Glossary

Glossary Glossary

Acetyl CoA: A metabolic intermediate produced through catabolism of many compounds, including fatty acids, and used as the initial substrate for the central respiratory pathway, the TCA cycle.

Acid: A molecule that is capable of releasing a hydrogen ion.

Acid hydrolases: Hydrolytic enzymes with optimal activity at an acid pH.

Activation energy: The minimal kinetic energy needed for a reactant to undergo a chemical reaction.

Active site: The part of an enzyme molecule that is directly involved in binding the substrate.

Adenosine triphosphate (ATP): Nucleotide consisting of adenosine bonded to three phosphate groups; it is the principal immediateenergy source for prokaryotic and eukaryotic cells.

Aerobes: Organisms dependent on the presence of oxygen to metabolize energy-rich compounds.

Alleles: Alternate forms of the same gene.

Allosteric modulation: Modification of the activity of an enzyme through interaction with a compound that binds to a site (i.e., allosteric site) other than the active site.

Alpha () helix: One possible secondary structure of polypeptides, in which the backbone of the chain forms a spiral (i.e., helical) conformation.

Amide bond: The chemical bond that forms between carboxylic acids and amines (or acidic and amino functional groups) while producing a molecule of water.

Amino acids: The monomeric units of proteins; each is composed of three functional groups attached to a central,  carbon: an amino group, a defining side chain, and a carboxyl group.

Amphipathic: The biologically important property of a molecule having both hydrophobic and hydrophilic regions.

Amphoteric: Structural property allowing the same molecule to act as an acid or as a base.

Anabolic pathway: A metabolic pathway resulting in the synthesis of relatively complex products.

Anaerobes: Organisms that utilize energy-rich compounds through oxygen-independent metabolic pathways such as glycolysis and fermentation. Angstrom: The unit, equivalent to 0.1 nm, used to describe atomic and molecular dimensions.

Anion: An ionized atom or molecule with a net negative charge.

Artifact: A structure seen in a microscopic image that results from the coagulation or precipitation of materials that had no existence in the living cell.

Assay: Some identifiable feature of a specific protein, such as the catalytic activity of an enzyme, used to determine the relative amount of that protein in a sample.

Atomic force microscope (AFM): A high-resolution scanning instrument that is becoming increasingly important in nanotechnology and molecular biology. The AFM operates by scanning a delicate probe over the surface of the specimen.

ATP synthase The ATP-synthesizing enzyme of the inner mitochondrial membrane, which is composed of two chief components: the F1 headpiece and the F0 basal piece, the latter of which is embedded in the membrane itself.

Autoradiography: A technique for visualizing biochemical processes by allowing an investigator to determine the location of radioactively labeled materials within a cell. Tissue sections containing radioactive isotopes are covered with a thin layer of photographic emulsion, which is exposed by radiation emanating from the tissue. Sites in the cells containing radioactivity are revealed under the microscope by silver grains after development of the overlying emulsion.

Autotroph: Organism capable of surviving on CO2 as its principal carbon source.

Base: Any molecule that is capable of accepting a hydrogen ion.

Base composition analysis: The relative amounts of each base in various samples of DNA.

Beta () pleated sheet: One possible secondary structure of a polypeptide, in which several -strands lie parallel to each other, creating the conformation of a sheet.

Beta () strand: One possible secondary structure of a polypeptide, in which the backbone of the chain assumes a folded (or pleate d) conformation.

Biochemicals: Compounds synthesized by living organisms.

Bioenergetics: The study of the various types of energy transformations that occur in living organisms.

Unit 1 reticulum or Golgi complex, modified during passage through the Golgi complex, and transported within the cytoplasm to various destinations such as the plasma membrane, a lysosome, or a large vacuole of a plant cell. The alternative term secretory pathway has been used because many of the materials synthesized in the pathway are destined to be discharged (secreted) outside the cell.

Buffers: Compounds that can interact with either free hydrogen or hydroxyl ions, minimizing a change in pH.

Carbohydrates: (Glycans) Organic molecules including simple sugars (monosaccharides) and multisaccharide polymers, which largely serve as energy-storage and structural compounds in cells.

Catabolic pathway: A metabolic pathway in which relatively complex molecules are broken down into simpler products.

Cation: An ionized atom or molecule with an extra positive charge.

