wanskiption

Question 1

Properties of RNA polymerase

Answer 1

• Completely processive – single enzyme transcribes complete RNA
• Catalyses both initiation and elongation of RNA – no primer needed
• No proof reading mechanism

Question 2

Different types of RNA polymerase where are they found

Answer 2

1: nucleolus

2+3: nucleoplasm

Question 3

What do RNA polymerase 1 2 and 3 make

Answer 3

1) rRNA
2) mRNA, snRNA, snoRNA,miRNA
3) tRNA, rRNA, some snRNAs

Question 4

What happens in initiation in transcription

Answer 4

• Specific GTFs that bind to correct promoter and recruit polymerase
• Binding of TATA box binding protein (TBP) and TBP associated factors to TATA box
• Causes sequential recruitment of other TFs for RNA polymerase 2 (TFIIs) e.g. TBII1,TF11B,TFIIF .
• Forms preinitiation complex: protein scaffold onto which polymerase is recruited
• On completion, the initiation complex/basal transcription apparatus unwinds stretch of double helix to reveal single stranded DNA that it will transcribe

Question 5

What happens in elongation

Answer 5

• RNA polymerase 2 selects correct ribonucleotide triphosphate and catalyses formation of phosphodiester bond.
• RNA molecule doesn’t require primer and is synthesised in 5’3’ direction
• Normal base pairing but U not T, so mRNA strand complementary to DNA template

Question 6

In what direction does polymerase move

Answer 6

• RNA pol 2 move unidirectionally away from promoter region along DNA

Question 7

What happens in protein dependent termination

Answer 7

self-complementary RNA in palindromic GC-rich region forms hair pin in RNA structure due to base pairing, this hair pin followed by oligo (U) sequence (caused by T rich region). This complex destabilises weak association between RNA and DNA so they dissociate

Question 8

What happens in protein independent termination

Answer 8

Rho protein binds to newly made RNA at C rich, G poor region scanning along RNA towards RNA polymerase (needs ATP). When it reaches RNA polymerase, it breaks DNA-RNA association, terminating transcription.

Question 9

Where is the signal for termination of RNA pol

Answer 9

Newly transcribed RNA

Question 10

How is preMrna processed

Answer 10

capping, polyadenylation and splicing.

Question 11

What happens in capping

Answer 11

• A GMP nucleotide/G residue is added to the 5’ end of preMRNA by 5’-5’ triphosphate bond ; G residue is methylated and binds to cap binding complex. (methyl guanosine cap

Question 12

What is the role of capping

Answer 12

protects the 5’ terminal of the mRNA against degradation (exonucleases can’t recognise 5’ end due to 5’-5’ linkage)

• improves ribosomal recognition for translation (recruits small ribosomal subunit)
• Provides scope for regulation of translation.
• Export machinery recognises and uses cap to help mRNA move out of nucleus

Question 13

What end does capping protect

Answer 13

5’ END

Question 14

How does splicing occur

Answer 14

• snRNA-mediated transesterification reaction results in 2 sequential breakages and rejoining of sugar phosphate backbone in RNA excision of introns and fusion of exons.

Question 15

What does a splicesome consist of

Answer 15

snRNA, (bound to) splicing factor, in complex known as snRNPs
And, premRNA being processed

Question 16

Describe importance of snRNAs

Answer 16

have complementary sequences to splice sites at each exon-intron junction so can hybridise with them in RNA-RNA interactions

Question 17

What are splice sites

Answer 17

there are 5’ and 3’ splice sites at border of each exon/intron

Question 18

Dinucletode found at 3’ and 5’ end of intron

Answer 18

5’ = GU

3’=AG

Question 19

What is nonsense mediated decay

Answer 19

surveillance mechanism in which exon junction proteins act as markers to identify faulty Mrna. Exon junction complex downstream of stop codon is recognised and indicates that it’s a premature stop codon so faulty mRNA containing premature stop codons are degraded.

Question 20

True of false, after normal stop codon, no more EJC complexes form

Answer 20

True

Question 21

What happens after splicing at exon exon junctions

Answer 21

marked by deposition of exon junction proteins/complex.

Question 22

Why is alternate splicing important

Answer 22

cells to generate several different proteins (i.e. exon skipping so many transcripts made) from a gene – enables tissue specific gene expression.

Question 23

The more introns per gene…

Answer 23

Increased complexity of organism and greater regulation of splicing

Question 24

How can alternatve splicing be enhanced

Answer 24

enhancer proteins, which bind to enhancer sequences packed into exons. Make splice site more attractive, provide binding site for components of spliceosome so more likely to include exon X in final mRNA.

Question 25

How can proteins silence splice sites of exon/intron junction

Answer 25

the proteins bind to silencer region prevent spliceosome associating with 3’ and 5’ splice site , weakens splice site

Question 26

What is polyadenylation consensus sequence

Answer 26

AAUAAA

Question 27

What does polyadenylation consensus sequence signal

Answer 27

premRNA should be cleaved 20 bases downstream by endonuclease.

Question 28

What happens in polyadenylation

Answer 28

1) Polyadenylation consensus sequence (AAUAAA) signals that premRNA should be cleaved 20 bases downstream by endonuclease.
2) Poly(A) polymerase adds poly(A) tail to 3’ end (around 250 adenosine residues) donated by ATP, which is then covered by poly(A) binding proteins

Question 29

Role of poly(A) tail

Answer 29

transport, stability, translatability

• Makes mRNA more stable because must be degraded by exonucleases before they reach coding mRNA, so more time for this to be translated
• Cap and poly (A) binding proteins interact, forming structure that recruits ribosome to mRNA- enhances translation

Question 30

How can mutations affect mRNA processing

Answer 30

Mutations affecting splice sites lead to reduced/abolished splicing of some introns, faulty mRNAs that contain intronic sequences changing the protein message or creating premature stop codon.
- Mutations affecting poly(A) signals can reduce/increase cleavage and polyadenylation so total output of mRNA affected.