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Biochemistry 2280A
Eric Ball

Term Definition abasic site a site on DNA which has lost the base portion of the nucleotide, while retaining the sugar-phosphate backbone acetyl CoA a molecule consisting of an acetyl group attached to coenzyme A acids substances that release hydrogen ions into solution (decrease pH) adipocytes fat cells; cells that form the adipose tissue affinity chromatography a type of chromatography in which a particular ligand is bound to the resin; only proteins that will bind that ligand will stick to the column aldolase an enzyme in glycolysis that cleaves fructose 1,6-bisphosphate to yield one molecule of dihydroxyacetone phosphate and one molecule of glyceraldehyde 3- phosphate aldol linkage a chemical structure in which an alcohol is attached to a carbon at the beta position relative to a carbonyl (e.g., ...-CO-CH2-CHOH-...) aldose a monosaccharide containing an aldehyde group in the straight-chain form allosteric regulation regulation of enzyme activity that occurs when a small molecule interacts non- covalently with a regulatory site distinct from the active site alpha-keto acid a molecule containing a ketone direclty adjacent to a carboxylic acid alpha carbon the carbon atom of an amino acid or amino acid residue to which the side chain is attached alternative splicing variations in splicing of a particular pre-mRNA, resulting in differential retention of exons and introns; also called differential splicing Alu repeats repeating, non-coding DNA sequences of about 300 base pairs found in the human genome that were originally characterized by the restriction enzyme Alu I amino acid a class of organic compounds in which an amino group and a carboxyl group are linked to a central carbon atom to which a variable side chain is also bound amino acid activation the process of attaching an amino acid to its tRNA by aminoacyltransferase amino acid residue the remaining portion of an amino acid after it has been incorporated into a polypeptide chain; the free amino acid loses a water molecule when the peptide bond is formed amphipathic describes a molecule that is hydrophobic on one side or end, and hydrophilic on the other anabolism the set of metabolic processes by which small molecules are combined into larger ones Ångstrom a unit of length. One Ångstrom is equal to 1 E-10 metres, or 0.1 nanometres annealing the process of allowing single-stranded DNA or RNA to hybridize to a complementary polynucleotide sequence anomeric carbon in a linear monosaccharide, the carbon atom of the carbonyl group; in a cyclized monosaccharide, the orientation of the hydroxyl at this carbon distinguishes anomers from one another apoenzyme an enzyme that is missing a subunit or cofactor required for full function apurinic site a position in a DNA strand at which the sugar-phosphate backbone is intact but a purine base is missing automated thermocyclers machines used for polymerase chain reactions; the cycler automatically changes the temperature of the reaction to allow the cycles of PCR to take place bases substances that acquire protons from solution (increase pH) base excision repair repair of damaged DNA that is initiated by the removal of the damaged base (except for repair of abasic sites) and involves synthesis of one (short-patch BER) or 2-10 (long-patch BER) new nucleotides beta-oxidation of fatty acids degradation of fatty acids into two-carbon units, accomplished by oxidizing the carbon beta to the carboxylic acid group biochemistry the study, primarily at the molecular level, of the chemical and physical processes that go on in the cell Bradford method a colorimetric assay for measuring the total amount of protein present in a solution, done using a dye that binds to certain common amino acid side chains carboxymethyl (CM) cellulose cellulose beads to which a carboxymethyl group has been added. The carboxymethyl group is negatively charged at neutral pH, allowing it to interact with positively charged proteins during ion exchange chromatography. catabolism the set of metabolic processes by which large molecules are broken down into smaller ones catabolite repression the process by which certain genes are not expressed when a particular catabolite (substrate for catabolism) is present in the media central dogma a phrase used to describe how genetic make-up determines the properties of an organism, based on flow of information from DNA to RNA to proteins centrifugation a purification method in which a sample is fractionated based on density by spinning it at high speed chaperone a protein that binds to unfolded or misfolded proteins, and promotes normal folding and formation of native three-dimensional structure chemiosmotic hypothesis the idea that ATP synthesis is driven by movement of ions across a membrane and down an electrochemical gradient chimeric protein a protein that results when genes encoding two or more distinct proteins (or parts of proteins) are fused to express a single polypeptide chain chiral carbon a carbon molecule that has four non-identical groups attached to it chromatin the complex of DNA and protein that comprises the eukaryotic chromosomes coding strand the DNA strand which has the same base sequence as the RNA transcript produced; also called the sense strand or non-template strand coenzyme a small organic molecule that is essential for particular enzymatic activities; vitamins are often converted to coenzymes coiled coil an arrangement of polypeptide chains in which several (usually two) alpha-helices wind around each other, as in alpha-keratin collagen the protein substance of the white fibres of connective tissue competitive inhibitor an enzyme inhibitor that competes with substrate for binding to the active site of the enzyme complementary DNA a DNA molecule, usually synthesized by the action of reverse transcriptase, that is (cDNA) complementary to an mRNA molecule consensus sequence a sequence that is representative of a group of related sequences that have similar functions. The consensus sequence is obtained by compiling the most common base or amino acid at each position within the group of sequences. cytochrome b-c1 complex Complex III of the electron transport chain, which accepts electrons from uibquinone and transfers them to cytochrome c via the Q cycle cytochrome oxidase Complex IV of the electron transport chain, which accepts electrons from complex cytochrome c and transfers them to oxygen cytoplasm everything inside the plasma membrane of the cell and outside the nucleus cytosol the aqueous solution inside the cytoplasm, excluding membrane-bound organelles deamination the spontaneous loss of an amine group from a nitrogenous base. When cytosine is deaminated it is coverted to uracil. dehydrogenase an enzyme that catalyzes a redox reaction; electron carriers are reduced, and the substrate is oxidized denaturation Separation of a DNA double helix into single strands, OR unfolding of a protein or RNA molecule from its native structure diabetes mellitus a condition characterized by a failure of