LEHNINGER PRINCIPLES OF BIOCHEMISTRY - VOLUME 3. INFORMATION PATHWAYS - 2017

PART III. INFORMATION PATHWAYS

GLOSSARY

ABC transporter: a member of a large family of membrane-spanning transporters containing ATP-binding domains (cassettes); they transport various substrates across Cell/30.html">The Plasma Membrane, including inorganic ions, Lipids, and nonpolar drug molecules, using ATP as an energy source.

ADP (adenosine diphosphate): a ribonucleoside-5'-diphosphate; a phosphate group acceptor in cellular METABOLISM/26.html">Energy Metabolism.

ATP (adenosine triphosphate): a ribonucleoside-5'-triphosphate; a phosphate group donor in cellular energy metabolism; carries chemical energy in metabolic pathways; a common intermediate in coupled endergonic and exergonic reactions.

ATPase: an enzyme that hydrolyzes ATP to ADP and phosphate, typically participating in energy-requiring processes.

ATP synthase: an enzyme complex that forms ATP from ADP and phosphate during Oxidative Phosphorylation in The inner mitochondrial membrane or bacterial plasma membrane, as well as during Photophosphorylation in Chloroplasts.

B lymphocyte (B cell): a Blood cell responsible for antibody production.

cAMP receptor protein: a specific regulatory protein in Bacteria that controls the transcriptional initiation of enzyme genes, which allow The Cell to shift to alternative carbon sources when glucose is scarce; also known as catabolite activator protein.

C-terminal residue: the unique amino acid residue in a polypeptide sequence with a free a-carboxyl group.

Escherichia coli (E. coli): a common bacterium inhabiting the Small Intestine of vertebrates; one of the most thoroughly studied organisms.

GLUT: a family of Membrane Proteins responsible for glucose transport.

G proteins: a family of heterotrimeric GTP-binding proteins involved in transmembrane signaling. Ligand binding to a G protein-coupled receptor triggers the exchange of GTP for GDP, allowing the protein to activate the next enzyme in the signaling pathway. G proteins possess intrinsic GTPase activity and thus self-inactivate.

In situ: in place, i.e., in a natural Setting.

In vitro: "in Glass," i.e., in artificial conditions, in a test tube.

In vivo: "in life," i.e., in a living cell or Organism.

NAD, NADP (nicotinamide adenine dinucleotide

(NAD), nicotinamide adenine dinucleotide phosphate

(NADP)): nicotinamide-containing Cofactors that function as hydrogen and electron carriers in oxidation-reduction reactions.

P/O ratio: the number of moles of ATP formed in oxidative phosphorylation per reduction of ¹/₂ O₂ (i.e., per pair of electrons transferred to O₂). The P/O ratio is typically assumed to be 2.5 when electrons are transferred from NADH to O₂, and 1.5 when transferred from FADH to O₂ (or 3.0 and 2.0, respectively, in other textbooks).

pH: the negative logarithm of the hydrogen ion concentration in an aqueous solution.

pK_a: the negative logarithm of an acid dissociation constant.

R group: (1) designation for an alkyl group; (2) sometimes used to denote substituents in Organic compounds.

SELEX: a method for the rapid identification of nucleic acid sequences (usually RNA) with specific catalytic or ligand-binding properties.

SH2 domain: a protein domain that binds tightly to a phosphotyrosine residue in specific proteins, such as receptor Tyrosine Kinases, initiating the assembly of a protein complex involved in signal Transduction.

Siglec: a family of cell-surface Lectins that bind sialic acid; they contain multiple immunoglobulin-like domains.

SOS Response: the coordinated induction of a diverse set of genes in bacterial Cells in response to severe DNA damage.

STS marker: a short, unique DNA sequence at a specific locus that can be used for its identification.

T lymphocyte (T cell): a blood cell that originates in the Thymus and participates in cell-mediated Immunity.

V_max: the maximum velocity of an enzymatic reaction, achieved when the binding sites on all enzyme molecules are saturated with substrate.

A

Absolute configuration: the spatial arrangement of four different substituents around an asymmetric carbon atom, determined relative to the standard configurations of D- and L-glyceraldehyde.

Autotroph: an organism that synthesizes complex molecules from simple carbon and nitrogen sources, such as carbon dioxide and ammonia.

Agonist: a substance (typically a hormone or neurotransmitter) whose binding to a specific receptor triggers a physiological response.

S-Adenosylmethionine (adoMet): a cofactor involved in enzymatic Transmethylation reactions.

Adipocyte: an animal cell specialized for the storage of fats (triacylglycerols).

Activator: (1) a DNA-binding protein that enhances Gene Expression (i.e., increases The rate of Transcription) of one or more genes; (2) a positive modulator of an allosteric enzyme.

Amino Acid Activation: an ATP-dependent enzymatic reaction that forms an ester linkage between the carboxyl group of an Amino Acid and the 3'-hydroxyl group of its corresponding tRNA.

Active (catalytic) site: the region On the surface of an enzyme where the substrate binds and undergoes catalytic conversion.

Active Transport: the trans-membrane movement of solutes against a concentration gradient, driven by the expenditure of energy.

Actin: a protein found in Muscle fibers and an essential component of the Cytoskeleton in many Eukaryotic cells.

Proton acceptor: a base or anion capable of accepting a proton from a donor.

Electron acceptor: a chemical entity that accepts electrons during a redox reaction.

Acceptor control: the Regulation of cellular Respiration rate through fluctuations in ADP concentration, which acts as a phosphate group acceptor.

Alkalosis: a metabolic condition characterized by a reduced ability of the body to bind hydroxide ions, typically resulting in an elevated blood pH.

Allosteric protein: a protein (usually multisubunit) with multiple ligand-binding sites, where ligand binding at one site influences binding at the others.

Allosteric enzyme: a regulatory enzyme whose catalytic activity is modulated by the noncovalent binding of a specific metabolite (effector) at a site other than the Active Site.

Allosteric site: a specific region on The surface of an allosteric enzyme molecule where a modulator (effector) molecule binds.

Aldose: a monosaccharide in which the carbonyl carbon is part of an aldehyde group located at one end of the carbon chain.

Aminoacyl-tRNA: an aminoacyl derivative of tRNA.

Aminoacyl-tRNA synthetases: Enzymes that catalyze the synthesis of aminoacyl-tRNA at the expense of ATP energy.

α-Amino acid: an α-amino-substituted carboxylic acid, which serves as a structural unit of Peptides and Proteins.

Aminotransferases (transaminases): enzymes that catalyze The transfer of amino groups from α-Amino Acids to α-keto acids.

Ammoniotelic organism: an organism that excretes excess nitrogen in the form of ammonia.

Amphibolic pathway: a metabolic pathway involved in both Catabolic and anabolic processes.

Amphitropic protein: a protein that reversibly binds to The cell membrane and is therefore capable of residing in both the Cytosol and the membrane.

Amphiphilic compound: a compound containing both polar and nonpolar regions.

Ampholyte: a substance capable of acting as both an acid and a base.

Amphoteric substance: a substance capable of accepting and donating protons and, consequently, acting as an acid or a base depending on conditions.

Anabolism: the energy-requiring phase of Intermediary Metabolism involving The Biosynthesis of cellular components from simpler precursors.

Analyte: the substance being analyzed (e.g., in mass spectrometry).

Anammox: anaerobic Oxidation of ammonia to molecular nitrogen, utilizing nitrite as an electron acceptor; carried out by specialized chemolithotrophic bacteria.

Anaplerotic reaction: an enzymatic reaction that replenishes intermediates in The Citric Acid Cycle.

Anaerobe: an organism that lives in an oxygen-free environment; obligate anaerobes are killed in the presence of oxygen.

Anhydride: a Condensation product of two carboxyl or phosphate groups, formed with the release of a Water molecule;

Class="center">

Angstrom (Å): a unit of length. 1 Å = 10^-8 cm. Used to express distances at the atomic and molecular levels.

Anion-exchange resin: a polymer resin with fixed cationic groups; used for the Separation of anions by Ion-exchange Chromatography.

Anomeric carbon: the carbon atom at the chiral center formed during the cyclization of a sugar molecule to create a hemiacetal; for example, the carbonyl carbon in aldehydes and ketones.

Anomers: two stereoisomers of a given sugar that differ in configuration at the carbonyl (anomeric) carbon atom.

Antagonist: a molecule that interferes with the physiological action of another molecule (agonist), specifically by blocking the binding of a hormone or neurotransmitter to its receptor.

Antibiotics: a large group of organic compounds synthesized and secreted by various microorganisms and plants—where they presumably perform a protective function—that are toxic to other organisms.

Antigen: a molecule capable of inducing the Synthesis of specific Antibodies in a vertebrate organism.

Anticodon: a specific three-nucleotide sequence in a tRNA molecule that is complementary to the codon for a specific amino acid in an mRNA sequence.

Antiparallel arrangement: the alignment of two linear polymer chains with opposite polarity or orientation.

Antiporter: the simultaneous transport (cotransport) of two substances across a cell membrane in opposite directions.

Antibody: a protective protein synthesized by the vertebrate immune system. See also Immunoglobulin.

Apolipoprotein: the protein component of a lipoprotein.

Apoprotein: the protein moiety of a protein molecule lacking the organic or inorganic cofactors or prosthetic groups that may be required for its activity.

Apoptosis: programmed cell death in response to an external signal or internal genetic instructions, characterized by the systematic dismantling of cellular contents.

Apoenzyme: the protein component of an enzyme lacking the organic or inorganic cofactors or prosthetic groups that may be required for catalytic activity.

Golgi apparatus (complex): a system of membrane-bound Organelles in eukaryotic cells involved in the Post-translational Modification of Proteins and their secretion from the cell or incorporation into the plasma membrane and organelle membranes.

Aptamer: an oligonucleotide that binds specifically to molecular targets; obtained through affinity-based enrichment Methods (the SELEX process).

Arrestins: a family of proteins that bind to the phosphorylated C-terminal domains of G protein-coupled receptors, preventing receptor interaction with G proteins and thereby terminating signal transduction through these receptors.

Archaea: a domain of living organisms, many species of which inhabit extreme environments characterized by high salinity, high Temperature, or low pH.

Asymmetric carbon atom: a carbon atom covalently bonded to four different chemical groups; can exist in two distinct tetrahedral configurations.

Carbon assimilation: The sequence of reactions by which atmospheric CO2 is converted into organic compounds.

Attenuator: An RNA sequence involved in The regulation of certain gene expression; acts as a transcription terminator.

Auxin: A plant Growth Hormone.

Auxotrophic mutant (auxotroph): A mutant organism that has lost The ability to synthesize certain molecules and must obtain them from an external source.

Autophosphorylation: Strictly speaking, the phosphorylation of a protein's amino acid residues catalyzed by the protein itself; sometimes refers to the phosphorylation of one subunit of a homodimer by the other subunit.

Acidosis: A metabolic state accompanied by a decreased capacity of the organism to neutralize protons; typically associated with a drop in blood pH.

Acyl phosphate: Any molecule with the general formula

Aerobe: An organism that lives in an oxygen-rich atmosphere and uses oxygen as the terminal electron acceptor for respiration.

B

Bacteriophage (phage): A virus capable of replicating within a bacterial cell.

Bacteria: A kingdom of living organisms; bacteria are bounded by a plasma membrane but lack membrane-enclosed internal organelles and a nucleus.

Cytology/practical/49.html">White adipose tissue: Non-thermogenic adipose tissue with a high content of triacylglycerols, which are stored and released in response to hormonal signals. Electron transport in the mitochondrial Respiratory Chain of white Adipose tissue is directly coupled to ATP synthesis.

Protein Data Bank (PDB): An international database (www.rcsb.org/pdb) containing information on the three-dimensional structures of most known macromolecules.

Protein: A macromolecule consisting of one or more polypeptide chains, each with a specific sequence of amino acids linked by peptide bonds.

Uncompetitive inhibitor: A reversible inhibitor that binds to the enzyme-substrate complex but not to the free enzyme.

DNA library: A collection of cloned DNA fragments.

cDNA library: A DNA library consisting of synthesized cDNA molecules complementary to all mRNA molecules of a specific organism or cell type.

Bioassay: An analytical METHOD FOR DETERMINING The amount of a biologically active substance (e.g., a hormone) in a sample by quantitatively measuring its activity in vitro.

Bioinformatics: Computer-based analysis of biological data using statistical, linguistic, mathematical, chemical, and physical methods; such biological data frequently include amino acid or nucleotide sequences, structural data, clinical trial results, etc.

