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Kaplan Biochemistry
| Term | Definition |
|---|---|
| A-Helix | An element of polypeptides secondary structure, marked by clockwise coiling of amino acids around a central axis |
| Acetyl-CoA | An important metabolic intermediate that links glycolysis and B-oxidation to the citric acid cycle; can also be converted into ketone bodies |
| Activation | Conversion of a biomolecule to its active or usable form, such as activating tRNA with an amino acid or activating a fatty acid with CoA to for a fatty acyl-CoA |
| Active Site | The catalytically active potion of an enzyme |
| Active Transport | The movement of a molecule against its concentration gradient with energy investment; primary active transport uses ATP, whereas secondary active transport couples energetically costly movement to that of a favorable transport gradient of a different mole |
| Activity(V_Max) | Also sometimes called velocity or rate, this is a measure of the catalytic activity of an enzyme; the measurement by which activity is often assessed, and may be analyzed after protein isolation |
| Adenosine Triphosphate (ATP) | The primary energy molecule of the body; energy is released by breaking the molecule's bond with terminal phosphate to form ADP and an inorganic phosphate |
| Aerobic Respiration | Energy-producing metabolic processes that require oxygen. These include the citric acid cycle, electron transport chain, and oxidative phosphorylation |
| Allosteric Enzymes | Enzymes that experience changes in their conformation as a result of interactions at sites other than the active site (allosteric sites); the conformational changes that result may increase or decrease enzyme activity |
| Alternative Splicing | The production of multiple different but related mRNA molecules from a single primary transcript of hnRNA |
| Amino Acid | A dipolar compound containing an amino group(-NH_2) and a carboxyl group (-COOH) |
| Amplification | Increase transcription (and translation) of a gene in response to hormones, growth factors, and other intracellular conditions |
| Anabolism | Metabolic processes that result in the consumption of energy and the synthesis of molecules |
| Anerobic Respiration | Energy-producing metabolic processes that do not require oxygen, including glycolysis and fermentation |
| Anomers | A subtype of epimers in which the chiral carbon with inverted configuration is the carbonyl carbon (anomeric carbon) |
| Anticodon | A three-nucleotide sequence on a tRNA molecule that pairs with a corresponding mRNA codon during translation |
| Apoenzyme | An enzyme devoid of the prosthetic group, coenzyme, or cofactor necessary for normal activity |
| Apolipoprotein | Protein component of lipoprotein complexes. Responsible for the interactions of the resultant lipoproteins with cells and the transfer of lipid molecules |
| B-Oxidation | The catabolism of fatty acids to acetyl-CoA |
| B-Pleated Sheet | An element of polypeptide secondary structure characterized by peptide chains lying alongside one another, forming rows or strands |
| Basal Metabolic Rate | The amount of energy consumes in a given period of time by an organism while in a resting, nonmobile state |
| Bradford Protein Assay | A colorimetric method of determining the concentration of protein in a sample as compared to a protein standard; relies on a transition of absorption between bound and unbound Coomassie Brilliant Blue dye |
| Catabolism | Metabolic processes that result in the release of energy and the breakdown of molecules |
| Cell Adhesion Molecules (CAMs) | Specialized structural proteins that are involved in cell-to-cell junctions as well as transient cellular interactions; common cell adhesion molecules include cadherins, integrins, and selectins |
| Central Dogma of Molecular Biology | The major steps in the transfer of genetic information from the transcription of DNA to RNA and resultant translation of the RNA to protein |
| Centrifugation | The process of separating components on the basis of their density and resistance to flow by spinning a sample at very high speeds; the most dense components form a solid pellet and the least dense components remain in the supernatant (liquid portion) |
| Ceramide | The simplest sphingolipid, with a single hydrogen as its head group |
| Cerebroside | A sphingolipid containing a carbohydrate as a head group |
| Chaperones | Proteins that assist in protein folding during posttranslational processing |
