Biochemistry, Cell Energetics, and Metabolic Pathways

Comprehensive vocabulary flashcards covering biomolecules, membrane dynamics, thermodynamics, enzyme kinetics, cellular respiration, fermentation, and photosynthesis based on lecture and recitation materials.

Organic Molecules

Carbon-based molecules that contain carbon covalently bonded to hydrogen ($\text{C}-\text{H}$ covalent bonds), typically forming hydrocarbon chains or rings such as glucose, amino acids, and lipids.

Inorganic Molecules

Molecules that lack covalent $\text{C}-\text{H}$ bonds (e.g., $H_2O$, $\text{NaCl}$, and $O_2$). Note that $CO_2$ contains carbon but lacks $\text{C}-\text{H}$ bonds, classifying it as inorganic.

Dry Cellular Biomass Composition

The four major molecular components of dry cellular biomass: proteins ($\sim 55\%$ dry weight), nucleic acids / RNA and DNA ($\sim 23\%$ total), lipids ($\sim 9\%$), and polysaccharides / carbohydrates ($\sim 9\%$).

Proteins

Macromolecular polymers composed of 20 amino acid monomer subunits linked by covalent peptide bonds, containing C, H, O, N, and S, functioning in enzyme catalysis, structural integrity, molecular transport, and signaling.

Nucleic Acids

Macromolecules composed of nucleotide monomers (NTPs/dNTPs) joined by phosphodiester bonds, containing C, H, O, N, and P, which function in genetic inheritance (DNA), protein translation (RNA), and cellular energy transfer (ATP).

Carbohydrates

Molecules formed from monosaccharide monomers linked by glycosidic bonds with an elemental ratio of C, H, and O of $1:2:1$, functioning as primary cellular fuels (glycogen/starch) and structural cell wall components (cellulose/chitin).

Lipids

Hydrophobic biomolecules assembled from glycerol and fatty acids via ester or ether linkages (containing C, H, O, and P in phospholipids), functioning as membrane permeability barriers, dense long-term energy reserves, and signaling molecules.

Primary Protein Structure ($1^\circ$)

The linear sequence of amino acids joined covalently by peptide bonds between adjacent carboxyl and amino groups.

Secondary Protein Structure ($2^\circ$)

Local conformations consisting of $\alpha$-helices and $\beta$-pleated sheets stabilized exclusively by hydrogen bonds between polypeptide backbone atoms ($C=O$ and $N-H$).

Tertiary Protein Structure ($3^\circ$)

The overall three-dimensional monomeric conformation governed by R-group interactions, including hydrophobic interactions, van der Waals forces, ionic bonds, hydrogen bonds, and covalent disulfide bridges between cysteine residues.

Quaternary Protein Structure ($4^\circ$)

The spatial association of two or more polypeptide subunits held together by non-covalent R-group interactions and covalent disulfide bonds.

Fluid Mosaic Model

A biological membrane model describing a dynamic phospholipid bilayer embedded with integral and peripheral proteins; lipids and proteins diffuse rapidly laterally within a leaflet, but spontaneous flip-flop between leaflets is extremely rare without flippase enzymes.

Archaeal Membrane Lipids

Membrane lipids consisting of a glycerol-1-phosphate backbone, ether linkages, and branched isoprenoid (phytanyl) chains, arranged as a bilayer or a heat-resistant tetraether monolayer.

Bacterial and Eukaryotic Membrane Lipids

Membrane lipids consisting of a glycerol-3-phosphate backbone, ester linkages, and unbranched fatty acid chains arranged in a bilayer (with eukaryotes incorporating sterols).

Membrane Fluidity Modulators

Structural factors controlling bilayer viscosity: cis double bonds in unsaturated fatty acids and shorter tails increase fluidity, saturated fatty acids decrease fluidity, and cholesterol hinders lipid movement at high temperatures while preventing tight packing at low temperatures.

Osmosis

The net physical movement of water across a selectively permeable membrane from an area of low solute concentration (high free water) toward an area of high solute concentration (low free water).

Hypertonic Environment

An external solution having a solute concentration higher than the cell interior, causing net water efflux and resulting in cellular crenation in animal cells or plasmolysis in plant cells.