Biomolecule: An organic compound present in living organisms that performs a physiological function.

Biopterin: A pterin-based cofactor involved in enzymatic oxidation-reduction reactions.

De novo biosynthesis: A pathway for synthesizing a biomolecule (e.g., a nucleotide) from simple precursors, as an alternative to metabolite recycling.

Biosphere: All living matter on our planet, including that in the oceans and the atmosphere.

Biotin: A vitamin and enzymatic cofactor involved in carboxylation reactions.

Biocytin: A conjugated amino acid formed by a covalent (amide) bond between a Lysine residue and a biotin molecule.

Fermentation: A non-oxidative anaerobic breakdown of a nutrient (e.g., glucose) accompanied by energy release; fermentation products include lactate, ethanol, and Other Compounds.

Brown adipose tissue: Thermogenic adipose tissue rich in Mitochondria containing the uncoupling protein thermogenin, which interrupts the proton flow between the Respiratory Chain and ATP synthesis.

Buffer: A solution that can resist changes in system pH; prepared from a corresponding acid and base (acid-base pair, proton acceptor and donor) taken in a molar ratio of ~1.

B

Structure/103.html">Van der Waals interactions: Weak intermolecular interactions arising from the mutual polarization of molecules.

Vector: A DNA molecule capable of autonomous Replication in a host cell; insertion of a foreign DNA fragment into a vector enables the replication of that fragment; for example, a plasmid or artificial chromosome.

Vectorial metabolism: Metabolic transformations that result in A change in the localization (rather than The chemical composition) of a substrate relative to the plasma membrane or a membrane between two cellular compartments. Viral vector: Viral DNA modified so that it can be used to transfer recombinant DNA.

Vitamin: An organic compound required in small amounts by certain organisms; typically a component of a coenzyme.

Extracellular matrix: A complex network of glycosaminoglycans, Proteoglycans, and proteins located directly on the outer surface of the plasma

membrane; provides Cell Adhesion, recognition, and migration.

Extrahepatic tissues: All tissues other than Liver tissue; a term that highlights the crucial role of the liver in metabolism.

Hydrogen bond: A weak electrostatic attraction between an electronegative atom (such as oxygen or nitrogen) and a hydrogen atom covalently bonded to a second electronegative atom. Excited state: A high-energy state of an atom or molecule; generated when an atom or molecule absorbs light energy. Reducing agent (reductant): An electron donor in a redox reaction.

Reducing end: the end of a polysaccharide chain that features a free anomeric carbon atom; this terminal residue can act as a reducing agent. Reducing sugar: a sugar molecule containing a carbonyl (anomeric) carbon atom that does not participate in a glycosidic bond and is therefore susceptible to oxidation. Reducing equivalent: a general term designating electrons or electron equivalents in the form of a hydrogen atom or hydride ion.

Fluorescence recovery after photobleaching (FRAP): a quantitative method for analyzing the diffusion of membrane components (lipids or proteins) within a bilayer.

Reduction (half-reaction): The addition of electrons to an atom or ion.

Half-life: the time required for half of a given substance in a system to decay.

Absorption: the process by which Digestion products are transferred from the intestine into the blood.

Accessory pigments: pigments found in plants and photosynthetic bacteria, active in the visible region of the solar spectrum (carotenoids, xanthophylls, and phycobilins), that Complement the function of chlorophylls in absorbing solar energy.

Secondary structure: the local spatial conformation of a segment of a polypeptide or polynucleotide chain.

Secondary Metabolism: metabolic pathways that lead to The formation of specialized products not found in all living cells.

Secondary messenger: an effector molecule synthesized within a cell in response to an external signal (primary messenger), such as a hormone.

Second law of Thermodynamics: the law stating that any chemical and physical processes in a closed system are accompanied by an increase in Entropy.

Code degeneracy: the capacity to represent a single element (word) in one language using multiple elements (words) of another language; the degeneracy of The Genetic Code lies in the fact that Certain amino acids are encoded by multiple nucleotide triplets.

High-Performance Liquid Chromatography (HPLC): an automated chromatographic method for separating substances under high pressure; the technique ensures reproducible results and allows the separation of highly similar substances.

G

Gametes: reproductive cells with a haploid set of genes; spermatozoa and egg cells. Gangliosides: Sphingolipids containing complex oligosaccharide HEAD groups; predominantly found in Nervous Tissue.

Haploid cell: a cell containing a single set of Genetic information, i.e., one chromosome of each type.

Hapten: a small molecule that can elicit an Immune Response when attached to a larger carrier molecule.

Hexose: a six-carbon carbohydrate (sugar).

Helicase: an enzyme that catalyzes the unwinding of DNA strands prior to replication.

Heme: an iron-porphyrin prosthetic group found in certain proteins.

Hemoprotein: a protein containing heme as a prosthetic group.

Hemoglobin: a heme-containing protein found in erythrocytes; an oxygen transporter.

Gene: a segment of a chromosome that encodes a specific functional polypeptide chain or RNA molecule. Tumor suppressor gene (antioncogene): a gene encoding a protein that negatively regulates Cell Division; defects in both copies of the gene lead to uncontrolled division and tumor transformation of the cell. Genetic information: hereditary information encoded by the sequence of nucleotide bases in chromosomal DNA or RNA.

Genetic map: a schematic representation of the relative positions of specific sequences and genes on a chromosome.

Genetic code: the set of DNA (mRNA) triplets that encode Proteinogenic Amino Acids.

Genome: all the genetic information encoded within a cell or virus.

Genomics: The branch of science that studies the genomes of cells and organisms.

Genomic library: A DNA library containing DNA fragments that represent the entire (or nearly entire) genome sequence of an organism.

Genotype: The genetic makeup of an organism, as opposed to its physical characteristics (phenotype). Geometric isomers (cis/trans isomers): Isomers that differ in the spatial arrangement of substituent groups with respect to a double bond.

Heparan sulfate: A sulfated polymer consisting of alternating units of N-acetylglucosamine and uronic acid (glucuronic or iduronic acid); a component of the extracellular matrix. Hepatocyte: The principal cell type of the liver.

DNA heteroduplex: A DNA duplex containing complementary strands derived from two different DNA molecules with similar sequences; frequently formed as a product of genetic recombination. Heteropolysaccharide: A polysaccharide consisting of multiple types of monosaccharide units. Heterotropic modulator: An allosteric modulator that is different from the normal ligand.

Heterotropic enzyme: An allosteric enzyme that requires a modulator different from its normal substrate.

Heterotroph: An organism that requires complex organic molecules (such as glucose) as sources of nutrients and energy.

Hyaluronate (hyaluronic acid): A high-molecular-weight acidic polysaccharide typically composed of GlcUA (β1 —> 3) GlcNAc disaccharide units; a major component of the extracellular matrix that forms large complexes (proteoglycans) with proteins and other acidic Polysaccharides.

Hydronium ion (Н₃O⁺): A hydrated proton.

Hydrolases: Enzymes (proteases, lipases, Phosphatases, Nucleases) that catalyze Hydrolysis reactions.

Hydrolysis: The Cleavage of a covalent bond (such as an anhydride or peptide bond) by the addition of a water molecule, yielding two or more products.

Hydropathic index: A scale reflecting the relative Hydrophobicity and hydrophilicity of chemical groups.

Hydrophilicity: The presence of polarity or charge that promotes the interaction of molecules or chemical groups with water (including their dissolution).

Hydrophobicity: The absence of polarity, which prevents molecules from dissolving in water.

Hydrophobic interactions: The association of nonpolar molecular groups in aqueous solution, driven by the tendency of surrounding water molecules to seek a thermodynamically more stable (disordered) state.

Hyperchromic effect: A substantial increase in Light absorption at 260 nm that occurs when the DNA double helix unwinds (melts). Hypoxia: A metabolic state caused by oxygen deficiency.

Histones: A family of basic proteins tightly bound to DNA in the Chromosomes of eukaryotic cells. Glycan: Synonym for polysaccharide; a polymer consisting of monosaccharide units linked by glycosidic bonds.

Glycogenesis: The process of converting glucose into Glycogen. Glycogenin: A protein that initiates glycogen chain synthesis and catalyzes the polymerization of the first few units in each chain before glycogen synthase takes over.

Glycogenolysis: The enzymatic breakdown of stored (non-dietary) glycogen.

Glycosaminoglycan: A heteropolysaccharide composed of two alternating units, one of which is N-acetylglucosamine or N-acetylgalactosamine and the other is a uronic acid (most commonly glucuronic acid); formerly called a mucopolysaccharide.

Glycosidic bond: A bond linking a sugar to another molecule (typically an alcohol, purine, pyrimidine, or another sugar) via an oxygen atom (O-glycosidic bond) or a nitrogen atom (N-glycosidic bond).

Glycoconjugate: A glycoprotein or glycolipid consisting of a carbohydrate moiety covalently linked to a protein or lipid.

Glycolysis: A catabolic pathway in which a glucose molecule is broken down into two Pyruvate molecules.

Glycolipid: A lipid containing a carbohydrate component.

Glycomics: The systematic Analysis of the carbohydrate complement of a cell or tissue, including components attached to proteins or lipids.

Glycoprotein: A protein containing a carbohydrate component.

Glyoxylate cycle: An alternative pathway of The Citric Acid cycle found in bacteria and certain plants, which converts acetate into succinate and ultimately into a new carbohydrate.

Glyoxysome: A specialized peroxisome containing the enzymes of The glyoxylate cycle; found in the cells of germinating seeds.

Glycerophospholipids: Amphiphilic lipids based on a glycerol backbone, in which Fatty acids are attached via ester bonds to the C1 and C2 carbon atoms of glycerol, and polar alcohols are attached via a phosphodiester bond to the C3 atom.

Globular proteins: Soluble proteins with a globular (spherical) conformation.

Glucogenic amino acids: Amino acids whose carbon skeletons can be converted into glucose or glycogen via Gluconeogenesis.

Gluconeogenesis: The biosynthesis of CARBOHYDRATES from simpler non-carbohydrate precursors, such as oxaloacetate or pyruvate.

Homeobox: A conserved 180-base-pair DNA sequence that encodes a protein domain found in many regulatory proteins involved in developmental processes.

Homeodomain: A regulatory protein domain that determines embryonic segmentation; encoded by a homeobox.

Homeostasis: The maintenance of a dynamic steady state through regulatory mechanisms that compensate for changes induced by external stimuli.

Homeotic genes: Genes that regulate The Development of embryonic segments in Drosophila; similar genes have been identified in most vertebrates.

Homologous genetic recombination: Recombination between two DNA molecules with similar sequences, occurring in all cells; in eukaryotes, it takes place during Mitosis and Meiosis. Homologous proteins: proteins from different organisms that share similar sequences and functions (e.g., Hemoglobins).

Homopolysaccharide: A polysaccharide composed of identical monosaccharide units.

Homotropic modulator: An allosteric modulator that is identical to the normal ligand.

Homotropic enzyme: An allosteric enzyme for which the substrate simultaneously acts as a modulator.

Hormone: A chemical compound synthesized in small amounts by Endocrine glands and transported via the blood to other tissues, where it regulates their function by acting as a chemical messenger. Gram-mole: A unit of the amount of substance, numerically equal to the molecular mass of that substance in grams. Granum: A stack of thylakoids (flattened membranous sacs or disks) within chloroplasts.

D

Dalton: A unit of atomic and molecular mass; 1 Da (1.66 • 10^-24 g) corresponds to the mass of a hydrogen atom.

Double helix: The native conformation of two complementary antiparallel DNA strands.

Lipid bilayer: The ordered arrangement of amphiphilic lipid molecules that forms the structural basis of Introduction/36.html">Biological Membranes, in which the hydrocarbon "tails" of the molecules point inward, creating a continuous nonpolar core.

Double-reciprocal plot (Lineweaver-Burk plot): A graphical representation in which 1/V₀ is plotted against 1/[S] instead of V₀ versus [S], used for a more accurate determination of V_max and K_m values.

Two-component signal transduction system: A signaling system in bacteria and plants comprising a receptor Histidine kinase that, upon ligand binding, autophosphorylates specific internal histidine residues and subsequently catalyzes the transfer of a phosphoryl group to the second component of the system—the response regulator—which in turn activates the transcription of a gene or a group of genes.

Diprotic acid: An acid capable of releasing two protons upon dissociation.

Dehydrogenases: Enzymes that catalyze the removal of two hydrogen atoms from a substrate molecule.

