Transcription

Question 1

RNA is synthesized by ___ ___. It requires a ____ template and synthesizes new RNA 5’ to 3’. No ____ is needed to initiate RNA synthesis. RNA polymerases do no _____

Answer 1

RNA polymerase; DNA; primer; proofread

Question 2

E. coli uses a single RNA polymerase for all transcript synthesis:

Answer 2

rRNA, tRNA, and mRNA

Question 3

Core enzyme of E. coli RNA polymerase is inefficient at initiating RNA synthesis and consists of 5 subunits. The sixth subunit ___ is req for efficient initiation and the complete enzyme is then called the RNA polymerase ____

Answer 3

1. 2 alpha subunits
2. 1 beta
3. 1 beta prime
4. w (gamma)

sigma factor; holoenzyme

Question 4

Transcription is initiated at ____ sites upstream. Things that are upstream have ____ numbers. The first base on the template transcribed strand copied is called the _____ ___ ___.

Answer 4

promoter; negative; transcription start site

Question 5

What are the E. coli promoter consensus sequences

Answer 5

regions within promoters that have similar DNA sequences…centered around -35 and -10 region (pribnow box)

Question 6

what does commonality of seq suggest?

Answer 6

functional importance for the regions and binding RNA polymerase for that region.

Question 7

RNA polymerase binds weakly to DNA until it binds to -35 site and closes tightly. RNA polymerase then moves forward to -10 site and unwinds about ____ bp in front and forms open complex.

Answer 7

17

Question 8

What is the first nucleotide brought into active site

Answer 8

a purine; pyrimidine on template

Question 9

Oncle nucleotides are brought in ____ units fall off.

Answer 9

sigma

Question 10

As elongation of transcript goes forward; DNA helix gets unwound in front of enzyme and rewinds behind which displaces growing RNA strand. At any one point, about ____ bp unwound

Answer 10

17

Question 11

RNA polymerase dissociates from the template. Where does it terminate?

Answer 11

3’ downstream of translation termination codon.

Question 12

what are the two mechanisms for transcriptional termination in E. coli?

Answer 12

1. Rho dependent

2. Rho independent

Question 13

How does Rho dependent termination occur

Answer 13

1. Req ATP
2. Binds to seq in 3’ untranslated region of mRNA and uses energy from ATP to break H bonds holding transcript to template.

Question 14

how does Rho independent termination occur

Answer 14

driven by secondary structure formation of RNA transcript and thermodynamics. Region of transcript folds into hairpin loop and reduces bp to template. This region following the loop is very U rich which favors DNA rewinding bc there is poor H bonding

Question 15

Eukaryotes have ____ diff kinds of RNA polymerases

Answer 15

3:
I: in nucleolus; transcribes rRNA
II: in nucleus; transcribes mRNA. extremely sensitive to alpha amanitin
III: in nucleus; transcribes tRNA & 5S rRNA

Question 16

In eukaryotes, typical mRNA promoter has ____box about ____ bases upstream of transc start site which is the core promoter.

Answer 16

TATA; 25

Question 17

RNA pol II catalyzes RNA synthesis. ____ recognizes TATA box. ____ stabilizes TFIIB and TBP binding to promoter. TFIIB binds ___ and recruits more Pol II-TFIIF complex. _____ recruits TFIIH. _____ binds Pol II and binds TFIIB and prevents nonspecific binding of Pol II. _____ unwinds DNA at promoter; phosphorylates Poll II within CTD (carboxy terminal domain)

Answer 17

TBP; TFIIA; TBP; TFIIE; TFIIF; TFIIH

Question 18

How is RNA processed? what is a newly synthesized RNA molecule called

Answer 18

Prokaryote mRNAs are ready to be used in translation w/o furhter modification. primary transcript.

Question 19

tRNA and rRNA never become _____. tRNA’s undergo ____ modifications and rRNAs are involved in cleavage of large primary trancript into functional fragments.

Answer 19

proteins! Base

Question 20

tRNA is single strand of RNA that base pairs with itself and makes unusual structures. Always a piece at 5’ end that gets removed by RNAse P. Always a piece at 3’ end that gets removed and replaced with a ____and where aa bind.

Answer 20

CCA addition

Question 21

rRNA is transcribed as a big precursor molecule. RNA cleavage occurs to give each RNA _____

Answer 21

intermediate (ind compennts of rRNA and tRNA)

Question 22

Where are tandem arrays of rRNA genes found?

Answer 22

found in nucleolar regions of 13, 14, 15, 21, and 22.

Question 23

In eukaryotes _____ also gets processed, but NOT in prokaryotes

Answer 23

mRNA; 5’ cap to 5’ end and 3’ polyA tail and splicing of introns

Question 24

hetero nuclear RNA means

Answer 24

it hasnt been processed yet

Question 25

processing of mRNA happens concurrently with:

Answer 25

transcription

Question 26

what is added to 5’ cap

Answer 26

7 methylguanosine adds to 5’ end to the transcript in opp orientation. Helps mRNA transcript stay in there longer.

Question 27

Cap binding complex

Answer 27

recognizes new cap and keeps it tethered. So as its transcribed intron can get spliced out and poly A tail can be added on the end.

Question 28

What is splicing mediated by? What is its role?

Answer 28

small nuclear RNAs (snRNAs) which form splicesome complex. They help bring 5’ splice junction and branch point close to each other. Form the loop. Cuts off one side and then the other side and helps ligate the exons.

Question 29

Introns always have GU at 5’ end and AG at 3’ end. What does the branch point help do?

Answer 29

Branch point helps make lariat structure.

Question 30

What do the OH groups serve as

Answer 30

nucleophiles to first form the lariat structure, then join the donor and acceptor junction.

Question 31

____ and transcription are coordinated

Answer 31

Splicing

Question 32

____ are larger than the exons

Answer 32

Introns

Question 33

____ splicing is often tissue dependent

Answer 33

Alternative

Question 34

Some mRNAs are edited before translation. Alteration usually involves enzymatic deamination of A or C to form inosine or ____. In intestine, deamination converts ____ to uridine.

Answer 34

uridine. cytidine

Question 35

what are differences in RNA processing in eukaryotes vs prokaryotes

Answer 35

1. No 5’ cap 3’ poly a tail or splicing of mRNA in prokaryotes.
2. There is no removal of UU at 3’ end for tRNA in prokaryotes.
3. There is some methylation of some bases in rRNA in prokaryotes whereas in eukaryotes, theres methylation of some riboses

Question 36

what are inhibitors of transcription

Answer 36

1. Rifamycin: antibiotic that inhibits prokaryote but not eukaryote RNA polymerase.
2. alpha amanitin: toxin from poisonous mushroom that mainy affects RNA pol II, blocks mRNA synthesis
3. Actinomycin D: planar molecule intercalates into double helix bet two GC base pairs which blocks polymerase movement.
4. acridine: research reagant that works in similar manner.