Gene Expression 1

Question 1

What elements are included in a gene control region?

Answer 1

Regulatory elements (bind TFs), promoter region (binds TFs and RNA poly), the proximal regulatory element (SP1), and spacer DNA.

Question 2

What complexes allow for TFs to bind to an exposed element in a regulatory gene region?

Answer 2

Chromatin remodeling complexes, aka SWI/SNF. They hydrolyze ATP to dissociate chromatin from their nucleosomes.

Question 3

Name three key histone modifications that allow for regulatory proteins to bind to DNA and how they work.

Answer 3

Lysine acetylation: HAT changes charge from +1 to 0, thereby freeing DNA from its strong histone interaction–>euchromatin. Binds a regulatory protein’s bromodomain.
Lysine methylation and arginine methylation: give signal to regulatory protein’s chromodomains

Question 4

What are the four major DNA binding motifs used in TFs?

Answer 4

Helix-Turn-Helix, Helix-Loop-Helix, Zn Finger, bZIP

Question 5

Name the three domains of a DNA binding protein.

Answer 5

DNA binding domain, dimerization domain, and activation domain

Question 6

An alpha helix dimer that binds to palindrome-like sequence, one monomer in adjacent major grooves; high binding constant

Answer 6

Helix-Turn-Helix (HTH) motif

Question 7

An alpha helix hetero or homodimer, one monomer is a recognition helix that binds to DNA major groove, the second a leucine zipper

Answer 7

Helix-Loop-Helix motif

Question 8

Has 3 subunits that bind in sequence in major grooves, each has an alpha helix for recognition and a beta strand (support) joined by Zn coordinated cysteines and histidines.

Answer 8

Zn finger motif

Question 9

Two alpha helices with basic amino acids present at the “scissor structure” DNA binding region. Can be heterodimers or homodimers (dimerization through Leu zipper).

Answer 9

bZIP motif