Protein Function and Ligand Binding

Flashcards on Protein Function and Ligand Binding from Biochemistry Lecture

Ligand

A molecule that binds (interacts) reversibly to a protein.

Binding Site

The region in the protein where the ligand binds.

Equilibrium Constant (Ka)

Characterizes the equilibrium composition in protein-ligand interactions, where association and dissociation rates are equal.

Association Rate Constant (Ka)

Describes the affinity of the protein-ligand interaction.

Dissociation Rate Constant (Kd)

Describes the affinity of the protein-ligand interaction; lower Kd corresponds to higher affinity.

Specificity (Protein-Ligand)

Proteins typically have high specificity, meaning only certain ligands bind, attributed to the 3D structure of the protein’s binding site.

Induced Fit

Conformational changes that often occur upon ligand binding, allowing for tighter binding of the ligand; both ligand and protein can change conformations.

Prosthetic Group

A non-amino acid containing group which is covalently attached to the protein and contributes to the function of the protein.

Heme

An organometallic compound (prosthetic group) that captures the oxygen molecule (ligand) and is bound to a protein.

Myoglobin (Mb)

An oxygen storage protein found in the muscle, having a single peptide chain and one site for O2 binding.

Haemoglobin (Hb)

A circulating oxygen transporter found in the blood, with four subunits (each similar to myoglobin), one heme per subunit, and 4 O2 binding sites, exhibiting cooperative binding and allostery.

Cooperativity

A phenomenon where binding sites are able to interact with each other, recognized by sigmoidal binding curves; the first binding event increases affinity at remaining sites (positive cooperativity).

Allosteric Proteins

Binding of a ligand to one site affects the binding properties of a different site on the same protein; can be positive or negative.

Homotropic Allostery

Ligand and allosteric regulator are the same.

Heterotropic Allostery

Ligand and allosteric regulator are NOT the same.

T State

Tense state of hemoglobin, which has low O2 affinity, assumed in the absence/low oxygen.

R State

Relaxed state of hemoglobin which has a higher O2 affinity; triggered by the binding of oxygen, causing a conformational change.

Bohr Effect

The effect of pH on O2 binding in hemoglobin. H+ binds to Hb and stabilizes the T state, leading to the release of O2 (in the tissues).