| Chemiosmotic Coupling | A more widely accepted method of ATP synthase activity. Utilization of the proton-motive force generated by the electron transport chain to drive ATP synthesis in oxidative phosphorylation |
| Cholesterol | A molecule containing four linked rings; provides both fluidity and stability to cell membranes and is the precursor for steroid hormones |
| Citric Acid Cycle | A metabolic pathway that produces GTP, energy carriers, and carbon dioxide as it burns acetyl-CoA; also called the Krebs cycle or tricarboxylic acid (TCA) cycle; can share intermediates with many other metabolic processes including fatty acid and choleste |
| Coding Strand | The strand of DNA that is not used as a template during transcription; also called the sense strand |
| Codon | A three-nucleotide sequence in an mRNA molecule that pairs with an appropriate tRNA anticodon during translation |
| Coenzyme | An organic molecule that helps an enzyme carry out its function |
| Cofactor | An inorganic molecule or ion that helps enzyme carry out its function |
| Competitive Inhibition | A decrease in enzyme activity that results from the interaction of an inhibitor with the active site of an enzyme; competitive inhibition can be overcome by addition of excess substrate |
| Conformational Coupling | A less-accepted mechanism of ATP synthase activity in which the protons cause a conformational change that releases ATP from ATP synthase |
| Conjugated Protein | A protein that derives part of its function from covalently attached molecules (prosthetic groups) |
| Cooperativity | The interaction between subunits of a multisubunit protein in which binding of substrate to one subunit increases the affinity of other subunits for the substrate; unbinding of substrate from one subunit decreases the affinity of other subunits for the su |
| Corepressor | A species that binds with a repressor, allowing the complex to bind to the operator region of an operon, stopping transcription of the relevant gene |
| Cristae | Infoldings of the inner mitochondrial membrane that increase the surface area available for electron transport chain complexes |
| Degenerate | Description of an aspect of the genetic code; specifically, that more than one codon can specify a single amino acid |
| Denaturation | The loss of tertiary structure in a protein, leading to loss of function |
| Deoxyribonucleic Acid (DNA) | A nucleic acid found exclusively in the nucleus that codes for all the genes necessary for life; transcribed to mRNA and always read 5' to 3' |
| Desmosomes | Cell-to-cell junctions that anchor layers of epithelial cells to one another |
| Disulfide Bond | A covalent interaction between the-SH groups of two cysteine residues; an element of tertiary and quaternary structure in protein |
| Electrochemical Gradient | An uneven separation of ions across a biological membrane, resulting in electrical potential across the membrane |
| Electrophoresis | The process of separating compounds on the basis of size and charge using porous gel and an electric field; protein electrophoresis generally uses polyacrylamide, while nucleus acid electrophoresis generally uses agarose |
| Elongation | The three-step cycle repeated for each amino acid being added to a protein during translation |
| Endocytosis | The transport of molecules into a cell through invagination of the cell and the formation of a vesicle; phagocytosis (cell eating) is the endocytosis of solids, pinocytosis (cell drinking) is the endocytosis of liquids |
| Enhancer | Portion of DNA that can be bound by transcription factors to increase transcription of a gene |
| Enzyme | A biological molecule with catalytic activity; includes many proteins and some RNA molecules |
| Epimers | A subtype of diastereomers that differ in absolute configuration at exactly one chiral carbon |
| Euchromatin | Loose, less dense collections of DNA that appear light-colored under the microscope; transcriptionally active |
| Exocytosis | The transport of molecules out of a cell by release from a transport vesicle; the vesicle fuses to the cell membrane during secretion |
| Exon | A portion of hnRNA that is spliced together with other exons to form mature mRNA |
| Facilitated Diffusion | The movement of solute molecules through the cell membrane down their concentration gradient via a transport protein or channel; used for ions and large or polar molecules |
| Fatty Acid | A monocarboxylic acid without additional substituents; fatty acids may be saturated (all single bonds) or unsaturated contain at least one double bond); natural unsaturated fatty acids are in the cis conformation |
