Enzyme Kinetics, Structure, and Regulation: A Comprehensive Review

Energy of Activation (EA)

The initial energy input required to start a chemical reaction; enzymes lower the EA so reactions run faster.

ΔG

"Gibbs free energy change: the difference in free energy between products and reactants; negative ΔG = spontaneous reaction, positive ΔG = nonspontaneous."

Enzymes lower the barrier of Activation Energy

"Enzymes reduce the activation energy (EA) of reactions by stabilizing the transition state, increasing reaction rate without changing ΔG."

Catalytic Cycle of an Enzyme

Sequence: substrate binds active site → transition state stabilized → substrate converted to product → product released → enzyme ready for next substrate. Cycle emphasizes specificity and turnover.

EA graph (reaction coordinate diagram) interpretation

"Shows reactants → transition state (peak = EA) → products. With enzyme, peak is lower (reduced EA) but product and reactant energy levels (ΔG) are unchanged."

Optimal Temperature (diagram) interpretation

"Bell-shaped curves for different enzymes: activity rises with temperature until an optimum (increased kinetic energy), then falls as denaturation reduces activity. Different enzymes have different optima."

Optimal pH (diagram) interpretation

"Each enzyme has a pH activity curve with an optimum where active site ionization and conformation are ideal; deviations alter charge and hydrogen bonding, decreasing activity."

Varying Substrate Concentration (Michaelis-Menten) interpretation

"Plot of reaction velocity (V) vs substrate [S] shows hyperbolic approach to Vmax. At low [S], rate ∝ [S]; at high [S], enzyme becomes saturated and rate approaches Vmax."

Varying Enzyme Concentration interpretation

"At constant [S] (non-saturating), reaction rate increases linearly with [enzyme]; at saturating [S], adding enzyme still increases Vmax proportionally but Km unchanged."

Saturation point

Condition when all enzyme active sites are occupied by substrate; adding more substrate won't increase rate. On Michaelis-Menten curve this causes plateau at Vmax.

Inhibitors of Enzyme Activity

"Molecules that decrease enzyme activity. Major types: competitive (bind active site), noncompetitive/allosteric (bind different site and change conformation), uncompetitive (bind enzyme-substrate complex)."

Competitive inhibitor

Competes with substrate for the active site; increases apparent Km (lower affinity) but Vmax unchanged (can be outcompeted by high [S]).

Noncompetitive (allosteric) inhibitor

Binds a site other than the active site and changes enzyme conformation; reduces Vmax without changing Km (substrate binding unaffected but catalysis reduced).

Uncompetitive inhibitor

"Binds only to enzyme-substrate complex, lowering both apparent Km and Vmax."

Allosteric Regulation

"Regulation of enzyme activity by binding of effectors at sites other than the active site; can be positive (activators) or negative (inhibitors), often causes sigmoidal kinetics."

Examples of inhibitors/toxins

DDT and parathion: toxins that inhibit essential enzymes in pests; penicillin: antibiotic that inhibits bacterial cell-wall enzymes (transpeptidases).

Feedback Inhibition

End-product of a metabolic pathway inhibits an upstream enzyme (often the first committed step) to regulate pathway flux and conserve resources.

Enzyme Cooperativity

A form of allosteric regulation where binding of substrate to one active site affects binding at other subunits (positive cooperativity → sigmoidal curve).

Oxygen Dissociation Curve & Cooperativity

Hemoglobin curve is sigmoidal because O2 binding at one heme increases affinity at remaining hemes — classic positive cooperativity; shifts left/right indicate affinity changes.

"2

3-Diphosphoglycerate (2,3-DPG)","A metabolite that binds hemoglobin and decreases its O2 affinity (right-shifts O2 dissociation curve), important in hypoxemia and anemia adaptation."

"Protein basic composition (""C:H:O:N"")"

"Proteins composed mainly of carbon, hydrogen, oxygen, and nitrogen (and sometimes sulfur); amino acids are the monomers."

