Genetics 11 Flashcards
Super secondary structure
When a DNA-binding protein attaches to the DNA.
-structure somewhere between a secondary and tertiary protein structure.
Allosteric regulation primarily affects the ____ whereas transcriptional control primarily affects the ____
Km, Vmax
Helix-turn-helix
- 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
Zinc finger
- 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.
Leucine zipper
- 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
trp operon
- 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.
Negative control
If binding of protein to DNA inhibits transcription.
-ex: trp operon
Positive control
If binding of protein to DNA activates transcription
-DNA-binding protein can only bind to DNA in absence of ligand
T/F Some gene regulatory proteins can function as both repressors and enhancers
True.
Depends on how they are positioned on the DNA within the promoter region.
lac operon
- 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.
TFs
-gene activator protein
2 main functions: bind to DNA, and bind to more proteins so transactivation can occur.
Functional domains of a TF
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.
Promiscuity
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.
Promoters
-Give RNA Polymerase the position and orientation information it needs in order to start transcription.
Enhancers
- 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
Constitutive transcription factors
Function in normal cell activity
Inducible transcription factors
- TFs we can turn on and off with signaling.
- can be 2nd messenger dependent, hormone receptors, or tissue-specific.
Chromatin remodeling complex
- 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)
Competitive DNA binding
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.
Direct interaction with general TFs
- when both repressor and activator proteins are bound
- hold TF out of reach of transactivation domain on gene activator protein.
What can gene repressor proteins recruit to silence DNA?
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.
How do you regulate regulatory sequences?
- Insulator sequences between genes prevent TFs from cross-regulating genes.
- Barrier sequences between genes block heterochromatin from spreading, prevents cross-regulation.
