W - BIOL200 - 2.5 PROTEIN FUNCTION

What is specificity in ligand binding?

Specificity is how specific the ligand-protein interaction is—whether a ligand can bind to multiple proteins or not.

What is affinity in ligand binding?

Affinity is how strong the ligand binds to the protein. Higher affinity = harder to dissociate.

What determines ligand-binding specificity and affinity?

The physical and chemical properties of the protein's ligand binding site.

What does K_d measure?

K_d measures affinity. Lower K_d = stronger affinity.

What are antibodies?

Proteins with high specificity and affinity for antigens

How do antibodies recognize antigens?

Each has six complementary determining regions (CDRs) that bind to a specific epitope.

What makes antibodies highly specific?

They can distinguish between similar proteins differing by one amino acid.

What do enzymes do?

Enzymes catalyze reactions by lowering activation energy.

Do enzymes increase product amount?

No, they increase reaction rate, not product amount.

What are the two regions of an enzyme's active site?

Substrate-binding site and catalytic site.

What happens at low substrate concentrations in Michaelis-Menten?

Reaction rate is proportional to substrate amount.

What happens at high substrate concentrations in Michaelis-Menten?

Reaction rate approaches V_max and is independent of substrate amount.

Write the Michaelis-Menten equation.

V₀ = (V_max[S]) / (K_m + [S])

 What does a low K_m mean?

High enzyme-substrate affinity.

 What do scaffold proteins do?

Hold together proteins in the same pathway.

What is allostery?

 A ligand binds to one site and affects binding at another by changing protein conformation.

 Example of allosteric protein?

Hemoglobin—O₂ binding to one subunit increases affinity of the others.

 What turns calmodulin ON and OFF?

Ca²⁺ binds → ON; no Ca²⁺ → OFF

What activates/inactivates GTPases?

GTP bound = ON, GDP bound = OFF.

 What is a GEF?

 Guanine nucleotide exchange factor releases GDP to allow GTP binding.

Heteromeric vs. Monomeric G proteins?

Heteromeric: surface receptors; Monomeric: signal transduction without surface receptors.

 What are non-competitive inhibitors?

Bind elsewhere than active site, change enzyme shape, and inhibit function.

 What are the 3 types of signal transduction?

 Endocrine (distant), paracrine (nearby), autocrine (self).

What do receptors do?

Detect and bind signaling molecules with high specificity/affinity.

 Can same molecule cause different responses?

Yes, depending on receptor type or cell context.

What do kinases do?

 Phosphorylate proteins on specific amino acids (Tyrosine or Serine/Threonine).

What can phosphorylation do?

Activate or inhibit protein function.

 What do phosphatases do?

 Dephosphorylate proteins.

 What does Michaelis-Menten say about reaction rate?

 It's dependent on substrate amount at low concentrations and independent at high concentrations.

 Which is NOT an allosteric switch?

An IgG antibody binding to its antigen.