Cellulose: Unbranched glucose polymer with (14) linkages that assembles into cables and serves as a principal structural element of plant cell walls.

Chaperones: Proteins that bind to other polypeptides, preventing their aggregation and promoting their folding and/or assembly into multimeric proteins.

Chaperonins: Members of the Hsp60 class of chaperones, e.g., GroEL, that form a cylindrical complex of 14 subunits within which the polypeptide folding reaction takes place.

Chemiosmotic mechanism: The mechanism for ATP synthesis whereby the movement of electrons through the electron-transport chain results in establishment of a proton gradient across the bacterial, thylakoid, or inner mitochondrial membrane, with the gradient acting as a high-energy intermediate, linking oxidation of substrates to the phosphorylation of ADP.

Chemoautotroph: An autotroph that utilizes the energy stored in inorganic molecules (such as ammonia, hydrogen sulfide, or nitrites) to convert CO2 into organic compounds.

Cholesterol: Sterol found in animal cells that can constitute up to half of the lipid in a plasma membrane, with the relative proportion in any membrane affecting its fluid behavior.

Coactivators: The intermediaries that help bound transcription factors stimulate the initiation of transcription at the core promoter.

Coenzyme: An organic, nonprotein component of an enzyme.

Cofactor The nonprotein component of an enzyme, it can be either inorganic or organic.

Competitive inhibitor: An enzyme inhibitor that competes with substrate molecules for access to the active site. Conjugate acid: Paired form created when a base accepts a proton in an acid-base reaction.

Conjugate base: Paired form created when an acid loses a proton in an acid-base reaction.

Conjugated protein: Protein linked covalently or noncovalently to substances other than amino acids, such as metals, nucleic acids, lipids, and carbohydrates.

Conserved sequences: Refers to the amino acid sequences of particular polypeptides or the nucleotide sequences of particular nucleic acids. If two sequences are similar to one another, i.e., homologous, they are said to be conserved, which indicates that they have not diverged very much from a common ancestral sequence over long periods of evolutionary time.

Constitutive: Occurs in a continual, non-regulated manner. Can relate to a normal process, such as constitutive secretion, or the result of a mutation that leads to a breakdown in regulation, which causes continual activity, such as the constitutive activation of a signaling pathway.

Copper atoms of the electron transport chain: A type of electron carrier; these atoms are located within a single protein complex of the inner mitochondrial membrane that accept and donate a single electron as they alternate between Cu 2+ and Cu 1+ states.

Covalent bond: The type of chemical bond in which electron pairs are shared between two atoms.

Cytochromes: A type of electron carrier consisting of a protein bound to a heme group.

Dalton: A measure of molecular mass, with one dalton equivalent to one unit of atomic mass (e.g., the mass of a 1 H atom).

Dehydrogenase: An enzyme that catalyzes a redox reaction by removing a hydrogen atom from one reactant.

Denaturation: Separation of the DNA double helix into its two component strands.

Denaturation: The unfolding or disorganization of a protein from its native or fully folded state.

Deoxyribonucleic acid (DNA): A double-stranded nucleic acid composed of two polymeric chains of deoxyribose-containing nucleotides. The genetic material of all cellular organisms. DNA may be duplicated as in DNA replication and produced in large quantities of a specific segment as in DNA cloning.

Disulfide bridge: Forms between two cysteines that are distant from one another in the polypeptide backbone or in two separate polypeptides. They help stabilize the intricate shapes of proteins.

DNA gyrase: A type II topoisomerase that is able to change the state of supercoiling in a DNA molecule by relieving the tension that builds up during replication. It does this by traveling along the DNA and

Unit 1 acting like a “swivel,” changing the positively supercoiled DNA into negatively supercoiled DNA.

Dolichol phosphate: Hydrophobic molecule built from more than 20 isoprene units that assembles the basal, or core, segment of carbohydrate chains within glycoproteins.

Domain: A region within a protein (or RNA) that folds and functions in a semi-independent manner.

Electrochemical gradient: The overall difference in electrical charge and in solute concentration that determines the ability of an electrolyte to diffuse between two compartments.

Electrogenic: Any process that contributes directly to a separation of charge across a membrane.

Electron-transfer potential: The relative affinity for electrons, such that a compound with a low affinity has a high potential to transfer one or more electrons in a redox reaction (and thus act as a reducing agent).

