EXAM 2: L7 Gene Expression I: Transcription and RNA Processing

Question 1

what does transcription produce?

Answer 1

transcription produces rna complentary to one strand of dna

Question 2

what direction are rna molecules syntheized?

Answer 2

5’ –> 3’ direction

Question 3

strand identity

Answer 3

template strand (anti-sense) strand

coding (sense strand) RNA is identical to the coding/sense strand (T replaced with U)

Question 4

what happens to rna molecules produced by transcription?

Answer 4

the are release from the dna as single strand

Question 5

5’ – ATG GCG TAA – 3’
What will be the sequence of the RNA transcript?

Answer 5

5’ – AUG GCG UAA – 3’

Question 6

An RNA molecule is being synthesized in the 5’ → 3’ direction.
What direction is RNA polymerase moving along the DNA template?

Answer 6

3’ –> 5’

Question 7

transcription in eukaryotes

Answer 7

three polymerases, introns, RNA processing (nucleus), monocistronic, mRNA
export

Question 8

transcription in prokaryotes

Answer 8

one polymerase, no introns, no nucleus, and genes can be polycistronic

Question 9

where does trx begin?

Answer 9

+1-

Question 10

what direction is upstream

Answer 10

towards 3’ end of template, contains promoter

Question 11

what direction is downstream

Answer 11

towards 5’ end of template, contains coding sequence

Question 12

polycistronic mRNA

Answer 12

multiple genes under the regulation of the same promoter (operon)

one single mrna transcript
prokaryotes

Question 13

monocistronic mRNA

Answer 13

each gene under the regulation of each promoter

eukaryotes and prokaryotes

Question 14

is helicased required?

Answer 14

no, RNA pol unzips the
DNA without a
helicase

Question 15

rna poly properties

Answer 15

high processivity

modest proofreading (fidelity)

Question 16

RNA polymerase binding

Answer 16

Facilitated by proteins that
recognize the
promotor region
Unwinding of double helix
Closed (dsDNA) – open (ssDNA)
complex

• Transcription bubble

Question 17

what is initiation?

Answer 17

transcription start site

Question 18

what is elongation?

Answer 18

unwidning dna, 5’ to 3’ synth

dna-rna hybrid

Question 19

termination

Answer 19

A terminator sequence is a DNA sequence that signals the end of transcription.

RNA transcript released and the polymerase dissociates from the DNA

Question 20

Which statement could NOT describe both eukaryotic and prokaryotic
transcription?

Answer 20

RNA polymerase catalyzes RNA synthesis from 3’-to-5’ of the new
strand.

Question 21

rRNA

Answer 21

ribosomal RNA

form the basic structure of the ribosome and catalyze protein syntehsis

Question 22

What happens to the DNA in the transcription bubble during elongation?

Answer 22

Only one strand is transcribed, and the bubble moves with RNA
polymerase

Question 23

holoenzyme

Answer 23

core enzyme + sigma
factor

Question 24

what does holoenzyme do

Answer 24

binding and initiation

promoter

Question 25

core enzyme - catalytic function

Answer 25

elongation and termination

Question 26

binding - transcription in e.coli

Answer 26

Binding RNA polymerase – promoter sequence 𝜎 (sigma) factor dictates binding to promoter Preferential binding to promoters of different 𝜎 factors Local unwinding of DNA

Question 27

initiation - transcription e.coli

Answer 27

First two rNTP base-pair with template – phosphodiester bond is formed RNA polymerase advances incorporating new nucleotides based on the templat

Question 28

elongation - transcription e.coli

Answer 28

After 10 nucleotides, 𝜎 (sigma) factor dissociates Core enzyme continues synthesis of RNA

Question 29

termination - transcription e.coli

Answer 29

ρ (rho) factor dependent - ATP-dependent unwinding enzyme Intrinsic termination - short GC-rich sequence (inverted repeats) followed by several U residues near their 3ʹ end Hairpin loop – pulls RNA molecule away from DNA

