Eukaryotic Gene expression

Question 1

what is control used for in euk gene expression?

Answer 1

regulate the genetic program that underlies embryonic development and tissue differentiation; gene expression patterns must remain permanent, even for decades–>activating signals may be transient

Question 2

what ar ethe RNA pols in a euk?

Answer 2

Pol I, Pol II, and Pol III

Question 3

what is the role of Pol II?

Answer 3

similar to bacterial RNA pol; transcribes the majority of protein coding genes and microRNAs

Question 4

what is the role of pol I?

Answer 4

transcribes for larger ribosomals RNA

Question 5

what is the role of pol III?

Answer 5

transcribes short RNAs such as 5S rRNAs and tRNAs

Question 6

each euk pol has more than just single sigma TF–alows for much more intricate gene control and need to displace chromatin

Answer 6

ya

Question 7

7 additional subunits attach to RNA pol II

Answer 7

ya

Question 8

what is the purpose of TFIID?

Answer 8

various subunits of it recognize the TATA, INR (initiator) and DPE (downstream promoter element) seq domains

Question 9

what composes TFIID?

Answer 9

12 subunits (human), including the TBP (TATA binding protein)

Question 10

what is the point of TBP?

Answer 10

to bind TATA in the minor groove at the con seq TATA(A/T)A(A/T)

Question 11

what is the purpose of BRE?

Answer 11

a sequence upstream of the TATA box for which TFIIB binds to

Question 12

what is TFIIB?

Answer 12

basal factor; binds BRE; binds both TFII-D and pol–>brings pol to promoter; gives polarity since the TATA box is symmetrical

Question 13

what is the purpose of TFIIA?

Answer 13

stabilizes the binding of TFIIB

Question 14

what is the purpose of TFIIF?

Answer 14

stabilizes the binding between TFIIB and RNA pol II

Question 15

genes aren’t in a total on/off state, but the rate of transcription can be increased or decreased

Answer 15

ya

Question 16

what is the purpose of the mediator complex?

Answer 16

integrates signals of whether a gene needs to be up- or down-regulated; it brings the Pol II complex to wherever it’s needed–>these signals increase or decrease; allows for long-range control (through bending of DNA); can also integrate multiple signals by binding to many different places on DNA–>the different signals may increase transcription by 20%, others may inhibit by 40%, etc

Question 17

TFIIS role

Answer 17

elongation factorl; keeps pol II from stalling, has proofreading activity, stimulates hydrolysis of incorrect rNTPs

Question 18

purpose of introns?

Answer 18

allows for multiple RNA forms to arise from one gene

Question 19

we can possible judge organism complexity based on number of introns

Answer 19

ya

Question 20

what is the role of GT/MT?

Answer 20

guanylyn transferase/methyl transferase; needed for capping

Question 21

What is the purpose of TFIIH?

Answer 21

helicase (requires TP) /kinase–phosphorylate other proteins in the complex; required for expression of some genes–creates the bubble to allow RNA synth

Question 22

what is the role of P-tef-B

Answer 22

modifies Pol II tail to release the initiation complex; (involved in elongation)

Question 23

what is the role of CstF and CPSF?

Answer 23

cut 35 bases after AAUAAA

Question 24

what does PAP do?

Answer 24

add the poly-A tail

Question 25

what is the purpose of PAB?

Answer 25

acts a ruler and binds As to set the length of the tail

Question 26

what is the purpose of TFIIE?

Answer 26

recruits TFIIH

Question 27

what is the heptad con seq in the C term domain of pol II?

Answer 27

Tyr-Ser-Pro-Thr-Ser-Pro-Ser; ser5 phos. RNA pol 2 for activation by a subunit of TFIIH; pTEFb transitionsRNA ol phos to ser2 (and dephos of ser 5 by phosphatases) as it moves through the gene

Question 28

why is RNA capping used, and what happens?

Answer 28

to improve stability of mRNA, as exonuclease has a substrate specificity for 5’ ends of RNA/DNAs
Step 1: 5’5’ bond between 5’ end of mRNA and guanine is catalyzed by guanylyl transferase
Step 2: Guanine cap is methylated by guanine-7-methyl transferase

Question 29

most plants and animals can also methylate the 2’ carbon of deoxyribose of the +1 nuc and vertebrates can methylate 2’ of 2+ nt

Answer 29

ya

Question 30

what creates the polyA tail?

Answer 30

cleavage stimulation factor (CstF) and CPSF (cleavage and polyadenylation specificity factor); PAP then works much more quickly when CstF and CPSF o their job–can add up to 250 As

Question 31

what signals may termination utilize?

Answer 31

2 signals: 1. Lack of CstF and CPSF attached to pol II tail (CTD tail)–antitermination factors–and possibly promoting other binding factors to leave (termination factors)
2. 5’ end of the cleaves mRNA now has no cap–5’3’ mRNA exonuclease (Xnr2)