| Feedback Inhibition | The inhibition of an enzyme by its product (or a product further down in a metabolic pathway); used to maintain homeostasis |
| Feed-Forward Activation | The stimulation of an enzyme by an intermediate that precedes the enzyme in a metabolic pathway |
| Fermentation | The conversion of pyruvate to either ethanol and carbon dioxide (yeast) or lactic acid (animal cells); does not require oxygen |
| Fischer Projection | A method of drawing organic molecules in which horizontal lines are coming out of the page (wedges) and vertical lines are going into the page (dashes) |
| Flavin Adenine Dinucleotide (FAD) | An energy carrier that participates as an electron acceptor and donor in the electron transport chain |
| Fluid Mosaic Model | The representation of the plasma membrane as a dynamic phospholipid bilayer that interacts with cholesterol and proteins |
| Furanose | A five-membered ring sugar |
| G Protein-Coupled Receptors | A special class of membrane receptors with an associated GTP binding protein; activation involves dissociation and GTP hydrolysis |
| Ganglioside | A sphingolipid with a head group containing an oligosaccharide and one or more N-acetylneuraminic acid (NANA) molecules |
| Gap Junctions | Cell-to-cell junctions that allow the passage of small molecules between adjacent cells |
| Globoside | A sphingolipid with multiple carbohydrate groups attached as a head group |
| Glucogenic | Describes amino acids that can be converted into intermediates that feed into gluconeogenesis; all amino acids except leucine and lysine |
| Gluconeogenesis | The production of glucose from other biomolecules; carried out by the liver and kidneys |
| Glucose | The primary monosaccharide used for fuel by all cells of the body; has the formula C_6 H_12 O_6 |
| Glycerol | A three-carbon alcohol that serves as the backbone for glycerophospholipids, sphingolipids, and triacylglycerols |
| Glycerophospholipid | A lipid containing a glycerol backbone with a phosphate group; bound by ester linkages to two fatty acids |
| Glycogen | A branched polymer of glucose that represents a storage form of glucose |
| Glycolysis | The breakdown of glucose into two molecules of pyruvate with the formation of energy carriers (NADH); occurs under both aerobic and anaerobic conditions |
| Glycosidic Linkage | The bond between the anomeric carbon of a sugar and another molecule |
| Glycosphingolipid | A sphingolipid with a head group composed of sugars; includes cerebrosides and globosides |
| Helicase | An enzyme that unwinds the double helix of a DNA molecule, allowing replication to take place |
| Heterochromatin | Dense, tightly coiled DNA that appears dark colored under the microscope; transcriptionally active |
| Heterogeneous Nuclear RNA (hnRNA) | Preprocessed mRNA; converted to mRNA by adding a poly-A tail and 5' cap and splicing out introns |
| Histone | A structural protein around which DNA is coiled in eukaryotic cells |
| Holoenzyme | An enzyme that has already bound a required prosthetic group, coenzyme, or cofactor |
| Hydrophilic | Being attracted to water; describes polar and charged compounds and those that can participate in hydrogen bonding |
| Hydrophobic | Being repelled by water describes nonpolar, uncharged compounds (usually lipids or certain R groups of amino acids) |
| Hypertonic | A solution that has a greater concentration than the one to which it is being compared |
| Hypotonic | A solution that has a lower concentration than the one to which it is being compared |
| Induced Fit Model | The best supported of the most prominent theories of enzyme specifically; states that the enzyme and substrate experience a change in conformation during binding to increase complementarity |
| Inducible System | An operon that requires an inducer to remove a repressor protein from the operator site to being transcription of the relevant gene; also called positive control system |
| Initiation | The start of translation, in which the small subunit of ribosome binds to the mRNA molecule and the first tRNA (methionine or N-formyl methionine) is bound to the start codon |
| Intron | A portion of the hnRNA that is spliced out to form mRNA; remains in the nucleus during processing |
| Irreversible Inhibition | A decrease in enzyme activity that results from the interaction of an inhibitor that bonds permanently at either the active site or an allosteric site; in laboratory settings, irreversible inhibitors are sometimes called suicide substrates |