Deamination: The enzymatic removal of amino groups from Biomolecules, such as amino acids or NUCLEOTIDES.

Deoxyribonucleotides: nucleotides containing 2-deoxy-D-ribose as their pentose component.

Deletion Mutations: mutations resulting from the deletion (removal) of one or more nucleotides from a gene or chromosome.

Denaturation: the complete or partial unfolding of a polypeptide chain, protein, or nucleic acid, leading to the loss of the molecule's biological function.

Desaturases: enzymes that catalyze the Introduction of a double bond into the hydrocarbon chain of a fatty acid molecule.

Desensitization: a universal process involving the attenuation of a cellular response upon prolonged exposure to a specific stimulus.

Desolvation: the removal of the Hydration shell surrounding a solute in an aqueous solution.

Dialysis: the removal of small molecules (low-molecular-weight substances) from a macromolecular solution by passing the solution through a semipermeable membrane.

Wild type: the normal (non-mutated) genotype or phenotype.

Diploid cell: a cell containing a double set of genetic information (two chromosomes of each type).

Disaccharide: a carbohydrate consisting of two monosaccharide units linked by a covalent bond.

Disulfide bond: a covalent bond formed under oxidizing conditions between two Cys residues of the same or different polypeptide chains, resulting in the formation of cystine.

Differential centrifugation: the separation of cell organelles or other particles of different sizes based on differences in their sedimentation rates during centrifugation.

Cell Differentiation: the transformation of precursor cells into specialized cells through the synthesis of new proteins and RNA.

Differentiation: the acquisition of specific Structural and functional features by a cell during GROWTH AND DEVELOPMENT.

Diffusion: the movement of solute molecules from a region of higher concentration to a region of lower concentration.

DNA (deoxyribonucleic acid): a polynucleotide with a specific sequence of deoxyribonucleotide units covalently linked by 3',5'-phosphodiester bonds; the repository of genetic information.

DNA ligase: an enzyme that catalyzes the formation of a phosphodiester bond between the 3' end of one DNA fragment and the 5' end of another.

DNA microarray: an array of DNA fragments positioned in a predetermined manner and immobilized on a solid support, used for Hybridization with target DNA sequences.

DNA polymerase: an enzyme that catalyzes the template-directed synthesis of DNA from deoxyribonucleoside-5'-triphosphates.

Domain: a clearly identifiable structural unit of a polypeptide; domains can perform independent functions and fold independently.

Proton donor: an acid or other chemical compound that donates protons in an acid-base reaction.

Electron donor: a substance that donates electrons during a redox reaction.

Respiration: any metabolic process accompanied by the consumption of oxygen and the release of carbon dioxide.

Respiratory chain: the Electron Transport Chain; a sequence of proteins in aerobic cells that transfer electrons from substrates to molecular oxygen.

Ж

Flagellum: a cellular appendage used for locomotion; bacterial flagella have a much simpler structure than eukaryotic flagella, which resemble cilia.

Iron-sulfur protein: a member of a large family of electron-transfer proteins in which electron transfer is mediated by iron atoms coordinated to inorganic sulfur atoms and the sulfur atoms of Cys residues within the protein.

Rieske iron-sulfur protein: an iron-sulfur protein in which two ligands to the central iron ion are provided by the side chains of His residues; it participates in numerous electron-transfer processes, including OXIDATIVE PHOSPHORYLATION AND photophosphorylation.

Iron-sulfur center (cluster): a prosthetic group in certain proteins involved in electron transfer; Fe²⁺ or Fe³⁺ is coordinated to inorganic sulfur and the sulfur atom of a Cys residue in the protein.

Bile salts: amphiphilic steroid derivatives that act as detergents and play a key role in the DIGESTION AND ABSORPTION of Lipids.

Fluid Mosaic Model: a model that views the biological membrane as a fluid lipid bilayer with embedded proteins; such a bilayer exhibits both structural and functional Asymmetry.

Fatty acid: an aliphatic carboxylic acid found in natural fats and oils; a structural component of membrane Glycolipids and Phospholipids.

Adipose tissue: a specialized Connective Tissue that stores large amounts of triacylglycerols; see also White adipose tissue; Brown adipose tissue.

I

Law of mass action: the rate of a chemical reaction is proportional to the product of the concentrations (or activities) of the reacting substances.

Closed system: a system that exchanges neither matter nor energy with its surroundings.

Nonessential amino acids: amino acids that can be synthesized by humans and other vertebrates from simple precursors and therefore do not need to be supplied in the diet.

Substitution mutation: a mutation caused by the replacement of one base by another.

Germ cell: an animal cell set aside at an early stage of Embryogenesis; it can divide by mitosis or undergo meiosis to give rise to gametes (sperm and egg cells).

Green fluorescent protein (GFP): a small protein from a marine organism that exhibits bright green fluorescence in the visible spectrum. Fusion proteins with GFP are widely used to determine the Intracellular Localization of proteins via Fluorescence Microscopy.

Zymogen: an inactive enzyme precursor; for example, the precursor to Pepsin is pepsinogen.

Probe: a labeled nucleic acid fragment containing a sequence complementary to a target gene or genomic sequence, used for hybridization.

I

Free-energy change (∆G): the amount of Free energy released (∆G <0) or absorbed (∆G> 0) during a reaction proceeding at constant temperature and pressure.

Enthalpy change (∆Н): in a chemical reaction, approximately equal to the difference between the energy required to break existing bonds and The energy released upon the formation of new bonds.

Isomerases: enzymes that catalyze the interconversion of positional isomers.

Isomers: molecules with the same molecular formula but different arrangements of chemical groups.

Isoprene: 2-methyl-1,3-butadiene, the repeating structural unit of Isoprenoids (terpenoids).

Isoprenoid (terpenoid): a member of a large class of natural compounds synthesized enzymatically from two or more isoprene units.

Isothermal conditions: constant temperature.

Isotopes: stable or radioactive atoms of the same chemical element. Isotopes of a given element share the same nuclear charge but have different atomic masses while remaining identical in their chemical properties. They are commonly used as tracers in chemical analysis.

Isoenzymes (isozymes): Multiple Forms of an enzyme that catalyze the same reaction but differ in Amino Acid Sequence, substrate Specificity, V_mах value, or regulatory properties.

Isoelectric focusing: an electrophoretic method for separating macromolecules based on differences in their isoelectric points.

Isoelectric point: the pH value at which the net electrical charge of a molecule is zero, rendering the molecule stationary in an electric field.

Immune response: the ability of a vertebrate organism to synthesize antibodies against macromolecules (Antigens) that are foreign to the body.

Immunoglobulin (antibody): a protein synthesized in response to the introduction of an antigen into the organism and capable of binding to it specifically.

Feedback inhibition (end-product inhibition): the inhibition of The activity of an enzyme operating at the early stage of a metabolic pathway by the end-product of that entire pathway.

Inhibitory G protein (G_i): a trimeric GTP-binding protein that, upon activation by an associated receptor in the plasma membrane, proceeds to inhibit adjacent membrane-bound enzymes such as adenylyl cyclase; its action is opposite to that of G_s.

Inducer: a signaling molecule that binds to a regulatory protein, thereby enhancing the expression of the corresponding gene.

Induction: the upregulation of GENE EXPRESSION IN response to a change in regulatory protein activity.

Induced fit: the conformational change of an enzyme upon substrate binding that shifts the enzyme into a catalytically active state; a model describing Conformational Changes in any macromolecule in response to ligand binding, whereby the macromolecule's binding site becomes more complementary to the ligand's shape.

Initiation complex: a complex comprising a ribosome, mRNA, and an initiator Met-tRNA^Met or fMet-tRNA^Met, ready for the elongation phase.

Insertion mutation: a mutation caused by the insertion of one or more Base Pairs into a DNA sequence.

Insertion sequence (IS element): Mobile Genetic Elements typically flanked by specific inverted repeats on both sides.

Integral protein: a protein firmly attached to a membrane via hydrophobic interactions (as opposed to a peripheral protein).

Integrin: a member of a large family of heterodimeric transmembrane proteins that mediate cell-cell and cell-extracellular matrix adhesion.

Intercalating agent: a substance (mutagen) that inserts itself between adjacent nucleic acid bases, causing a reading frameshift.

Intercalation: the insertion of a molecule between aromatic or planar ring systems, such as between two adjacent nucleic acid bases.

Interferons: a class of Glycoproteins exhibiting antiviral activity.

Intron: a nucleotide sequence located between exons that is transcribed but removed prior to Translation.

Informational macromolecules: biomolecules that store information in the form of specific monomer sequences, such as proteins, lipids, polysaccharides, and Nucleic Acids.

Ionizing radiation: a type of radiation (e.g., X-rays) that induces electron loss in certain molecules, thereby enhancing their reactivity.

Ion product of water (К_w): the product of the concentrations of Н⁺ and ОН^- ions in pure water.

К_w = [Н⁺][ОН^-] = 1 • 10^-14 at 25 °С.

Ion channel: an integral protein that facilitates the regulated transport of specific ions across the cell membrane.

Ion-exchange resin: A polymer resin containing immobilized charged groups; used in chromatography to separate ionic compounds.

Ionophore: A compound that binds one or more Metal Ions and diffuses across a membrane, transporting the bound ion.

K

Calorie: A unit of thermal energy. 1 cal is the amount of heat required to raise the temperature of 1.0 g of water from 14.5 to 15.5 °C; 1 cal = 4.18 J.

Capsid: The protein shell of a virus particle.

Carbanion: A carbon atom bearing a negative charge.

Carbocation: A carbon atom bearing a positive charge.

Scaffold protein: A non-catalytic protein that facilitates the assembly of multienzyme complexes by providing multiple specific binding sites for enzymes.

Carnitine shuttle: The transport mechanism that carries fatty acids as carnitine esters from the cytosol into the mitochondrial matrix.

Carotenoids: Fat-soluble Photosynthetic Pigments composed of isoprene units. Catabolism: The stage of intermediary metabolism involving The breakdown of nutrient molecules with the release of energy.

Catenanes: Compounds consisting of two or more rings interlocked mechanically via non-covalent topological bonds, resembling links in a chain.

Catecholamines: Hormones (such as epinephrine) that are amino derivatives of catechol.

Cation-exchange resin: An insoluble polymer matrix with fixed negatively charged groups; used for the chromatographic separation of cationic compounds. Wobble pairs: Pairs formed by relatively weak interactions between the base at the 3' end of a codon and the complementary base at the 5' end of an anticodon.

Keratins: Insoluble protective or structural proteins composed of parallel polypeptide chains with an α-helical or β-conformation.

Ketogenic amino acids: Amino acids whose carbon skeletons can be used for the synthesis of Ketone Bodies.

Ketosis: An abnormally high concentration of ketone bodies in the blood, tissues, and urine.

Ketose: A simple monosaccharide in which the carbonyl group is a ketone.

Ketone bodies: Acetoacetate, D-β-hydroxybutyrate, and acetone; water-soluble energy molecules normally produced by the liver, but present in excess during starvation or uncompensated Diabetes Mellitus.

Kinases: Enzymes that catalyze the phosphorylation of specific molecules using ATP. Kinetics: The branch of physical chemistry that studies Chemical Reactions over time and reaction rates.

Oxygen debt: The additional amount of oxygen consumed by the body during the recovery period following intense physical exertion, compared to the resting consumption rate.

Clone: The progeny of a single cell.

Cloning: The process of producing A large number of identical DNA molecules, cells, or organisms from a single DNA molecule, single cell, or single organism.

Covalent bond: A chemical bond formed by the sharing of valence electrons between two atoms to create a shared electron pair.

Codon: A sequence of three nucleotides that encodes a specific amino acid.

3'-End: The terminus of a nucleic acid molecule that bears a free hydroxyl group on the ribose or deoxyribose sugar.

5'-End: the terminus of a nucleic acid molecule that bears a free phosphate group.

Conservative substitution: the replacement of one amino acid residue in a polypeptide chain with another having similar properties, resulting in no significant change in polymer function, such as replacing Glu with Asp. Instability (dissociation) constant (Kd): the reciprocal of the association constant; characterizes the tendency of a complex to dissociate into its component parts; for example, the dissociation of an enzyme-substrate complex.

Acid dissociation constant (K_a): characterizes the dissociation reaction of an acid into a proton and its conjugate base.

Equilibrium Constant (K_eq): characterizes any chemical reaction; expressed in terms of the equilibrium concentrations of all reactants and products (at chemical equilibrium) at a given temperature and pressure.