"Functional groups: Amine

Carboxyl, Hydroxyl, Phosphate, Carbonyl, Methyl","Common organic functional groups in biomolecules: amine (-NH2), carboxyl (-COOH), hydroxyl (-OH), phosphate (-PO4), carbonyl (C=O), methyl (-CH3). Each confers distinct chemical properties."

Central carbon (amino acid)

"The alpha carbon (central carbon) in amino acids bonded to an amino group, carboxyl group, hydrogen, and side chain (R group)."

Amino terminal (N-terminus)

The end of a polypeptide with a free amino group (—NH2); synthesis starts at N-terminus → C-terminus.

Carboxyl terminal (C-terminus)

The end of a polypeptide with a free carboxyl group (—COOH).

Functional group

"The reactive part of a molecule (like —OH, —NH2, —COOH) that largely determines chemical behavior."

If there are 20 different functional groups how many possible amino acids are there?

The packet's rhetorical point: many different side chains (R groups) yield many amino acids; biologically there are 20 common amino acids with distinct R groups.

Amino Acids (categories)

"Classified by side chain properties: nonpolar (hydrophobic), polar uncharged, acidic (negatively charged at physiological pH), basic (positively charged at physiological pH)."

Non-Polar Amino Acids

"Amino acids with hydrophobic side chains (e.g., leucine, isoleucine, valine, phenylalanine) often found in protein cores or membranes."

Polar Amino Acids

"Contain side chains that can hydrogen bond (e.g., serine, threonine, asparagine, glutamine); often on surfaces or active sites."

Acidic Amino Acids

Aspartic acid (Asp) and glutamic acid (Glu): negatively charged at physiological pH; can coordinate cations or participate in catalysis.

Basic Amino Acids

"Lysine, arginine, histidine: positively charged at physiological pH (histidine can act as proton donor/acceptor near pH 7)."

Monomers (in proteins)

Amino acids are the monomers that polymerize to form proteins (polypeptides).

Dehydration Synthesis (peptide bond formation)

"Reaction that joins two amino acids: carboxyl of one reacts with amino of another, releasing water, forming a peptide bond (—CONH—)."

Peptide bond

Covalent bond formed between the carboxyl carbon of one amino acid and the amino nitrogen of another; planar and has partial double-bond character.

Polypeptides

Chains of amino acids linked by peptide bonds; a protein may be a single polypeptide or multiple polypeptides.

Polymer

"Large molecule made of repeating subunits (monomers) — proteins, nucleic acids, polysaccharides are biological polymers."

Primary Structure

Linear sequence (order) of amino acids in a polypeptide; determined by DNA and held together by peptide bonds.

Secondary Structure

Local folding patterns stabilized by hydrogen bonds between backbone atoms: α-helix and β-pleated sheet are common motifs.

α-Helix

Right-handed coil stabilized by hydrogen bonds between backbone N—H and C=O groups 4 residues apart; common in transmembrane and structural regions.

β-Pleated Sheet

Sheets of polypeptide strands aligned side-by-side with hydrogen bonds between backbone C=O and N—H groups; can be parallel or antiparallel.

Tertiary Structure

"3-D shape of a single polypeptide chain stabilized by side-chain interactions: hydrophobic interactions, disulfide bridges (covalent), ionic bonds, hydrogen bonds."

Hydrophobic interactions

"Nonpolar side chains cluster away from water, driving folding and stabilizing tertiary structure."

Disulfide bridges

"Covalent bonds between cysteine residues (—S—S—) that stabilize folded protein structures, especially extracellular proteins."

Ionic bonding (in proteins)

Electrostatic interactions between oppositely charged side chains (salt bridges) that stabilize tertiary/quaternary structures.

Quaternary Structure

"Association of multiple polypeptide subunits into a functional protein complex (e.g., hemoglobin: 4 subunits)."

Examples of quaternary proteins

"Collagen (triple helix), hemoglobin (tetramer), some enzymes assembled from multiple subunits."

