Lecture 09

Question 1

Helix-turn-helix motif

Answer 1

Simplest, most common DNA-binding motif. 2 alpha helices connected by short chain of amino acids. Longer helix = recognition module/DNA binding module fits into major groove.

Question 2

Zinc finger domain motif

Answer 2

Includes Zn atom, amino acid sequence looks like “finger projection”. Binds to major groove of DNA. Found in tandem clusters, stabilizers interaction with DNA

Question 3

Leucine zipper motif

Answer 3

2 alpha helical DNA binding domain, dimerizes through leucine zipper region; leucine residue every 7 amino acids forming zipper structure

Question 4

Helix-loop-helix motif

Answer 4

Consists of short alpha chain connected to second longer alpha chain via a loop. Contains a binding domain, dimerization domain, and activation domain

Question 5

A mutation in the Klf1 gene causes an absence of Erythrocyte Membrane Skeleton (EMS) proteins leading to hereditary spherocytosis (HS). What motif is disrupted in the Klf1 gene?

Answer 5

Zinc finger motif

Question 6

What techniques can be used to identify transcription factors?

Answer 6

Electrophoretic mobility shift assay (EMSA) or Affinity chromatography

Question 7

What technique can be used to identify the DNA binding sequence with a known transcription factor?

Answer 7

CHIP assay

Question 8

How do activators modify DNA to favor transcription?

Answer 8

Nucleosome remodeling and histone removal (example: histone acetylation)

Question 9

Explain the action of the repressor in competitive DNA binding

Answer 9

Inhibits transcription by competing with activator for same binding site

Question 10

Explain the action of the repressor in masking the activation surface

Answer 10

Inhibits transcription - both proteins bind to DNA, but repressor binds to activation domain of activator protein

Question 11

Explain the action of the repressor in direct interaction with general transcription factors

Answer 11

Repressor binds to DNA and blocks assembly of transcription factors, thereby inhibiting transcription

Question 12

Explain the action of the repressor in the recruitment of chromatin remodeling complexes

Answer 12

Repressor recruits chromatin remodeling complex, returning promoter to the pre-transcriptional nucleosome state, preventing transcription

Question 13

Explain the action of the repressor in the recruitment of histone deacetylases

Answer 13

Repressor attracts histone deacetylase to promoter, making deacetylated histone harder to remove/open up DNA; inhibits transcription

Question 14

Explain the action of the repressor in the recruitment of histone methyl transferase

Answer 14

Repressor attracts histone methyl transferase which methylates histones (bound to proteins which act to maintain chromatin in transcriptionally silent form)

Question 15

List the ways that regulatory proteins are controlled.

Answer 15

Synthesis, Ligand Binding, Covalent modification/phosphorylation, Addition of subunit, Unmasking, Nuclear entry, Proteolysis

Question 16

True or False: Gene repressors inhibit transcription when repressor and activator proteins compete for the same or overlapping DNA binding site.

Answer 16

True