Rate constant: a proportionality constant that relates the rate of a chemical reaction to the concentrations of the reacting substances.

Constitutive enzyme: an enzyme that is continuously required by a cell and is present at a constant concentration, such as many enzymes of central metabolic pathways.

Contig: a set of overlapping clones or a continuous sequence spanning a whole chromosomal fragment.

Transcriptional control: the Regulation of Protein Synthesis by controlling The production of its mRNA.

Translational control: the regulation of Protein Synthesis by controlling the rate of its translation on Ribosomes. Contour length: the length of a helical polymer molecule measured along the axis of the helix. β-Conformation: an extended, zigzag folding pattern of a polypeptide chain; frequently found as a secondary structure in proteins.

N-Terminal residue: the unique amino acid residue in a polypeptide chain that carries a free α-amino group.

Cooperativity: the ability of an enzyme or other protein to alter its affinity for subsequent ligand molecules upon binding the first; in positive cooperativity, binding of the first ligand molecule increases affinity for the next ones, whereas in negative cooperativity, it decreases affinity.

Short tandem repeat (STR): multiple adjacent repetitions of two or more (typically 3 to 6) base pairs in a DNA sequence; widely used in forensics and pathology.

Corticosteroids: Steroid Hormones produced in the adrenal cortex.

Cotransport: the simultaneous transport of two solutes across a membrane by the same carrier protein. See also Antiporter; Symport.

Activity coefficient: a proportionality factor relating the concentration of a solute to its thermodynamic activity in a solution.

Partition coefficient: The ratio of concentrations of a compound in a mixture of two immiscible phases at equilibrium.

Sedimentation coefficient: a measure of the rate at which a particle settles during centrifugation.

Krebs cycle: see Citric acid cycle

Cruciform DNA (RNA) structure: a Secondary structure of double-stranded RNA or DNA formed when The Double Helix denatures and self-complementary palindromic sequences pair up to form cross-like or hairpin structures.

Titration curve: a plot of pH values against the amount of base added during the titration of an acid.

Cristae: folds of the inner mitochondrial membrane. Nitrogen cycle: the overall biogeochemical cycle of nitrogen. Various Forms of biologically available nitrogen circulate in nature, passing through plants, animals, and microorganisms, with free nitrogen present in the atmosphere and mineral forms residing in the geosphere.

Tissue culture: a technique for the long-term maintenance and growth (cultivation) of cells extracted from a multicellular organism on artificial nutrient media.

L

Lineweaver-Burk equation: an algebraic transformation of the Michaelis-Menten Equation that allows a more accurate determination of V_max and K_m values through extrapolation.

1/V₀ = K_M/V_max[S] + l/V_max.

Levorotatory isomer: A stereoisomer that rotates the plane of polarization of plane-polarized light counterclockwise.

Leukotrienes: Lipids formed in the body from arachidonic acid, containing a 20-carbon chain. They belong to Eicosanoids and play a role in the Pathogenesis of Bronchial Asthma (mediators of bronchoconstriction in asthma).

Leukocytes: White Blood Cells; the leukocyte count characterizes the state of the body's defense mechanisms (in humans and animals).

Leucine zipper: A structural protein motif required for Protein-Protein Interactions in many eukaryotic regulatory proteins; it consists of two interacting α-chains with a leucine residue at every seventh position.

Lectin: A protein that binds to a carbohydrate (usually an oligosaccharide) with very high affinity and specificity, thereby mediating cell-cell interactions.

Lethal mutation: Inactivates a vital function of a cell or organism.

Lyases: Enzymes that catalyze the removal of a functional (chemical) group, leading to the formation of a double bond, or addition across a double bond.

Ligases: Enzymes that catalyze a condensation reaction in which a bond between two atoms is formed at the expense of ATP energy or another high-energy compound.

Ligand: A small molecule that binds in a specific manner to a larger molecule; for example, a hormone is a ligand for a specific protein receptor.

Leader sequence: A short N-terminal protein sequence or 5’-terminal RNA sequence with a specialized directing or regulatory function.

Lysis: Disruption of the plasma membrane or Cell wall (in bacteria) leading to the release of intracellular contents and cell death.

Lysosome: A membrane-bound organelle of a Eukaryotic Cell containing various hydrolytic enzymes, serving as a center for the degradation and recycling of currently unnecessary components.

Rate-limiting step: (1) in general terms, the enzymatic reaction with the maximum activation energy or maximum Transition State free energy; (2) in particular terms, the slowest step of a metabolic pathway.

Lymphocytes: A type of leukocyte; the principal cells of The Immune System responsible for humoral immunity.

Lipases: Enzymes that catalyze the hydrolysis of triacylglycerols.

Lipid: A low-molecular-weight compound insoluble in water, typically containing fatty acid residues, sterols, or isoprenoid fragments.

Lipidome: The complete lipid profile of a cell or tissue under specific conditions.

Sticky ends: Ends of DNA fragments with identical or different sequences featuring short, mutually complementary single-stranded overhangs that facilitate the ligation of these fragments.

Lipoate (Lipoic Acid): An intermediate carrier of hydrogen atoms and acyl groups in α-keto acid dehydrogenase reactions; a vitamin for certain microorganisms.

Lipoprotein: A lipid-protein aggregate through which water-insoluble lipids are transported in the blood; the protein component of a lipoprotein is called an apolipoprotein.

Liposome: A small spherical vesicle bounded by a lipid bilayer, spontaneously formed in a suspension of phospholipids in an aqueous buffer.

M

Macromolecule: A molecule with a molecular weight ranging from several thousand to several million.

High-energy compounds: A group of natural substances whose molecules contain energy-rich bonds; upon hydrolysis under standard conditions, they release energy (a decrease in free energy). They are present in all living cells.

Small nuclear RNA (snRNA): A small RNA molecule (typically 100 to 200 nucleotides) found in The Nucleus that participates in the splicing of eukaryotic mRNA.

Small nucleolar RNA (snoRNA): a small RNA molecule (typically 60 to 300 nucleotides long) involved in the chemical modification of rRNA.

Matrix: the aqueous interior of a cell or organelle (such as a mitochondrion) containing dissolved solutes.

Template: a macromolecular structure that serves as a pattern for the synthesis of a new informational macromolecule.

Messenger RNA (mRNA): an RNA molecule complementary to one of the DNA strands, which carries genetic information from the chromosomes to the ribosomes.

Template strand: a nucleic acid strand used by a polymerase to synthesize a complementary strand.

Meiosis: a type of cell division in which a diploid cell gives rise to haploid cells—gametes.

Membrane Potential (V_m): the electrical potential difference across the inner and outer surfaces of a biological membrane, measurable using a microelectrode; a typical membrane potential ranges from -25 mV to -100 mV (found in the vacuolar membranes of certain plant species). A negative sign indicates that the electrical potential is more negative on the inner surface of the membrane than on the outside.

Membrane transport: the movement of polar solutes across a membrane facilitated by specific membrane proteins (transporters).

Metabolism: the enzymatic transformation of organic molecules within a living organism; the sum of all catabolic and anabolic processes.

Metabolite: a chemical intermediate in a metabolic reaction.

Metabolic Regulation: a mechanism that enables a cell to maintain constant concentrations of individual metabolites despite fluctuations in flux through a metabolic pathway under Metabolic control.

Metabolic control: a mechanism that allows the flux of metabolites through a metabolic pathway to be adjusted in response to changing conditions.

Metabolome: the complete set of low-molecular-weight metabolites (intermediates, signaling molecules, secondary metabolites) present within a given cell under specific conditions.

Metabolon: a supramolecular complex of enzymes carrying out specific metabolic functions, together with the cellular structural element to which this complex is localized.

Metalloprotein: a protein containing a metal ion as a prosthetic group.

Metamerism: segmental body Organization, characteristic of insects, for example.

Branch migration: the movement of the branch point in a branched DNA molecule formed by two DNA molecules of identical sequence.

MicroRNA (miRNA): small RNA molecules (20 to 25 nucleotides long after Processing) involved in silencing gene expression by inhibiting translation and/or cleaving the corresponding mRNA.

Microsomes: membrane vesicles formed upon the fragmentation of The Endoplasmic reticulum of a eukaryotic cell, isolated by differential centrifugation.

Microbodies: membrane-bound cytoplasmic vesicles containing enzymes involved in the generation and degradation of peroxides; this category includes Peroxisomes, Lysosomes, and glyoxysomes.

Microtubules: thin tubules assembled from Two Types of globular tubulin subunits; found in cilia, flagella, centrosomes, and other motile and contractile structures of the cell.

Microfilaments: thin actin filaments found in the Cytoplasm of eukaryotic cells, serving structural and motile functions.

Myosin: a fibrous protein, the major component of thick filaments in Skeletal Muscle and of Actomyosin complexes.

Myofibril: a structural element composed of thin and thick filaments within muscle fibers.

Myocyte: a muscle cell.

Mitosis: A multi-step process in eukaryotic cells that results in Chromosome replication and cell division.

Mitochondrion: A double-membrane-bounded organelle of eukaryotic cells; the cellular powerhouse that supplies energy for ATP synthesis; contains the enzymatic machinery for the citric acid cycle, Fatty acid oxidation, electron transport, and oxidative phosphorylation.

Michaelis constant (K_м): Equal to the Substrate Concentration at which the velocity V of an enzymatic reaction is half of the maximum velocity V_mах.

Michaelis-Menten kinetics: The kinetics of an enzymatic reaction characterized by a hyperbolic dependence of the initial reaction velocity on substrate concentration.

Michaelis-Menten equation: The equation of a hyperbola; describes the dependence of the initial reaction velocity V₀ on the substrate concentration [S] observed in many enzymatic reactions:

_V0 = V_max[S]/(К_м + [S]).

Micelle: An aggregate of amphiphilic molecules in water in which the nonpolar PARTS OF THE molecules are directed inward, while the polar parts face outward, forming an outer surface that contacts the aqueous phase.

Modulator: A metabolite that binds to an allosteric site of an enzyme and alters its catalytic properties.

Silent mutation: Does not lead to visible Changes in the biological activity of the product of a given gene.

Mole: The mass of a substance in grams, numerically equal to its molecular weight.

Molar solution: An (aqueous) solution containing 1 mole of a substance per 1000 ml of solution.

Monoclonal Antibodies: Produced by a single cell clone using hybridoma technology; monoclonal antibodies are identical and directed against a single epitope of a target antigen.

Monosaccharide: A carbohydrate consisting of a single sugar unit.

Monolayer: A single layer of properly oriented lipid molecules.

Monocistronic mRNA: An mRNA that can be translated into a single, unique protein.

Motif: Any characteristic arrangement of Protein secondary structure elements found in one or more proteins; a motif can be simple or complex and may span the entire protein or only a part of it; synonymous with fold or supersecondary structure.

Mutases: Enzymes that catalyze the rearrangement of functional groups within a molecule.

Mutarotation: The change in optical rotation accompanying the interconversion of α- and β-anomeric forms of Monosaccharides.

Mutation: A stable, i.e., heritable, change in the genotype caused by external or internal environmental factors.

N

Saturated fatty acid: A fatty acid with no double bonds in its carbon Skeleton.

Native conformation: The biologically active conformation of a macromolecule.

Non-heme iron proteins: Proteins that contain iron but lack a porphyrin ring; typically involved in oxidation-reduction reactions.

Essential Amino Acids: Amino acids that are not synthesized in The Human Body (and other vertebrates) and must be obtained from the diet.

Essential Fatty Acids: Polyunsaturated fatty acids that are synthesized by plants but not by the human body; an essential component of the human diet.

Neurotransmitter: a low-molecular-weight compound (usually nitrogen-containing) secreted at the axon terminals of a neuron that binds to a specific receptor on the next neuron, thereby transmitting a Nerve Impulse.

Neuron: a cell of the nervous tissue specialized for conducting nerve impulses.

Non-coding RNA (ncRNA): does not encode information for the synthesis of a protein product.

Unsaturated fatty acid: a fatty acid containing one or more double bonds.

Inorganic pyrophosphatase: an enzyme that hydrolyzes an inorganic phosphate molecule to yield pyrophosphate.

Nonpolar substance: a hydrophobic substance that is poorly soluble in water.

Non-cyclic electron flow: light-driven electron transport from water to NADP⁺ in oxygen-dependent reactions of Photosynthesis; involves Photosystems I and II.

Low-energy phosphate compounds: phosphorylated compounds with a relatively low Standard Free Energy of hydrolysis.