Electron-transport or respiratory chain: Membrane-embedded electron carriers that accept high-energy electrons and sequentially lower the energy state of the electrons as they pass through the chain, with the net results of capturing energy for use in synthesizing ATP or other energy-storage molecules.

Electronegative atom: The atom with the greater attractive force; the atom that can capture the major share of electrons of a covalent bond.

Endergonic reactions: Reactions that are thermodynamically unfavorable and cannot occur spontaneously, possessing a ΔG value.

Endoplasmic reticulum (ER): A system of tubules, cisternae, and vesicles that divides the fluid content of the cytoplasm into a luminal space within the ER membrane and a cytosolic space outside the membranes.

Endothermic reactions: Those gaining heat under conditions of constant pressure and volume.

Energy: The capacity to do work, it exists in two forms: potential and kinetic.

Enthalpy change (ΔH): The change during a process in the total energy content of the system.

Entropy (S): A measure of the relative disorder of the system or universe associated with random movements of matter; because all movements cease at absolute zero (0 K), entropy is zero only at that temperature.

Enzyme inhibitor: Any molecule that can bind to an enzyme and decrease its activity, classified as noncompetitive or competitive based on the nature of the interaction with the enzyme. Enzyme–substrate complex: The physical association between an enzyme and its substrate(s), during which catalysis of the reaction takes place.

Enzymes: The vitally important protein catalysts of cellular reactions.

Equilibrium constant of a reaction (Keq): The ratio of product concentrations to reactant concentrations when a reaction is at equilibrium.

Ester bond: The chemical bond that forms between carboxylic acids and alcohols (or acidic and alcoholic functional groups) while producing a molecule of water.

Excited state: Electron configuration of a molecule after absorption of a photon has energized an electron to shift from an inner to an outer orbital.

Exergonic reactions: Reactions those are thermodynamically favorable, possessing a -ΔG value.

Exonuclease: A DNA- or RNA-digesting enzyme that attaches to either the 5’ or 3’ end of the nucleic acid strand and removes one nucleotide at a time from that shrinking end.

Exothermic reactions: Those releasing heat under conditions of constant pressure and volume.

Fats: Molecules consisting of a glycerol backbone linked by ester bonds to three fatty acids, also termed triacylglycerols.

Fatty acid: Long, unbranched hydrocarbon chain with a single carboxylic acid group at one end.

Feedback inhibition: A mechanism to control metabolic pathways where the end product interacts with an enzyme in the pathway, resulting in inactivation of the enzyme.

Fermentation: An anaerobic metabolic pathway in which pyruvate is converted to another molecule (often lactate or ethanol, depending on the organism) and NAD+ is regenerated for use in glycolysis.

First law of thermodynamics: The law of conservation of energy, which states that energy can neither be created nor destroyed.

Flavoproteins: A type of electron carrier in which a polypeptide is bound to one of two related prosthetic groups, either FAD or FMN.

Free energy change: (ΔG) The change during a process in the amount of energy available to do work.

Free radical: Highly reactive atom or molecule that contains a single unpaired electron.

Functional groups: Particular groupings of atoms that tend to act as a unit, often affecting the chemical and physical behavior of the larger organic molecules to which they belong.

Unit 1 Genes: In nonmolecular terms, a unit of inheritance that governs the character of a particular trait. In molecular terms, a segment of DNA containing the information for a single polypeptide or RNA molecule, including transcribed but non-coding regions.

Genetic code: Manner in which the nucleotide sequences of DNA encode the information for making protein products.

Glycogen: Highly branched glucose polymer that serves as readily available chemical energy in most animal cells.

Glycolysis: The first pathway in the catabolism of glucose, it does not require oxygen and results in the formation of pyruvate.

Glycosidic bond: The chemical bond that forms between sugar molecules.

Glycosylation: The reactions by which sugar groups are added to proteins and lipids.

Glycosyltransferases: A large family of enzymes that transfer specific sugars from a specific donor (a nucleotide sugar) to a specific receptor (typically the growing end of an oligosaccharide chain).

Glyoxysomes: Organelles found in plant cells that serve as sites for enzymatic reactions including the conversion of stored fatty acids to carbohydrate.

Guanosine triphosphate (GTP): A nucleotide of great importance in cellular activities. It binds to a variety of proteins (called G proteins) and acts as a switch to turn on their activities.

