[W7-8] Transcription

Question 1

What is transcription?

Answer 1

The process by which information in DNA is copied into a complementary RNA sequence.

Question 2

In which direction does transcription occur?

Answer 2

5′ to 3′ direction on a DNA strand running 3′ to 5′.

Question 3

What are the three stages of transcription?

Answer 3

Initiation, Elongation, Termination.

Question 4

What is the central dogma of molecular biology?

Answer 4

DNA → RNA → Protein.

Question 5

What does RNA polymerase do?

Answer 5

Synthesizes RNA from a DNA template without a primer.

Question 6

What forms the transcription bubble?

Answer 6

RNA polymerase melts 12–14 bp of DNA, forming an 8–9 bp RNA-DNA hybrid.

Question 7

What types of RNA are made by transcription?

Answer 7

• mRNA
• tRNA
• rRNA
• snRNA
• snoRNA
• miRNA
• siRNA
• piRNA
• lncRNA
• crRNA

Question 8

What subunits form the bacterial RNA polymerase core enzyme?

Answer 8

• α₂
• β
• β′
• ω

Question 9

What is the role of the sigma factor?

Answer 9

Directs RNA polymerase to promoters and is released after ~10 nt.

Question 10

What are the key promoter elements in bacteria?

Answer 10

• -10 (TATAAT)
• -35 (TTGACA) boxes.

Question 11

What are the two classes of prokaryotic terminators?

Answer 11

• Intrinsic (hairpin + U’s)
• Rho-dependent.

Question 12

What is abortive initiation?

Answer 12

RNA polymerase produces short transcripts before elongation.

Question 13

What does RNA polymerase I transcribe?

Answer 13

18S, 28S rRNA in the nucleolus.

Question 14

What does RNA polymerase II transcribe?

Answer 14

mRNA and some small RNAs (e.g. miRNA).

Question 15

What does RNA polymerase III transcribe?

Answer 15

tRNA, 5S rRNA, and other small RNAs.

Question 16

What is the CTD of RNA Pol II?

Answer 16

The C-terminal domain that is phosphorylated to regulate transcription and processing.

Question 17

Why do eukaryotic RNA polymerases need transcription factors?

Answer 17

They cannot recognize DNA promoters on their own.

Question 18

What is the core promoter?

Answer 18

The minimal DNA sequence required to initiate transcription.

Question 19

What is TBP and its function?

Answer 19

TATA-binding protein that bends DNA and helps position RNA polymerase.

Question 20

What are the steps of RNA Pol II initiation?

Answer 20

• TFIID binds TATA
• TFIIB binds BRE
• Pol II/TFIIF recruited
• TFIIE and TFIIH join
• TFIIH unwinds DNA and phosphorylates CTD.

Question 21

Describe RNA Pol I promoter.

Answer 21

Bipartite: core (−45 to +20) and UPE (−180 to −107).

Question 22

Describe RNA Pol III promoter types.

Answer 22

• Type I/II: internal (e.g. tRNA, 5S rRNA)
• Type III: upstream (e.g. snRNAs).

Question 23

What happens during elongation?

Answer 23

RNA polymerase moves along DNA, synthesizes RNA, displaces histones.

Question 24

Which enzymes relieve transcription-induced supercoiling?

Answer 24

• Gyrase
• Topoisomerase.

Question 25

What causes promoter clearance?

Answer 25

TFIIH-mediated DNA melting and CTD phosphorylation.

Question 26

What are key CTD phosphorylation events?

Answer 26

* Ser5 (capping) by TFIIH * Ser2 (elongation/splicing) by P-TEFb * Ser7 by unknown kinase.

Question 27

What signals termination in Pol II transcription?

Answer 27

Polyadenylation signal (AAUAAA) and RNA cleavage.

Question 28

What proteins are involved in polyadenylation?

Answer 28

* Specificity factor * Endonuclease * Poly(A) polymerase * Exonuclease.

Question 29

What is the 5′ cap and its function?

Answer 29

7-methylguanosine cap via 5′–5′ linkage; stabilizes RNA, aids export, splicing, and translation.

Question 30

What is the function of the poly(A) tail?

Answer 30

Enhances mRNA stability, export, and translation efficiency.

Question 31

What must happen to chromatin for transcription to proceed?

Answer 31

Nucleosomes must be displaced/remodeled.

Question 32

What is chromatin remodeling?

Answer 32

ATP-dependent repositioning or eviction of nucleosomes to allow transcription.

Question 33

What is a cis-acting element?

Answer 33

DNA sequences (e.g., promoter, enhancer, silencer) near the gene that regulate expression.

Question 34

What is a trans-acting factor?

Answer 34

Proteins (e.g., TFs, coactivators) that bind cis-elements to control transcription.

Question 35

What’s the difference between general and specific TFs?

Answer 35

* General TFs are required for all genes (e.g. TFIID, TFIIB) * Specific TFs regulate individual genes.

Question 36

What is antitermination?

Answer 36

A mechanism where RNA polymerase ignores termination signals (seen in phage and rRNA genes).

Question 37

What are riboswitches?

Answer 37

RNA elements that bind metabolites and regulate transcription or translation in response.

Question 38

Where does transcription occur in prokaryotes?

Answer 38

Cytoplasm.

Question 39

Where does transcription occur in eukaryotes?

Answer 39

Nucleus.

Question 40

Is transcription coupled to translation in prokaryotes?

Answer 40

Yes.

Question 41

Is transcription coupled to translation in eukaryotes?

Answer 41

No.

Question 42

How many subunits in RNA polymerase core (prokaryotes)?

Answer 42

5 subunits.

Question 43

How many subunits in RNA polymerase (eukaryotes)?

Answer 43

12–17 subunits.

Question 44

Can prokaryotic RNA polymerase recognize promoters alone?

Answer 44

Yes, with sigma factor.

Question 45

Can eukaryotic RNA polymerase recognize promoters alone?

Answer 45

No, it needs transcription factors.

Question 46

Is mRNA processing common in prokaryotes?

Answer 46

No, minimal or none.

Question 47

Is mRNA processing common in eukaryotes?

Answer 47

Yes — capping, splicing, polyadenylation.

Question 48

What type of mRNA is typical in prokaryotes?

Answer 48

Polycistronic.

Question 49

What type of mRNA is typical in eukaryotes?

Answer 49

Monocistronic.

Question 50

How is transcription terminated in prokaryotes?

Answer 50

Rho-dependent or intrinsic (hairpin structure).

Question 51

How is transcription terminated in eukaryotes?

Answer 51

Poly(A) signal and downstream terminator.