Ninhydrin reaction: a color reaction occurring between amino acids or peptides and ninhydrin upon heating; used for the qualitative and Quantitative determination of Amino Acids and peptides.

Nitrogenase complex: an enzymatic system capable of reducing atmospheric nitrogen to ammonia in the presence of ATP.

Nonsense codon (stop codon): one of the DNA base triplets (UAG, UAA, UGA) that does not encode any amino acid; serves as a translation terminator and is therefore sometimes called a termination codon.

Nonsense mutation: a point mutation resulting in the formation of a stop codon and the premature termination of Polypeptide chain synthesis.

Nonsense suppressor: a mutant tRNA gene that encodes a molecule with an altered anticodon.

Nucleases: enzymes that hydrolyze internucleotide (phosphodiester) bonds in nucleic acids.

Nucleic acids: naturally occurring polynucleotides whose subunits form specific sequences and are linked together by phosphodiester bonds; DNA and RNA.

Nucleoside: a compound consisting of a purine or pyrimidine base covalently linked to a pentose sugar.

Nucleoside diphosphate kinase: an enzyme that catalyzes the transfer of the terminal phosphate group from a nucleoside 5'-triphosphate to a nucleoside 5'-diphosphate.

Nucleoside diphosphate sugars: coenzyme-like molecules involved in the enzymatic synthesis of polysaccharides and sugar derivatives.

Nucleoside monophosphate kinase: an enzyme that catalyzes the transfer of the terminal phosphate group of ATP to a nucleoside 5'-monophosphate.

Nucleoid: meaning "nucleus-like"; an irregularly shaped region within a Prokaryotic Cell that contains the genetic material; the bacterial genome.

Nucleoplasm (nuclear matrix): the portion of The Eukaryotic Cell contents enclosed by the nuclear membrane.

Nucleosome: the structural unit of Chromatin in eukaryotes; consists of a DNA strand wrapped around a histone core.

Nucleotide: a phosphate ester of a nucleoside at one of the hydroxyl groups of the pentose sugar.

Nucleophile: an electron-rich functional group capable of donating electrons to electron-deficient atoms (electrophiles); active in bimolecular substitution reactions.

O

Facilitated Diffusion (passive transport): The diffusion of polar substances across a biological membrane mediated by a carrier protein.

Reversible inhibitor: An inhibitor that binds to an enzyme in a reversible manner, such that enzyme activity is restored upon the inhibitor's removal.

Reverse (reversion) mutation: A mutation that restores the original phenotype to an organism.

Reverse Transcriptase: An RNA-dependent DNA polymerase found in Retroviruses; capable of synthesizing DNA complementary to an RNA template.

General Acid-Base Catalysis: Catalysis accompanied by proton transfer to or from molecules other than water.

Monoprotic acid: An acid that yields one proton upon dissociation.

Oxidation (half-reaction): The loss of electrons by an atom or ion.

α-Oxidation: The oxidation pathway for β-methylated fatty acids in peroxisomes.

β-Oxidation: The oxidative breakdown of fatty acids into acetyl-CoA via the sequential oxidation of the β-carbon atom.

ω-Oxidation: An alternative pathway of fatty acid oxidation in which the carbon atom most distant from the carboxyl group is oxidized first.

Oxidizing agent: An electron acceptor in a redox reaction.

Redox pair (oxidation-reduction pair): An electron-donor compound and its corresponding oxidized form, for example, NАDН/NАD⁺.

Redox reaction (oxidation-reduction reaction): A chemical reaction in which electrons are transferred from a donor to an acceptor.

Oxygenases: Enzymes that catalyze reactions in which oxygen atoms are directly incorporated into reaction products, forming a hydroxyl or carboxyl group. In Reactions Catalyzed by Monooxygenases, only one oxygen atom is incorporated, while the other is reduced to Н_2O. In reactions catalyzed by Dioxygenases, two oxygen atoms are incorporated into the product.

Mixed-function oxidases: Enzymes (such as monooxygenases) that catalyze The oxidation of two reducing agents: typically one is NАDРН and the other is a substrate. In this process, one oxygen atom is incorporated into the product, while the other is reduced to Н_2O. To transfer electrons from NАDРН to O₂, these enzymes often utilize cytochrome P450.

Oxidases: Enzymes that catalyze oxidation reactions in which molecular oxygen serves as the electron acceptor, but oxygen atoms are not incorporated into the final products.

Oligomer: A short polymer consisting of no more than 50 amino acids, nucleotides, or sugars.

Oligomeric protein: A protein composed of two or more identical polypeptide chains.

Oligonucleotide: A short nucleotide sequence (typically no more than 50 bases).

Oligopeptide: A sequence of several amino acid residues linked by peptide (amide) bonds.

Oligosaccharide: A sequence of monosaccharide units linked by glycosidic bonds.

Saponification: The alkaline hydrolysis of triacylglycerols yielding fatty acids.

Oncogene: A gene encoding a protein that, when dysregulated, can cause rapid and uncontrolled cell division, leading to tumor development. Mutations that activate an oncogene increase the risk of malignant cell transformation.

Operator: A specific region of DNA that controls the expression of a gene or a group of genes through interaction with a repressor protein.

Operon: A functional unit of prokaryotic genomic DNA comprising a cluster of genes under the control of a single promoter.

pH optimum: The range of pH values at which an enzyme exhibits maximum catalytic activity.

Optical activity: The ability of a substance to rotate the plane of polarization of plane-polarized light.

Organelles: Membrane-bound structures within eukaryotic cells that contain enzymes and other components with specific functions.

Orthologs: Genes from different organisms that share marked sequence similarity and functional relatedness.

Osmosis: The diffusion of a substance, typically water (or a solvent in general), through a semipermeable membrane from a solution of lower solute concentration to one of higher solute concentration.

Osmotic pressure: The pressure exerted on a semipermeable membrane resulting from the diffusion of solvent from a solution of lower solute concentration to one of higher concentration.

Central dogma of molecular biology: The fundamental principle of molecular biology stating that genetic information flows from DNA to RNA to protein.

Ground state (as opposed to excited state): The stable state of an atom or molecule.

Basal metabolic rate (BMR): An indicator of the rate of Metabolism and Energy Exchange in an organism under conditions of thermal comfort and fasting (at complete rest, long after a meal).

Open Reading Frame (ORF): A continuous sequence of non-overlapping nucleotide codons in a DNA or RNA molecule that does not contain a stop codon.

Open system: A system that exchanges both matter and energy with its surroundings.

Mass action ratio (Q): For the reaction

аА + bВ <-> сС + dD

Q = [С]c[D]d/[А]a[В]b.

Negative cooperativity: A property of certain multimeric enzymes and proteins whereby the binding of a ligand or substrate to one subunit hinders its binding to another subunit.

Negative feedback: A mechanism of biochemical pathway regulation in which the reaction product inhibits earlier steps of the pathway.

Lagging strand: The DNA strand that is synthesized during replication in the opposite direction to the movement of the Replication fork.

Mismatched base pairing: The pairing of bases in a way other than standard Watson-Crick base pairing.

P

Palindrome: A segment of double-stranded DNA in which the base sequences of the two strands are symmetrical with respect to a central axis.

Paradigm: A set of fundamental scientific concepts and terms accepted by the scientific community; in biochemistry, an experimental model or archetype.

Pathogen: An organism that causes disease.

Pentose: A simple sugar whose carbon skeleton consists of five carbon atoms.

Pentose Phosphate Pathway (hexose monophosphate shunt): A metabolic pathway found in most organisms involving the interconversion of hexoses and pentoses; it serves as a source of reducing equivalents (NADPH) and pentoses for biosynthetic reactions, beginning with glucose-6-phosphate and proceeding via the formation of 6-phosphogluconate.

Peptide: Two or more amino acids linked by a peptide bond.

Peptidases: Enzymes that hydrolyze peptide bonds.

Peptidyl transferase: A ribozyme that catalyzes peptide bond formation in proteins; part of the large ribosomal subunit rRNA.

Peptide bond: An amide linkage formed between the α-amino group of one amino acid and the α-carboxyl group of another, accompanied by the release of a water molecule.

Peptide mapping: A characteristic two-dimensional pattern (on paper or in a gel) produced by the separation of a mixture of peptides generated through partial Protein Hydrolysis.

Peptidoglycan: A major component of the Bacterial cell wall; typically composed of parallel heteropolysaccharide chains cross-linked by short peptide fragments.

Primary Structure: The linear sequence of building blocks in a biopolymer.

Primary transcript: The immature RNA molecule produced by transcription, which subsequently undergoes post-transcriptional processing.

First law of thermodynamics: The principle stating that the total energy of a system remains constant in any physical or chemical process.

Signal transduction: The Amplification of an extracellular signal (chemical, mechanical, or electrical) and its conversion into a cellular response.

Electron transport: The movement of electrons from a donor to an acceptor, such as from substrates to oxygen via carriers in the respiratory (electron transport) chain.

Electron carrier: A protein (such as a flavoprotein or cytochrome) capable of reversibly accepting and donating electrons; involved in Electron transfer from organic nutrients to oxygen or other terminal acceptors.

Transporters (transport proteins, permeases): Integral membrane proteins that facilitate the translocation of specific nutrients, metabolites, ions, or other proteins across the plasma membrane.

Translational reprogramming: Programmed shifting of the reading frame during mRNA Translation on ribosomes.

Transition state: The activated state of a molecule undergoing partial conversion during a chemical reaction; it represents the highest energy point along the reaction coordinate.

Peripheral membrane proteins: Proteins weakly or reversibly bound to the plasma membrane via Hydrogen Bonds or Electrostatic Interactions; they typically dissociate into aqueous media upon extraction.

Peroxisome: A membrane-bound organelle in eukaryotic cells containing enzymes that generate and degrade peroxides.

DNA loops: Loops formed in DNA segments between distant sites As a result of interactions between proteins bound to those specific regions.

Pyranose: A simple sugar containing a six-membered pyran ring.

Pyridine nucleotide: A nucleotide coenzyme containing a pyridine derivative, nicotinamide; either NAD or NADP.

Pyridoxal phosphate: A coenzyme containing pyridoxine (vitamin B₆); participates in amino group transfer reactions.

Pyrimidine: A nitrogenous heterocyclic base found in nucleotides and nucleic acids.

Pyrimidine dimer: A dimer formed by the covalent linkage of two adjacent pyrimidine residues in DNA, induced by UV irradiation; thymine dimers are the most common.

Digestion: The enzymatic breakdown of major dietary constituents into simpler substances within the gastrointestinal tract.

Plasmalogen: A phospholipid in which the C1 position of the glycerol moiety is attached to an aliphatic alcohol via an ether bond.

Plasma membrane: The outer membrane enclosing the cytoplasm of a cell.

Plasmid: An extrachromosomal, autonomously replicating small circular DNA molecule; used in Genetic Engineering.

Plastid: A self-replicating plant cell organelle capable of differentiating into a chloroplast.

Plectonemic coil: A biopolymer structure in which one strand winds around another in a simple and regular manner.

Superhelix density: The number of extra turns in a helical molecule (such as DNA) compared to the number of turns in a relaxed molecule.

Beta-turn (P-turn): A segment of a protein sequence formed by four amino acid residues that forces the polypeptide chain to reverse direction; an element of protein secondary structure.

Poly(A) tail: A sequence of adenosine residues at the 3' end of many mRNA molecules in eukaryotic cells and certain bacteria.

Polyclonal antibodies: A heterogeneous pool of antibodies produced by different B lymphocytes in response to an antigen; the different antibodies in the pool recognize different parts of the antigen molecule (epitopes).

Polylinker: A short, often synthetically produced DNA sequence containing recognition sites for several Restriction Endonucleases.

Polymerase Chain Reaction (PCR): A laboratory method involving the multiple amplification of a specific DNA sequence.

Polymorphism: The existence of different, yet fully functional variants of a protein/gene within an organism population.

Restriction fragment length polymorphism (RFLP): Variations in the length of restriction fragments containing specific DNA sequences among individuals in a population; the result of rare Changes in DNA that create or abolish specific sequences recognized by restriction enzymes.

Sequence polymorphism: Any variation in a genomic sequence (nucleotide substitutions, insertions, deletions, rearrangements) that allows the identification of a group of individuals within a population or the differentiation of organisms of different species.

Single nucleotide polymorphism (SNP): A nucleotide pair substitution that allows one individual to be distinguished from another or a specific group of individuals to be identified within a population.

Polyunsaturated fatty acid: A fatty acid containing multiple double bonds, usually not conjugated with one another.

