Gene expression 2

Question 1

Protein subunits of RNA polymerase?

Answer 1

AlphaX2
Beta’
Beta
Omega

Question 2

Subunits of holo RNA polymerase?

Answer 2

AlphaX2
Beta’
Beta
Omega
Sigma

Question 3

In prokaryotic transcription, what enzyme recognises promoter?

Answer 3

Holo RNA polymerase.

Question 4

What binds the consensus sequence in the core promoter?

Answer 4

Sigma factor.

Question 5

Consensus element?

Answer 5

-35 and -10 elements

Question 6

What is found to be the optimum spacing in consensus?

Answer 6

17

Question 7

Open complex formation?

Answer 7

Promoter opening allows for exposure of template strand for complementary RNA strand.
This formation is in equilibrium.

Question 8

Anchored transcription?

Answer 8

Only short transcripts can be synthesized whilst sigma factor remains bound to the promoter.

Question 9

Promoter escape?

Answer 9

Sigma factor released from the promoter.
Elongation factor binds and transcription proceeds.
Enzyme becomes processive and makes longer transcripts.

Question 10

Transcription termination in prokaryotic cells?

Answer 10

The palindromic sequence in the RNA forms a hairpin loop causing RNA polymerase to stall.
The u-rich stretch downstream of the termination signal allows the transcript to fall off the template, thereby terminating.

Question 11

4 rough steps of prokaryotic transcription.

Answer 11

Open complex.
Anchored transcription.
Promoter escape.
Termination.

Question 12

Rho-independent termination?

Answer 12

A terminating hairpin forms on the mRNA interacting with the NusA protein to stimulate release of transcript from the RNA polymerase complex.

Question 13

Rho-dependent termination?

Answer 13

The Rho protein binds at the upstream rut site, translocates down the mRNA, and interacts with the RNA polymerase complex to stimulate release of transcript.

Question 14

RNA polymerase I structure?

Answer 14

5.8S, 18S and 28S rRNA genes.

Question 15

RNA polymerase II structure?

Answer 15

All protein-coding genes, plus snoRNA genes, miRNA genes, siRNA genes, IncRNA genes and most snRNA genes.

Question 16

RNA polymerase III structure?

Answer 16

tRNA genes, 55rRNA genes, some snRNA genes and genes from other small RNAs.

Question 17

How many subunits make up bacteria?

Answer 17

5

Question 18

How many subunits make up eukaryotes?

Answer 18

12-17

Question 19

What are the two important DNA sequences in Eukaryotic transcription?

Answer 19

Core promoters
Promoter proximal and distal elements.

Question 20

Core promoters role in eukaryotic transcription?

Answer 20

Recognised by general transcription factors that recruit RNA polymerase.

Question 21

Steps of general transcription at core promoters?

Answer 21

-RNA polymerase itself cannot find promoters.
-TFIID makes multiple specific contacts with core promoter elements such as TBP interacting with TATA box.
-TFIID recruits TFIIB.
TFIID is critical for recruitments of RNA polymerase II (with TFIIF)
-This complex cannot initiate transcription even though RNA polymerase II is there.
-Once TFIIE and TIFFIH have joined a transcription initiation component pre-initiation complex has formed.
-TFIIE and TFIIH stimulate and stabilize promoter opening to allow initiation of transcription by RNA polymerase.

Question 21

Role of promoter proximal and distal elements in eukaryotic transcription?

Answer 21

Regulatory sequences and binding sites for transcriptional activators and repressors.

Question 21

Order of TF complex in general transcription at core promoter?

Answer 21

TFIID
TFIIB
TFIIE TIFFIH

Question 21

Role of TFIIB

Answer 21

Recruits RNA polymerase.

Question 22

Role of TFIID?

Answer 22

Makes multiple specific contacts with core promoter elements. Recruits TFIIB

Question 22

What happens when TFIIE and TIFFIH joins.

Answer 22

Transcription initiation competent pre-initiation complex forms. Stimulates and stabilizes promoter opening to allow initiation of transcription by RNA polymerase.

Question 22

What can affect the rate of transcription initiation?

Answer 22

-Sequences that bind specific transcription factors may be far from actual transcription site -DNA bending allows specific transcription factors to interact with the RNA polymerase complex and rate of transcription.

Question 23

DNA binding of transcription factors?

Answer 23

-Specific hydrogen bond between an amino acid and a base -A typical protein-DNA interaction might involved about 29 similar contacts.

Question 24

4 dimerization domains?

Answer 24

-Helix-turn-helix motif -Zinc finger motif Leucine zippers motif Helix-loop-helix motif

Question 25

Role of dimers?

Answer 25

Dimers of transcription factors binds sequence-specifically to those short sequence-specifically to those short sequence elements, which are often arranged in palindrome.

Question 26

What determines differential gene expression?

Answer 26

Transcription factors.

Question 27

How in mRNA processed in eukaryotes?

Answer 27

-A 5' cap (modified GTP) is added at the 5' end, which facilitates binding to a ribosome and protects mRNA from being digested and protects mRNA from being digested by ribonucleases. -A poly A tail is added at 3' end: sequence AAUAAA after the last codon signals an enzyme to cut the pre-mRNA; the another enzyme added 100-300 adenine (to form tail). The tail assists in export from the nucleus and is important for stability in mRNA.

Question 28

Explain how genes are split in eukaryotes?

Answer 28

In eukaryotes, the coding sequences are interrupted with non-coding sequences (introns) that are spliced out of the mature mRNA transcript.

Question 29

Explain RNA processing?

Answer 29

RNA splicing removes intron sequences from newly transcribed pre-mRNAs. The precursor mRNA transcript introns are removed by a process called RNA splicing, leaving the protein coding sequences (exons) in the mature mRNA.

Question 30

Steps of RNA splicing involving the spliceosome?

Answer 30

- Small nuclear ribonucleoprotein particle bind to consensus sequences in RNA near 5' donor and 3' acceptor splice sites. - Binding of snRNAs recruits other proteins - A cut is made between the 5' exon and the intron - After the first cut at the 5' end, the intron forms a closed loop. - The free 3' end OH group ,at end of cut, exons' reacts with 5' phosphate group of other exon. - The 3' exon is cleaved and spliced to the 5' exon and the mature mRNA is exported to cytoplasm for translation - The excised intron is degraded in the nucleus.

Question 31

Explain alternative RNA splicing?

Answer 31

Alternative splicing can give more than one product from single genes. Alternative splicing can be regulated to give differential gene expression.

Question 32

Eukaryotic and prokaryotic order of transcription and translation.

Answer 32

Prokaryotic cells are translated at the same time and transcribed. Eukaryotic cells RNA transcripts must be processed and transported to cytoplasm before being translated. Leaves nucleus through nuclear pore complexes.