| Isoelectric Focusing | A specialized method of separating proteins by their isoelectric point using electrophoresis; the gel is modified to possess a pH gradient |
| Isoelectric Point (pl) | The pH at which an amino acid is predominantly in zwitterionic form |
| Isoform | A slightly different version of the same protein, often specific to a given tissue |
| Isotonic | A solution that has the same concentration as the one to which it is being compared |
| Jacob-Monod Model | The description of the structure and function of operons in prokaryotes, in which operons have structural genes, an operator site , a promoter site, and a regulator gene |
| Ketogenesis | The synthesis of ketone bodies from the metabolic products of B-oxidation or amino acid metabolism; occurs under conditions of starvation |
| Ketogenic | Describes amino acids that can be converted into intermediates that feed into ketogenesis |
| Kinase | A specific transferase enzyme that catalyzes the movement of a phosphate group, generally from ATP, to a molecule of interest |
| K_m | The concentration of substrate at which an enzyme runs at half its maximal velocity; a measure of enzyme affinity (high the measurement the lower the affinity) |
| Lagging Strand | The strand of DNA that is synthesized in small fragments, called Okazaki fragments, and then ligated together. Okazaki fragments are synthesized in the 5' to 3' direction, but the overall synthesis is in the 3' to 5' direction |
| Lariat | The lasso-shaped structure formed during the removal of introns in mRNA processing |
| Leading Strand | The strand of DNA that is continuously synthesized in the 5' to 3' direction. Template strand is read in the 3' to 5' direction |
| Ligase | An enzyme that catalyzes the joining of large polymeric biomolecules, most commonly nucleic acids |
| Lipoprotein | The transport mechanism for lipids within the circulatory and lymphatic systems; includes chylomicrons and VLDL, which transport mostly triacyclglycerols, and HDL, IDL, and LDL, which transport mostly cholesterol and cholesteryl ester |
| Lock and Key Theory | One of the two most prominent theories of enzyme specificity; states that the enzyme and the substrate have a static but complementary state. Less supported than the induced fit model |
| Lyase | An enzyme that catalyzes the cleavage or synthesis of a molecule without the addition of loss of water |
| Matrix | Contents of the inner mitochondrial membrane; includes soluble enzymes of the electron transport chain and mitochondrial DNA |
| Membrane Receptors | Transmembrane protein molecules that act enzymatically or as ion channels to participate in signal transduction |
| Messenger RNA (mRNA) | The strand of RNA formed after transcription of DNA; moves to the cytoplasm to be translated |
| Micelle | A collection of fatty acid or phospholipid molecules oriented to minimize free energy through hydrophobic and hydrophilic interactions; generally a sphere with a hydrophobic core and hydrophilic exterior |
| Mixed Inhibition | A decrease in enzyme activity that results from the interactions of an inhibitor with allosteric site; mixed inhibitors bind to the free enzyme and to the substrate-bound enzyme with different affinities. Cannot be over come by addition of substrate and i |
| Monocistronic | The coding pattern seen in the vast majority of eukaryotic proteins in which one mRNA molecule codes for only one protein |
| Motor Proteins | Proteins that are involved in cell mobility through interactions with structural proteins; motor proteins have ATPase activity and include myosin, kinesin, and dynein |
| Mutarotation | The rapid interconversion between different anomers of a sugar |
| Nicotinamide Adenine Dinucleotide (NAD+) | An energy carrier that accepts electrons through carious processes and feeds them into the electron transport chain |
| Nicotinamide Adenine Dinucleotide Phosphate (NADP+) | An electron acceptor important in the pentose phosphate pathway that is involved in biosynthesis, oxidative stress, and immune function |
| Noncompetitive Inhibition | A decrease in enzyme activity that results from the interaction of an inhibitor with an allosteric site; noncompetitive inhibitors bind equally well to free enzymes and to substrate-bound enzymes. Cannot be overcome by the addition of substrate |
| Nontemplate Synthesis | The method of de novo synthesis of lipids and carbohydrates that relies on gene expression and enzyme specificity rather than the genetic template of DNA or RNA |