Hypotonic Environment

An external solution having a solute concentration lower than the cell interior, causing water to enter the cell and leading to cell swelling or lysis (while maintaining turgor in walled plant cells).

Facilitated Diffusion

Passive transport down a concentration gradient requiring channel or carrier proteins without energy input; displays hyperbolic kinetics that plateau at $V_{\text{max}}$ when transporting polar or charged solutes such as glucose and ions.

Active Transport

The movement of solutes against their concentration gradient requiring transmembrane protein pumps and metabolic energy input (ATP hydrolysis in primary active transport; electrochemical ion gradients in secondary active transport), characterized by hyperbolic saturable kinetics.

Second Law of Thermodynamics

The thermodynamic principle stating that every spontaneous process increases universal entropy ($\Delta S_{\text{universe}} > 0$); cells create internal order by consuming environmental energy and releasing unusable heat and waste.

Exergonic Reaction

A spontaneous chemical reaction characterized by a negative change in Gibbs free energy ($\Delta G < 0$) that proceeds forward and releases usable free energy.

Endergonic Reaction

A non-spontaneous chemical reaction with a positive change in Gibbs free energy ($\Delta G > 0$) that requires energy input to proceed forward and proceeds backward spontaneously.

Catalyst / Enzyme Function

A biological agent that increases reaction rates by lowering the activation energy barrier ($E_a$) via transition state stabilization, without altering $\Delta G$, reactant free energy, product free energy, or reaction equilibrium.

Michaelis Constant ($K_m$)

The substrate concentration at which an enzymatic reaction reaches half of its maximal velocity ($\frac{1}{2}V_{\text{max}}$), where a lower value reflects higher enzyme-substrate affinity.

Competitive Inhibitor

An inhibitor that competes directly with the substrate for the enzyme active site, increasing the apparent $K_m$ while leaving $V_{\text{max}}$ unchanged; overcome by high substrate concentrations.

Noncompetitive Inhibitor

An inhibitor that binds to an allosteric site rather than the active site, reducing $V_{\text{max}}$ while leaving $K_m$ unchanged; cannot be overcome by adding excess substrate.

Allosteric Regulation

The modification of enzymatic activity caused by the binding of an effector molecule to an allosteric site away from the active site, altering affinity ($K_m$) or activity ($V_{\text{max}}$) and generating sigmoidal kinetic curves in multi-subunit enzymes.

Oxidation and Reduction

Coupled redox processes where oxidation is the loss of electrons (loss of H atoms, gain of O bonds) and reduction is the gain of electrons (gain of H atoms, loss of O bonds).

$\text{NAD}^+$ / NADH

A soluble mobile coenzyme that accepts $2\,e^-$ and $1\,H^+$ during catabolic nutrient oxidation to become NADH, transporting these high-energy electrons directly to Complex I of the electron transport chain.

Electron Transport Chain (ETC)

A sequence of membrane-bound multiprotein complexes (I $\rightarrow$ III $\rightarrow$ IV) that couples exergonic electron transfer to active proton ($H^+$) pumping into the intermembrane or periplasmic space to establish a proton motive force.

Uncouplers (e.g., DNP, Thermogenin)

Compounds that create proton leaks across the inner mitochondrial membrane, dissipating the proton motive force without ATP synthase activity, dissipating energy as heat while accelerating ETC activity and $O_2$ consumption.

Chemiosmosis and ATP Synthase

The mechanism wherein protons flow down their electrochemical gradient through the $F_0$ rotor channel of ATP synthase, driving mechanical shaft rotation that induces conformational changes in the $F_1$ domain to synthesize ATP from ADP and $P_i$.

Substrate-Level Phosphorylation

The direct enzymatic transfer of a phosphate group from a high-energy phosphorylated metabolic substrate to ADP, generating ATP in glycolysis and the citric acid cycle with low overall yield.

Oxidative Phosphorylation

The indirect synthesis of ATP across the inner mitochondrial membrane where electron transport drives chemiosmosis via ATP synthase, producing approximately $90\%$ of total cellular ATP ($\sim 26-28\text{ ATP}$ per glucose).

Glycolysis

A 10-step catabolic pathway occurring in the cytosol that converts $1\text{ glucose } (6\text{C})$ into $2\text{ pyruvate } (3\text{C})$, producing a net yield of $2\text{ ATP}$ via substrate-level phosphorylation and $2\text{ NADH}$.

