Mid-term

Question 1

Transcription Definition

Answer 1

The process by which regions of DNA are copied into RNA molecules

Question 2

What are Cis-Acting elements

Answer 2

features embedded in the DNA that regulate transcription

Question 3

What are some examples of cis-acting elements

Answer 3

promoters, regulatory sequences, terminator

Question 4

What are trans-acting elements

Answer 4

features that bind to the cis-acting element of a gene to control its expression

Question 5

what are some examples of trans-acting elements

Answer 5

RNA polymerase, transcription factors, gene regulatory proteins.

Question 6

What direction is the template strand read

Answer 6

3’ to 5’

Question 7

What direction are transcripts made in

Answer 7

5’ to 3’

Question 8

What is the non-coding strand

Answer 8

The template strand used for transcription

Question 9

What is the coding strand

Answer 9

the non-template strand is the coding because it is almost identical to RNA

Question 10

RNA polymerase definition

Answer 10

catalyzes phosphodiester bond between NTPS

Question 11

What are some differences between prokaryotic transcription and eukaryotic transcription

Answer 11

prokaryotes have no membrane-bound organelles (aka no nucleus), circular genome, transcription and translation occur at the same time, there are no post transcriptional modifications like introns, extrons, 5’ cap, or poly-a tail

Question 12

What is the holoenzyme

Answer 12

core enzyme + sigma factor

Question 13

What is the core enzyme

Answer 13

No sigma factor

Question 14

What is the sigma factor

Answer 14

a specificity factor that tells the polymerase which strand to use.

Question 15

How did we figure out the purpose of sigma factor

Answer 15

core enzyme created double-stranded RNA by using both strands of DNA as a template. Holoenzyme only created one strand of RNA

Question 16

Why is the sigma important for initiation of transcription

Answer 16

it recognizes the promoter at the -10 and -35 box, weakly binds to the double stranded DNA, then binds strongly to the single stranded DNA

Question 17

How does sigma recognize the promoter

Answer 17

at the -35 and -10 box. there is always a conserved TT at the -35 box.

Question 18

After sigma binds to the promoter, what happens?

Answer 18

The RNA polymerase moves to the right elongating the RNA and sigma dissociates. It can now rejoin with a different core, thereby creating another holoenzyme

Question 19

How can sigma factors change in response to the different needs of the cell

Answer 19

There are multiple sigma factors and they each have different sequence specificities for promoters so they can bind to different promoters. The -10 and -35 box are still important for all sigma factors.

Question 20

How does prokaryotic transcription terminate

Answer 20

Via Rho-independent or Rho-dependent termination

Question 21

Explain Rho-independent termination

Answer 21

There is an inverted repeat in DNA followed by string of A residues that creates a hairpin structure. This structure helps pull apart the weak dA-rU interaction and RNA polymerase falls off

Question 22

Explain Rho-dependent termination

Answer 22

RNA is thought to be threaded through Rho center and then when the polymerase stalls at the termination signal, Rho may break apart the DNA-RNA interaction

Question 23

What is Rho

Answer 23

a protein that reduces ability of RNA polymerase to transcribe

Question 24

Operon

Answer 24

a group of genes involved in the same response pathway that are regulated together

Question 25

How are operons regulated

Answer 25

by specialized proteins (repressors) binding to specific DNA elements (operators)

Question 26

Explain the lac operon with glucose only

Answer 26

LacI gene encodes the repressor monomer which binds to the operator blocking transcription

Question 27

Explain the lac operon with lactose only

Answer 27

allolactase binds to the repressor tetramer which blocks the repressor from binding to the operator. cAMP-CAP which rises when glucose levels fall, helps the RNA polymerase bind to the promoter.

Question 28

Explain the lac operon with glucose and lactose

Answer 28

only medium level of transcription of lac genes

Question 29

What is the trp operon

Answer 29

codes for protein that the bacterium needs to make the amino acid tryptophan

Question 30

Explain the trp operon with high tryptophan

Answer 30

trpR encodes the repressor. When tryptophan is bound to the repressor, it is able to interact with the operator and block it from transcribing but not 100%. There is an attenuator sequence that forms a stable hairpin causing ribosome to fall if transcription occurs.

Question 31

Explain the trp operon with low tryptophan

Answer 31

trpR encodes the repressor but no tryptophan can activate the repressor so transcription occurs and forms an unstable hairpin and ribosome stalls.

Question 32

Difference between operons and sigma factors

Answer 32

operons only control a handful of genes while alternative sigma factors change a lot more.

Question 33

anti-sigma factors

Answer 33

proteins that can bind to sigma factors and control their activity

Question 34

anti-anti sigma factors

Answer 34

promote sigma factors

Question 35

What helps regulation of sigma factors

Answer 35

anti-sigma factors, anti-anti sigma factors, transcription factors (assist sigma factor recognition of promoter elements)

Question 36

Difference between eukaryotic RNA polymerase II and prokaryotic polymerase II

Answer 36

eukaryotic polymerase cant recognize promoters without general transcription factors

Question 37

What binds to the TATA box

Answer 37

TBP (TFIID)

Question 38

What binds to BRE (B recognition element)

Answer 38

TFIIB

Question 39

What is the purpose of the Inr

Answer 39

Together with TATA and BRE promotes basal transcription of any gene

Question 40

what is the purpose of DCE

Answer 40

can replace TATA in TATA-less promoters

Question 41

What is the order of binding

Answer 41

TFIID binds to DNA via TBP at TATA box, TFIIA stabilizes binding of TFIIB and TBP, TFIIB binds to BRE and recruits RNA polymerase, TFIIF binds polymerase II and TFIIB, TFIIE recruits TFIIH, TFIIH unwinds promoter DNA and phosphorylates C-terminal domain of polymerase

Question 42

What are the two forms of RNA polymerase II

Answer 42

hypo-phosphorylated which can join the pre-initiation complex, hyper-phosphorylated which can mediate RNA synthesis initiation and elongation

Question 43

What transcription factors remain at the promoter

Answer 43

TBP and TFIIB

Question 43

What transcription factors remain at the promoter

Answer 43

TBP and TFIIB

Question 44

What transcription factors remain at the promoter

Answer 44

TBP and TFIIB

Question 45

What transcription factors that dissociate from the elongation complex

Answer 45

TFIIE and TFIIH

Question 46

What are activators

Answer 46

bind upstream of the promoter

Question 47

What are repressors

Answer 47

bind to silencers and inhibit transcription

Question 48

what are co-activators

Answer 48

aid activators by serving as a bridge

Question 49

How does acetylation of histones affect transcription

Answer 49

cause DNA to loosen up

Question 50

HATs

Answer 50

writer enzymes, they add acetylation

Question 51

HDACs

Answer 51

Eraser enzymes, that remove acetylation making DNA not active

Question 52

What is the purpose of polyadenylation

Answer 52

stability / protection from degradation, translation, gene expression regulation