| Operator Site | A component of the operon in prokaryotes; a nontranscribable region of DNA that is capable of binding a repressor protein |
| Operon | In prokaryotes, a cluster of genes transcribed as a single mRNA that can be regulated by repressors or inducers, depending on the system |
| Osmosis | The simple diffusion of water |
| Osmotic Pressure | The pressure necessary to counteract the effect of an osmotic gradient against pure water; one of the colligative properties; can be thought of as a 'sucking' pressure created by solutes drawing in water |
| Oxidative Phosphorylation | The transfer of phosphate group, generally to ATP, which is powered by a gradient formed by oxidation reduction reactions; occurs in the mitochondria |
| Pancreatic Proteases | The enzyme that are primarily responsible for the digestion of proteins in the small intestine; they include trypsin, chymotrypsin, and carboxypeptidases A and B, all of which are secreted as zymogens |
| Paracellular Transport | Transport of material through the interstitial space without interactions with the cytoplasm or cell membrane |
| Passive Transport | The movement of a molecule down its concentration gradient without energy investment, includes simple diffusion and facilitated diffusion and osmosis |
| Pentose Phosphate Pathway | A metabolic process that produces NADPH and ribose 5-phosphate for nucleotide synthesis |
| Peptide | A molecule composed of more than one amino acid; can be divided into dipeptides (two amino acids), tripeptides (three), oligopeptides (up to 20), and polypeptides (more than 20) |
| Peptide Bond | An amide bond between the carboxyl group of one amino acid and the amino group of another amino acid |
| Phospholipid | A lipid containing a phosphate and an alcohol (glycerol or sphingosine) joined to hydrophobic fatty acid tails |
| Polycistronic | The coding pattern of prokaryotes, in which one mRNA may code for multiple proteins |
| Polysaccharide | A long chain of monosaccharides linked by glycosidic bonds; can be divided into homopolysaccharides (only one type of monosaccharide is used) and heteropolysaccharides (more than one type of monosaccharide is used) |
| Primary Structure | The linear sequence of amino acids in a polypeptide |
| Promoter Region | Portion of DNA upstream from a gene; contains the TATA box, which is the site where RNA polymerase II binds to start transcription |
| Prostaglandins | A group of 20-carbon molecules that are unsaturated carboxylic acids derived from arachidonic acid; act as a=paracrine or autocrine hormones |
| Prosthetic Group | A cofactor or coenzyme that is covalently bonded to a protein to permit its function |
| Pyranose | A six-membered ring sugar |
| Pyruvate | An important metabolic intermediate that can feed into the citric acid cycle, fermentation, or gluconeogenesis |
| Quaternary Structure | The interaction between different subunits of a multisubunit protein; stabilized by R group interactions |
| Reaction Coupling | The tendency of energetically unfavorable biological reactions to occur concurrently with favorable reactions, often catalyzed by a single enzyme |
| Reducing Sugar | A sugar that can reduce other compounds and that can be picked up by Tollens' or Benedict's reagent |
| Release Factor | The protein that binds to the stop codon during termination of translation |
| Renaturation | Regaining the correct tertiary structure after denaturation of a protein |
| Repressible System | An operon that requires a repressor to bind to a corepressor before bonding to the operator site to stop transcription of the relevant gene; also called negative control system |
| Respiratory Quotient | A numerical representation that can be sued to determine the prevalent type of biomolecule being used in metabolism; the ratio of carbon dioxide produced to oxygen consumed |
| Resting Membrane Potential | The electrical potential that results from the unequal distribution of charge around the cell membrane; resting membrane potential characterizes a cell that has not been stimulated |
| Ribosomal RNA (rRNA) | The structural ad enzymatic RNA found in ribosomes that takes part in translation |
| Ribozyme | An RNA molecule with enzymatic activity |
| Saponification | The reaction between a fatty acid and a strong base resulting in a negatively charged fatty acid anion bound to a metal ion; creates soap |
| Saturation | Refers to the presence or absence of double bonds in a fatty acid; saturated fatty acids have one only single bonds, whereas unsaturated fatty acids have at least one double bond |
