Transcription (Chapter 36)

Question 1

Difference between RNA and DNA synthesis?

Answer 1

• RNA doesn’t need primers.
• Ribonucleotides used.
• One strand is used.
• RNAP has OWN helicase activity.
• RNAP does not have proofreading ability.

Question 2

Name the types of small RNA and their function.

Answer 2

snRNA - involved in pre-mRNA ripening 
snoRNA- involved in chemical modifications of tRNA etc
miRNA - prevents translation
siRNA - degrades RNA molecules
piwiRNA - protects against transpoons.

Question 3

Which direction is template strand read in?

Which direction is RNA Synthesised?

Answer 3

Read in 3-5.

Synth in 5-3

Question 4

What makes up the Prokaryotic RNAP?

What does each subunit do?

Answer 4

two alpha subunits.
1 b’ and b subunit.
w(omega) subunit.

alpha binds to regulatory sequences.

b - binds to mg2+ to form the catalytic subunit which forms PDEB
b’ - holds the DNA template.

Question 5

What is the importance of the Sigma Subunit in Prokaroyes?

Answer 5

It binds to the RNAP’s core to form a holoenzyme.
This then binds to specific promotors.
SO DIFFERENT SIGMA FACTORS HAVE DIFFERENT AFFINITIES TO DIFFERENT PROMOTORS.

Question 6

Steps of Transcription cycle?

Answer 6

1) closed promotor complex
2) open promotor complex
3) chain initiation
4) Promotor clearance
5) Chain elongation
6) Termination

Question 7

What is happening during the: Closed Promotor complex?

Answer 7

RNAP binds to DNA and is looking for a promotor.

Question 8

What is happening during the: Open Promotor complex?

What else do we call the open promotor complex?

Answer 8

RNAP had bound to the DNA, causing it to melt and unwind.

We call it the “initiation complex”

Question 9

What happens during: Chain Initiation?

Answer 9

RNAP catalysed the coupling of the first base (usually purine) with second.

Question 10

What happens in: Promotor clearance?

Answer 10

The RNAP undergoes a conformational change after adding 10ish Nucleotides. and moves away from the promotor.

Question 11

What happens during: Chain Elongation?

Answer 11

As RNAP moves, DNA unwinds infront, reanneals behind.

Nucleotides added to 3-OH of the Nascent RNA.

Question 12

Importance of Ubiquitious Pyrophosphatases?

Answer 12

It breaks ppi into pi.

ensuring irreverisibility in every cycle of polymerisation

Question 13

Termination in Prokaryotes?

Answer 13

Rho-independent:

• palindromic sequences
• cause hair loop

Rho-dependent:
Rho is an ATP dependent RNA stimulated Helicase.

Question 14

When RNAP bound to -35BP of DNA promotor what does it form?

Answer 14

Closed complex.

Question 15

Bacterial promotor?

Answer 15

-35 and -10.

• 10 (TATA BOX):
  
  • AT rich region
  • Has low melting temperature thus allows easy dissociation of the two strands.

Question 16

Explain the Rho-dependent Signals?

Answer 16

They consist of inverted repeats.
Followed by AT.
They cause a hairpin to form, which slows down RNAP allowing Rho (an ATP depedent RNA stimulated helicase) to bind to it.

Question 17

Where is Methylated Cytosine most commonly found?

Answer 17

In regions of high transcription activity.

Question 18

1) How many Eukaryotic RNA Polymerase can be found?

2) What are their products and how are they affected by al-amantin?

Answer 18

1) 3RNAP and 1 Mitochondrial RNAP.

RNAP1: Forms rna like 28s, 5,8s, 18s
Not sensitive to a-amantin

RNAP2: Forms mRNA and small RNA
It is very affected by a-amantin

RNAP3: Forms tRNA and 5s rRNA, mitochondria RNA
It is slightly affected by a-amantin

Question 19

What is the location of TATA box in Eukaryotic Promotors?

Answer 19

-25bp

Question 20

What is the location of Inr in Eukaryotic Promotors?

Answer 20

-3 to +5

Question 21

What is the location of DPE in Eukaryotic Promotors?

Answer 21

+25Bp

Question 22

What happens in a mutation of TATA?

Answer 22

A mutation in Tata box causes a decrease in transcription.

Question 23

What are GC and CAAT Cis elements? What are they bound by?

Answer 23

GC and CAAT are found upstream.
Upstream cis-elements tend to affect the frequency of transcription.
GC bound by SP1 (has a zinc finger motiff)
CAAT bound by CTF

Question 24

What is TATA box bound by?

Answer 24

Tata box is bound by TBP.
TBP is found in: - TFIID
- SAGA
- P-caf

Question 25

What does TFIID consist of?

Answer 25

• TBP

- TAFS (14 of them)

Question 26

What does binding of TBD to DNA cause?

Answer 26

• Binds to Tata Box
• Causes 100 degree kind in DNA.
• This bending allows TAFS to interact with other cis element

Question 27

What is the significance of TAFS?

Answer 27

• TAFS are specific to polymerases.

- Which specify a certain promotor.

Question 28

what is swi/snf

Answer 28

swi/snf is a - Coregulator

Question 29

How many subunits does Eukaryotic RNAP 2 consist of?

Answer 29

12 subunits.

There are two similiar to Bacterial RNAP’s B subunits.

Question 30

Which Amino Acids make up the CTD?

Answer 30

-Tyr
-Ser
-Pro
-Ther
-Ser
The Stupid Prostitute Thor Sket…

Question 31

What is CTD a substrate for?

Answer 31

• kinases
• phosphatases
• proyly isomerases
• glycolysases

Question 32

How does TFIIH help in activation of RNAP2?

Answer 32

TFIIH has a kinase subunit.

It can phosphorylate Ser and Thr residues.

Question 33

What are classified as Basal Components?

Answer 33

• RNA pol 2
• TBP
• TFIIA
• TFIIB etc etc

Question 34

What are classified as co-regulators?

Answer 34

• TAFS
• TFIID
• Mediators
• Chromatin Remodelling modifiers.

Question 35

What are classified as Activators?

Answer 35

• SP1
• ATF
• CTF
• AP1

Question 36

What makes up the splicosome?

Answer 36

-U1,U2,U4,U5,U6
-60 other proteins which have (RRM and SARM)
They form a small nuclear ribonucleoprotein complex.

Question 37

Explain the: 1st Transesterification

Answer 37

• cut at 5’.
• nucleophilic attack from 3OH of Adenyly on brained point.
• Forms 5’-2’ bond