Globular Proteins
What is a ligand?
It is a molecule that binds to a protein.
Explain the lock and key model.
Lock and key - high specificity explained by the complementary binding sites between the site and ligand.
Who discovered it?
What are macrophages?
The are large phagocytes that ingest bacteria that are tagged by antibodies.
What is covalent catalysis and what does it require?
It is a transient covalent bond between the enzyme and the substrate. It requires a nucleophile on the enzyme. (Can be a reactive serine, thiolate, amine, or carboxylate.)
What are inhibitors?
They are compounds that decrease an enzymes activity.
What is the binding site?
It is the region of a protein where the ligand binds.
Explain the induced fit model.
Induced fit - Conformational changes may occur upon ligand binding.
What are antigens/ antibodies?
Antigens are substances that stimulate the production of antibodies. Antibodies are proteins that are produced by B cells and that specifically bind to antigens.
What is metal ion catalysis?
It involves a metal ion bound to the enzyme, it interacts with substrates to facilitate binding.
Whats the difference between irreversible and reversible inhibitors?
Irreversible inhibitors can permanently shut off one enzyme molecule. Reversible inhibitors can bind to and dissociate from the enzyme.
What is positive/ negative cooperativity?
Positive cooperativity: First binding event increases affinity at remaining sites recognized by sigmoidal binding curves.
Negative cooperativity: First binding event reduces affinity at remaining sites.
In the lock and key model in what ways are the binding site and ligand complementary?
Size, shape, charge, and hydrophobic/ hydrophilic character.
How does pH affect hemoglobin binding to oxygen?
The lower the pH, the more H+ is available to bind to hemoglobin, stabilizing the T state.
What is chemotrypsin?
It is one of several proteases that cuts peptides at specific locations on the peptide backbone. The protease is able to cleave the peptide bond adjacent to aromatic amino acids.
What is competitive inhibition?
They compete with the substrate for binding. They bind to the active site and doesn't affect catalysis.
What are the biological problems in oxygen binding proteins?
Protein side chain lacks affinity for O2, some transition metals bind O2 well but will generate free radicals, organometallic compounds such as heme are suitable but can be oxidized (Fe2+ -> Fe3+)
What is Ka and Kd and how does that relate to equilibrium?
Ka is association rate constant, Kd is dissociation rate constant. Equilibrium is where the association and dissociation rates are equal.
What is the tense and relaxed state in hemoglobin and what is involved in the conformational change between the two?
Tense state is more stable and has lower affinity for O2.
Relaxed state has fewer interactions and higher affinity for O2.
The conformational change from T to R involves breaking ion pairs between the alpha 1 and beta 2 interface.
What is the kinetic mechanism?
What is uncompetitive inhibition?
It bind to the enzyme substrate complex. It doesn't affect substrate binding and inhibits catalytic function.
List the 5 functions of globular proteins and examples.
Storage of ions and molecules - Myoglobin/Ferritin
Transport of ions and molecules - Hemoglobin/ Serotonin Transporter
Defense against pathogens - Antibodies/ Cytokines
Muscle Contraction - Actin/ Myosin
Biological Catalysis - Chymotrypsin/ Lysozymes
Why is induced fit more accurate then lock and key?
Induced fit allows tighter binding of the ligand and allows higher affinity for different ligands.
What is the antibody, Immunoglobin G, made out of?
Two heavy chains and two light chains, composed of constant domains and variable domains.
Light chain: one constant and one variable domain
Heavy Chain: Three constant and one variable domain
Whats the difference between sequential and ping-pong mechanism?
In Ping-Pong mechanism the enzyme reacts with the first substrate, releases the first product and the second substrate binds. (One in, one out, then the next in, next in)
What is mixed inhibition?
It binds to enzymes with or without substrate. It binds to the regulatory site and inhibits both binding and catalysis.