lectures 1-3

Question 1

heterochromatin

Answer 1

dark stained, inactive genes, condensed chromatin

Question 2

euchromatin

Answer 2

lightly stained, active genes, decondensed chromatin

Question 3

histone acetylase complex

Answer 3

interact with activators, acetylate Lys on N-termini of histone tails decondensing chromatin

Question 4

TFIID

Answer 4

TATA binding protein, interacts with TATA box

Question 5

TFIIA, TFIIB

Answer 5

attach to TFIID to join PIC

Question 6

RNA pol. II & TFIIF

Answer 6

attach to TFIIA, TFIIB

Question 7

TFIIH

Answer 7

kinase (phosphorylate CTD of pol. II), helicase (open txn bubble)

Question 8

NELF, DSIF

Answer 8

negative elongation factor, pauses pol. II

Question 9

P-TEFb

Answer 9

positive elongation factor, phosphorylates NELF and CTD of pol. II

Question 10

pioneer transcription factors

Answer 10

de-condense chromatin using histone acetylase and chromatin remodeling

Question 11

txn. regulation overview

Answer 11

1. pioneer tf’s decondense chromatin
2. mediators/activators associate on promoter / repressors bind and inhibit pol. II
3. pol. II transcribes -100bp, pauses due to NELF/DSIF
4. P-TEFb phosphorylates CTD of pol.II and NELF, continue elongation

Question 12

RNA pol. I

Answer 12

pre-rRNA - protein synthesis

Question 13

RNA pol. II

Answer 13

mRNA, snRNA, siRNA, miRNA

Question 14

RNA pol. III

Answer 14

tRNA

Question 15

eukaryotic RNA pol.II components (4)

Answer 15

clamp - accomodate DNA
bridge - close clamp over DNA
catalytic centre - RNA synthesis (with Mg 2+)
channel - synthesized RNA exits

Question 16

TATA box promoters

Answer 16

-highly conserved genes
-unidirectional transcription
-promoter-proximal and enhancers

Question 17

CpG island promoters

Answer 17

-housekeeping genes
-promoter-proximal only

Question 18

core promoter elements

Answer 18

-37/-32 - BRE / TFIIB recognition
-31/-26 - TATA box
-2/+4 - Initiator
+28/+32 - downstream promoter element

Question 19

components of antibody

Answer 19

constant, variable, hyper-variable regions (variable, diversity & junction sections)

Question 20

immunofluorescence

Answer 20

primary and secondary ab with dye to visualize

Question 21

immunoprecipitation

Answer 21

use agarose beads and western blot, IN VITRO

Question 22

chromatin immuno-precipitation

Answer 22

1. formaldehyde -> crosslinking
2. sonicate / fragment DNA
3. add ab, immunoprecipitate
4. reverse cross linking, DNA sequencing
   -IN VIVO

Question 23

RT-PCR

Answer 23

-quantitative
-convert RNA -> DNA with reverse transcriptase