Exam 4 RNA Metabolism

Question 1

What is the primary structure of RNA?

Answer 1

An unbranched, single-stranded polymer of ribonucleotides linked by phosphodiester bonds.

Question 2

What is the secondary structure of RNA?

Answer 2

Local folding into motifs like hairpins or stem-loops via intrastrand base pairing.

Question 3

What is the tertiary structure of RNA?

Answer 3

Complex 3D folding stabilized by interactions between secondary structures (e.g., tRNA L-shape).

Question 4

Name three noncoding RNAs and their functions.

Answer 4

rRNA(ribosomal structure/catalysis),tRNA(delivers amino acids),miRNA(gene regulation).

Question 5

What is the difference between a genome and a transcriptome?

Answer 5

Genome: Complete set of genetic material of an organism
Transcriptome: All RNA transcripts produced by the genome under specific conditions, reflecting active gene expression

Question 6

Why doE. colipromoters have more AT base pairs?

Answer 6

AT pairs (2 H-bonds) are easier to unwind than GC pairs (3 H-bonds), reducing energy for transcription initiation.

Question 7

What is the structure ofE. coliRNA polymerase holoenzyme?

Answer 7

Core enzyme (α₂ββ′ω) + σ factor for promoter recognition.

Question 8

What is the role of the σ (sigma) factor?

Answer 8

Recognizes promoter sequences and dissociates after ~10–20 nucleotides of RNA synthesis.

Question 9

In what direction is RNA synthesized?

Answer 9

5′→3′, with nucleotides added to the 3′-OH end of the growing chain.

Question 10

What are the steps inE. colitranscription initiation?

Answer 10

σ binds to the promoter region forms closed complex → converted to open complex (DNA unwinds) → RNA synthesis → σ dissociation → elongation.

Question 11

Given RNA: 5′-AUGCCAUGA-3′, what is the template strand?

Answer 11

3′-TACGGTACT-5′ (antisense, complementary to RNA).

Question 12

Given RNA: 5′-AUGCCAUGA-3′, what is the coding strand?

Answer 12

5′-ATGCCATGA-3′ (sense, matches RNA but with T instead of U).

Question 13

Do RNA polymerases require a template?

Answer 13

Yes, they use a DNA template to synthesize complementary RNA.

Question 14

Does reverse transcriptase require a template?

Answer 14

Yes, it uses RNA to synthesize complementary DNA (cDNA).

Question 15

What activities occur during eukaryotic RNA Pol II initiation?

Answer 15

TF binding (e.g., TFIID), DNA unwinding (TFIIH helicase), Pol II CTD phosphorylation.

Question 16

What distinguishes exons from introns?

Answer 16

Exons: Coding sequences retained in mRNA.Introns: Noncoding, spliced out.

Question 17

How is eukaryotic pre-mRNA processed?

Answer 17

5′ capping, 3′ polyadenylation, and intron removal (splicing).

Question 18

What is the structure of the 5′ mRNA cap?

Answer 18

7-methylguanosine linked via 5′-5′ triphosphate bridge (+ possible 2′-O-methylation).

Question 19

Which nucleoside is required for group I intron splicing?

Answer 19

Guanine (G) as a cofactor.

Question 20

When is a lariat structure formed during splicing?

Answer 20

During spliceosome splicing of group II introns and nuclear pre-mRNAs, where the 2′-OH of an adenosine (the branch point) attacks the 5′ splice site, creating the lariat.

Question 21

How does differential RNA processing affect gene expression?

Answer 21

Produces multiple proteins from one gene via alternative splicing/polyadenylation.

Question 22

Are rRNA and tRNA synthesized from the same primary transcript inE. coli?

Answer 22

Yes, as polycistronic RNA, later processed into individual rRNAs/tRNAs.

Question 23

How do mRNA secondary structures (e.g., hairpins) affect stability?

Answer 23

Slow degradation by protecting against ribonucleases.

Question 24

What is the term for all RNAs produced by a cell?

Answer 24

Transcriptome.

Question 25

What is the term for all proteins produced by a cell?

Answer 25

Proteome.

Question 26

Transcribe this DNA template: 3′-TACGGTACT-5′.

Answer 26

5′-AUGCCAUGA-3′ (RNA replaces T with U).

Question 27

What is the mRNA sequence for DNA coding strand 5′-ATGCCATGA-3′?

Answer 27

5′-AUGCCAUGA-3′

Question 28

Compare ρ-dependent and ρ-independent termination.

Answer 28

ρ-independent: Formation of hhairpin + poly-U cause pausing -> dissociation of RNA & pol of DNA template...termination. ρ-dependent: Requires ρ protein to dissociate RNA polymerase.

Question 29

How many RNA polymerases do eukaryotes have?

Answer 29

Three: Pol I (rRNA), Pol II (mRNA), Pol III (tRNA/5S rRNA).

Question 30

Which RNA polymerase synthesizes mRNA in eukaryotes?

Answer 30

RNA polymerase II.

Question 31

True or False: RNA polymerase I synthesizes 5S rRNA.

Answer 31

False (Pol III synthesizes 5S rRNA).

Question 32

What are three post-transcriptional RNA modifications?

Answer 32

5′ capping, 3′ polyadenylation, splicing.

Question 33

How is mature tRNA formed in E. coli?

Answer 33

RNase P/D trim ends of short sequences at 5' & 3' of primary transcript, CCA added to 3′, bases modified (forming pseudouridine or methylguanosine), introns spliced (sometimes).

Question 34

What is the key difference between DNA and RNA polymerases?

Answer 34

DNA pol: Needs primer, has proofreading. RNA pol: No primer, no proofreading.

Question 35

Which enzyme synthesizes RNA primers for DNA replication?

Answer 35

Primase (a DNA-dependent RNA polymerase).

Question 36

In transcription, which DNA strand is the coding strand?

Answer 36

The 5′→3′ strand

Question 37

What is the template strand in transcription?

Answer 37

The 3′→5′ strand read by RNA polymerase to synthesize complementary RNA.

Question 38

What is the role of TFIIH in eukaryotic transcription?

Answer 38

Helicase activity unwinds DNA; kinase phosphorylates Pol II CTD for elongation.

Question 39

What signals transcription termination in eukaryotes?

Answer 39

Polyadenylation signal (AAUAAA) and cleavage/polyadenylation.