -58
the -35 element: -35 to -30
the extended -10 element (Ext): -17 to -14
the -10 element: -12 to -7
the discriminator element (Dis): -6 to -4

*the exact position of each element may vary

Question 19

how does RNAPol recognize the bacterial gene promoter?

Answer 19

specific elements are recognized by individual domains of sigma factor and alpha-RNAPol

Question 20

where does transcription start in the gene?

Answer 20

at the +1 bp

Question 21

what is the composition of E.coli during growing conditions?

Answer 21

55% protein
10% lipid
3% DNA
20% RNA
<1% mRNA

Question 22

why is RNA found in much higher quantities within the bacterial cell than mRNA?

Answer 22

mRNA has a half-life od 3-8mins
RNA has a half-life of days

Question 23

what is E.coli house keeping sigma factor?

Answer 23

sigma 70

Question 24

what is the role of sigma70 (house keeping sigma factor)?

Answer 24

has lots of domains, each responsible for recognising a section of promoter
- sigma 70 recognizes most promoters

Question 25

what are the domains of sigma70?

Answer 25

3&4 - correct position of the promoter
1&2 - open complex

Question 26

what mediates binding of RNAP to the promoter?

Answer 26

initiation factor

Question 27

what is the role of sigma factor in initiation of transciption?

Answer 27

ensures the correct orientation of the dsDNA in the RNApol

Question 28

what does elongation of the RNA transcript occur?

Answer 28

once the sigma factor is released

Question 29

what is the role of RNAPs catalytic core?

Answer 29

RNAP catalytic core is capable of RNA polymerization

Question 30

what eukarotic polymerase is similar to bacterial RNA pol?

Answer 30

Pol II

Question 31

what is the structures involved in elongation?

Answer 31

Initiation factors are exchanged for elongation factors during the early stages of RNA synthesis

in E.coli- initiation factor (sigma 70) and elongation factor (NusG) bind to the same RNAP region

Question 32

what happens during elongation?

Answer 32

DNA-RNA hybrid of 8 to 9 base pairs is formed in the transcription bubble
The downstream DNA is not yet transcribed; the upstream DNA has regained the duplex form

Question 33

what is the function of backtracking in elongation during transcription?

Answer 33

incorrectly incorporated nucleotides can be excised

Question 34

what is the role of the rudder loop in elongation?

Answer 34

separates DNA

Question 35

what maintains the transcription bubble in elongation?

Answer 35

a series of loops

Question 36

where is the active site of the RNApolymerase?

Answer 36

the active site is located at the floor of the cleft

Question 37

when does the elongation phase start?

Answer 37

after RNAP synthesizes 9-10 RNA nts, it escapes from the promoter region

Question 38

what occurs during the termination of bacterial transcription?

Answer 38

intrinsic termination- DNA and RNA sequence
the helicase Rho associate with C-rich RNA sequences and expeles RNAP from the DNA

the helicase Rho engages with NusG, NusA, and RNAP during transcription elongation

RNAP dissociation from the DNA