Lecture 4: Protein Folding, Energy, and Enzymes - Bio 172

Vocabulary flashcards covering protein structure, denaturation, energy, ATP, and enzyme concepts from Lecture 4.

Primary structure

Linear sequence of amino acids in a polypeptide, linked by covalent peptide bonds.

Peptide bond

Covalent bond connecting adjacent amino acids in a protein.

Secondary structure

Local folding into alpha helices and beta sheets stabilized by backbone hydrogen bonds.

Alpha helix

Right-handed helical secondary structure stabilized by intrachain hydrogen bonds.

Beta sheet

Pleated sheet secondary structure formed by beta strands held together by hydrogen bonds.

Tertiary structure

Three-dimensional shape of a single polypeptide, stabilized by interactions among R-groups.

Disulfide bond

Covalent link between cysteine residues that helps stabilize protein structure.

Quaternary structure

Complex formed when two or more polypeptide subunits assemble.

Denaturation

Loss of native protein conformation due to heat, pH change, or chemicals.

Renaturation

Reformation of native protein structure in some cases; can be inhibited by chaperones.

Chaperone

Protein that assists in folding and prevents misfolding or aggregation.

Hydrophobic interaction

Clustering of nonpolar residues away from water, driving proper folding.

Hydrogen bond

Bond between a carbonyl and amide hydrogen stabilizing structures.

Ionic bond

Electrostatic attraction between oppositely charged side chains.

Covalent bond

Bond formed by sharing electrons; includes disulfide bonds in proteins.

Active site

Region of an enzyme where the substrate binds and the reaction occurs.

Enzyme

Biological catalyst, typically a protein, that speeds reactions.

Substrate

Molecule that binds to an enzyme’s active site and is converted into product.

Enzyme-substrate complex

Transient complex formed when the substrate is bound to the enzyme.

Transition state

High-energy configuration at the peak of the reaction pathway.

Activation energy (EA)

Energy barrier that must be overcome for a reaction to proceed.

Catalysis

Process by which enzymes lower activation energy without changing overall ∆G.

Gibbs free energy (∆G)

Free energy change; negative values indicate spontaneous processes.

Exergonic

Reactions that release free energy and are spontaneous (∆G < 0).

Endergonic

Reactions that require input of energy (∆G > 0).

∆H

Change in enthalpy (bond energy) during a process.

∆S

Change in entropy (disorder) of a system.

∆G

Gibbs free energy change; ∆G = ∆H − T∆S.

ATP

Adenosine triphosphate, a high-energy molecule that donates phosphate groups.

ATP hydrolysis

Breakdown of ATP to ADP and inorganic phosphate, releasing energy.

Coupled reactions

Pairing an exergonic reaction with an endergonic one so the overall ∆G is negative.

Enzyme kinetics

Study of how reaction rate depends on factors like substrate and enzyme concentration.

Vmax

Maximum rate of an enzyme-catalyzed reaction when the enzyme is saturated.

Km

Substrate concentration at 1/2 Vmax; reflects enzyme affinity for the substrate.

Allosteric regulation

Regulation by molecules binding at a site other than the active site.

Allosteric activator

Molecule that increases enzyme activity by stabilizing the active form.

Allosteric inhibitor

Molecule that decreases enzyme activity by stabilizing an inactive form.

Competitive inhibition

Inhibitor binds the active site, increasing Km with no change to Vmax.

Noncompetitive inhibition

Inhibitor binds away from the active site, often lowering Vmax and sometimes affecting Km.

Irreversible inhibition

Inhibitor binds permanently to an enzyme, inactivating it.

Enzyme regulation

Control of enzyme activity via environmental factors and inhibitors.

Allosteric site

Regulatory site outside the active site where effectors bind.

Amyloid fibers

Misfolded protein aggregates associated with neurodegenerative diseases.

Renaturation

Reformation of the native structure after denaturation (possible for some proteins).

R-group

Side chain of an amino acid; determines properties and interactions in folding.