CHM41-1 Biochemistry Week 3: Proteins and Enzymes Vocabulary

Vocabulary flashcards focusing on biochemical definitions, structural levels, kinetic terms, and clinical biomarkers from CHM41-1 Week 3.

Zwitterion

A dipolar molecule carrying one positive and one negative charge; at $\text{pH } 7$, an amino acid exists as a neutral zwitterion with a -$NH_3^+ group and a -$COO^- group.

Peptide Bond

A covalent amide linkage formed between the $\alpha$-carboxyl group of one amino acid and the $\alpha$-amino group of another via a condensation reaction that eliminates a water molecule.

Primary Structure

The linear sequence of amino acid residues in a polypeptide chain, held together and determined by covalent peptide bonds.

Secondary Structure

The regular, recurring conformational patterns of a polypeptide chain—principally the $\alpha$-helix and $\beta$-pleated strand—stabilized by backbone hydrogen bonds.

Tertiary Structure

The compact three-dimensional fold assumed by a single polypeptide chain, typically yielding a globular conformation with a low surface-to-volume ratio.

Quaternary Structure

The spatial organization and interaction of two or more individual polypeptide chains (subunits) in a multi-subunit protein complex.

Hydrophobic Effect

The principal, entropically driven force for protein folding in which nonpolar side chains cluster together in the interior core away from water.

Denaturation

The unspooling or loss of native protein three-dimensional structure and functional activity caused by disrupting weak noncovalent interactions, leaving covalent peptide bonds intact.

Hydrolysis

The covalent cleavage of peptide bonds in the polypeptide backbone by the addition of water, serving as the reverse of condensation.

Hemoglobin

A heterotetrameric oxygen-carrier protein in the blood composed of two $\alpha$ and two $\beta$ polypeptide chains ($\alpha_2\beta_2$).

Albumin

The most abundant plasma protein ($3.4$–$4.7\text{ g/dL}$) synthesized by the liver, which contributes $75$–$80\%$ of plasma osmotic pressure and binds various ligands for transport.

Substrate

The specific chemical reactant or substance upon which an enzyme acts during a biochemical reaction.

Active Site

The specific region of an enzyme molecule where substrate binding and catalysis occur.

Activation Free Energy ($\Delta G^\ddagger$)

The energy barrier separating reactants from the transition state; enzymes lower this barrier ($\Delta G_e^\ddagger < \Delta G_u^\ddagger$) to accelerate reaction rates.

Lock-and-Key Hypothesis

Emil Fischer's historical model of enzyme specificity proposing that the active site is a rigid template complementary in shape to the substrate.

Induced Fit

Daniel Koshland's model stating that substrate binding dynamically modifies the conformation of the enzyme active site and substrate to achieve optimal catalytic fitting.

Initial Velocity ($v_i$)

The rate of the forward enzymatic reaction measured over very short time periods where product concentration is minimal and reverse reaction is negligible.

Substrate Saturation

The state wherein high substrate concentration occupies virtually all enzyme active sites as the $ES$ complex, causing reaction velocity to reach a plateau at $V_{\max}$.

Michaelis Constant ($K_m$)

The operational substrate concentration at which the initial reaction velocity ($v_i$) reaches exactly half of maximum velocity ($V_{\max}/2$).

Reversible Inhibition

Enzyme inhibition characterized by noncovalent, equilibrium association and dissociation reactions between the inhibitor and the enzyme.

Irreversible Inhibition

Enzyme inhibition involving the formation of covalent bonds with active-site side chains or prosthetic groups, permanently decreasing the concentration of active enzyme.

Competitive Inhibition

A form of reversible inhibition in which the substrate and inhibitor compete for the same active site on the enzyme in a mutually exclusive manner.

Apoenzyme

The catalytically inactive protein component of an enzyme that lacks its required nonprotein cofactor or prosthetic group.

Holoenzyme

The complete, catalytically active enzyme system consisting of an apoenzyme combined with its necessary cofactor or prosthetic group.

Prosthetic Group

A tightly or permanently bound nonprotein component (metal ion or organic coenzyme) essential for an enzyme's catalytic activity.

Biomarkers

Molecules (such as tissue enzymes) whose presence or quantitative levels in biological fluids assist in the diagnosis, prognosis, and treatment monitoring of disease.

Plasma

The liquid component of unclotted blood obtained by centrifugation after adding an anticoagulant.

Serum

The fluid phase remaining after blood has been permitted to clot naturally.