| Secondary Structure | The local structure of neighboring amino acids in a polypeptide or protein; most common are a-helices and B-pleated sheets |
| Shine-Dalgarno Sequence | The site of initiation of translation in prokaryotes |
| Shuttle Mechanism | A method of functionally transferring a compound across a membrane without the actual molecule crossing; common examples are the glycerol 3-phosphate shuttle and the malate-aspartate shuttle |
| Side Chain | The variable component of an amino acid that gives it its identity and chemical properties; also called an R group |
| Simple Diffusion | The movement of solute molecules through the cell membrane down their concentration gradient without a transport protein; used for small, nonpolar, lipophilic molecules and water |
| Sphingolipid | A lipid containing a sphingosine or spingoid backbone bound to fatty acid tails; includes ceramide, sphingomyelins, glycosphingolipids, and gangliosides |
| Sphingomyelin | A sphingophospholipid containing a sphingosine backbone and a phosphate head group |
| Spliceosome | The apparatus used for splicing out introns and brining exons together during mRNA processing |
| Start Codon | The first codon in an mRNA molecule that codes for an amino acid |
| Stop codon | The last codon translation; release factor bonds here terminating translation |
| Structural Proteins | Proteins that are involved in the cytoskeleton and extracellular matrix; they are generally fibrous in nature and include collagen, elastin, keratin, actin, and tubulin |
| Substrate | The molecule upon which an enzyme acts |
| Substrate-Level Phosphorylation | The transfer of a phosphate group from a her-energy compound to ATP or another compound; occurs in glycolysis |
| Surfactant | A compound that lowers surface tension by acting as a detergent or emulsifier |
| TATA Box | The site of binding for RNA polymerase II during transcription; named for its high concentration of thymine and adenine bases |
| Template Strand | The strand of DNA that is transcribed to form mRNA; also called the antisense strand |
| Termination | The end of translation, in which the ribosome finds a stop codon and release facto bind to it, allowing the peptide to be freed from the ribosome |
| Terpene | A class of lipids built from isoprene moieties; have carbon groups in multiples of five |
| Tertiary Structure | The three-dimensional shape of a polypeptide, stabilized by numerous interactions between R groups |
| Tight Junctions | Cell-to-cell junctions that prevent that paracellular transport of materials; tight junctions form a collar around cells and link cells within a single layer |
| Transcellular Transport | Transport of materials through the cell; requires interaction with the cytoplasm and may require transport proteins |
| Transcription | Production of an mRNA molecule from a strand of DNA |
| Transcription Factors | Proteins that help RNA polymerase II locate and bind to the promoter region of DNA |
| Transfer RNA (tRNA) | A folded strand of RNA that contains a three-nucleotide anticodon that pairs with an appropriate mRNA codon during translation and is charge with the corresponding amino acid |
| Transferase | An enzyme that catalyzes the transfer of a functional group |
| Translation | Production of a protein from an mRNA molecule |
| Triacylglycerol | A glycerol molecule esterified to three fatty acid molecules; most common form of fat storage within the body |
| Uncompetitive Inhibition | A decrease in enzyme activity that results from the interaction with an inhibitor at the allosteric site; uncompetitive inhibitors bind only to the substrate-bound enzyme and cannot be overcome by addition of substrate. Functionally increase affinity (K_m |
| Vitamin | An essential organic coenzyme that assists an enzyme in carrying out its action |
| Wax | A lipid with a high melting point that is composed of a very long chain alcohol and a very long chain fatty acid |
| Wobble Hypothesis | Hypothesis describing the binding of the third nucleotide of a codon to an anticodon, which is not specific and can occur with mismatched bases. In the genetic code, the third nucleotide often plays no role in specifying an amino acid. Theorized to be an |
| Zwitterion | A molecule that contains charges, but is neutral overall. Most often used to describe amino acids |
| Zymogen | An enzyme that is secreted in an inactive form and must be activated by cleavage; common examples are digestive enzymes |
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