Final 19 Flashcards
What are house keeping genes?
Genes that are always on, they are constitutively expressed genes.
What are regulated genes?
Inducible or repressible genes.
They are either turned on or off with the effect of activators/repressors and specificity factors.
What are cis-acting regulatory sequences?
Sequences on the same gene that regulates expression.
What are trans-acting regulatory genes?
Sequences that code for a regulatory protein that act on a different molecule.
What are specificity factors? Name an example.
Factors are are only expressed or turned on during a specific point in time.
Sigma-subunits of RNAP.
Sigma-70 (normal) vs. Sigma-32 (heat shock)
What do activators and repressors do?
Activators will promote expression of a gene, and repressors will inhibit expression of a gene.
They will affect gene expression through protein-DNA interactions.
What do co-activators/co-repressors do?
They affect gene expression through protein-protein interactions.
What are two ways that negative regulation takes place through repressors?
- The repressor is bound to the operator, making the gene turned off. A molecular signal binds to the repressor, turning the gene on.
- The gene is turned on, then a molecular molecule binds to the repressor, causing it to bind the the operator, turning the gene off.
What do repressors bind to?
Operators
What do activators bind to?
Enhancers
What are two ways that positive regulation takes place through activators?
- An activator ran be bound to RNAP, turning the gene on, but then a molecular signal can bind to the activator, causing it to fall off, turning it off.
- A gene can be turned off, but then a molecular signal binds to an activator, causing it to bind to RNAP, turning the gene on.
What is the net result of a repressor?
Reduces RNAP-promoter interactions or it can completely block RNAP from binding.
What is the net result of activators
It improves RNAP-promoter interaction.
How do protein-DNA interacts that place?
Through specific DNA sequences called motifs.
How do motifs work?
They consist of an alpha-helix that fits inside the major groove on DNA and interacts with it via dipole-dipole interactions with DNA’s negative charges.
Interactions can distort the DNA allowing for H-bonding between protein and DNA.
What are the 5 types of DNA-binding motifs?
- Helix-turn-helix
- Homeodomain/Homeobox
- Zinc Finger
- Leucine Zipper
- Helix-Loop-Helix
What is the structure of a helix-turn-helix?
Two alpha-helices connected by a small string of AA.
What are some characteristics of a HTH?
It is vert tight and tends to stay in this shake.
Many proteins that use this kind of motif will bind as dimers, therefore you will see palindrome sequences.
What operon do you see HTH being used. What is unique about this one?
The Lac Operon uses HTH.
Instead of binding as a dimer, it binds as a quatramer.
What is the structure of a homeodomain?
It is a HTH with a third conserved alpha-helix.
What is the structure of a Zinc Finger?
Anti-parallel Beta-Sheet + alpha-helix
AND
2 Cys + 2 His + Zn Ion.
What is unique about Zinc Fingers?
They are the most common DNA-binding domains in the human genome.
The alpha-helices interact with the MINOR GROOVE. This interaction is weak, therefore you need a cluster of Zn-Fingers to produce a strong association.
What is the structure of a Leucine Zipper?
Two much longer alpha helices.
The helices will have hydrophobic and hydrophilic regions. The hydrophilic regions will typically have Leucines evenly spaced to create this zipper-like interaction.
What is a Helix-Loop-Helix.
It is like a Leucine Zipper, except the part that brings together the two monomers that makes up the dimer is another helix.