the body to respond to high blood glucose dialysis a procedure in which solvent molecules and solutes smaller than the pores in a semipermeable membrane freely exchange between a sample and a larger volume of medium, while larger solutes are retained. This process changes the buffer in which the larger molecules are dissolved a type of local protein structure that permits binding to DNA, commonly through DNA binding motif interactions with the major groove DNA polymerase an enzyme responsible for DNA chain elongation domain a functional unit of a protein; can be either a single polypeptide chain or multiple chains downstream on a DNA molecule, towards the 3' end (usually to the right, depending on how the molecule is written) enantiomers molecules that are nonsuperimposable mirror images of one another; a type of stereoisomer endonuclease an enzyme that cleaves at internal sites in DNA or RNA enzyme a protein that catalyzes a chemical reaction enzyme assay a way of detecting enzyme activity; specific assays vary epimers isomeric structures with more than one chiral centre that only differ in the configuration of a single carbon atom exonuclease an enzyme that removes nucleotides from the end of a DNA or RNA chain extrinisic factors factors that are related to the environmental conditions; for example, salt concentration or solvent composition facultative anaerobe an organism that can survive in the absence of oxygen but can use oxidative phosphorylation to make ATP when oxygen is present FAD flavin adenine dinucleotide (oxidized form) FADH 2 flavin adenine dinucleotide (reduced form) feedback inhibition the inhibition of an earlier step in a reaction sequence by the product of a later step feedforward activation the activation of a later step in a reaction sequence by the product of an earlier step fermentation a process by which ATP is generated through a series of reactions involving no net change in the overall oxidation state of the atoms of the substrate flux the rate at which molecules flow through a metabolic pathway free energy (G), also Gibbs free energy a thermodynamic quantity, the change of which for a reaction at constant pressure indicates the spontaneity of the reaction; for a spontaneous reaction, delta G is negative French pressure cell a piece of equipment commonly used to shear cells, in which the cells are forced through a small opening at high pressure furanose a monosaccharide that exists as a five-membered ring in the cyclic form gene disruption replacing a large part of a gene (or the entire gene) with other DNA, often acquired by homologous recombination. This technique is usually used to knock out a particular gene and introduce markers in its place that can be followed to ensure that the resulting strain is now missing the targeted gene gene-specific regulatory proteins that regulate the transcription of one specific gene, as opposed to a group proteins of related genes genetic instability a general term that refers to a variety of phenomena, including DNA rearrangements, which all result in changes in the genomic DNA genome the complete set of genetic instructions in an organism genomic library a set of cloned DNA fragments representing an organism's entire genome globular protein a water-soluble protein characterized by a compact, highly folded structure glycosylation the attachment of carbohydrate chains to a protein through N- or O-glycosidic linkages helicase an enzyme responsible for the unwinding of the template DNA double helix at the replication fork helix-turn-helix motif a protein motif that forms two alpha-helices that cross; this motif binds in DNA's major groove to specific base sequences heterodimer a dimer that consists of two non-identical subunits "high energy" molecule a molecule that releases a lot of free energy when hydrolyzed hinge region of an IgG; a region that allows for the Fab and Fc regions to move more or less independently histones highly conserved basic proteins that constitute the protein core to which DNA is bound to form a nucleosome core particle and a 30-nm chromatin fibre holoenzyme a complete and active enzyme that includes all subunits and bound cofactors homologous recombination a process in which similar sequences of DNA from different chromosomes exchange places; also describes DNA repair in which DNA from one chromosome is used as a template to regenerate the analogous sequence on the damaged sister chromosome homodimer a dimer which consists of two identical subunits hot probe a probe labeled with a radioactive element (has nothing to do with temperature) housekeeping genes genes that are expressed in all cells and that encode proteins necessary for maintenance and essential cellular functions hybridization annealing of two nucleic acid strands hydrogen bond an electrostatic interaction between a weakly acidic donor group such as O--H or N--H and a weakly basic acceptor atom such as O or N hydrophobic column a type of chromatography in which the column resin has hydrophobic groups stuck chromatography to it; therefore, proteins with exposed hydrophobic areas will bind to the resin hydrophobic/hydrophilic interactions non-covalent attractions between molecules; not types of bond hydroxyapatite deposition when calcium is deposited as a brittle substance which forms bone hydroxyproline/hydoxylysine in the formation of collagen, these molecules both stabilize the collagen fibrils through aldol crosslinks between the collagen fibers hypervariable when referring to a region of DNA, means that this region can be quite different from one individual to the next imino acid a molecule like an amino acid except that the nitrogen is bound to two carbon atoms and only one hydrogen; for example, proline immunodetection detection of a protein using an antibody that binds to that protein induced fit model of enzyme a model that states that the active site of an enzyme undergoes conformational function change to adapt to the binding of a substrate integral membrane protein a protein that interacts with the hydrophobic centre of a lipid bilayer, either directly or via a covalently attached lipid. Integral membrane proteins cannot be removed from a membrane without disrupting the membrane. interchain bonding bonding between two or more distinct chains intermediate filaments a family of fibrous protein filaments that provide tensile strength to cells intrachain bonding bonding within the same polypeptide chain ion exchange chromatography a fractionation procedure in which ions are selectively retained by a matrix bearing groups of charge opposite to the bound ions isoelectric point (pI) the pH at which a molecule has no net charge, and thus does not migrate in an electric field ketose a monosaccharide containing a ketone group in the straight-chain form kinases a family of enzymes that add a phosphate group to a substrate Km, the Michaelis constant for an enzyme-catalyzed reaction that obeys Michaelis-Menten kinetics, Km is the substrate concentration at which reaction velocity equals half the
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