Half-life: A measure of the instability of a radioisotope, or, equivalently, the amount of time required for one-half of the radioactive material to disintegrate.

Head group: The polar, water-soluble region of a phospholipid that consists of a phosphate group linked to one of several small, hydrophilic molecules.

Heat shock response: Activation of the expression of a diverse array of genes in response to temperature elevation. The products of these genes, including molecular chaperones, help the organism recover from the damaging effects of elevated temperature.

Hemicelluloses: Branched polysaccharides of the plant cell wall whose backbone consists of one sugar, such as glucose, and sidechains of other sugars, such as xylose.

Heterotroph: Organism that depends on an external source of organic compounds.

Highly repeated fraction: Typically short (a few hundred nucleotides at their longest) DNA sequences that are present in at least 105 copies per genome. The highly repeated sequences typically account for about 10 percent of the DNA of vertebrates. hnRNP (heterogeneous nuclear ribonucleoprotein): The result of the transcription of each hnRNA which becomes associated with a variety of proteins; hnRNP represents the substrate for the processing reactions that follow.

Hydrocarbons: The simplest group of organic molecules, consisting solely of carbon and hydrogen.

Hydrogen bond: The weak, attractive interaction between a hydrogen atom covalently bonded to an electronegative atom (thus, with a partial positive charge) and a second electronegative atom.

Hydrophilic: The tendency of polar molecules to interact with surrounding water molecules, which are also polar; derived from “water loving.”

Hydrophobic interaction: The tendency of nonpolar molecules to aggregate so as to minimize their collective interaction with surrounding polar water molecules; derived from “water fearing.”

Induced fit: The conformational change in an enzyme after the substrate has been bound that allows the chemical reaction to proceed.

Introns: Those parts of a split gene that correspond to the intervening sequences.

Ion: An atom or molecule with a net positive or negative charge because it has lost or gained one or more electrons during a chemical reaction.

Ionic bond: A noncovalent bond occurring between oppositely charged ions, also called a salt bridge.

Iron-sulfur proteins: A group of protein electron carriers with an inorganic, iron-sulfur center.

Irreversible inhibitor: An enzyme inhibitor that binds tightly, often covalently, thus inactivating the enzyme molecule permanently.

Isoelectric point: The pH at which the negative charges of the component amino acids of a protein equal the positive charges of the component amino acids, so the protein is neutral.

Isoforms: Different versions of a protein. Isoforms may be encoded by separate, closely related genes, or formed as splice variants by alternative splicing from a single gene.

Kinetic energy: Energy released from a substance through atomic or molecular movements.

Lipids: Nonpolar organic molecules, including fats, steroids, and phospholipids, whose common property of not dissolving in water contributes to much of their biological activity.

Macromolecules: Large, highly organized molecules crucial to the structure and function of cells; divided into polysaccharides, certain lipids, proteins, and nucleic acids.

Mass spectrometry: Methodology to identify molecules (including proteins). A protein or mixture of proteins is fragmented, converted into gaseous ions, and propelled through a tubular component of a mass spectrometer, causing the ions to separate according to their mass/charge (m/z) ratio. Identification of the protein(s) is made by comparison with a computer database of the sequence of proteins encoded by a particular genome.

Maximal velocity (Vmax): The highest rate achieved for a given enzymatically catalyzed reaction, it occurs when the enzyme is saturated with substrate.

Membrane potential: The electrical potential difference across a membrane.

Messenger RNA (mRNA): The intermediate molecule between a gene and the polypeptide for which it codes. Messenger RNA is assembled as a complementary copy of one of the two DNA strands that encodes the gene.

Metabolic intermediate: A compound produced during one step of a metabolic pathway.

Metabolic pathway: A series of chemical reactions that results in the synthesis of an end product important to cellular function.

Metabolism: The total of the chemical reactions occurring within a cell.

Methylguanosine cap: Modification of the 5’ end of an mRNA precursor molecule, so that the terminal “inverted” guanosine is methylated at the 7’ position on its guanine base, while the nucleotide on the internal side of the triphosphate bridge is methylated at the 2’ position of the ribose. This cap prevents the 5’ end of the mRNA from being digested by nucleases, aids in transport of the mRNA out of the nucleus, and plays a role in the initiation of mRNA translation.

