Biochemistry: Bioenergetics, Enzyme Kinetics, Carbohydrates, and Membrane Lipids

Comprehensive vocabulary flashcards covering bioenergetics, thermodynamics, enzyme kinetics and inhibition mechanisms, carbohydrate structures and polysaccharides, and membrane lipid biochemistry.

Bioenergetics

The quantitative study of energy transductions and chemical transfers that occur within living cells.

Gibbs Free Energy ($G$)

The thermodynamic quantity representing the amount of energy capable of doing work during a chemical reaction at constant temperature and pressure.

Exergonic Reaction

A chemical process that occurs with a negative free energy change ($-\Delta G$), releasing energy and proceeding spontaneously under defined conditions.

Endergonic Reaction

A non-spontaneous chemical reaction characterized by a positive free energy change ($+\Delta G$), requiring an input of free energy to proceed.

Standard Transformed Free Energy Change ($\Delta G^{\circ \prime}$)

The free energy change of a biochemical reaction under standard conditions: temperature of $298\,\text{K}$ ($25^\circ\text{C}$), pressure of $1\,\text{atm}$, initial reactant and product concentrations of $1\,\text{M}$, $[\text{H}_2\text{O}] = 55.5\,\text{M}$, and $[\text{H}^+] = 10^{-7}\,\text{M}$ ($\text{pH} = 7.0$).

Reaction Coupling

The biological process of driving a thermodynamically unfavorable endergonic reaction by linking it to a highly exergonic reaction, such that the sum of their individual free energy changes ($\Delta G_1 + \Delta G_2$) is negative.

Activation Energy ($\Delta G^{\ddagger}$)

The threshold of energy required to convert reactant molecules from their ground state to the transition state, determining the rate of the reaction.

Oxyanion Hole

A pocket in an enzyme active site that stabilizes the negatively charged oxygen atom of the tetrahedral transition-state intermediate via hydrogen bonds with peptide backbone amide groups, such as Gly 193 and Ser 195.

Catalytic Triad

A conserved active-site trio of amino acid residues in serine proteases—specifically Asp 102, His 57, and Ser 195—that coordinate to carry out acid-base and nucleophilic catalysis during peptide bond cleavage.

Steady-State Assumption

The condition in enzyme kinetics where the concentration of the enzyme-substrate complex ($[ES]$) remains virtually constant over time because its rate of formation equals its rate of breakdown.

Michaelis Constant ($K_m$)

The substrate concentration at which an enzyme-catalyzed reaction attains half of its maximal velocity ($v = \frac{1}{2}V_{\max}$), serving as an inverse indicator of an enzyme's affinity for its substrate.

Turnover Number ($k_{\text{cat}}$)

The first-order rate constant that measures the maximum number of substrate molecules converted to product per unit of time by an individual enzyme active site when fully saturated.

Double-Reciprocal Plot (Lineweaver-Burk Plot)

A linear algebraic plot of $\frac{1}{v_0}$ against $\frac{1}{[S]}$ with a y-intercept of $\frac{1}{V_{\max}}$, an x-intercept of $-\frac{1}{K_m}$, and a slope equal to $\frac{K_m}{V_{\max}}$.

Competitive Inhibition

A type of reversible inhibition where an inhibitor binds directly to the active site of the free enzyme, competing with the substrate and increasing the apparent $K_m$ while leaving $V_{\max}$ unchanged.

Uncompetitive Inhibition

A reversible inhibition mode where the inhibitor binds exclusively to the enzyme-substrate ($ES$) complex, resulting in a proportional decrease in both $V_{\max}$ and apparent $K_m$, generating parallel Lineweaver-Burk lines.

Mixed Inhibition

An enzyme inhibition mechanism where an inhibitor can bind to either the free enzyme or the enzyme-substrate complex, reducing $V_{\max}$ and causing an apparent change in $K_m$, with double-reciprocal lines intersecting to the left of the y-axis.

Aldose

A monosaccharide characterized by an aldehyde functional group located at the terminus of the carbon chain.

Ketose

A monosaccharide containing an internal carbonyl ketone group.

Epimers

Two stereoisomeric monosaccharides that differ in spatial configuration around only one chiral carbon atom, such as D-glucose and D-mannose at C-2, or D-glucose and D-galactose at C-4.

Pyranose

A six-membered cyclic hemiacetal ring structure formed by intramolecular reaction between a carbohydrate's C-5 hydroxyl group and its C-1 aldehyde group.

Furanose

A five-membered cyclic carbohydrate ring formed by internal hemiacetal or hemiketal cyclization, as observed in D-fructofuranose.

Sucrose

A nonreducing disaccharide composed of D-glucose and D-fructose joined by anomeric glycosidic linkages designated as $\beta\text{-D-fructofuranosyl } \alpha\text{-D-glucopyranoside}$ ($\text{Glc}(\alpha 1 \leftrightarrow 2\beta)\text{Fru}$).

Amylose

An unbranched homopolysaccharide constituting approximately $20\%$ of starch, composed entirely of linear D-glucose residues connected by $(\alpha 1 \rightarrow 4)$ glycosidic bonds.

Amylopectin

A branched homopolysaccharide making up approximately $80\%$ of starch, containing linear $(\alpha 1 \rightarrow 4)$ glucose chains with $(\alpha 1 \rightarrow 6)$ glycosidic branch points occurring every $24$ to $30$ residues.

Cellulose

A tough, water-insoluble linear homopolysaccharide of plant cell walls composed of D-glucose units linked by $(\beta 1 \rightarrow 4)$ glycosidic bonds, allowing long parallel chains to assemble into rigid fibrils.

Chitin

A linear structural homopolysaccharide formed from $(\beta 1 \rightarrow 4)\text{-linked } N\text{-acetylglucosamine}$ ($\text{GlcNAc}$) units, serving as the major component of arthropod exoskeletons.

Amphipathic Lipid

A dual-affinity molecule possessing both a hydrophilic polar head group and one or more nonpolar hydrophobic hydrocarbon tails.

Fatty Acid

A carboxylic acid containing an unbranched hydrocarbon chain ranging from $4$ to $36$ carbons in length, typically having an even number of carbon atoms and a $\text{p}K_a$ near $4.5$.

Triacylglycerol

A nonpolar, neutral storage lipid composed of a glycerol backbone ester-linked to three fatty acid chains, stored primarily in the lipid droplets of adipocytes.

Glycerophospholipid

A primary membrane structural lipid containing a glycerol backbone with two fatty acids esterified at C-1 and C-2, and a polar or charged alcohol head group attached at C-3 through a phosphodiester linkage.

Lipid Bilayer

A two-layered supramolecular sheet assembled from cylindrical phospholipids, featuring hydrophilic interfacial regions on the exterior surfaces and a central hydrophobic core measuring approximately $30\,\text{\AA}$ thick within a total width of roughly $60\,\text{\AA}$.

Sterol

A class of structural membrane lipids characterized by a rigid tetracyclic steroid nucleus composed of four fused rings (A, B, C, D), a polar hydroxyl group at C-3, and an alkyl side chain, exemplified by cholesterol.

Facilitated Diffusion

Passive transmembrane transport that permits polar molecules or ions to diffuse down their electrochemical gradient via protein pores, channels, or carrier transporters without consuming metabolic energy.

Primary Active Transport

The uphill movement of a solute against its electrochemical gradient directly powered by an exergonic chemical reaction, most commonly the hydrolysis of ATP.

Secondary Active Transport

The active accumulation of a solute against its concentration gradient achieved by coupling its transport to the downhill flow of a secondary ion moving along an established electrochemical gradient.