lecture 6- transcription factors

Question 1

___ is a protein that binds to DNA and affects the transcription of that gene

Answer 1

TF

Question 2

5-25 bp stretch of DNA that regulates expression of a gene on the same stretch of DNA via protein binding (often in promoter or 5’ region, but can be in intron or 3’ region)

Answer 2

cis regulatory element

Question 3

classic example of cis element

Answer 3

TATA box

TBP (tata binding protein) binds TATA box and allow RNA poly II to bind and begin transcription

Question 4

regions further upstream from promoter have have binding sites for __ and __ proteins

Answer 4

enhancer and repressor

Question 5

___ allows transcription to begin

__ prevent enhancers from acting

Answer 5

enhancers

repressors

Question 6

transcription factors are transcribed in the ___ but are translated in the cell’s ___

Answer 6

nucleus
cytoplasm

Question 7

many proteins that are active in the nucleus contain a ___that direct them to the nucleus

Answer 7

nuclear localization signal

Question 8

for many transcription factors, ___ is the KEY point of their regulation

Answer 8

NLS

Question 9

4 major classes of transcription factors

Answer 9

1- basic domain TF (leucine zipper, basic helix loop helix)

2- zinc related TF (zinc finger)

3- helix turn helix (homeodomain)

4- beta scaffold factors (STAT, p53, TATA)

Question 10

leucine zippers consists of two alpha helical protein segments with ___ facing each other along the lengths of their helices, this allows the protein to ___ and form a symmetric interface, like a ___, that can bind to DNA on both sides of the double helix

Answer 10

leucine
dimerize
zipper

Question 11

basic helix loop helix (bHLH) transcription factors are named after their highly ___ consisting of 1 ___ basic region and 2 ___ separated by a variable loop region

they can have diff protein interacting helix regions leading to formation of ___ or ___ complexes

Answer 11

conserved domain
DNA-binding
alpha-helices

homodimeric or heterodimeric

Question 12

zinc finger motif contains the metal ion, ___, that helps to stabilize its ___

the structure consists of 2 ___ and 1 ___ held together by the ___

Answer 12

zinc
3D structure

beta sheets
alpha helix
zinc ion

Question 13

helix-turn-helix motif consists of 20 AA, with 2 ___ separated by a turn

the 2 blank do what?

Answer 13

helixes

one helix stabilizes, the other involved in DNA cis-motif recognition (stabilization & recognition helix)

Question 14

beta scaffolding formed from ____ do what?

Answer 14

beta sheets
bind to a specific DNA sequence (cis element) and bends it

Question 15

most signaling pathways contain these 4 things:

Answer 15

1- ligand
2- receptor
3- signaling cascade
4- TF

Question 16

name 6 major signaling pathways in development

Answer 16

1- receptor tyrosine kinase (RTK)
2- Jak/Stat
3- Hedgehog
4- TGFbeta / BMP
5- Wnt/Wingless - beta catenin
6- Notch

Question 17

why phosphorylation is often used

Answer 17

1- occurs quickly
2- no need to make or break down proteins
3- easily reversible process

Question 18

this signaling pathway is important in all sorts of growth factors, stem cell factors, cancer, blood vessel formation, limb development

Answer 18

RTK