Gene Expression (L13)

Question 1

What is the main strucutral difference b/w DNA and RNA?

Answer 1

RNA has a 2’ OH, DNA does not

Question 2

How do DNA and RNA react differently in alkaline conditions?

Answer 2

DNA is resistant to alkaline conditions,

RNA is hydrolyzed to mononucleotides by alkaline conditions

Question 3

What are the subunits in E. coli RNAP?

Answer 3

2 alpha subunits, a beta, and a beta’. There is also a sigma factor that joins the core enzyme, enabling it to bind to promoter regions of genes.

Question 4

What is the TATA box?

What is significant upstream of the TATA box?

Answer 4

TATAA(T) is the main DNA site that RNAP binds to, it is a site before transcription begins (designated +1).

The TATA box is found b/w -7 and -10. There is another sequence sometimes present upstream that regulate the sigma factor binding.

Question 5

What are the 3 names for each DNA strand during transcription?

Answer 5

Template strand, Non-coding strand, Antisense strnd

vs

Non-template strand, coding strand, sense strand

Question 6

RNA molecules in E. coli is mostly made of what type of RNA?

Answer 6

Ribosomal RNA (rRNA)

rRNA>tRNA>mRNA

Question 7

E. coli mRNA is polycistronic. what does this mean?

Answer 7

The single mRNA strand can encode for multiple proteins.

NOTE: Eukaryote mRNA cannot do this.

Question 8

What is the start codon in E. coli RNA for translation and what AA does it code for?

Answer 8

AUG; Methionine

Question 9

Describe the 2 ways of transcription termination in E. coli.

Answer 9

Rho-INdependent termination: NusA protein (associated w/ RNAP) binds to a GC stable loop structure on nascent (new) RNA, which stalls RNAP at a U-rich site. RNAP unbinds b/c of weak association.

Rho-dependent termination: An ATP-dependent helicase (rho) binds nascent RNA chain and pulls it away from RNAP and the DNA template

Question 10

What is essential for tRNA that is not in mRNA?

Answer 10

tRNA gets base modifications and need them to function. Also there is a 5’-CCA-3’ end of all tRNAs

Question 11

What is one of the main class of antibiotics that inhibit bacterial RNAP and how does it do it?

What is it usually used to treat?

Answer 11

Rifamycins inhibit transcriptional elongation but not transcriptional initiation.

It is the first-line anti-Tuberculosis agent in the clinic

Question 12

Why can RNA transcription and translation in prokaryotes occur closely on ribosomes?

Answer 12

B/c prokaryotes have no nucleus.

Question 13

How is DNAP and RNAP different (main difference)

Answer 13

DNAP can’t initiate DNA synthesis but RNA polymerases can (note that primase is an RNAP)

Question 14

What are the 4 classes of antibiotics that can inhibit bacterial RNAP?

Answer 14

1. Rifamycins
2. Streptolydigin
3. Sorangicin
4. Myxopyronin