Denaturation

"Loss of a protein's native tertiary/quaternary structure (and function) due to heat, pH, salts, or chemicals; often irreversible in vivo."

Renaturation

Refolding of a denatured protein back to its native conformation under favorable conditions; possible for some proteins in vitro.

Chaperonins

Protein complexes that assist other proteins to fold correctly by providing protected environment and preventing aggregation.

X-Ray Crystallography

Experimental technique to determine 3-D structures of proteins by diffracting X-rays through protein crystals and computing electron density.

"Primary examples of proteins (structural

regulatory, enzymatic)","Structural: keratin, actin/myosin; Regulatory/hormonal: insulin, glucocorticoids; Signaling: neuropeptides; Enzymes: salivary amylase, lipase, lactase, peroxidase."

Enzymes (nomenclature)

"Most enzyme names end in '-ase' and often reflect the substrate or reaction (e.g., lactase cleaves lactose)."

Lipids (general)

"Hydrophobic or amphipathic organic molecules mostly made of C, H, O; include fats (triglycerides), phospholipids, steroids; energy storage and membrane roles."

Non-polar molecules

Molecules with even electron distribution and little or no net polarity; insoluble in water and often form hydrophobic cores or membranes.

Triglyceride (structure)

Glycerol backbone + 3 fatty acids joined by ester linkages; main form of long-term energy storage in organisms.

Saturated fatty acid

"Fatty acid with only single bonds between carbons (no double bonds), straight chain, typically solid at room temp (animal fats)."

Unsaturated fatty acid

Fatty acid containing one or more C=C double bonds that introduce kinks; usually liquid at room temperature (plant/fish oils).

Phospholipid (structure and properties)

Glycerol + 2 fatty acids + phosphate head group: amphipathic — hydrophilic head and hydrophobic tails; forms bilayers in aqueous environments.

Micelle

Spherical structure formed when amphipathic lipids assemble with hydrophobic tails inward and hydrophilic heads outward (typical for single-tailed lipids).

Phospholipid bilayer

Fundamental structure of cell membranes: two layers of phospholipids with hydrophobic tails inward and hydrophilic heads facing aqueous environments.

Sterols / Steroids

"Ring-structured lipids (e.g., cholesterol, testosterone, estrogen) that function in membranes and as hormones."

Cholesterol

A sterol that modulates membrane fluidity and is precursor for steroid hormones; has LDL/HDL health associations in humans.

"Bonding basics (valence electrons

carbon skeletons)",Atoms form bonds to achieve stable electron configurations; carbon's 4 valence electrons allow versatile skeletons for organic molecules.

Functional groups (list again briefly)

"Key groups: hydroxyl, carbonyl (aldehyde/ketone), carboxyl, amino, phosphate, methyl — each affects reactivity and solubility."

Isomers (structural types)

"Molecules with same formula but different arrangement: structural (different connectivity), geometric (cis/trans), enantiomers (mirror-image optical isomers)."

Dehydration Synthesis (general)

Reaction that joins monomers into polymers by removing a water molecule (condensation reaction).

Hydrolysis

Reaction that breaks polymers into monomers by adding a water molecule.

Carbohydrate formula and classes

"General formula approx C:H:O = 1:2:1; classes: monosaccharides (single sugars), disaccharides, polysaccharides (starch, glycogen, cellulose)."

Monosaccharides (examples)

"Single-ring sugars like glucose, fructose, galactose, ribose; primary cellular energy sources and building blocks for nucleotides."

Disaccharides

"Two monosaccharides joined by glycosidic linkage (e.g., sucrose = glucose+fructose, lactose = glucose+galactose, maltose = glucose+glucose)."

Glycosidic linkage

Covalent bond formed between monosaccharides via dehydration synthesis; orientation (α or β) affects digestibility and structure.

Polysaccharides (functions)

"Long chains of sugars for energy storage (starch in plants, glycogen in animals) or structural roles (cellulose in plant cell walls)."

Starch: amylose vs amylopectin

"Amylose = mostly unbranched α-1,4 linkages (helical); amylopectin = branched α-1,4 with α-1,6 branch points."