Polynucleotide: A sequence of covalently linked nucleotides in which the 3'-hydroxyl group of the pentose in one nucleotide residue is linked via a phosphodiester bond to the 5'-hydroxyl group of the pentose of the adjacent residue.

Polypeptide: A long sequence of amino acid residues (typically up to 10,000 Da) linked by peptide bonds.

Polysaccharide: A linear or branched polymer consisting of monosaccharide units linked by glycosidic bonds.

Polysome (polyribosome): A complex of an mRNA molecule with two or more ribosomes.

Multienzyme system (complex): A group of functionally interrelated enzymes operating within a metabolic pathway.

Polycistronic mRNA: An mRNA template encoding the translation of two or more proteins.

Positive cooperativity: A property of the subunits of a protein molecule whereby the binding of the first ligand or substrate molecule to one subunit facilitates the binding of subsequent molecules to other subunits.

Polar molecule: A hydrophilic substance that is readily soluble in water.

Polarity: (1) In chemistry, the uneven distribution of electrons within a molecule; polar molecules are typically water-soluble; (2) in molecular biology, the directional orientation from the 5' end of a nucleic acid to the 3' end and vice versa.

Porphyrin: A complex of nitrogenous compounds containing four substituted pyrroles joined in a ring via covalent bonds; often binds a metal atom at its central position.

Porphyria: A hereditary disorder associated with a deficiency of one or more enzymes involved in porphyrin biosynthesis.

Linking number: a topological parameter reflecting the degree of DNA Supercoiling, which indicates the number of times one closed circular DNA strand winds around the other.

Post-transcriptional processing: enzymatic modifications of a primary transcript that result in the formation of functional mRNAs, tRNAs, rRNAs, and many Other types of RNA.

Post-translational modification: enzymatic modification of a polypeptide chain following mRNA translation.

Group transfer potential: characterizes a compound's ability to donate an activated group (such as a phosphoryl or acyl group); typically expressed as the standard Free energy of hydrolysis.

Phosphorylation potential (∆G_p): the actual free energy change of ATP hydrolysis under non-standard cellular conditions.

Dextrorotatory isomer: a stereoisomer that rotates the plane of plane-polarized light clockwise.

Primase: an enzyme that catalyzes the synthesis of short RNA oligonucleotides used as primers by DNA polymerases.

Primer: a short oligomer (such as sugar or nucleotide residues) to which an enzyme adds subsequent monomer units.

Priming: (1) the phosphorylation of an amino acid residue that serves as a binding center and checkpoint for the phosphorylation of other residues within the same protein; (2) the synthesis of a short nucleotide sequence to which DNA polymerases can add further nucleotides during DNA replication.

Primosome: an enzyme complex responsible for synthesizing primers for lagging strand DNA Synthesis during replication.

Projection formulas (Fischer projections): a method for depicting molecules to illustrate the configuration of substituents around chiral centers.

Haworth projection formulas: a method for representing cyclic chemical structures that shows the configuration of all substituents; frequently used for sugars.

Prokaryotes: a historically accepted term for all members of the kingdoms Bacteria and Archaea. However, because the differences between bacteria (formerly eubacteria) and archaea are substantial, this Classification is largely obsolete. Moreover, the term is frequently used to refer exclusively to bacteria, which can cause confusion, and the word "prokaryote" itself incorrectly implies that they were the evolutionary ancestors of eukaryotes.

Intermediate: any chemical species with a finite and short lifetime formed during a reaction pathway.

Holliday junctions: intermediate structures formed During genetic recombination, where two double-stranded DNA molecules are held together by strand exchange interactions between each molecule.

Intermediary metabolism: the interconnected enzymatic pathways that extract chemical energy from nutrients and utilize it to synthesize and assemble cellular components.

Promoter: a DNA sequence to which RNA polymerase binds to initiate transcription.

Prostaglandins: lipid-soluble, hormone-like regulatory molecules derived from arachidonic acid and other polyunsaturated fatty acids.

Simple diffusion: the movement of solute molecules across a membrane down their concentration gradient without the assistance of a carrier protein.

Prosthetic group: a metal ion or organic molecule (non-amino acid) tightly or covalently bound to a protein and essential for its activity.

Proteasome: a multisubunit protein complex that degrades damaged or unneeded cellular proteins.

Protein kinases: enzymes that transfer the terminal phosphoryl group of ATP or another nucleoside triphosphate to the side chain of a Ser, Thr, Tyr, Asp, or His residue in a target protein, thereby regulating its activity or other functional properties.

Proteoglycan: a hybrid macromolecule composed of a core protein covalently linked to glycosaminoglycan chains; the carbohydrate component typically predominates by weight.

Proteome: the entire set of proteins expressed by a given cell, tissue, or organism at a given time, or the full complement of proteins encoded by a genome.

Proteomics: broadly defined, the large-scale Study of the structure, function, and expression of proteins within a cell or organism.

Protomer: a general term describing any repeating unit of one or more tightly bound protein subunits within a larger Protein Structure. The subunits of a multisubunit protomer may be identical or different.

Proton-motive force: the Electrochemical Potential associated with the transmembrane proton concentration gradient; the driving force for ATP Synthesis in oxidative phosphorylation and photophosphorylation.

Protooncogene: a cellular gene, typically encoding a regulatory protein, that can be converted into an oncogene as a result of mutation.

Protoplasm: a general term describing the entire contents of a living cell.

Prochiral molecule: a symmetric molecule that can react asymmetrically with an enzyme possessing a chiral center, yielding a chiral product.

Processivity: the ability of enzymes that catalyze the synthesis of biological polymers to add multiple monomer units to a polymer without dissociating from the substrate complex.

Purine: a nitrogenous heterocyclic base found in nucleotides and nucleic acids; consists of fused pyrimidine and imidazole rings.

Puromycin: an antibiotic that disrupts polypeptide synthesis by incorporating into the growing polypeptide chain and causing premature termination of synthesis.

P

Equilibrium: a state of a system in which no net change occurs; the free energy of such a system is at a minimum.

Radical (free radical): an atom or group of atoms possessing an unpaired electron.

Radioactive isotope: an isotope of an element with an unstable nucleus capable of emitting ionizing radiation.

Radioimmunoassay (RIA): a sensitive quantitative method for determining BIOLOGICALLY ACTIVE SUBSTANCES based on competitive binding to specific antibodies.

Uncoupling agent: for example, 2,4-dinitrophenol, a substance that uncouples ADP phosphorylation from electron transport.

Reading frame: a contiguous, nonoverlapping sequence of trinucleotide codons in DNA or RNA.

Racemic mixture (racemate): an equimolar mixture of the D- and L-stereoisomers of an optically active substance.

Reactive oxygen species (ROS): highly reactive products of the partial reduction of O₂, including hydrogen peroxide (Н₂О₂), superoxide radical (•О₂), and hydroxyl radical (•ОН), formed as by-products of oxidative phosphorylation.

Regulon: a group of coordinately regulated genes or operons, sometimes located at distant sites on the chromosome or genome.

Regulatory sequence: a DNA sequence involved in the Regulation of Gene Expression, such as a promoter or operator.

Regulatory gene: a gene whose product regulates the expression of another gene, such as the gene encoding a repressor protein.

Regulatory enzyme: an enzyme that carries out a regulatory function through its ability to alter catalytic activity via allosteric interactions or covalent modifications.

RNA editing: posttranscriptional modifications of mRNA that alter the meaning of certain codons.

Recombinant DNA: DNA formed by joining genes in a new combination.

Recombinational repair: recombination aimed at repairing breaks or cross-links in DNA, particularly at stalled replication forks.

Recombination: any enzymatic process in which chromosome fragments are cleaved and linearly rearranged.

Relaxed DNA: Any DNA existing in its most stable and unstressed form, typically in the B-form, under nearly all intracellular conditions.

Renaturation: The refolding of an unfolded (denatured) globular protein to restore its native Structure and function.

X-ray crystallography: The Determination of the three-dimensional structure of crystals using X-Ray Diffraction Analysis.

Repair: The correction of errors made during the synthesis of informational Biopolymers by removing incorrect units after they have been incorporated into the polymer chain.

Mismatch Repair: The enzymatic removal of abnormally paired bases in DNA. Replicase complex: A complex of enzymes and specialized proteins that carries out DNA replication within cells.

Replication fork: The Y-shaped structure formed at the site of DNA replication.

Replicative form: The full-length structural form of viral DNA produced at an intermediate stage of replication in certain Viruses.

Replication: The synthesis of daughter nucleic acid molecules identical to the parent molecules. Replisome: A multi-enzyme complex involved in DNA synthesis at the replication fork.

Repressible enzyme: A bacterial enzyme whose synthesis is inhibited by the product of the reaction it catalyzes.

Repression: The reduction of gene expression in response to a change in regulatory protein activity.

Translational repressor: A repressor that binds to mRNA and blocks translation.

Repressor: A protein that binds to a regulatory sequence or operator of a gene, thereby blocking transcription.

Response element: A DNA segment located just upstream of a gene's start site that binds a specific protein, which influences the rate of gene transcription.

Restriction endonucleases (restriction enzymes): Site-specific endodeoxyribonucleases that cleave both strands of DNA near a specific site recognized by the enzyme; an essential tool in genetic engineering.

Restriction fragment: A DNA segment excised from a longer DNA sequence by a restriction enzyme.

Retrovirus: An RNA virus that contains reverse transcriptase.

Salvage pathway: The synthesis of biomolecules, such as nucleotides, from intermediate breakdown products of those molecules; recycling as opposed to de novo synthesis.

Hormone receptor: A protein inside or on the surface of a target cell that binds a specific hormone and initiates a cellular response.

Receptor tyrosine kinases: A large family of plasma membrane proteins consisting of a ligand-binding extracellular domain, a single transmembrane helix, and a cytoplasmic domain with tyrosine kinase activity regulated by the extracellular ligand.

Peroxisome proliferator-activated receptors (PPARs): A family of nuclear transcription factors activated by lipid ligands that alter the expression of specific genes, including those encoding enzymes involved in lipid Synthesis and degradation.

G protein-coupled receptors (GPCRs): A large family of receptor membrane proteins consisting of seven transmembrane helical segments that associate with G proteins to transmit extracellular signals and alter cellular metabolism; also known as seven-transmembrane receptors.

Ribozymes: RNA molecules that possess catalytic activity.

Ribonuclease: A nuclease that catalyzes the hydrolysis of certain internucleotide bonds in RNA.

Ribonucleotide: A nucleotide containing D-ribose as its pentose component.

Riboswitch: A structural element within an mRNA molecule that binds a specific ligand and affects mRNA translation or processing.

Ribosome: A supramolecular complex of rRNA and proteins; 18 to 22 nm in diameter; the site of protein synthesis.

Ribosomal RNA (rRNA): A type of RNA molecule that is a structural component of ribosomes.

Releasing hormones (liberins): Hypothalamic hormones that stimulate the Pituitary Gland to release Other Hormones.

Release factors (termination factors): Cytosolic protein factors that participate in the release of the completed polypeptide chain from the ribosome.

RNA (ribonucleic acid): A polyribonucleotide with a specific sequence, whose units are linked by 3',5'-phosphodiester bonds.

RNA polymerase: An enzyme that catalyzes the synthesis of RNA from ribonucleoside-5'-triphosphates using a DNA or RNA template.

C

Site-Directed Mutagenesis: A genetic engineering technique used to introduce specific changes into a gene sequence.

Site-Specific Recombination: A type of genetic recombination that occurs only at specific DNA sequences.

Sarcomere: The functional structural unit of the muscle contractile apparatus.

Satellite DNA: A non-coding region of eukaryotic chromosomes containing large numbers of repeated sequences; most commonly found in the centromere; function unknown.

Southern blot: A laboratory Procedure used to detect one or more specific DNA fragments via hybridization with a complementary labeled probe.

Diabetes mellitus: A group of Metabolic Disorders associated with insufficient Insulin synthesis or impaired insulin action, resulting in disrupted glucose Transport from the blood into cells.

Svedberg (S): A unit of measurement for the Sedimentation Rate of a particle during centrifugation.

Supercoil: A helical molecule twisted around itself.

Supercoiled DNA: DNA that is coiled around itself due to torsional stress caused by underwinding or overwinding of the double helix relative to the B-form.

Light reactions: Photosynthetic reactions that cannot take place in the dark.

Free energy (G): The portion of a system's total energy that is available to perform work at constant temperature and pressure.

