Biochemistry: Metabolism, Enzyme Regulation, Mechanisms, Kinetics, and Inhibition

Comprehensive practice flashcards covering metabolic pathways, high-energy intermediates, GPCR regulation, enzyme catalytic mechanisms, Michaelis-Menten kinetics, and enzyme inhibition patterns.

Catabolism

The oxidative, exergonic metabolic process in which energy-yielding nutrients (carbohydrates, fats, and proteins) are degraded into simple, energy-poor end products ($CO_2$, $H_2O$, and $NH_3$), conserving released free energy as ATP and NADPH.

Anabolism

The reductive, endergonic biosynthetic process in which precursor molecules (amino acids, sugars, fatty acids, and nitrogenous bases) are assembled into cell macromolecules (proteins, polysaccharides, lipids, and nucleic acids) using the chemical energy of ATP and reducing power of NADPH.

The ATP Cycle

The cyclical cellular energy transfer system where ATP is synthesized from ADP and $P_i$ via catabolism or light-driven photosynthesis, and subsequently hydrolyzed back to ADP and $P_i$ to power biosynthesis, osmotic work, and cell motility or muscle contraction.

Energy Charge

A quantitative index of the cellular energy state defined by the ratio: $\text{Energy charge} = \frac{[\text{ATP}] + \frac{1}{2}[\text{ADP}]}{[\text{ATP}] + [\text{ADP}] + [\text{AMP}]}$.

Phosphorylation Potential

A thermodynamic measure of the chemical capacity for ATP synthesis or phosphate group transfer, defined by the ratio: $\frac{[\text{ATP}]}{[\text{ADP}] + [P_i]}$.

Flavin Adenine Dinucleotide (FAD)

A redox cofactor consisting of riboflavin bonded to an adenosine diphosphate unit; it accepts $2\,e^-$ and $2\,H^+$ to form $\text{FADH}_2$ through semiquinone intermediate states (semiquinone form at $\lambda_{\max} = 570\,nm$; semiquinone anion at $\lambda_{\max} = 490\,nm$).

Coenzyme A (CoA)

An acyl group carrier composed of a $\beta$-mercaptoethylamine unit, a pantothenate unit, and a phosphorylated ADP moiety; its reactive terminal thiol ($-\text{SH}$) group forms high-energy thioester bonds ($\Delta G^{\circ\prime} = -31.4\,kJ\,mol^{-1}$).

Phosphocreatine

A high-energy phosphagen that transfers its phosphoryl group to ADP via creatine kinase ($\Delta G^{\circ\prime} = -13\,kJ\,mol^{-1}$, $K_{eq} = 162$) to rapidly replenish ATP during exercise before oxidative metabolism responds.

Zymogen

An inactive enzyme precursor (proenzyme)—such as pepsinogen, chymotrypsinogen, or trypsinogen—that requires irreversible, selective proteolytic cleavage of specific peptide bonds to become catalytically active.

Heterotrimeric G Protein

A membrane-associated signaling complex composed of $\alpha$, $\beta$, and $\gamma$ subunits that mediates signal transduction between GPCRs and adenylyl cyclase; ligand binding triggers GDP-to-GTP exchange on $G_\alpha$, causing $G_\alpha(GTP)$ to dissociate and activate its effector.

Protein Kinase A (PKA)

A cyclic AMP-dependent kinase configured as an inactive tetramer ($R_2C_2$); binding of four $cAMP$ molecules to the regulatory dimer ($R_2-(\text{cAMP})_4$) induces dissociation and releases two active catalytic ($C$) subunits.

Glycogen Phosphorylase

A dimeric enzyme that catalyzes phosphorolysis of glycogen to generate $\alpha\text{-D-glucose-1-phosphate}$; it is regulated covalently by phosphorylase kinase (phosphorylation of Ser 14 converting inactive $b$ to active $a$) and allosterically by AMP (activator), ATP, glucose-6-phosphate, glucose, and caffeine.

ADME

The pharmacokinetic framework describing the disposition of a pharmaceutical compound within an organism: Absorption (entry into bloodstream), Distribution (dispersion through compartments), Metabolism (biotransformation), and Excretion (elimination).

Lipinski's Rules for Bioavailability

A set of four structural guidelines predicting poor oral absorption if a drug candidate violates more than one of the criteria: molecular mass $> 500\,g\,mol^{-1}$, $> 5$ hydrogen-bond donors, $> 10$ hydrogen-bond acceptors, and partition coefficient $\log(P) > 5$.

Phase I Transformation

A metabolic functionalization reaction, predominantly carried out by cytochrome P450 enzymes (e.g., CYP3A4, CYP2D6) using $O_2$ and NADPH, that introduces or unmasks polar functional groups (such as $-OH$) on lipophilic drugs.

Phase II Transformation

A conjugation reaction in which an endogenous hydrophilic molecule—such as glucuronic acid from UDP-glucuronic acid, sulfate from PAPS, or glutathione—is covalently attached to a drug or Phase I metabolite to accelerate excretion.

Enzyme Commission (EC) Numbers

A hierarchical numerical classification system categorizing enzyme-catalyzed reactions into seven classes: EC 1 (Oxidoreductases), EC 2 (Transferases), EC 3 (Hydrolases), EC 4 (Lyases), EC 5 (Isomerases), EC 6 (Ligases), and EC 7 (Translocases).