Pyruvate Oxidation

The conversion of $2\text{ pyruvate}$ into $2\text{ acetyl-CoA}$ and $2\,CO_2$ inside the mitochondrial matrix (or cytosol in prokaryotes), yielding $2\text{ NADH}$ and $0\text{ ATP}$.

Citric Acid Cycle

A series of reactions in the mitochondrial matrix (or cytosol in prokaryotes) that completely oxidizes $2\text{ acetyl-CoA}$ into $4\,CO_2$, producing $6\text{ NADH}$, $2\text{ FADH}_2$, and $2\text{ ATP/GTP}$ via substrate-level phosphorylation per glucose.

Fermentation

An anaerobic metabolic pathway in which NADH transfers electrons to an organic molecule (such as pyruvate or acetaldehyde) solely to regenerate $\text{NAD}^+$ and sustain glycolysis without an electron transport chain.

Fermentation End Products

The distinct organic outputs of anaerobic glycolysis: yeast cells produce ethanol and $CO_2$, whereas mammalian muscle cells produce lactate (lactic acid).

Beta-Oxidation ($\beta$-Oxidation)

The catabolic breakdown of fatty acids within the mitochondrial matrix, cleaving hydrocarbon chains into 2-carbon acetyl-CoA units along with NADH and $\text{FADH}_2$ to fuel the citric acid cycle and ETC.

Deamination

The removal of amino groups from amino acids (excreted as urea or ammonia), allowing the remaining carbon skeletons to enter cellular respiration as pyruvate, acetyl-CoA, or citric acid cycle intermediates.

Phosphofructokinase-1 (PFK-1)

The primary regulatory enzyme of glycolysis that is inhibited via feedback inhibition by high levels of ATP and citrate, and activated allosterically by high levels of AMP and ADP.

Endosymbiotic Evidence of Mitochondria

Structural and evolutionary markers indicating mitochondria arose from engulfed aerobic bacteria: a double membrane with cardiolipin, their own circular DNA, antibiotic-sensitive 70S ribosomes, and division by binary fission.

Secondary Production

The generation of biomass from preformed organic material by heterotrophic organisms (secondary producers).

Photosystem II (PSII / P680)

A photosystem whose oxidized reaction center ($\text{P680}^+$) splits $H_2O$ to evolve $O_2$ and release $H^+$ into the thylakoid lumen, transferring electrons through pheophytin and plastoquinone (PQ) to cytochrome $b_6f$.

Photosystem I (PSI / P700)

A photosystem whose reaction center (P700) receives electrons from plastocyanin and re-energizes them via absorbed photons, delivering electrons to ferredoxin and $\text{NADP}^+$ reductase to produce NADPH in the stroma.

Linear Electron Flow (Non-Cyclic)

The one-way light reaction pathway: $H_2O \rightarrow \text{P680} \rightarrow \text{pheophytin} \rightarrow \text{plastoquinone} \rightarrow \text{cytochrome } b_6f \rightarrow \text{plastocyanin} \rightarrow \text{P700} \rightarrow \text{ferredoxin} \rightarrow \text{NADP}^+ \text{ reductase} \rightarrow \text{NADPH}$, yielding ATP, NADPH, and $O_2$.

Cyclic Photophosphorylation

An alternate photosynthetic pathway wherein electrons from ferredoxin loop back to cytochrome $b_6f$, plastoquinone, and plastocyanin before returning to P700, generating a proton gradient that produces ATP only, without generating $O_2$ or NADPH.

Calvin Cycle

The light-independent stroma pathway that fixes $3\,CO_2$ using $9\text{ ATP}$ and $6\text{ NADPH}$ to generate a net yield of $1\text{ G3P}$ (3C sugar), returning $9\text{ ADP}$, $6\text{ NADP}^+$, and $P_i$ to the light reactions.

Rubisco

Ribulose-1,5-bisphosphate carboxylase/oxygenase; an enzyme capable of productive carbon fixation ($\text{RuBP} + CO_2 \rightarrow 2\text{ 3-PGA}$) and wasteful photorespiration ($\text{RuBP} + O_2 \rightarrow 1\text{ 3-PGA} + 1\text{ 2-phosphoglycolate}$) when stomata close.