Additional stuff for midterm

Question 1

2nd function of DNase I footprinting

Answer 1

Assay for TF purification

Question 2

Chromatory modelling complexes what processes they are involved in

Answer 2

transcription AND REPLICATION

Question 3

unmethylated to methylated what enzyme

Answer 3

methyl transferase

Question 4

Cap will be recognized ___________

Answer 4

by molecules in ribosomes at beginning of splicing

Question 5

GTFs in prokaryotes

Answer 5

NO GTFs ! Only GTFs in eukaryotes

Question 6

RNAP where it binds

Answer 6

promoter AND +1 start site (in strong promoters) but active site positionned at +1 start site

Question 7

What is coordinate expression

Answer 7

Arrangement of genes in linear operons in prokaryotes (they are transcribed on same mRNA so that’s why you say that they expression is coordinated)

Question 8

What is coregulation and eukaryotes/prokaryotes

Answer 8

Process buy which analogous genes (related prots) are transcribed simultaneoulsy. In prokaryotes, achieved by physical linkage, but not in eukaryotes.

Question 9

CTD tail state at transcription initiation

Answer 9

unphosphorylated (until TFIIH kinase does it)

Question 10

T/F : EMSA/DNase I footprinting can replace each other

Answer 10

false. Footprinting can’t replace EMSA : too difficult in lab.

Question 11

T/F : EMSA can give quantity of protein bound to DNA

Answer 11

false. quantitative because +/- for different fractions

Question 12

T/F : mediator complex can mediate repressing

Answer 12

true. can bind activators and repressors too. mediates everything from repressors to RNAP II

Question 13

How to purify TFs

Answer 13

Put sequence that it influences in cell. (TFs will bind it there) and perform chromatography (living cell as start) to isolate TF

Question 14

what to do before EMSA

Answer 14

chromatography

Question 15

T/F : you can use chromatography to isolate DNA fragments

Answer 15

false. only proteins

Question 16

G-T pairs in DNA helix consequence

Answer 16

no major distortion. it is viable

Question 17

additional substance that can denature DNA strands

Answer 17

formaldehyde

Question 18

Something you can not do to denature DNA

Answer 18

raise ionic concentrations

Question 19

Where sxl binds on genes it regulates

Answer 19

on Sxl gene, binds on 3’ end of intron between exons 2/3. On Tra, seems to bind on 3’ end of intron between exons 1/2.

Question 20

Which subunits in U2AF bind what

Answer 20

subunit 65 binds pyrimidine track (and U2 snRNP since it’s same subunit ?). Subunit 35 binds AG sequence at 3’ end of intron

Question 21

how do you call PPi

Answer 21

pyrophosphate

Question 22

What adds (A) residues in Poly(A)

Answer 22

PAP, not PABPII

Question 23

where PABPII binds and how

Answer 23

A residues with RRM motif, binding allows fast poly(A)

Question 24

order of processing in long genes

Answer 24

splicing can happen before poly(A) and before end of transcription

Question 25

element(s) of spliceosome SR proteins can recruit

Answer 25

U1 and U2