Catalytic Triad

The hydrogen-bonded active site network of Asp 102, His 57, and Ser 195 in serine proteases that operates as a charge-relay system: Asp 102 polarizes His 57, which abstracts a proton from Ser 195 to convert it into a potent nucleophilic alkoxide ion.

Oxyanion Hole

A structural pocket in serine proteases formed by the backbone NH amide groups of Gly 193 and Ser 195 that preferentially binds and stabilizes the negatively charged tetrahedral intermediate through hydrogen bonds.

Substrate Specificity Pocket

A defined cavity adjacent to the catalytic triad that determines substrate selectivity: chymotrypsin possesses a deep hydrophobic pocket for bulky aromatic residues; trypsin features Asp 189 at the base to bind positively charged Arg/Lys; elastase has Val 190 and Val 216 restricting entry to small, uncharged residues.

Chorismate Mutase

An enzyme that catalyzes the intramolecular Claisen rearrangement of chorismate to prephenate via a chair conformation, stabilizing the pericyclic transition state through electrostatic interactions and hydrogen bonding.

Near-Attack Complex (NAC)

A pre-organized ground-state conformation in an enzyme active site where substrate reacting groups are positioned within van der Waals contact distances and approaching transition-state angles, lowering the entropic barrier to reaction.

Diisopropylphosphofluoridate (DIPF)

A group-specific, irreversible organophosphate inhibitor that covalently reacts with the catalytic Ser 195 hydroxyl of serine proteases, releasing HF and completely inactivating the enzyme.

Steady-State Approximation

The kinetic assumption in the Michaelis-Menten derivation that the concentration of the enzyme-substrate complex remains constant during the reaction because its rate of formation ($V_{\text{form}} = k_1[E][S]$) equals its rate of decomposition ($V_{\text{decomp}} = (k_{-1} + k_2)[ES]$).

Michaelis Constant ($K_M$)

The substrate concentration at which the initial reaction velocity equals half of the maximal velocity ($V = \frac{1}{2}V_{\max}$), mathematically expressed as $K_M = \frac{k_{-1} + k_2}{k_1}$.

Turnover Number ($k_{cat}$)

The catalytic rate constant representing the maximum number of substrate molecules converted to product per enzyme active site per unit time at saturating substrate levels: $k_{cat} = \frac{V_{\max}}{[E_{\text{Total}}]}$ (units of $s^{-1}$).

Catalytic Efficiency

The apparent second-order rate constant given by $\frac{k_{cat}}{K_M}$, which measures enzyme efficiency at low substrate concentrations ($[S] \ll K_M$); it is physically constrained by diffusion limits to $10^8 - 10^9\,M^{-1}\,s^{-1}$.

Lineweaver-Burk Plot

A linear double-reciprocal plot of $\frac{1}{V}$ versus $\frac{1}{[S]}$ described by $\frac{1}{V} = \frac{K_M}{V_{\max}}\frac{1}{[S]} + \frac{1}{V_{\max}}$, where the slope is $\frac{K_M}{V_{\max}}$, the y-intercept is $\frac{1}{V_{\max}}$, and the x-intercept is $-\frac{1}{K_M}$.

Inhibition Constant ($K_I$)

The equilibrium dissociation constant of the enzyme-inhibitor complex: $K_I = \frac{[E][I]}{[EI]}$, where a lower value reflects stronger inhibitor binding to the free enzyme.

Competitive Inhibition

A reversible inhibition mechanism in which the inhibitor binds exclusively to the free enzyme ($E$) at the active site, competing directly with substrate; it increases the apparent $K_M$ without altering $V_{\max}$.

Pure Noncompetitive Inhibition

A reversible inhibition mechanism where the inhibitor binds with equal affinity to both free enzyme ($E$) and enzyme-substrate complex ($ES$) at an allosteric site ($K_I = K_I^\prime$); it reduces $V_{\max}$ without affecting $K_M$.

Uncompetitive Inhibition

A reversible inhibition mechanism in which the inhibitor binds only to the enzyme-substrate complex ($ES$); it reduces both $V_{\max}$ and apparent $K_M$ by the exact same factor, yielding parallel lines on a Lineweaver-Burk plot.

Mixed Inhibition

A form of reversible inhibition where the inhibitor binds to both free enzyme ($E$) and the enzyme-substrate complex ($ES$) with unequal affinities ($K_I \neq K_I^\prime$), altering both $V_{\max}$ and apparent $K_M$.

Cyclooxygenase (COX)

The enzyme (prostaglandin $H_2$ synthase-1) that converts arachidonic acid ($20:4\,\omega 6$) into prostaglandin $H_2$ ($PGH_2$); it is irreversibly inactivated by aspirin through covalent acetylation of a critical active-site serine, and reversibly inhibited by ibuprofen.

Suicide Inhibitor

A mechanism-based inhibitor that mimics normal substrate and is processed by the target enzyme to generate a reactive intermediate, which then covalently inactivates the enzyme (exemplified by clavulanic acid inactivating bacterial $\beta$-lactamase).