FSU Marks PCB 3134 Exam 4: Transcription

Central Dogma

DNA -> RNA -> Protein

Can RNA be the final product of some genes?

yes

T/F DNA is changed by transcription

False (just opened and read)

If one gene is being coded for in transcription, does that impact if other genes are transcribed?

No (genes are transcribed independently)

What strand is actually used to make RNA?

template strand

What does the coding strand do?

It specifies the sequence of amino acids in polypeptides. Opposite to one used to make RNA

In what way is template strand read?

3-5

Which types of RNA are involved in translation?

mRNA, tRNA, rRNA

What compound was used to test the triplet code hypothesis?

proflavin

Why was proflavin used to test the triplet code hypothesis?

it induces frameshift mutations by inserting or deleting one nucleotide.

degenerate code means

multiple codons encode for the same amino acid

DNA is non-overlapping. What does this mean?

always shifts three nucleotides.

Indel mutations involve

insertion or deletion of a base pair

How can an indel not cause a frameshift?

three nucleotides added or removed

A gene has one insertion and one deletion. What is this called?

revertant mutant

What side are nucleotides added to?

3' end

N to C is

5' to 3'

C to N is

3' to 5'

template must be read in the

3' to 5'

Where does RNA polymerase bind?

promoter

How is transcription mediated in eukaryotes?

Transcription factors and enhancer regions

What type of cell does RNA polymerase directly bind to DNA?

prokaryote

In bacterial transcription, the start is almost always

adenine

Upstream is towards

5'

Downstream is towards

3'

what is about 10 bp upstream?

pribnow box

A minus indicates

something is upstream

Where does the alpha subunit bind?

UP-element

What does the B subunit do?

carry out transcription

What does the sigma subunit do?

binds -10 and -35

What is the only part of RNA polymerase actually responsible for prokaryotic transcription?

B

In order for the polymerase to move in prokaryotes, what subunit has to leave?

sigma

What subunit of polymerase slides along DNA in prokaryotes?

B

How is transcription terminated in prokaryotes?

Hairpin loop pulls U's and A's

What mostly makes up a hairpin loop?

GC rich

What's at the end of a hairpin loop?

U's

How many types of polymerase do prokaryotes have?

one

T/F promoters vary widely in prokaryotes

False (they're pretty uniform)

How many types of polymerase do eukaryotes have?

three

Where can promoters occur in eukaryotes?

downstream of a gene

Which type of cell has prevalent protein-protein interactions for transcription?

eukaryotes

What happens to RNA molecules during and after transcription?

RNA processing

What does RNA polymeras 1 make?

rRNA

What does RNA polymerase 2 make?

mRNA

What does RNA polymerase 3 make?

tRNA and a little rRNA

What is the core promoter?

relatively short DNA sequence that is necessary for transcription to take place

BRE

TFIIB recognition element

DPE

downstream promoter element

What are the two types of promoters for RNA polymerase II?

TATA driven promoter, DPE driven promoter

What are the parts of a TATA driven promoter?

TATA box

INR

maybe BRE

No DPE

What are the parts of a DPE driven promoter?

DPE sequence

INR

no BRE

no TATA Box

What types of promoters does tRNA have for RNA polymerase III?

box A and B

What types of promoters does rRNA have for RNA polymerase III?

box A and C

What makes polymerase more efficient in eukaryotes?

upstream control elements

If a transcriptional start site is upstream of a promoter, what happens?

the promoter is also transcribed

What is always required for RNA polymerase to bind to promoters in eukaryotes?

general transcription factors

What is the first transcription factor to bind in euks?

TFIID

What are the two main characteristics of a TATA driven promoter?

No BRE sequence

Only TATA box and INR

What allows TFIID to bind to TATA Box?

TATA binding protein (in TFIID)

What does TFIID do after binding to the TATA box?

recruit TFIIA and B

What determines if TFIIA will bind?

if promoter had a BRE

After TFIIA and B bind, what happens?

other TFs bind

After all the necessary TFs bind to the DNA, what happens?

RNA Pol II is recruited

Can RNA pol II immediately start transcription after it binds?

No (needs TFIIH)

What has to bind to allow RNA Pol II to move?

TFIIH

How does TFIIH activate polymerase?

phosphorylation

How does RNA pol III initiate termination?

short run of U's (kind of like a hairpin loop)

T/F RNA pol III does not need protein factors to initiate termination

true

What's the first step of termination for RNA Pol II?

cleave at specific sites before termination begins

Is the stop sequence included when transcribing RNA Pol II?

yes

After the cleavage site is reached for RNA Pol II, what binds?

RNAse and Poly-A polymerase

What is a primary transcript?

the initial RNA transcript from any gene prior to processing

What's the. initial pre-tRNA structure?

cloverleaf (four hairpin loops)

How is the 3' end of pre-tRNA modified?

cut and add nucleotides

How is the 5' end of pre-tRNA modified?

cut nucleotides only (get rid of SSRNA)

Besides splicing, what else is edited in pre-tRNA?

nucleotides

How does tRNA make individual binding sites for all amino acids?

nucleotide modification

What 3 pieces make pre-mRNA into mRNA?

splicing

5' cap

poly-A tail

how does the 5' cap work

5' 5' triphosphate bond. nuclease doesn't recognize that

What is methylated in the 5' cap?

guanosine at position 7

What adds Poly A tail to mRNA?

poly-A polymerase

What is required for mRNA export into the cytoplasm?

Poly-A tail

A poly-A tail does not need a ______

template strand

what does the 5' end of mRNA start with?

GU

What does the 3' end of mRNA end with?

AG

What does snRNA do?

use complementary base pairing to bring proteins to right spot.

Where does the U1 snRNP bind?

5' splice site

Where does the U2 snRNP bind?

branch site (near 3')

Besides U1 and U2, what other proteins complete a spliceosome?

U4,5,6

Transcription and splicing are almost ____

simultaneous

A spliceosome has cut out an intron. what's left behind?

EJC's

What has to happen to the C-terminal domain of RNA pol-II?

phosphorylated

What's the first step of phosphorylation of the 5' cap?

swap out the phosphates

What is the second step of phosphorylation of the 5' cap?

recruit snRMPs with another P

What is the last step of phosphorylation of the 5' cap?

swap another phosphate to cleave

how long does mRNA last in a euk?

several hours to a few days

How long does mRNA last in a prok?

a few minutes