Transcription and Transcriptional Regulation

Question 1

What about bacterial mRNA is different from eukaryotes?

Answer 1

Instead of capping, bacteria have actual ribosome binding sites that are translated into proteins.

Question 2

What is the transcription cycle?

Answer 2

1) Initiation
2) Elongation
3) Termination

Question 3

What direction does RNA polymerase synthesize?

Answer 3

In the 5’ to 3’ direction (binding to the strand that is 3’ to 5’)

Question 4

What are the RNAP subunits, their corresponding gene, and their function?

Answer 4

-Alpha: gene rpoA and enzyme assembly
-beta: gene rpoB and nucleotide binding
-beta prime: gene rpoC and template binding
-sigma: gene rpoD and promoter binding

Question 5

What is the overall structure of RNAP?

Answer 5

-2 cores
-1 holoenzyme: only one to recognize a promoter (RNAP core +sigma)

Question 6

What region of DNA interacts with sigma region?

Answer 6

-10 and -35 touch the Sigma regions

Question 7

What is a consensus sequence?

Answer 7

The closer -10 and -35 sequences are to the consensus the tighter the binding between the holoenzyme and the promoter

Question 8

What genes would have consensus promoters?

Answer 8

necessity genes that you want constantly being transcribed

Question 9

What genes would have promoters that diverged from the consensus sequence?

Answer 9

Something that you want heavily regulated.

Question 10

What happens in the initiation step?

Answer 10

1)sigma binds to the RNAP core and causes a conformational change in which RNAP goes from a “closed hand” to an “open hand” complex.
2) This open conformation allows RNAP to bind DNA
3) the DNA wraps around the holoenzyme
4) holoenzyme then closes around the DNA

Question 11

What are the steps in elongation?

Answer 11

1)incorporation of monomers into polymer until a length of about 10
2) holoenzyme loses sigma factor (if sigma stayed bound that holoenzyme would be stuck and not able to move)
3) When RNAP makes a polymer of 15 to 30 bases the core enzyme contacts only 30 to 40 bases of DNA
4) incorporation of monomers continues at about 45 per second
5) at a distance of ~5 nucleotides away from the active site, the mRNA molecule emerges onto the surface of RNAP
6) As mRNA arrives on the surface it folds up into secondary structures unless it is being actively translated

Question 12

What are the steps in Rho-dependent Termination?

Answer 12

1) Rho pursues polymerase
2) Hairpin forms, polymerase pauses, Rho catches up
3) Rho causes termination (type of regulation)

Question 13

How do sigma factors act as regulation?

Answer 13

Different sigma factors recognize different promoters that transcribe different genes that tell them to do specific things (housekeeping, nitrogen regulation, heat shock response, and staying in stationary phase)

Question 14

What type of regulation is repression

Answer 14

negative regulation

Question 15

What is Attenuation?

Answer 15

RNA leader sequences are responsible for the modulation of gene expression.
NOTE: does not involve DNA binding proteins. Typically involves the mRNA leader sequence and the formation of either an anti-terminator or a terminator

Question 16

What are riboswitches?

Answer 16

-RNA molecules that control their expression
-Translation of Anti Trap involves a riboswitch

Question 17

What is an operon?

Answer 17

A cluster of genes that are transcribed together to give a single messenger RNA (mRNA) molecule, which therefore encodes multiple proteins

Question 18

What is the purpose of Pribnow box?

Answer 18

Where DNA strands begin to separate for transcription (usually in the -10 region)

Question 19

Compare and Contrast Rho-dependent vs. Rho-independent termination

Answer 19

In Rho-dependent termination, the Rho protein is responsible for termination, while the formation of a hairpin loop structure triggered Rho-independent termination.

Question 20

In Rho-dependent termination, how is Rho identified?

Question 21

What is the purpose of RNAP?

Answer 21

To transcribe DNA into RNA