Michaelis constant (Km) In enzyme kinetics, the value equal to the substrate concentration present when reaction rate is one-half of the maximal velocity.

MicroRNAs (miRNAs): Small RNAs (20-23 nucleotides long) that are synthesized from many sites in the genome and involved in inhibiting translation or increasing degradation of complementary mRNAs.

Mitochondrial matrix: The aqueous compartment within the interior of a mitochondrion. Mitochondrial membranes The outer membrane serves as a boundary with the cytoplasm and is relatively permeable, and the inner membrane houses respiratory machinery in its many invaginations and is highly impermeable.

Mitochondrion: The cellular organelle in which aerobic energy transduction takes place, oxidizing metabolic intermediates such as pyruvate to produce ATP. genome. The moderately repeated fraction of the DNA can vary from about 20 to about 80 percent of the total DNA. These sequences may be identical to each other or nonidentical but related.

Molecular chaperones: Various families of proteins whose role is to assist the folding and assembly of proteins by preventing undesirable interactions.

Motif: A substructure found among many different proteins, such as the  barrel, which consists of  strands connected by an -helical region.

Multiprotein complex: The interaction of more than one complete protein to form a larger, functional complex.

Nanometer: Measure of length equaling 10 -9 meters.

Nascent protein: A protein in the process of being synthesized, i.e., not yet complete.

Noncompetitive inhibitor: An enzyme inhibitor that does not bind at the same site as the substrate, and so the level of inhibition depends only on the concentration of inhibitor.

Noncovalent bond: A relatively weak chemical bond based on attractive forces between oppositely charged regions within a molecule or between two nearby molecules.

Nonpolar molecules: Molecules whose covalent bonds have a nearly symmetric distribution of charge because the component atoms have approximately the same electronegativities.

Nonrepeated fraction: Those DNA sequences in the genome that are present in only one copy per haploid set of chromosomes. These sequences contain the greatest amount of genetic information including the codes for virtually all proteins other than histones.

Nucleic acid: Polymers composed of nucleotides, which in living organisms are based on one of two sugars, ribose or deoxyribose, yielding the terms ribonucleic acid (RNA) and deoxyribonucleic acid (DNA).

Nucleic acid hybridization: A variety of related techniques that are based on the fact that two single-stranded nucleic acid molecules of complementary base sequence will form a double-stranded hybrid.

Nucleotide: The monomer of nucleic acids, each consists of three parts: a sugar (either ribose or deoxyribose), a phosphate group, and a nitrogenous base, with the phosphate linked to the sugar at the 5’ carbon and the base at the 1’ carbon.

Oils: Fats that are liquid at room temperature.

Oligosaccharides: Small chains composed of sugars covalently attached to lipids and proteins; they distinguish one type of cell from another and help mediate interactions of a cell with its surroundings.

Unit 1 Operon: A functional complex on a bacterial chromosome comprising a cluster of genes including structural genes, a promoter region, an operator region, and a regulatory gene.

Oxidation: The process through which an atom loses one or more electrons to another atom, in which the atom gaining electrons is considered to be reduced.

Oxidation-reduction (redox) potential: The separation of charge, measured in voltage, for any given pair of oxidizing-reducing agents, such as NAD + and NADH, relative to a standard couple (e.g., H+ and H2 ).

Oxidation-reduction (redox) reaction: One in which a change in the electronic state of the reactants occurs.

Oxidative phosphorylation: ATP formation driven by energy derived from high-energy electrons removed during substrate oxidation in pathways such as the TCA cycle, with the energy released for ATP formation by passage of the electrons through the electron- transport chain in the mitochondrion.

Oxidizing agent: The substance in a redox reaction that becomes reduced, causing the other substance to become oxidized

Peptide bond: The chemical bond linking amino acids in a protein, which forms when the carboxyl group of one amino acid reacts with the amino group of a second amino acid.

pH: The standard measure of relative acidity, it mathematically equals -log[H + ].

Phosphoglycerides: The name given to membrane phospholipids that are built on a glycerol backbone.

Photoautotroph: An autotroph that utilizes the radiant energy of the sun to convert CO2 into organic compounds.

PiwiRNAs (piRNAs): Small RNAs (24-32 bases) that are encoded by a small number of large genomic loci and act to suppress the movement of transposable elements in germ cells. piRNAs are derived from single-stranded precursors and do not require Dicer for processing.

