LECTURE 13

Question 1

what are direct removal of lesions methods?

Answer 1

error free systems because there is no synthesis of new DNA, which leads to errors
- thymine dimers (photoreactivation, photolyase)
- methyls (methylguanine methyltransferase)
- alkyls (alkyltransferase)

Question 2

what does recombination repair deal with?

Answer 2

recombination is the last resort: deals with big problems
complex mutations such as double strand breaks or multiple lesions in one area

Question 3

recombination repair picture:

Answer 3

there is 2 issues here: there is a thymine gap but also a gap opposite of that, which means you cannot use the opposing strand to synthesize DNA
a piece from strand A needs to go onto strand C to fix this problem

Question 4

what types of RNA does transcription generate?

Answer 4

mRNAs
tRNAs
rRNAs (16S, 23S, 5S)

Question 5

in what direction does RNA synthesis go?

Answer 5

5’ to 3’

Question 6

at what rate does RNA polymerase go?

Answer 6

highly processive
adds 40 nucleotides/second at 37°C

Question 7

how does RNA polymerase move on the gene?

Answer 7

forms a transcription bubble of 12-20 base pairs

Question 8

where does transcription start/stop?

Answer 8

start: promoter
stop: terminator

Question 9

characteristics of RNA structure?

Answer 9

• mostly single single stranded
• coils back on itself to make complementary base pairing
• secondary structure stem loops which can fold again to make tertiary structures
• sugars are riboses, contain OH group at the 2’ position
• the bases are ACGU

Question 10

how does mRNA come out of the transcription bubble?

Answer 10

comes out during transcription
the first base still has the triphosphate, since it is not linked to any other base
when the RNA polymerase reaches the end, the mRNA is detached

Question 11

what is the structure of a bacterial promoter?

Answer 11

• at -35 there is the RNA polymerase recognition site
• the consensus sequence is TTGACA
• at -10 there is the RNA polymerase binding site
• the TATA box, and the consensus sequence is TATAAT (also pribnow box)

the RNA polymerase binds to the TATA box and begins transcription

Question 12

what is Rho?

Answer 12

protein factor
helicase involved in transcriptional termination

Question 13

what are the two types of terminators for transcription in bacteria?

Answer 13

Rho independent:
- hairpin in the RNA strand
- 6 uridines after the hairpin structure
- no need for Rho

Rho dependent:
-no poly U tract
- sometimes no hairpin

Question 14

how do the rho dependent vs rho independent terminators work?

Answer 14

Rho independent:
- the RNA pol is stuck on the hairpin
- AU base pair is so weak that this releases the mRNA and the RNA polymerase

Rho dependent:
-the RNA pol is stuck on the hairpin
- Rho, which follows the RNA polymerase, catches up to it, and the helicase action releases the mRNA and the polymerase

Question 15

why do pictures of transcription of rRNA genes look like christmas trees?

Answer 15

bacteria needs lots of ribosomes
therefore need lots of rRNA
each branch coming out of the gene is an rRNA that is being synthesized
=> there are lots of RNA polymerases on each gene
as the rRNAs come out they already start to coil on themselves, making those secondary structures

Question 16

differences between eukaryotic and prokaryotic mRNA?

Answer 16

Question 17

what are polycistronic genes useful to bacteria?

Answer 17

genes on the same mRNA are usually related
very useful to express them at the same time, since they are most likely needed all together for the pathway in question

Question 18

what does the 5’ end of eukaryotic mRNA look like?

Answer 18

has a 7-methylguanosine cap added to the 5’ end
the first base has a methyl added to it

Question 19

what does the 5’ end of prokaryotic mRNA look like?

Answer 19

no cap and no methyl on the first nucleotide

Question 20

what is coupled transcription and translation in bacteria?

Answer 20

translation and transcription happen in the same place, therefore they can happen simultaneously
as the mRNA exits the transcription bubble, a ribosome can bind to it to begin translation

Question 21

what is a polysome?

Answer 21

an mRNA with multiple ribosomes on it