Glycogen

"Highly branched animal storage polysaccharide (α-1,4 main chains with α-1,6 branches) allowing rapid glucose release."

Cellulose

"Structural plant polysaccharide of β-1,4 linked glucose; straight chains form hydrogen-bonded fibers resistant to most animal digestion."

Properties of Water: polarity and hydrogen bonding

"Water is polar; hydrogen bonds between molecules give it high cohesion, surface tension, heat capacity, and solvent power."

Cohesion

Attraction of water molecules to each other via hydrogen bonding; important for water transport in plants and surface tension.

Adhesion

Attraction between water molecules and other surfaces; contributes to capillary action.

Specific Heat

Amount of heat needed to raise temperature of 1 g water by 1°C (~1 cal/g°C); water's high specific heat stabilizes environmental temperatures.

Heat of Vaporization

Energy required to convert 1 g of liquid water to gas; high for water (~580 cal/g at 25°C) enabling evaporative cooling (sweating).

Evaporative Cooling

"Cooling effect that occurs when high-energy (hot) molecules leave as vapor, lowering the temperature of the remaining substance (e.g., sweat)."

Water as Solvent

"Water's polarity dissolves polar and ionic substances (solutes), facilitating biochemical reactions in cells."

"Dissociation of Water

H3O+/OH-",Water can dissociate to H3O+ (often simplified to H+) and OH−; [H+][OH−]=10^-14 at 25°C; pH measures [H+].

Acids and Bases

Acids donate protons (H+); bases accept protons. Strong acids/bases dissociate completely; weak ones partially.

pH and pH scale

"pH = -log[H+]; neutral = pH 7 at 25°C; acidic < 7, basic > 7. Small pH changes can significantly affect protein structure and enzyme activity."

Buffers

"Systems (weak acid + conjugate base) that minimize pH changes by absorbing or releasing H+; vital for homeostasis (e.g., blood bicarbonate buffer)."

Carbonic acid / bicarbonate buffer system

"CO2 + H2O ⇌ H2CO3 ⇌ HCO3− + H+; important in blood buffering around pH 7.4, can shift to maintain pH with respiratory changes."

Blood buffering (physiological range)

Normal blood pH ≈ 7.4; small deviations (7.35-7.45) are tightly regulated; buffers and respiration/renal systems maintain balance.

Why atoms bond?

Atoms bond to achieve more stable electron configurations (filled valence shells); bonding releases energy and forms molecules.

How atoms bond? (share vs transfer electrons)

Covalent bonds = sharing of electrons; ionic bonds = transfer of electrons (resulting in charged ions); hydrogen bonds and Van der Waals are weaker intermolecular forces.

Polar vs Non-polar bonds

Polar covalent bonds have unequal electron sharing (partial charges); nonpolar covalent bonds have equal sharing (no charge separation).

Hydrogen bonds

"Weak attraction between a hydrogen atom covalently bound to an electronegative atom (O, N) and another electronegative atom; critical for water properties and biomolecular structure."

Van der Waals forces

"Very weak, transient attractions due to fluctuating electron distributions; important for close-range molecular packing."

Spectrum of bond strengths

"From strongest to weakest: covalent (polar/nonpolar), ionic, hydrogen, Van der Waals (note context and environment can change relative importance)."

Chemical reactions: make/break bonds

Chemical reactions involve breaking and forming bonds; these processes require or release energy depending on bond energies.

Exothermic reaction

Reaction that releases net energy (products have lower energy than reactants); often releases heat.

Endothermic reaction

Reaction that absorbs net energy (products have higher energy than reactants); requires input of heat.

Activation Energy (restate)

Energy barrier that reactants must overcome to reach transition state and form products; enzymes lower this barrier.

Enzyme examples (restate)

"Peroxidase (breaks down peroxides), salivary amylase (starch→maltose), lipase (lipid hydrolysis), lactase (lactose → glucose + galactose)."