Transcription

Question 1

RNAs transcribed in both prokaryotes and eukaryotes

Answer 1

• mRNA (messenger)
• rRNA (ribosomal)
• tRNA (transfer)

Question 2

RNA produced only in eukaryotes

Answer 2

• pre-mRNA (pre-messenger)
• snRNA (small nuclear)
• snoRNA (small nucleolar)
• miRNA (micro)
• siRNA (small interfering)
• piRNA (piwi-interacting)

Question 3

RNA produced only in prokaryotes

Answer 3

CRISPR RNA (crRNA)

Question 4

Function of rRNA

Answer 4

Ribosomal rna : structural and functional components of ribosome

Question 5

Function of mRNA

Answer 5

Messenger RNA: Carrie’s genetic code for proteins

Question 6

Function of tRNA

Answer 6

Transfer RNA: helps incorporate amino acids into polypeptide chain

Question 7

Function of snRNA

Answer 7

Small nuclear RNA: processing of pre-mRNA

Question 8

Function of snoRNA

Answer 8

Small nucleolar RNA : processing and assembly of tRNA

Question 9

Function of miRNA

Answer 9

MicroRNA: inhibits translation of mRNA

Question 10

Function of siRNA

Answer 10

Small interfering RNA: triggers degradation of other RNA molecules

Question 11

Function of piRNA

Answer 11

Piwi-interacting RNA : suppresses the transcription of transposable elements in reproductive cells

Question 12

function of crRNA

Answer 12

CRISPR RNA: assists destruction of foreign DNA

Question 13

What direction does transcription proceed

Answer 13

5’ —> 3’

Question 14

Components of bacterial RNA polymerase

Answer 14

• 2x α subunits, β, β’,ω & σ

Core enzymes (without σ) is catalytically active, but binds non-specifically

σ directs RNA polymerase to the promoter

Question 15

What are the 3 stages of bacterial transcription

Answer 15

Initiation
Chain elongation
Termination

Question 16

What happens in initiation of bacterial transcription

Answer 16

• promoter recognition
• formation of transcription bubble
• creation of first bonds between rNTPs
• escape of transcription apparatus from promoter

Question 17

What happens during chain elongation of bacterial transcription

Answer 17

RNA polymerization reaction

Question 18

What happens during termination of bacterial transcription

Answer 18

• ρ dependent termination

- ρ independent termination

Question 19

What is TTGACA

Answer 19

Consensus sequence on bacterial promoter with charge -35

Question 20

What is TATAAT

Answer 20

The pribnow box consensus sequence on bacterial promoter with charge -10

Question 21

What charge does the transcription start site on bacteria have

Answer 21

+1

Question 22

6 steps of initiation of transcription in bacteria

Answer 22

1. Sigma factor associates with core enzyme to form Holoenzyme
2. Bind to -35 and -10 consensus sequences in promoter
3. Holoenzyme bind the promoter tightly and unwinds the double stranded DNA
4. RNTP complementary to base at start site serves as first nucleotide in RNA molecule
5. Two phosphate groups are cleaved from subsequent nRTP, creating rna nucleotide that is added to 3’ ends of growing mRNA
6. Sigma factor released as the RNA polymerase moves beyond promoter

Question 23

Discuss DNA bending in the operon- promoter complex

Answer 23

• rna polymerase forms a closed complex in which dna is not unwound
• stable open complex forms where the -10 region is unwound
• an mg2+ dependent isomerization further unwinds the DNA from -12 to +2

Question 24

How does transcription bubble occur

Answer 24

Nucleophilic attack by the 3’-OH of the first nucleotide on the α-phosphate of the seconds nucleotide forms a phosphodiester bind in a manner analogous to dna replication (5’ to 3’)

As process continues, the dna is continuously unwound in a transcription bubble

Question 25

What does topoisomerase do during elongation

Answer 25

Remove negative supercoils

Question 26

What does gyrase do during elongation

Answer 26

Introduce negative supercoils

Question 27

Is rna polymerase activity continuous or discontinuous ? | Explain

Answer 27

Discontinuous When the RNA polymerase reaches a site difficult to transcribe it may pause or shift backwards Transcription can then resume either by the polymerase sliding forward or by cleavage of the non-base-paired part of the transcript

Question 28

6 steps of rho -independent transcription termination in bacteria

Answer 28

1. Rho-independent terminator contains an inverted repeat followed by a string of approximately 6 adenine nucleotides 2. The inverted repeated are transcribed into rna 3. String of Us cause the rna polymerase to pause 4. The inverted repeats fold into a hairpin 5. Destabilize DNA-RNA pairing 6. Rna transcript separates from the template, terminating transcription

Question 29

3 steps of Rho-dependent termination in bacteria

Answer 29

1. Rho binds to rut site and moves toward the 3’ end 2. When rna polymerase encounters a terminator sequence it pauses and rho catches up 3. Using helicase activity, rho unwinds the dna-rna hybrid and brings an ends to transcription

Question 30

3 steps of factor-dependent termination

Answer 30

1. Binding of ρ to dna-rna-polymerase complex 2. ρ moves toward 3’ end, displacing dna template strand 3. Weakens interaction between template and transcript, causing them the dissociate

Question 31

What happens during the initiation of eukaryotic mRNA transcription

Answer 31

- assembly of basal transcriptional apparatus on core promoter - binding of TFs to enhancers - formation of transcription bubble - first binds between rNTPs - escape of rna polymerase II from promoter

Question 32

What are the 4 regions on the eukaryotic core promoter

Answer 32

1. TFIIB recognition element (-35) 2. TATA box (-25) 3. Initiator element (+1) 4. Downstream core-promoter element (+30)

Question 33

5 steps of eukaryotic transcription initiation

Answer 33

1. TFIID binds to TATA box in core promoter 2. Transcription factors and RNA polymerase II bind to core promoter 3. Transcriptional activator proteins bind to sequences in enhancers 4. Dna loops out, allowing the proteins bound to the enhancer to interact with the basal transcription apparatus 5. Transcriptional activator proteins bind to sequences in the regulatory promoter and interact with the basal transcription apparatus through the mediator

Question 34

6. Steps of eukaryotic transcription termination

Answer 34

1. Rna polymerase II transcribed well past coding sequence 2. Cleavage near 3’ end of rna 3. Rna polymerase continues to transcribe 4. Rat1 endonuclease attached to 5’ ends of trailing rna 5. Moves toward rna polymerase degrading the rna as it goes 6. When rat1 reaches the polymerase, transcription is terminated

Question 35

What does mRNA processing involve

Answer 35

- capping - cleavage of transcript - polyadenylation - splicing - rna export from nucleus

Question 36

What function does the addition of 5’ cap have

Answer 36

Facilitates binding of ribosome to 5’ end of mRNA, increases rna stability and enhances RNA splicing

Question 37

What functions do 3’ cleavage and addition of polyAtail have

Answer 37

Increases stability of mRNA, facilitates binding of ribosome to mRNA

Question 38

What function does RNA splicing have

Answer 38

Removes non coding introns from pre-mRNA, facilitates export of mRNA to cytoplasm, allows for multiple proteins to be produced through alternative splicing

Question 39

What is alternative splicing

Answer 39

Producing different mRNAs from the same nRNA by linking together different combinations of potential exons