Eukaryotic Transcription Regulation Part 1 Flashcards Preview

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Flashcards in Eukaryotic Transcription Regulation Part 1 Deck (35):
1

gene-specific transcription factors

- stimulate or inhibit transcription by RNA pol II

2

2 functional domains of gene-specific transcription factors

- DNA binding domains
- transcription activation domains

3

other domains of gene-specific transcription factors

- dimerization domain
- binding sites for effectors

4

DNA binding domains percentage

- 80% of all transcription factors belong to 4 families

5

4 families

- helix-turn-helix
- zinc-containing modules
- bZIP motifs
- Helix-loop-helix

6

three types of activation domains

- acidic domains
- glutamine-rich domains
- proline-rich domains

7

functional domains within transcription factors can be “swapped"

- they are independent modules.

8

transcription factors interact

- to form protein dimers to facilitate binding to a DNA target site

9

specific factors bound to different DNA target sites

- collaborate to stabilize a transcription complex.

10

affinity of binding between a protein and DNA

- depends on the number of protein-DNA contacts

11

doubling the contacts by using a DNA dimer

- quadruples the affinity between the protein and DNA

12

most activators concentration

- most have to work at very low concentrations in the nucleus
- this helps to dimerize

13

dimerization of DNA binding proteins

- incapable of binding DNA as monomers
- must first dimerize to bind DNA

14

many classes of DNA binding proteins contain

- alpha helix that contacts the major groove

15

DNA binding protein length and binding

- DNA-binding domains are usually short polypeptide chains of ~ 100 amino acids
- bind to short DNA regions

16

various DNA-binding motifs provide

- 3D scaffolds that match contours of DNA to facilitate binding

17

most common motif in DNA binding domains

- Two hydrogen bonds between an arginine side chain of the transcription factor and a guanine base of the DNA

18

recognition helix binds where

- major groove

19

N-terminus binds where

- opposite side
- minor groove of helix

20

homeodomain proteins

- contain a homeobox
- the DNA binding domain

21

homeobox

- encodes a 60 AA DNA-binding region of transcriptional activators

22

three-dimensional structure of a zinc-containing transcription factor

- complex formation does not change structure of protein or DNA
- N terminal region of each finger point into the major groove

23

how many types of zinc fingers

- 2

24

hormone receptors and how they regulate gene expression

- bind to DNA as a dimer on one face of the DNA double helix, with each subunit in successive major grooves.

25

that the number of nucleotides separating successive binding sites

- help determine which receptor binds DNA

26

what a hormone receptor looks like

- 2 half sites separated by a spacer

27

RXR

- form heterodimers
- only bind to response element that differ only in their inter half-site spacing

28

heterodimerization of leucine zipper proteins

- alter their DNA-binding specificity

29

bZip and bHLH transcription factors

- bind to the major groove in DNA.

30

consensus DNA binding sequence of bHLH proteins

- 5’ CANNTG 3’.

31

leucine zipper

- hydrophobic AA on one face of the protein
- interact with hydrophobic molecules to form dimers

32

b/z

- only basic AA and zipper

33

b/HLH

- missing zipper

34

MyoD

- required for muscle development
- 4 helix bundle involved in dimer formation

35

Myc

- contains both a leucine zipper and HLH region
- alone cannot bind DNA
- Myc/max heterodimers bind DNA