Lecture 19

Question 1

What is transcription mediated by?

Answer 1

RNAP 2 machinery
Sequence specific DNA binding transcription factors
coactivators and corepressors
elongation factors

Question 2

Transcription factor activity can be altered by what?

Answer 2

protein degradation, post translational modifications, and ligand binding

Question 3

What are the possible mechanisms for how a transcription factor works?

Answer 3

it stimulates the recruitment and binding of general transcription factors (GTFs) and RNAP 2
or
it stimulates the enzymatic activity of GTFs and RNAP 2
or
interacts with chromatin remodeling and modification complexes

Question 4

What is the binding of DNA binding domain motifs?

Answer 4

specific hydrogen bonds and or hydrophobic interactions between amino acid functional groups and base pairs

Question 5

What is the most common motif (recognition pattern)?

Answer 5

interaction between an alpha-helical domain of the protein and about 5 base pairs within the major groove of the DNA
exception is TATA box binding protein

Question 6

What is the helix turn helix DNA binding motif?

Answer 6

2 alpha helices linked by a short turn
the 2nd, the recognition helix, fits into the major groove of the DNA where its amino acid side chains make specific contacts to recognize and bind to a particular DNA sequence and the other helix helps stabilize this interaction

Question 7

How are homobox genes and homeodomain proteins an example of the H2H motif?

Answer 7

homobox genes produce homeodomain proteins and in the fruit fly they have colinear expression
the order of the gene is important and a homeotic mutation could cause body parts to be in the wrong place

Question 8

What do Hox genes do? What codes for it?

Answer 8

encode transcription factors
the homeobox codes for the DNA binding domain (homeodomain) of the Hox protein

Question 9

How does the position of Hox genes matter in the fruit fly?

Answer 9

their position in the cluster correlates with its expression in the fruit fly… 3’ and 5’ Hox genes are expressed in the anterior and posterior portions of developing embryos

Question 10

What is the Zinc finger (Zif) DNA binding motif? What is the classic finger?

Answer 10

protein motif that contains a zinc atom coordinated by cysteine and/or histidine amino acids
it binds to specific DNA sequences acting like a key in a lock to stabilize a folded structure…alpha helix that fits into the major groove of the DNA double helix
Classic finger is Cys2-His2 pattern

Question 11

What are glucocorticoid receptor zinc fingers?

Answer 11

zinc finger motif
structural domains within the GR’s DNA binding region that are essential for binding to specific DNA sequences and regulating gene transcription
the GR binds DNA as a homodimer

Question 12

Which part of the zinc finger interacts with the major groove of the DNA?

Answer 12

the alpha helix

Question 13

What are 2 examples of a dimerization domain?

Answer 13

Basic Leucine zipper (bZIP)
Basic helix loop helix (BHLH)

Question 14

What is a basic leucine zipper? How does dimerization take place?

Answer 14

a sequence of amino acids that folds into a long alpha helix with leucines in every seventh position
leucine is a hydrophobic amino acid, and hydrophobic interactions make sure dimerization takes place and the zipper is what facilitates the dimerization (interaction happens when it’s not leucine rich)

Question 15

What is a basic helix-loop-helix? How does it work?

Answer 15

protein structural motif that allows 2 proteins to bind together to form a dimer
the basic region binds to DNA and the helix loop helix region forms 2 alpha helices linked by a loop and is responsible for the dimerization of the 2 bHLH proteins

Question 16

Why does it make sense that there are positively charged amino acids in the DNA binding domain?

Answer 16

positive charges can interact with negatively charged DNA

Question 17

What are examples of BHLH?

Answer 17

Myc-Max and Mad-Max

Question 18

What is Myc-Max?

Answer 18

a transcriptional activator

Question 19

What is Mad-Max?

Answer 19

a transcriptional repressor that has a structure that blocks the excess of other transcriptional assisting proteins in the DNA

Question 20

What do transactivation domains of transcription factors do? Compare them to DNA binding motifs?

Answer 20

activate transcription via protein-protein interactions
they are structurally more elusive than DNA binding motifs and many contain intrinsically disordered regions

Question 21

What are examples of transactivation domains?

Answer 21

acid blobs (flexible)
glutamine rich regions (flexible)
proline rich regions (cyclic structure so present in DNA where kinks or turns are required)
hydrophobic beta sheets (hydrophobic provides structure)