Week 2

Question 1

coding strand

Answer 1

5’ to 3’ strand mRNA would look just like this strand except T’s are U’s

Question 2

template strand

Answer 2

3’ to 5’ strand Transcription starts at +1 BP

Question 3

upstream

Answer 3

The bases before the the transcribed bases Houses the promoter

Question 4

Downstream

Answer 4

the bases after the starting transcribed BP

Question 5

numbering system

Answer 5

+ numbers indicated the start of transcription and movement downstream - numbers indicated upstream base pairs

Question 6

Function RNA polymerase

Answer 6

Directs transcriptions Catalyzes the formation of phosphodiester bonds between nucleotides Synthesis occurs 5’ to 3’ direction and doesn’t require a free 3’ OH

Question 7

Structure of RNA Polymerase

Answer 7

Classified as a Holoenzyme An enzyme with multiple subunits that each carry out specific structural, enzymatic, or regulatory functions

Question 8

Promoters

Answer 8

Contains the TATA box A sequence of BPs that initiates transcription Tends to be highly conserved

Question 9

Prokaryotic Transcription Initiation

Answer 9

Uses a protein called sigma factor to bind to the promotor region, which triggers RNA poly. to also bind. Initiation stage is completed when DNA strands separate near the promoter to form open complex

Question 10

Promoters in prokaryotes

Answer 10

are recognized and binds to a sigma factor which triggers RNA polymerase to also bind

Question 11

Do prokaryotes need assistance to unwind DNA

Answer 11

No. Prokaryotic RNA poly. opens the strands and the strands come back together at the rewinding point

Question 12

Prokaryotic Transcription Elongation

Answer 12

Sigma factor falls off and RNA poly. continues to add nucleotides in a 5’-3’ direction

Question 13

Prokaryotic transcription Termination

Answer 13

Require sequences tha signal RNA polymerase to pause, release the RNA transcript, and dissociate

Question 14

Two types of Prokaryotic terminators

Answer 14

Intrinsic: RNA structures that do not require protein factors for function. “Hairpin structure” Extrinsic: factor-dependent . ATP-dependent Rho helices

Question 15

Eukaryotic forms of RNA polymerase

Answer 15

RNA poly I, II, III

Question 16

RNA polymerase I and III

Answer 16

transcribes nonstructural genes for rRNA and tRNA

Question 17

RNA polymerase II

Answer 17

transcribes mRNA. Requires 5 general transcription factors to initiate transcription

Question 18

Eukaryotic Transcription Initiation

Answer 18

promoter is recognized and bound by transcription factors and forms an initiation complex which is then recognized by RNA polymerase holoenzyme

Question 19

Eukaryotic Transcription Termination

Answer 19

Different strategies depending on the RNA polymerase being used.

RNA Poly I terminates using DNA sequences and binding proteins.

RNA Poly II terminates RNA processing, cleavage and polyadenylation of the transcript

RNA Poly III terminates using RNA sequences

Question 20

Splicing

Answer 20

Intron removal

Question 21

Spliceosome structure

Answer 21

Composed of an RNA molecule and proteins called snRNPs (small nuclear ribonucleoprotein particles)

Question 22

Spliceosome function

Answer 22

A portion of the RNA component of the spliceosome will recognize conserved signal sequences in the intron via complementarity

Several snRNP subunits will bind to the pre-mRNA, cause the intron loop, then excise the intron and re-litigate the exon pieces together