lecture 23

Question 1

what is the general structure of a prokaryotic cells in the transcription

Answer 1

promoter
coding region (including termination)
termination

Question 2

what happens in the initiation of prokaryotic?

Answer 2

RNA polymerase binds, unwinds and joins first 2 nucleotides.
-initiation of RNA synthesis DOES NOT
require a primer

Question 3

what happens during the elongation of the prokaryotic

Answer 3

Complementary nucleotides
continue to be added during the elongation
process.
-localized DNA unwinding ahead of RNA
polymerase generates a “transcription
bubble”.
-transcription bubble moves with the
RNA polymerase and the unwound DNA
rewinds behind it.

Question 4

what happens during the termination of the prokaryotic

Answer 4

Transcription stops when RNA polymerase reaches the “terminator” region of the gene.
-the newly-synthesized RNA together with
RNA polymerase are released

Question 5

what are E. coli RNA polymerase

Answer 5

Core: a2 b b’ω
Holoenzyme: a2 b b’ ω s

Question 6

what does a2 b b’ω do

Answer 6

Transcribes any DNA sequence

Question 7

what does a2 b b’ω s do

Answer 7

the structure of the complete RNA polymerase, This structure is specific for transcribing genes

Question 8

what is the role of alpha

Answer 8

a: (alpha subunit)-involved in the assembly of the tetrameric
core

Question 9

what is the role of beta

Answer 9

b: (beta subunit) – contains the ribonucleoside triphosphate
(rNTP) binding site

Question 10

what is the role of beta prime

Answer 10

b’: (beta-prime subunit- contains the DNA template binding
region

Question 11

what is the role of omega

Answer 11

ω : (omega subunit)-it helps to stabilize the tetrameric (a2 b b’)
core

Question 12

what is the role of sigma subunit

Answer 12

(sigma subunit) – it binds to the RNA polymerase tetrameric core and assists in the correct initiation of transcription specifically at the promoter region of the
prokaryotic gene. Sigma give the RNA polymerase specificity for the gene.
-Transcribes any DNA sequence (not gene specific)
-the structure of the complete RNA polymerase,
This structure is specific for transcribing genes
3. Transcription in Prokaryotes (cont’d)
E. coli RNA polymerase

Question 13

what happens in the Initiation of transcription

Answer 13

recognition of the gene promoter region requires the intact RNA polymerase holoenzyme,
-Sigma factor recognizes and binds
to the -35 element in the promoter region, properly positioning the RNA polymerase to begin transcription

Question 14

where does alpha factor binds

Answer 14

-35 position

Question 15

what is -10 element

Answer 15

which due to its very A/T rich content, is prone to unwinding

Question 16

where does the transcription initiates

Answer 16

Transcription initiates about 5-9 base pairs
down from the end of the -10 sequence

Question 17

where is the +1 position

Answer 17

5’ end of the RNAis usually a purine (the +1
position

Question 18

-35 and -10 elements are examples of ……………

Answer 18

-35 and -10 elements are examples of consensus sequences

Question 19

what is the sequences of the -35

Answer 19

35 sequences has the consensus TTGACA which is important in unwinding DNA during transcriptional initiation.

Question 20

what is the consequences of the -10

Answer 20

TATAAT

Question 21

how many base pairs are in the Transcription bubble

Answer 21

-a localized region of unwinding of
~18 base pairs

Answer 22

Elongation occurs when Sigma factor is
released and RNA polymerase begins to move along the 3’ to 5’ DNA template strand.
-A localized region of unwinding called the
“transcription bubble” occurs as RNA
polymerase moves along the DNAtemplate.

Question 23

where does positive supercolis form and which enzyme remove it ?

Answer 23

-Positive supercoils formed in the double-
stranded DNA ahead of the advancing RNA
polymerase are removed by topoisomerases

Question 24

how does the termination happens

Answer 24

Common mechanism of transcription
termination in bacteria
-Weak H-bonding at U:A residues
allows mRNA release from DNA when
RNA polymerase pauses at terminator

Question 25

what are the promoters in the eukaryotic transcription

Answer 25

There are specific promoter sequences for genes transcribed by RNA
polymerases I, II or III.

Question 26

what is RNA polymerase II promoter consist of

Answer 26

It consists of a core promoter and a regulatory promoter that aid in positioning transcription proteins and RNA polymerase II to begin transcription
4. Transcription in eukaryotes (cont’d)

Question 27

what do Y, R, N abbreviation mean

Answer 27

Abbreviations:
Y = pyrimidine, either C or T
R= purine, either A or G
N= any nucleotide, A,G,C orT

Question 28

what is TFII

Answer 28

Transcription Factors of Pol. II (TFII A, B, D, E, F and H)

Question 29

how is transcription in the eukaryotic

Answer 29

TFIID assembles first at the
TATAbox followed by the remaining general transcription factors (TFs) and Pol. II.
-this forms the “preinitiation complex” or PIC: that is sufficientto initiate transcription.
-More complex transcriptional regulation involves a multi-subunit complex called
“Mediator” that permits interactions with other activator proteins bound to
upstream/downstream regulatory regions or enhancer sequences.

Question 30

what does core promoter do in the eukaryotic transcription

Answer 30

Core promoters assemble the transcriptional
machinery, but enhancer sequences determine how efficiently they transcribe, by
influencing them with cofactors (COFs)

Question 31

what are TF, COF, PIC, GTF

Answer 31

TF= transcription factor; COF = transcription co-factor; PIC =pre- initiation complex;
GTF = general transcription factors

Answer 32

at this stage, many of the general
transcription factors remain
at the promoter providing for quick
re-initiation with a new Pol.II.

-this together with DNAunwinding,
ensures that the free RNA 3’-OH
terminus is available for new rNTP
addition.

Question 33

how does transcription bubble generated

Answer 33

-an ~8 nucleotide “transcription bubble”
is generated by RNA:DNA binding.

Question 34

what is alpha aminitin

Answer 34

potent inhibitor RNA polymerase