Genetics 11

Question 0

Super secondary structure

Answer 0

When a DNA-binding protein attaches to the DNA.

-structure somewhere between a secondary and tertiary protein structure.

Question 1

Allosteric regulation primarily affects the ____ whereas transcriptional control primarily affects the ____

Answer 1

Km, Vmax

Question 2

Helix-turn-helix

Answer 2

• consists of an a helix, b turn, and b helix.
• structure sits comfortably in major groove of DNA, facilitating binding to specific sequences.
• most common DNA binding motif.
• functions as a dimer

Question 3

Zinc finger

Answer 3

• DNA binding motif
• Zinc chelates 2+ histidine or cytosine residues, forming finger-like structure.
• binds to major groove of DNA
• commonly found in hormone receptors.
• Bind to each half of a palindrome and form a dimer.

Question 4

Leucine zipper

Answer 4

• Leucine repeat every 7th AA
• alpha helix with 3.5 aa/turn means every 7th AA is on the same side of the helix.
• Gives leucines along helix, forming zipper structure.
• Leucine zipper creates hydrophobic domain that excludes water
• binds to major groove, forms dimers.
• You can get heterodimerization- a dimer of 2 leucine zippers can bind to different sequences on DNA

Question 5

trp operon

Answer 5

• contains all enzymes necessary for tryptophan synthesis
• DNA-binding protein functions as a repressor- turns operon off when bound to DNA.
• want switch off in presence of tryptophan
• DNA binding protein can’t bind to DNA in absence of tryptophan, RNA Polymerase can bind, turns switch on.

Question 6

Negative control

Answer 6

If binding of protein to DNA inhibits transcription.

-ex: trp operon

Question 7

Positive control

Answer 7

If binding of protein to DNA activates transcription

-DNA-binding protein can only bind to DNA in absence of ligand

Question 8

T/F Some gene regulatory proteins can function as both repressors and enhancers

Answer 8

True.

Depends on how they are positioned on the DNA within the promoter region.

Question 9

lac operon

Answer 9

• controlled by glucose and lactose.
• Only want to metabolize lactose when you have lactose and do not have glucose.
• to turn lac operon on, glucose must be absent, lactose must be present.

Question 10

TFs

Answer 10

-gene activator protein

2 main functions: bind to DNA, and bind to more proteins so transactivation can occur.

Question 11

Functional domains of a TF

Answer 11

1) DNA-binding domain (TF doesn’t have to have one)
2) transactivation domain: functionally more important.
- If TF lacks DNA binding domain, it must have 2+ transactivation domains.

Question 12

Promiscuity

Answer 12

Ability of one DNA-binding domain to bind specifically to multiple DNA sequences.
-Gene regulatory proteins that bind to multiple DNA sequences typically only have one DNA binding domain.

Question 13

Promoters

Answer 13

-Give RNA Polymerase the position and orientation information it needs in order to start transcription.

Question 14

Enhancers

Answer 14

• regulate transcription, -either enhance or inhibit transcription.
• enhancer sequences are almost always palindromes. Can be found far away from promoter sequence (remember, 3D structure, loops around)
• Do not function as promoters

Question 15

Constitutive transcription factors

Answer 15

Function in normal cell activity

Question 16

Inducible transcription factors

Answer 16

• TFs we can turn on and off with signaling.

- can be 2nd messenger dependent, hormone receptors, or tissue-specific.

Question 17

Chromatin remodeling complex

Answer 17

• alters chromatin structure to create transcription bubble (necessary so only one strand is read during transcription)
  1) remodels nucleosomes
  2) removes histones from nucleosomes
  3) replaces histones from nucleosomes
  4) modifies histones (methylation, acetylation)

Question 18

Competitive DNA binding

Answer 18

gene repressor proteins block gene activator proteins from binding to DNA by competing for binding at the same DNA sequence.
-gene repressor might let the gene activator protein bind to the DNA, but then bind to its activator–> masks the activation surface.

Question 19

Direct interaction with general TFs

Answer 19

• when both repressor and activator proteins are bound

- hold TF out of reach of transactivation domain on gene activator protein.

Question 20

What can gene repressor proteins recruit to silence DNA?

Answer 20

1) chromatin remodeling complexes: create heterochromatin, inhibit transcription
2) Histone deacetylase: removes acetyl groups attached to promoter to open DNA up for transcription
3) histone methyl transferase: methylate/silence chromatin.

Question 21

How do you regulate regulatory sequences?

Answer 21

• Insulator sequences between genes prevent TFs from cross-regulating genes.
• Barrier sequences between genes block heterochromatin from spreading, prevents cross-regulation.