Biochemistry Glossary

The specific region of an enzyme where substrate molecules bind and undergo a chemical reaction. The shape and chemical properties of the active site are complementary to the substrate, following the induced-fit model.

An organic molecule containing an amino group, a carboxyl group, a hydrogen atom, and a variable R group (side chain) attached to a central alpha-carbon. Twenty standard amino acids serve as the building blocks of proteins.

The set of metabolic pathways that construct complex molecules from simpler ones, requiring an input of energy typically in the form of ATP. Examples include protein synthesis, gluconeogenesis, and fatty acid synthesis.

The set of metabolic pathways that break down complex molecules into simpler ones, releasing energy that is captured as ATP or reduced coenzymes (NADH, $\text{FADH}_2$). Examples include glycolysis, beta-oxidation, and the citric acid cycle.

A small organic molecule, often derived from a vitamin, that transiently associates with an enzyme and participates in the reaction by carrying chemical groups between enzymes. Examples include $\text{NAD}^+$, FAD, and coenzyme A.

The loss of a protein's native three-dimensional structure due to disruption of non-covalent interactions by heat, extreme pH, detergents, or other agents. Denatured proteins typically lose their biological function.

A series of membrane-bound protein complexes (Complexes I-IV) and mobile electron carriers in the inner mitochondrial membrane that transfer electrons from NADH and $\text{FADH}_2$ to molecular oxygen, pumping protons to create the gradient used for ATP synthesis.

A biological catalyst, usually a protein, that accelerates a specific chemical reaction by lowering the activation energy. Enzymes are highly specific, regulated, and not consumed in the reactions they catalyze.

A long hydrocarbon chain with a terminal carboxyl group that serves as a major component of lipids. Fatty acids can be saturated (no double bonds) or unsaturated (one or more double bonds) and are a rich source of metabolic energy via beta-oxidation.

A highly branched polysaccharide of glucose that serves as the principal storage form of carbohydrate energy in animals, found mainly in the liver and skeletal muscle. It is rapidly mobilized by glycogen phosphorylase when blood glucose levels fall.

A ten-step cytoplasmic metabolic pathway that converts glucose into two molecules of pyruvate, producing a net gain of 2 ATP and 2 NADH. It is the most ancient and universal energy-yielding pathway and operates under both aerobic and anaerobic conditions.

The tendency of nonpolar molecules or nonpolar portions of molecules to aggregate in aqueous solution, minimizing their contact with water. Hydrophobic interactions are a major driving force in protein folding and membrane assembly.

An enzyme that catalyzes the structural rearrangement of a molecule, converting it from one isomer to another without adding or removing atoms. Examples include phosphoglucose isomerase in glycolysis and triose phosphate isomerase.

The substrate concentration at which an enzyme-catalyzed reaction proceeds at half its maximum velocity ($V_{max}$). It is an inverse measure of enzyme-substrate affinity; a lower $K_m$ indicates tighter binding between the enzyme and substrate.

A diverse group of hydrophobic or amphipathic biological molecules including fats, phospholipids, steroids, and waxes. Lipids serve as energy storage, structural components of membranes, and signaling molecules.

A single-stranded RNA molecule transcribed from DNA that carries the genetic code from the nucleus to the ribosome, where it serves as the template for protein synthesis during translation.

Nicotinamide adenine dinucleotide (reduced form), a key electron carrier in cellular metabolism. NADH is produced during glycolysis, the citric acid cycle, and other oxidative reactions, and donates its electrons to Complex I of the electron transport chain. Its oxidized form is $\text{NAD}^+$.

The monomer unit of nucleic acids, consisting of a nitrogenous base (purine or pyrimidine), a five-carbon sugar (ribose or deoxyribose), and one or more phosphate groups. Nucleotides form the building blocks of DNA and RNA.

The loss of electrons from a molecule, often accompanied by the loss of hydrogen atoms or the gain of oxygen. In metabolic pathways, oxidation reactions are coupled with reduction reactions (redox reactions) to transfer energy.

An amphipathic lipid molecule consisting of a glycerol backbone, two fatty acid tails (hydrophobic), and a phosphate-containing head group (hydrophilic). Phospholipids spontaneously form bilayers in aqueous environments, providing the structural basis of biological membranes.

A three-carbon molecule that is the end product of glycolysis. Under aerobic conditions, pyruvate enters the mitochondrion and is converted to acetyl-CoA by pyruvate dehydrogenase. Under anaerobic conditions, it is reduced to lactate or ethanol.

A large molecular machine composed of ribosomal RNA and proteins that catalyzes protein synthesis (translation). Ribosomes read the mRNA sequence and link amino acids together in the order specified by the codons.

The specific reactant molecule upon which an enzyme acts. The substrate binds to the enzyme's active site, where it is converted into product(s). Enzyme specificity is determined by the complementarity between the active site and the substrate.

The process by which RNA polymerase synthesizes a complementary RNA strand from a DNA template. In eukaryotes, the primary transcript (pre-mRNA) undergoes processing including 5' capping, 3' polyadenylation, and splicing before being exported as mature mRNA.

The maximum rate of an enzyme-catalyzed reaction, achieved when all enzyme active sites are saturated with substrate. $V_{max}$ is directly proportional to the total enzyme concentration and reflects the catalytic capacity of the enzyme.