Question 30

Rna polymerases in eukaryotic transcription

Answer 30

RNA I, II, and III

Question 31

general transcription factors

Answer 31

regulatory sequence - promoter -enhancer dna packaging

Question 32

Binding RNA poly

Answer 32

promoter sequence TATA box

Question 33

transcription initiation complex

Answer 33

Sequential binding to promotor sequence – recruitment of RNA polymerase

Question 34

initiation (Eukaroytic transcription)

Answer 34

Phosphorylation of RNA pol II CTD ‘tail’ by TFIIH – protein kinase (CTD – carboxy terminal domain)

Question 35

elongation - euk trans

Answer 35

Elongation factors – prevent RNA pol falling of DNA

Question 36

termination - euk trans

Answer 36

RNA cleavage and RNA pol dissociates from DNA mRNA - poly(A)-dependent pathway

Question 37

Which of the following best explains how RNA polymerase recognizes the transcription start site in eukaryotic cells?

Answer 37

C. It is recruited by general transcription factors bound to the promoter

Question 38

mRNA product (EUKARYOTES)

Answer 38

5' cap 5'UTR- 5' untranslated coding sequence 3'UTR 3' untranslated 3' poly-A-tail

Question 39

mRNA product (PROKARYOTES)

Answer 39

5'UTR- 5' untranslated coding sequence 3'UTR 3' untranslated

Question 40

where does rna processing occuer in eukaryotes

Answer 40

cell nucleus

Question 41

what is rna splicing

Answer 41

removal of introns

Question 42

exons

Answer 42

expressedsequences

Question 43

introns

Answer 43

interveinng sequences

Question 44

how is rna prcoessing done?

Answer 44

? Phosphorylation of RNA Pol-II CTD ‘tail’ coordinates RNA processing by recruiting proteins and factors required for processing

Question 45

what happens after rna processing

Answer 45

the transcript is exported into cytosol

Question 46

5' cap function

Answer 46

Prevents degradation of mrna (protects against exonuclease) orients mRNA on ribosme during translation

Question 47

3' poly-A tail

Answer 47

RNA transcript is cleaved at sequence and poly-A tail added – poly-A polymerase Length of poly-A tail determines life span of mRNA (long tails = long life span) Export into cytoplasm

Question 48

Which of the following best describes what happens at the end of transcription in eukaryotic cells?

Answer 48

C. Cleavage of the RNA transcript and polyadenylation signal trigger termination

Question 49

splicing in eukaryotes

Answer 49

exons: protein domains introns: removed by splicing

Question 50

spliceosome

Answer 50

snRNP (small nuclear ribonucleoproteins) = snRNAs + proteins Ribozymes

Question 51

splicing mechanism

Answer 51

Introns form a branched structure during splicing and is released as a lariat.

Question 52

RNA Editing

Answer 52

nucleotides may be inserted, removed, or chemically altered within the coding sequence of an mRNA

Question 53

alternative splicing

Answer 53

Alternative splicing is the process by which a **single pre-mRNA transcript** (from one gene) can be spliced in** different ways** to produce** multiple mature mRNA variants,** leading to the production of **different proteins from the same gene.** | (one gene, multiple proteins)

Question 54

mRNA export

Answer 54

transport into cytosol

Question 55

selective transport

Answer 55

only processed mrna

Question 56

selective transport mechanisms

Answer 56

Poly-A binding proteins Cap-binding complex Exon junction complex

Question 57

Which of the following RNA modifications could best be described as "removal of intervening sequences"?

Answer 57

splicing

Question 58

Gradual shortening of poly-A tail

Answer 58

A. 3’→5’ exonuclease B. Decapping → 5’→3’ exonuclease C. Endonuclease dependent decay

Question 59

Order the following events of eukaryotic mRNA synthesis: A. 3'-polyadenylation B. termination C. splicing D. 5'-capping E. initiation

Answer 59

initiation 5' splicing 3' terminaiton

Question 60

Which of the following RNA molecules is fully processed and ready for export to the cytoplasm in eukaryotes?

Answer 60

C. Spliced mRNA with 5ʹ cap and poly-A tail