Polar molecules: Molecules with an uneven distribution of charge because the component atoms of various bonds have greatly different electronegativities.

Poly(A) tail: A string of adenosine residues at the 3’ end of an mRNA added posttranscriptionally.

Polyacrylamide gel electrophoresis (PAGE): Protein fractionation technique in which the proteins are driven by an applied current through a gel composed of a small organic molecule (acrylamide) that is cross-linked to form a molecular sieve.

Polypeptide chain: A long, continuous unbranched polymer formed by amino acids joined to one another by covalent peptide bonds. Potential difference: The difference in charge between two compartments, often measured as voltage across the separating membrane.

Potential energy: Stored energy that can be used to perform work.

Pre-RNA: An RNA molecule that has not yet been processed into its final mature form (e.g., a pre-mRNA, pre-rRNA, or pre-tRNA).

Primary structure: The linear sequence of amino acids within a polypeptide chain.

Primary transcript (or pre-RNA): The initial RNA molecule synthesized from DNA, which is equivalent in length to the DNA from which it was transcribed. Primary transcripts typically have a fleeting existence, being processed into smaller, functional RNAs by a series of “cut-andpaste” reactions.

Prosthetic group: A portion of a protein that is not composed of amino acids, such as the heme group within hemoglobin and myoglobin.

Proteins: Structurally and functionally diverse group of polymers built of amino acid monomers.

Proteoglycan: A protein-polysaccharide complex consisting of a core protein molecule to which chains of glycosaminoglycans are attached. Due to the acidic nature of the glycosaminoglycans, proteoglycans are capable of binding huge numbers of cations, which in turn draw huge numbers of water molecules. As a result, proteoglycans form a porous, hydrated gel that acts like a “packing” material to resist compression.

Proteome: The entire inventory of proteins in a particular organism, cell type, or organelle.

Proton-motive force (Δp): An electrochemical gradient that is built up across energy-transducing membranes (inner mitochondrial membrane, thylakoid membrane, bacterial plasma membrane) following the translocation of protons during electron transport. The energy of the gradient, which is comprised of both a pH gradient and a voltage and is measured in volts, is utilized in the formation of ATP.

Purine: A class of nitrogenous base found in nucleotides that has a double-ring structure, including adenine and guanine, which are found in both DNA and RNA.

Pyrimidine: A class of nitrogenous base found in nucleotides that has a single-ring structure, including cytosine and thymine, which are found in DNA, and cytosine and uracil, which are found in RNA.

Quaternary structure: The three-dimensional organization of a protein that consists of more than one polypeptide chain, or subunit.

rDNA: The DNA sequences encoding rRNA that are normally repeated hundreds of times and are typically clustered in one or a few regions of the genome.

Unit 1 Reannealing (renaturation): Reassociation of complementary single strands of a DNA double helix that had been previously denatured.

Reducing agent: The substance in a redox reaction that becomes oxidized, causing the other substance to become reduced.

Reducing power: The potential in a cell to reduce metabolic intermediates into products, usually measured through the size of the NADPH pool.

Reduction: The process through which an atom gains one or more electrons from another atom, in which the atom losing electrons is considered to be oxidized.

Ribonucleic acid (RNA): A single-stranded nucleic acid composed of a polymeric chain of ribose-containing nucleotides.

Ribosomal RNAs (or rRNAs): The RNAs of a ribosome. rRNAs recognize and bind other molecules, provide structural support, and catalyze the chemical reaction in which amino acids are covalently linked to one another.

Riboswitches: mRNAs that, once bound to a metabolite, undergo a change in their folded conformation that allows them to alter the expression of a gene involved in production of that metabolite. Most riboswitches suppress gene expression by blocking either termination of transcription or initiation of translation.

Ribozyme: An RNA molecule that functions as a catalyst in cellular reactions.

RNA interference (RNAi): A naturally occurring phenomenon in which double-stranded RNAs (dsRNAs) lead to the degradation of mRNAs having identical sequences. RNAi is believed to function primarily in blocking the replication of viruses and restricting the movement of mobile elements, both of which involve the formation of dsRNA intermediates. Mammalian cells can be made to engage in RNAi by treatment of the cells with small (21 nt) RNAs. These small RNAs (siRNAs) induce the degradation of mRNAs that contain the same sequence.

