General Cell Bio Exam 1 Review

Enzyme

A biological catalyst (usually a protein) that speeds up chemical reactions by lowering activation energy without being consumed or changing ΔG.

Active site

The specific region of an enzyme where the substrate binds and catalysis occurs.

Substrate

The reactant molecule an enzyme acts upon.

Product

The molecule(s) produced after an enzymatic reaction.

Activation energy (Ea)

The minimum energy required for reactants to reach the transition state.

Activation energy barrier

The energy hill separating reactants from products.

Transition state

A high-energy, unstable state where bonds are partially broken and formed.

Catalyst

A substance that speeds up a reaction without being consumed.

Cofactor

A non-protein component required for enzyme activity (metal ion or organic molecule).

Coenzyme

An organic cofactor, often derived from vitamins (e.g., NAD⁺, FAD).

Turnover number (kcat)

The maximum number of substrate molecules converted to product per enzyme per second when saturated.

Induced fit

Model where enzyme changes shape upon substrate binding to improve catalysis.

Substrate orientation

Enzyme mechanism that aligns substrates properly to increase reaction probability.

Altering substrate reactivity

Enzyme mechanism that changes charge or bonding properties of substrate.

Inducing strain

Enzyme mechanism that distorts substrate bonds to promote reaction.

Michaelis constant (Km)

Substrate concentration at which reaction rate equals ½ Vmax.

Km and affinity relationship

Low Km indicates high affinity; high Km indicates low affinity.

Vmax

Maximum reaction velocity when all enzyme active sites are saturated.

Vmax/2

Half of the maximum velocity; occurs at substrate concentration equal to Km.

Saturation state

Condition where increasing substrate concentration does not increase reaction rate.

Michaelis-Menten model

Hyperbolic relationship between reaction rate and substrate concentration.

Lineweaver-Burk plot

Double reciprocal plot of 1/V vs 1/[S].

Lineweaver-Burk y-intercept

Equal to 1/Vmax.

Lineweaver-Burk x-intercept

Equal to −1/Km.

Competitive inhibitor

Inhibitor that competes with substrate for active site.

Effect of competitive inhibitor on Km

Km increases.

Effect of competitive inhibitor on Vmax

Vmax remains unchanged.

Noncompetitive inhibitor

Inhibitor that binds outside the active site.

Effect of noncompetitive inhibitor on Km

Km unchanged.

Effect of noncompetitive inhibitor on Vmax

Vmax decreases.

Internal energy (E)

The total energy contained within a system.

Exothermic reaction

A reaction that releases heat to the surroundings (ΔH < 0).

Endothermic reaction

A reaction that absorbs heat from the surroundings (ΔH > 0).

Entropy (ΔS)

A measure of disorder or randomness.

Free energy (G)

Energy available to do work at constant temperature and pressure.

ΔG

Change in free energy used to predict spontaneity.

Exergonic reaction

A reaction with negative ΔG that releases free energy.

Endergonic reaction

A reaction with positive ΔG that requires energy input.

Spontaneous reaction

A reaction that occurs without continuous external energy input.

Thermodynamically favorable

A reaction with ΔG < 0.

First law of thermodynamics

Energy cannot be created or destroyed, only transformed.

Second law of thermodynamics

Entropy of the universe always increases.

Downhill reactions

Reactions that move toward lower free energy and higher entropy.

Reaction coupling

Linking an endergonic reaction to an exergonic one.

ATP coupling

Using ATP hydrolysis to drive unfavorable reactions.

Equilibrium constant (Keq)

Ratio of products to reactants at equilibrium.

Keq and reaction direction

Keq > 1 favors products; Keq < 1 favors reactants.

Effect of enzymes on Keq

Enzymes do not change Keq.

Equilibrium

State where forward and reverse reaction rates are equal.

Steady state

A constant concentration of metabolites despite ongoing reactions.

Open system

A system that exchanges energy and matter with surroundings.

Prokaryotic cell

A cell lacking nucleus and membrane-bound organelles.

Eukaryotic cell

A cell containing nucleus and membrane-bound organelles.

Protein folding

Process by which a polypeptide acquires its functional 3D structure.

Protein unfolding (denaturation)

Loss of native protein structure due to disrupted interactions.

Native structure

The lowest-energy, biologically active conformation of a protein.

Chaperone

A protein that assists folding without determining final structure.

Hsp70

Chaperone that binds exposed hydrophobic regions of nascent polypeptides.

Hsp60 (chaperonin)

Barrel-shaped chaperone that encloses proteins for folding.

GroEL/GroES

Bacterial Hsp60 chaperonin system.

PrPC

Normal prion protein, α-helix rich and soluble.

PrPSc

Misfolded prion protein, β-sheet rich and infectious.

Prion infection model

PrPSc induces misfolding of PrPC.

Creutzfeld-Jacob Disease (CJD)

Neurodegenerative disease caused by prion protein misfolding.

Alzheimer's disease

A neurodegenerative disease involving amyloid plaques and tau tangles.

Difference between CJD and Alzheimer's

CJD is infectious; Alzheimer's is not.

pKa

The pH at which 50% of a functional group is protonated.

pH < pKa

Group is protonated.

pH > pKa

Group is deprotonated.

Carboxyl group below pKa

COOH (neutral).

Carboxyl group above pKa

COO⁻ (negative).

Amino group below pKa

NH₃⁺ (positive).

Amino group above pKa

NH₂ (neutral).

Amino acid structure

Central α-carbon bonded to amino group, carboxyl group, hydrogen, and R group.

Polar charged amino acids

Amino acids with fully charged side chains at physiological pH.

Polar uncharged amino acids

Amino acids with polar but uncharged side chains.

Nonpolar amino acids

Amino acids with hydrophobic side chains.

Glycine

Smallest amino acid; provides flexibility.

Proline

Rigid amino acid that introduces kinks.

Cysteine

Amino acid that forms disulfide bonds.

Disulfide bond

Covalent bond between two cysteine residues.

Primary protein structure

Amino acid sequence.

Secondary protein structure

Local folding stabilized by backbone hydrogen bonds.

Alpha helix

Coiled secondary structure stabilized by internal hydrogen bonds.

Beta pleated sheet

Sheet-like secondary structure stabilized by inter-strand hydrogen bonds.

Tertiary protein structure

Overall 3D folding of a single polypeptide.

Quaternary protein structure

Association of multiple polypeptide subunits.

Hydrophobic interactions

Attraction between nonpolar residues in proteins.

Ionic bonds in proteins

Attraction between oppositely charged side chains.

Van der Waals forces

Weak attractions between closely packed atoms.

Antibiotic

A compound that kills or inhibits bacteria.

Cell wall synthesis inhibitors

Antibiotics that block peptidoglycan formation (e.g., penicillin).

Protein synthesis inhibitors

Antibiotics that target bacterial ribosomes.

DNA replication inhibitors

Antibiotics that inhibit DNA gyrase or topoisomerase.

Transcription inhibitors

Antibiotics that block RNA polymerase.

Metabolic inhibitors

Antibiotics that block essential metabolic pathways.

Antibiotic resistance

The ability of bacteria to survive antibiotic treatment.

Beta-lactamase

Enzyme that degrades beta-lactam antibiotics.

Efflux pump

Protein that exports antibiotics out of bacterial cells.