Ch. 5 Protein Function Flashcards
How is genomic information regulated (2)?
RNA and proteins, but this section focuses on proteins.
What are the three types of genomic regulatory protiens?
- Reversible binding proteins (RNA does this too)
- Catalytic proteins (RNA does this too)
- Motor proteins
What are reversible binding proteins?
Proteins that reversibly bind to nucleic acids.
What are the six principles of reversible binding proteins?
- The DNA bound by a protein is the ligand, which is NOT chemically modified
- Ligand binds to a binding site of a protein through various non-covalent interactions
- Proteins have conformational flexibility: they have different shapes when bound and unbound by ligand
- Protein/ligand interactions often require induced fit: the protein conformation changes to better fit a ligand
- Cooperativity: conformation change of a subunit may lead to altered conformation of a different protein subunit
- The activity of proteins can be altered through interactions with one or more ligands
How many binding sites do proteins have?
A single protein may have multiple binding sites for different ligands.
What are DNA binding proteins?
Proteins that can bind DNA and can modify genome structure or function WITHOUT covalently modifying the DNA.
What are nonspecific DNA binding proteins?
Proteins that bind to DNA WITHOUT a strong preference for base sequence.
What are specific DNA binding proteins?
Proteins that bind to DNA WITH a stronger preference for base sequence based on DNA surface features.
How do DNA binding proteins that bind both specifically and nonspecifically work?
The attach at the major groove of DNA and search for their target sequence.
What are some examples of nonspecific DNA binding proteins (3)?
chromosome packaging proteins
DNA replication proteins
histones, etc.
How do nonspecific DNA binding proteins interact?
noncovalently
How do many specific DNA binding proteins bind to DNA?
Often bind nonspecifically to the major groove of DNA and move along the major groove until they interact with the target sequence.
Why do specific DNA binding proteins often bind at the major groove?
It is likely due to greater base exposure and opportunity for interactions between bases and amino acids.
What is an example of a DNA binding protein that is specific and nonspecific?
LacI
What is LacI and how does it work?
LacI is a regulatory protein for the lac operon.
1. It nonspecifically bids DNA and moves until recognizing a specific inverted repeat
2. It binds the repeat more strongly and causes a structural change in the DNA
What is the binding region of LacI?
A helix-turn-helix motif, which is common in bacterial and some eukaryotic proteins.
What is a DNA motif?
A pattern of bases (i.e. inverted repeat)
What are reaction catalysts (catalytic proteins)?
Proteins that speed up the rate of a reaction by decreasing the activation energy.
What does catalytic activity depend on for catalytic proteins?
Catalytic activity depends on conformation. Activity could be denaturing, slightly altering structure, etc.
What are the two things some enzymes require?
cofactors and coenzymes
What is a cofactor?
An inorganic metal ion like Mg²⁺.
What is a coenzyme?
A metallo-organic compound like a vitimin.
What is a holoenzyme?
A complete, catalytically active enzyme containing the necessary cofactor and/or coenzyme.
What are the four key principles of catalysis?
- An enzyme binds a substrate, which IS chemically altered during the reaction
- The substrate specifically interacts with the active site of an enzyme
- Catalysis requires conformational flexibility, induced fit, and cooperativity
- Activity of many enzymes is REGULATED