RNA silencing: A process in which small, noncoding RNAs, typically derived from longer double-stranded precursors, trigger sequencespecific inhibition of gene expression.

RNA splicing: The process of removing the intervening DNA sequences (introns) from a primary transcript.

Saturated fatty acids: Those lacking double bonds between carbons.

Second law of thermodynamics: Events in the universe proceed from a state of higher energy to a state of lower energy.

Secondary structure: The three-dimensional arrangement of portions of a polypeptide chain.

Side chain or R group: The defining functional group of an amino acid, which can range from a single hydrogen to complex polar or nonpolar units in the 20 amino acids most commonly found in cells. Small interfering RNAs (siRNAs): Small (21-23 nucleotide), doublestranded fragments formed when double-stranded RNA initiates the response during RNA silencing.

Small nuclear RNAs (snRNAs): RNAs required for mRNA processing that are small (90 to 300 nucleotides long) and that function in the nucleus.

Small-nucleolar RNAs (snoRNAs): RNAs required for the methylation and pseudouridylation of pre-rRNAs during ribosome formation in the nucleolus.

snoRNPs: (small, nucleolar ribonucleoproteins) Particles that are formed when snoRNAs are packaged with particluar proteins; snoRNPs play a role in the maturation and assembly of ribosomal RNAs.

snRNPs: Distinct ribonucleoprotein particles contained in spliceosomes, so called because they are composed of snRNAs bound to specific proteins.

Specific activity: The ratio of the amount of a protein of interest to the total amount of protein present in a sample, which is used as a measure of purification.

Specificity: The property of selective interaction between components of a cell that is basic to life.

Spontaneous reactions: Reactions that are thermodynamically favorable, capable of occurring without any input of external energy.

Standard free-energy change (ΔG°’): The change in free energy when one mole of each reactant is converted to one mole of each product under defined standard conditions: temperature of 298 K and pressure of 1 atm.

Starch: Mixture of two glucose polymers, amylose and amylopectin, that serves as readily available chemical energy in most plant cells.

Steady state: Metabolic condition in which concentrations of reactants and products are essentially constant, although individual reactions may not be at equilibrium.

Stereoisomers: Two molecules that structurally are mirror images of each other and may have vastly different biological activity.

Steroid: Lipid molecule based on a characteristic four-ring hydrocarbon skeleton, including cholesterol and hormones such as testosterone and progesterone.

Structural isomers: Molecules having the same chemical formula but different structures.

Substrate: The reactant bound by an enzyme.

Substrate-level phosphorylation: Direct synthesis of ATP through the transfer of a phosphate group from a substrate to ADP.

Subunit: A polypeptide chain that associates with other chains (subunits) to form a complete protein or protein complex.

tDNA: The DNA encoding tRNAs.

Tandem repeats: A cluster in which a DNA sequence repeats itself over and over again without interruption.

Telomere: An unusual stretch of repeated DNA sequences, which forms a “cap” at each end of a chromosome.

Template: A single strand of DNA (or RNA) that contains the information (encoded as a nucleotide sequence) for construction of a complementary strand.

Tertiary structure: The three dimensional shape of an entire macromolecule.

Thermodynamics: Study of the changes in energy accompanying events in the physical universe.

Transfer potential: A measure of the ability of a molecule to transfer any group to another molecule, with molecules having a higher affinity for the group being the better acceptors and molecules having a lower affinity better donors. Transfer RNAs (tRNAs): A family of small RNAs that translate the information encoded in the nucleotide “alphabet” of an mRNA into the amino acid “alphabet” of a polypeptide.

Transition state: The point during a chemical reaction at which bonds are being broken and reformed to yield products.

Triacylglycerols: Polymers consisting of a glycerol backbone linked by ester bonds to three fatty acids, commonly called fats.

Tricarboxylic acid cycle (TCA cycle): The circular metabolic pathway that oxidizes acetyl CoA, conserving its energy; the cycle is also known as the Krebs cycle or the citric acid cycle.

Turnover number: The maximum number of substrate molecules that can be converted to product by one enzyme molecule per unit of time.

Ubiquinone: A component of the electron transport chain, ubiquinone is a lipid-soluble molecule containing a long hydrophobic chain composed of five-carbon isoprenoid units.

Van der Waals force: A weak attractive force due to transient asymmetries of charge within adjacent atoms or molecules.

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END OF UNIT 1