Frameshift mutation: A mutation (insertion or deletion) of A number of nucleotides that alters the reading frame of codons during protein synthesis; from the point of mutation onward, an aberrant amino acid sequence is translated.

Selectins: A large family of cell-surface membrane proteins that bind tightly and specifically to Oligosaccharides on the surface of other cells, thereby enabling signal transduction across the plasma membrane.

Sickle-Cell Anemia: A human genetic disease characterized by the presence of defective hemoglobin in homozygous individuals carrying the mutant allele that encodes the hemoglobin $eta$-chain.

Sickle-cell trait: The formation of sickle-shaped erythrocytes in heterozygous individuals carrying one mutant allele responsible for sickle-cell anemia; manifested under conditions of low ambient oxygen.

Sialoadhesin: A cell-surface lectin that binds to carbohydrate ligands terminating in a sialic acid residue; a member of the siglec family of lectins.

Signal sequence: An amino acid sequence, most commonly located at the N-terminus, that directs the destination or subcellular localization of a newly synthesized cellular protein.

London dispersion forces: Weak, transient attractive forces between molecules arising from the induction of instantaneous molecular dipoles.

Symbionts: two or more interdependent organisms, usually living in direct contact.

Symport: the simultaneous transport of dissolved substances across a membrane in the same direction.

Synthases: enzymes that catalyze condensation reactions occurring without The Use of nucleoside triphosphates as Energy Sources.

Synteny: the conservation of gene order in the chromosomes of different species of organisms.

Synthetases: enzymes that catalyze condensation reactions driven by the energy derived from the cleavage of ATP or other nucleoside triphosphates.

Systems biology: The Study of complex biochemical systems, including all or some of the functions of cellular macromolecules (RNA, DNA, proteins).

β-Sheet (Pleated sheet): an arrangement of polypeptide chains with a β-conformation resembling a stretched accordion, held together by hydrogen bonds.

Scramblases: membrane proteins that catalyze the movement of phospholipids across The Lipid Bilayer, resulting in an even Distribution of lipids between the outer and inner leaflets.

Trace element: a chemical element required by an organism only in minute amounts.

Fusion protein: (1) a member of a family of proteins that facilitate membrane fusion; (2) a protein product of a gene formed by joining two different genes or parts of genes. Somatic cell: any cell of the body except a germ cell.

Coupled reactions: two chemical reactions that share a common intermediate and are able to exchange energy.

Base pairing: the formation of hydrogen bonds between nucleotides in nucleic acid chains; for example, A pairs with T or U, and G pairs with C.

Nuclear magnetic Resonance spectroscopy (NMR spectroscopy): a physicochemical analytical method that utilizes quantum mechanical

properties of atomic nuclei to study Molecular structure and dynamics.

Specific acid-base catalysis: acid or base catalysis involving the components of a water molecule (the hydroxide ion or the hydronium ion).

Specificity: the ability of an enzyme (or receptor) to distinguish between competing substrates (or ligands). α-Helix: a helical conformation of a polypeptide chain (typically right-handed) characterized by the maximum number of hydrogen bonds; one of the most common secondary structures in proteins.

Alcoholic Fermentation: the anaerobic conversion of glucose into ethanol during glycolysis. Splicing: the removal of introns and the joining of exons in a primary RNA transcript.

Spliceosome: a complex of RNA and proteins that carries out mRNA splicing in eukaryotic cells.

Standard free energy change (∆G°): the change in free energy in a reaction occurring under standard conditions: temperature 298 K, pressure 1 atm (101.3 kPa), concentration of all solutes 1 mol/L; ∆G'° corresponds to the free energy change at pH 7.0 in 55.5 M water.

Standard reduction potential (E'°): the electromotive force generated at an electrode in a 1 M solution of a reducing agent and its oxidized form at 25 °C and pH 7.0; a measure of a reductant's tendency to donate electrons.

Start codon: AUG (sometimes GUG or, even more rarely, UUG in bacteria and archaea); encodes the first amino acid of a polypeptide sequence—N-formylmethionine in bacteria, and Methionine in archaea and eukaryotes.

Steady state: a condition of a system in which the concentrations of all components remain constant. Stem cells: self-renewing Bone Marrow cells that undergo differentiation to produce blood cells such as erythrocytes and lymphocytes.

Stereoisomers: compounds with the same Chemical Composition and connectivity of atoms, but with a different spatial arrangement of atoms. Sterols: lipids containing a steroid nucleus.

Stimulatory G protein (G_s): a trimeric regulatory GTP-binding protein that is activated upon binding to a receptor in the plasma membrane and stimulates nearby membrane-bound enzymes, such as adenylate cyclase; its action is opposite to that of Gi.

Stop codon (termination codon): UAA, UAG, and UGA. During protein synthesis, they serve as a signal for the termination of polypeptide chain synthesis.

Stroma: the region within a chloroplast that surrounds the thylakoids.

Structural gene: a gene that encodes a protein or RNA (as opposed to a regulatory gene).

Substrate: a specific compound whose transformation is catalyzed by an enzyme.

Substrate channeling: the transfer of intermediate compounds of an enzymatic process within a protein complex directly from the Active Site of one enzyme to the active site of another enzyme that catalyzes the subsequent step of the process.

Substrate-level phosphorylation: the phosphorylation of ADP or another nucleoside 5'-diphosphate coupled with the dehydrogenation of an organic substrate, independently of The electron transport chain.

Suicide inhibitor: a relatively inactive molecule that binds to the active site of an enzyme, is converted into an active form, and irreversibly inactivates the enzyme.

Suppressor mutation: a mutation that partially or fully restores a function lost as a result of a previous mutation, but occurs at a different site than the original mutation (i.e., unlike a reverse mutation, it restores the phenotype rather than the genotype).

Sphingolipid: an amphiphilic lipid consisting of sphingosine with attached fatty acid residues and a polar alcohol.

T

Telomere: a specialized structure at the ends of linear eukaryotic chromosomes.

Terminal transferase: an enzyme that catalyzes the addition of specific nucleotide units to the 3'-end of a DNA chain.

Termination sequence: a DNA sequence at the end of a transcriptional unit that signals the cessation of transcription.

Thermogenesis: the generation of heat through muscle activity, uncoupled oxidative phosphorylation, or a futile metabolic cycle.

Thermogenin (uncoupling protein 1): a protein of the inner mitochondrial membrane in brown adipose tissue that allows protons to cross the membrane, prevents protons from being used for ATP synthesis, and dissipates energy from substrate oxidation as heat.

Terpenes: organic Hydrocarbons or their derivatives composed of repeating isoprene units; they impart taste and aroma to plant products.

Tetrahydrobiopterin: a coenzyme; the reduced form of biopterin.

Tetrahydrofolate: a coenzyme; the reduced, active form of folate.

Thiamine pyrophosphate: a coenzyme, the active form of Vitamin B1; participates in aldehyde group transfer reactions.

Thylakoids: closed cisternae or disks formed by the pigment-containing inner membrane of chloroplasts.

Thioester: an ester formed from a carboxylic acid and a thiol or mercaptan.

Tocopherol: a form of vitamin E.

Toxins: proteins synthesized by certain organisms that are toxic to other organisms.

Topoisomerases: enzymes that introduce positive or negative supercoils into a closed circular DNA duplex.

Topoisomers: forms of a circular DNA molecule that differ only in their linking number.

Origin of replication (ori): a region of a DNA sequence where replication is initiated.

Transamination: the enzymatic transfer of an amino group from an α-amino acid to an α-keto acid.

Transgenic organism: an organism whose genome has been modified by the introduction of genes from another organism using recombinant DNA techniques.

Transduction: (1) The conversion of one form of energy or signal into another; (2) the transfer of genetic material from one cell to another via a viral vector.

Transcriptome: the complete set of RNA transcripts produced in a given cell or tissue under specific physiological conditions.

Transcription factor: a eukaryotic protein that regulates the transcription of genes by binding to specific DNA sequences and interacting with RNA polymerase or other transcription factors to initiate transcription.

Transcription: the enzymatic process by which the genetic information encoded in a single-stranded DNA template is used to synthesize a complementary mRNA sequence.

Translocase: (1) an enzyme that catalyzes The transport of solutes across a membrane; (2) an enzyme involved in the movement of macromolecules, such as the translocation of ribosomes along an mRNA molecule.

Transpiration: the evaporation of water absorbed by plant roots, passing through The Vascular System and out to the leaves.

Transposition: the movement of a gene or a group of genes from one genomic Location to another.

Transposon: a DNA sequence that can change its position within a genome.

Transfer RNA (tRNA): a class of RNA molecules with a molecular weight ranging from 25,000 to 35,000, each of which binds a specific amino acid During the first step of Protein Biosynthesis.

Transformation: the introduction of foreign DNA into a cell, resulting in a newly acquired phenotype.

Triacylglycerols (neutral fats): esters of glycerol combined with three fatty acid molecules.

Triose: a monosaccharide containing three carbon atoms in its backbone.

Thromboxanes: derivatives of arachidonic acid that play a key role in platelet aggregation during blood clotting.

Platelets (thrombocytes): small, anucleated blood cells that initiate Blood Coagulation, derived from bone marrow precursor cells known as megakaryocytes.

Tropic hormone (tropin): a peptide hormone that stimulates a specific endocrine gland to secrete its own hormones; for example, thyrotropin synthesized by the pituitary gland stimulates The Thyroid Gland to secrete thyroxine.

Tunneling: the direct transfer of a reaction intermediate from the active site of one enzyme to the active site of another enzyme catalyzing the subsequent step in a metabolic pathway.

U

Ubiquitin: a small, highly conserved regulatory protein that tags intracellular proteins destined for degradation by the proteasome. Multiple ubiquitin molecules are covalently attached to lysine residues on the target protein via a cascade of specific enzymatic reactions.

Specific enzyme activity: the amount of substrate, in micromoles, converted per minute per milligram of protein at 25 °C; a standard measure of enzyme purity.

Specific heat capacity: the amount of thermal energy (in joules or calories) required to raise the temperature of 1 g of a pure substance by 1 °C.

Specific rotation: the angular rotation (in degrees) of the plane of plane-polarized light passing through a solution of an optically active substance at a specified path length at 25 °C, typically measured using the sodium D-line.

wavelength at 25 °C; usually light at the wavelength of the sodium D-line.

Ultraviolet (UV) radiation: electromagnetic radiation with wavelengths ranging from 200 to 400 nm.

Uniport: a transport system that carries only a single type of solute (unlike symport).

Ureotelic organism: an organism that excretes excess nitrogen in the form of urea.

Uricotelic organism: an organism that excretes excess nitrogen in the form of uric acid (urates).

Leaving group: the part of a molecule that is removed or displaced in an elimination or substitution reaction.

F

Growth factors: proteins or other molecules acting on a cell from the outside to stimulate its growth and division.

Elongation factors: (1) proteins involved in the transcription of eukaryotic DNA during the elongation phase; (2) proteins required for the extension of the polypeptide chain on ribosomes.

Facultative aerobes/anaerobes: cells capable of living in the presence or absence of oxygen.

Phenotype: the observable traits of an organism.

Enzyme: a protein or RNA that catalyzes a specific chemical reaction; an enzyme does not shift the reaction equilibrium, but increases its rate by providing a new reaction pathway with a lower activation energy.

Enzyme cascade: a series of regulatory reactions in which one enzyme activates another (often via phosphorylation), the second activates a third, and so on. This cascade results in a significant amplification of the initial signal.

Enzymes with a cryptic function: enzymes that perform two distinct functions, of which at least one is catalytic; the other function may be regulatory, catalytic, or structural.

Ferredoxin: an iron-sulfur protein (2Fе-2S) of chloroplasts that transfers electrons from iron-sulfur centers associated with Photosystem I to NАDР⁺ during photophosphorylation.

Fibrous proteins: insoluble proteins that perform a protective or structural function; they consist of polypeptide chains with a characteristic secondary structure.

Fibroblast: a CONNECTIVE TISSUE CELL that secretes proteins such as Collagen.

Nitrogen Fixation: the conversion of atmospheric nitrogen into a reduced, biologically available form by nitrogen-fixing organisms.

Carbon fixation: the initial reaction in photosynthesis, catalyzed by rubisco or other carboxylases, in which atmospheric СO₂ is incorporated into an organic compound.

Flavin adenine dinucleotide (FAD): a coenzyme for certain redox enzymes; it contains riboflavin.

Flavin-dependent dehydrogenases: dehydrogenases that use FMN or FAD as cofactors.

Flavin mononucleotide (FMN): riboflavin phosphate, a coenzyme for certain redox enzymes.

Flavin nucleotides: nucleotide Coenzymes (FMN and FAD) containing riboflavin.

Flavoprotein: an enzyme containing a flavin nucleotide as a prosthetic group.

Flippases: membrane proteins belonging to the ABC transporter family that catalyze the movement of phospholipids from the outer leaflet of the bilayer to the cytosolic leaflet.

Floppases: membrane proteins belonging to the ABC transporter family that catalyze the transfer of phospholipids from the cytosolic leaflet of the bilayer to the outer leaflet.

Fluorescence: the emission of light by molecules as they return from an excited state to the ground state.

Phosphatases: enzymes that cleave phosphoester or phosphoanhydride bonds, releasing inorganic phosphate.

Phosphodiester bond: a chemical linkage consisting of two alcohols forming esters with a single molecule of phosphoric acid, which acts as a bridge between them.

Phospholipid: a lipid containing one or more phosphate groups.

Phosphorylases: enzymes that catalyze phosphorolysis.

Phosphorylation: the formation of a phosphate derivative of a biomolecule, usually via the enzymatic transfer of a phosphoryl group from ATP.

Phosphorolysis: the cleavage of bonds by the action of a phosphate group; a process analogous to hydrolysis.

Photoreduction: light-induced reduction of an electron acceptor in photosynthetic cells.

Photorespiration: light-dependent oxygen consumption in plant cells, occurring primarily as a result of phosphoglycolate oxidation.

Photon (quantum): the smallest unit of light energy. Photosynthesis: the use of light energy to synthesize carbohydrates from carbon dioxide and water (with water acting as the reducing agent).

Photosystem: specific Functional groups of light-absorbing pigments and a reaction center in photosynthetic cells.

Phototroph: an organism capable of using light energy to synthesize fuel molecules from simple compounds such as water, carbon dioxide, and oxygen (as opposed to a chemotroph).

Photophosphorylation: the enzymatic formation of ATP from ADP, coupled with light-dependent electron transport in photosynthetic cells. Photochemical reaction center: the part of a photosynthetic complex in which the energy of an absorbed photon causes charge separation, initiating electron transfer.

Fractionation: the process of separating proteins or other complex mixtures into fractions based on properties such as solubility, charge, molecular weight, or function.

Fraction: a portion of a biological sample obtained after a specific procedure designed to separate macromolecules based on their solubility, charge, molecular weight, or function. Functional group: a specific atom or group of atoms that confers specific chemical properties on a biomolecule.

Furanose: a simple sugar containing a five-membered furan ring.

Footprinting: a method for identifying nucleic acid sequences bound by DNA- or RNA-binding proteins.

X

Chemiosmotic theory: the theory that energy from electron-transport reactions is stored as a transmembrane electrical potential and pH gradient, which is subsequently used to drive ATP synthesis in oxidative phosphorylation and photophosphorylation.

Chemiosmotic Coupling: the coupling of ATP synthesis to the flow of protons driven by a transmembrane potential and pH gradient.

Chemotaxis: the ability of cells to sense specific chemical signals and move toward or away from the source.

Chemotroph: an organism that obtains energy through the metabolism of organic substances synthesized by other organisms.

Henderson-Hasselbalch equation: an equation relating pH, pK_a, and the ratio of concentrations of a proton acceptor (A^-) and proton donor (HA) in solution: pH = pK_a + log[A^-]/[HA].

Hill coefficient: a measure of cooperative interaction between protein subunits.

Hill reaction: oxygen evolution and the reduction of an artificially introduced electron acceptor in a chloroplast preparation.

Chylomicron: a plasma lipoprotein consisting of a triacylglycerol core coated with a monolayer of protein and phospholipids, which transports dietary lipids from the intestine to tissues.

Chimeric DNA: DNA containing genetic information from different species of organisms.

Chymotrypsin: a well-studied protease that cleaves the polypeptide chain at the C-terminal side of aromatic amino acid residues. Chymotrypsinogen: the inactive precursor (zymogen) of chymotrypsin.

Chiral compound: a compound containing an asymmetric center (chiral atom or chiral center) that exists as two non-superimposable mirror-image forms (enantiomers).

Chiral center: an atom whose substituents are arranged in such a way that the molecule as a whole cannot be superimposed on its mirror image. Chloroplast: a chlorophyll-containing photosynthetic organelle found in certain eukaryotic cells. Futile cycle: a cycle of enzymatic reactions in which ATP hydrolysis results solely in the release of heat energy.

Holoenzyme: a catalytically active enzyme containing all subunits, prosthetic groups, and cofactors necessary for catalysis.

Chondroitin sulfate: a member of the sulfated glycosaminoglycan family and an essential component of the extracellular matrix.

Chromatin: a filamentous complex formed by DNA, histones, and other proteins that makes up the eukaryotic chromosome.

Chromatography: a method for separating complex mixtures of substances based on their differential distribution between a mobile and a stationary phase.

Chromosome: a single large DNA molecule associated with proteins, containing numerous genes; the structural unit for storing and transmitting genetic information.

C

Zwitterion: a dipolar ion with spatially separated positive and negative charges.

Binding site: a cleft or pocket in a protein molecule that binds a ligand molecule.

Centromere: a specialized region of a chromosome where the spindle fibers attach during mitosis and meiosis.

Cerebroside: a sphingolipid whose polar head group consists of a single sugar residue.

Calvin cycle: a cyclic metabolic pathway in plants that results in carbon dioxide fixation and the formation of triose phosphates.

Citric acid cycle (Krebs cycle or Tricarboxylic Acid Cycle): a cyclic metabolic pathway involving the oxidation of acetyl groups to carbon dioxide; The First stage of the cycle is the formation of citrate (the salt of citric acid).

Urea Cycle: a cyclic metabolic pathway in the liver of vertebrates that converts amino groups and carbon dioxide into urea.

Cyclin: a member of a protein family that regulates the Cell Cycle by activating cyclin-dependent protein kinases.

Cyclic AMP (cAMP): a secondary messenger whose synthesis by adenylate cyclase is stimulated by certain hormones and other signaling molecules.

Cyclic electron flow: a light-driven flow of electrons in chloroplasts that both starts and ends in photosystem I.

Cyclic photophosphorylation: the synthesis of ATP driven by cyclic electron flow through photosystem I.

Zinc fingers: a specific protein structural motif involved in the binding of certain proteins to DNA; it features a zinc atom coordinated to four Cysteine residues or two cysteine and two histidine residues.

Cistron: a segment of DNA or RNA corresponding to a single gene.

Cytosol: the aqueous, organelle-free phase of the cytoplasm containing dissolved solutes.

Cytokine: a member of a family of small secreted proteins (such as interleukins or interferons) that trigger the differentiation or division of target cells by binding to receptors on their plasma membrane.

Cytokinesis: The final division of daughter cells following mitosis.

Cytoplasm: The intracellular content between the nucleus and the plasma membrane; contains various organelles, including mitochondria.

Cytoskeleton: A filamentous network that provides the Structural organization of the cytoplasm; contains actin filaments, microtubules, and Intermediate filaments.

Cytochrome P-450: A family of heme-containing enzymes with a characteristic absorption band at 450 nm, involved in biological hydroxylation reactions.

Cytochromes: Heme proteins that function as electron carriers in respiration, photosynthesis, and other oxidation-reduction reactions.

C

Quaternary structure: The three-dimensional structure of a multimeric protein, describing, in particular, the spatial arrangement of its subunits.

Avogadro number (A): The number of molecules in 1 mole of any substance (N = 6,02 • 10²³ molecules).

Turnover number: The number of substrate molecules converted into product by an enzyme molecule per unit time, under conditions of maximum enzyme activity and at saturating substrate concentration.

S

Shine-Dalgarno sequence: A region of mRNA essential for binding to the bacterial ribosome.

Shuttle vector: A vector DNA capable of replicating in multiple types of host cells.

Hairpin: A secondary structure of single-stranded RNA or DNA; an antiparallel duplex closed at one end, formed by the pairing of palindromic repeats.

E

Ames test: A method for evaluating the carcinogenic (mutagenic) activity of chemical substances using bacterial cells.

Exergonic reaction: A chemical reaction that proceeds with the release of energy (∆G <0).

Exon: A region of a eukaryotic gene that encodes a portion of the final gene product; a region of RNA retained in mature RNA that is translated into protein or incorporated into RNA Structure.

Exonuclease: An enzyme that cleaves terminal nucleotides from a nucleic acid sequence.

Exothermic reaction: A chemical reaction that proceeds with the release of heat (∆H <0).

Exocytosis: The fusion of intracellular vesicles with the plasma membrane, resulting in the release of vesicle contents into the extracellular space.

Size-exclusion chromatography (Gel filtration): A method for separating molecules by size using porous polymers that retain solutes only of specific sizes.

Gene expression: The production of a gene product — transcription and (in the case of a protein-coding gene) translation; evidence of gene expression is the presence of its active product.

Electroporation: The introduction of macromolecules into a cell through the temporary increase in cell membrane permeability induced by a high electrical voltage.

Electrophile: An electron-deficient group with a strong tendency to accept electrons from an electron-rich group (nucleophile).

Electrophoresis: The movement of ions in an electric field; commonly used to separate mixtures of ions, proteins, or nucleic acids.

Electrochemical gradient: associated with the concentration gradient and electrical charge of an ion across a membrane; the driving force for oxidative phosphorylation and photophosphorylation.

Electrochemical potential: the energy required to maintain charge separation and ion concentration across different sides of a membrane.

Hormone response elements (HREs): short DNA sequences (12 to 20 bp) that bind receptors for steroid, retinoid, and THYROID HORMONES as well as vitamin D, thereby altering the expression of target genes. Each hormone has its own consensus sequence.

Eluate: the liquid phase emerging from a chromatography Column.

Enantiomers: stereoisomers that are non-superimposable mirror images of each other.

Endergonic reaction: a chemical reaction that requires an input of energy (∆G> 0).

Endocrine gland: a group of specialized cells that synthesize and secrete hormones into the bloodstream to regulate the activity of other cells.

Endonuclease: an enzyme that hydrolyzes internal phosphodiester bonds within nucleic acid molecules.

Endoplasmic reticulum: an extensive network of bilayer membranes within the cytoplasm of a eukaryotic cell; the region studded with ribosomes is referred to as the rough endoplasmic reticulum.

Endothermic reaction: a chemical reaction that proceeds with the absorption of heat (∆Н> 0).

Endocytosis: a cellular process by which extracellular substances are engulfed into vesicles (endosomes) formed by the invagination of the plasma membrane.

Energy charge: the proportion of high-energy phosphate groups within the ATP/ADP/AMP system.

Energy coupling: the transfer of energy between two processes.

Activation energy (∆G⁺): the amount of energy (in joules) required to convert 1 mole of reactant molecules from their ground state to the transition state.

Bond energy: the energy required to break a chemical bond.

Binding energy: the energy of non-covalent interaction between an enzyme and a substrate or a receptor and a ligand.

Enthalpy (H): the heat content of a system.

Entropy (S): the degree of disorder (randomness) of a system.

Enhancer: a DNA sequence that boosts the expression of a specific gene; it can be located hundreds or even thousands of base pairs away from the gene it regulates.

Epigenetics: the acquisition of a trait by an organism not through changes in The nucleotide sequence of parental chromosomes, but, for example, as a result of covalent histone modifications.

Epimerase: an enzyme that catalyzes the reversible interconversion of two epimers.

Epimers: two stereoisomers that differ in configuration at only one of their asymmetric centers in a molecule containing two or more asymmetric centers.

Epithelial cells: any lining or covering cells of an organism or organ.

Epitope (antigenic determinant): a specific region on the surface of a macromolecule (antigen) that is recognized and bound by a specific antibody.

Epitope tag: a protein sequence or domain that is bound by a well-characterized antibody.

Erythrocytes: red blood cells containing a high concentration of hemoglobin, specialized for Oxygen transport.

Eukaryotes: unicellular or Multicellular Organisms whose cells feature a membrane-bound nucleus, multiple chromosomes, and internal organelles.

Euchromatin: a lightly stained region of an interphase chromosome—in contrast to condensed and heavily stained heterochromatin; frequently corresponds to a transcriptionally active chromosomal region.

I

Nucleus: a membrane-bounded organelle of a eukaryotic cell that contains the chromosomes.

Nucleolus: a prominent, densely stained structure within the nucleus of a eukaryotic cell, involved in rRNA synthesis and ribosome assembly.