OXFORD DICTIONARY OF
`Biochemistry and
`Molecular Biology
`REVISED EDITION
`
`Managing Editor
`Professor R. Cammack King's College London
`General Editors
`Professor T.K. Attwood University of Manchester
`Professor P.N. Campbell University College London
`Dr J.H. Parish University of Leeds
`Dr A.D. Smith University College London
`Dr J.L. Stirling King's College London
`Professor F. Vella University of Saskatchewan
`
`3 Gilead 2013
`I-MAK v. Gilead
`IPR2018-00125
`
`1
`
`

`

`Editors
`
`Teresa K. Attwood Professor of Bioinformatics,
`Faculty of Life Sciences & School of Computer Science,
`University of Manchester
`
`Richard Cammack (Managing Editor) Professor of
`Biochemistry, King's College London
`
`Peter N. Campbell (deceased) Emeritus Professor of
`Biochemistry and Honorary Research Fellow,
`University College London
`
`J. Howard Parish Life Fellow, University of Leeds
`
`Anthony D. Smith Emeritus Reader in Biochemistry,
`University College London
`
`John L. Stirling
`Senior Lecture in Molecular Genetics,
`King's College London
`
`Francis Vella Former Professor of Biochemistry,
`Faculty of Medicine, University of Saskatchewan,
`Saskatoon, Canada
`
`2
`
`

`

`OXFORD DICTIONARY OF
`Biochemistry and
`Molecular Biology
`
`3
`
`

`

`1 G
`
`reat Clarendon Street, Oxford OX2 6DP
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`First edition published 1997
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`4
`
`

`

`chenodeoxycholate
`
`chi sequence
`
`cells are derived has a different coat colour from that of the strain
`producing the blastocyst. Production of chimeras is a step in the
`generation of mice carrying gene knockouts produced by homolo-
`gous recombination in ES cells. See mosaic, transgenic, chimeric mol-
`ecule. —chimeric or chimaeric adj.
`chimeraplast any RNA–DNA chimeric oligonucleotide used to in-
`duce base pair conversions at the genomic level and used in gene re-
`pair strategies for gene therapy. –chimeraplastic adj.
`chimeric molecule 1 any of the hybrid DNA molecules formed
`when DNAs from different sources are digested with the same re-
`striction endonuclease and the digests are mixed. The DNA frag-
`ments in the mixture become associated by hydrogen bonds be-
`tween complementary sequences to form new arrangements, which
`may be converted into covalently linked molecules by the action of
`DNA ligase. This process can produce chimeric plasmids and other
`chimeric structures. 2 a chimeric protein (or fusion protein) is a pro-
`tein obtained by the insertion or substitution of a partial sequence
`from one protein into another, typically using cDNA technology.
`The resultant protein thus has elements of both the original pro-
`teins. Such proteins frequently form naturally as a result of chro-
`mosomal translocations during neoplastic transformation. See
`acute myeloid leukemia. 3 a recombinant antibody that has, e.g.,
`structural characteristics of both human and mouse antibodies.
`chimerin any of several related proteins that function as GTPase-
`activating proteins, specific for the p21 Ras-related Rac GTPase.
`They include n-chimerin, and a- and b-chimerins. n-Chimerin is a
`cerebellar protein, and b-chimerin is expressed in testis. They are
`phorbol ester receptors, with an N-terminal domain similar to the
`zinc-finger region of protein kinase C, and a C-terminal domain
`similar to the product of BCR. Through their action on Rac, they
`lead to changes in cytoskeletal organization.
`chimyl alcohol glycerol 1-hexadecyl ether, (+)-3-(hexadecyloxy)-
`1,2-propanediol; a hydrolysis product of ether lipids.
`Chinese restaurant syndrome see monosodium glutamate.
`ChIP abbr. for chromatin immunoprecipitation.
`CHIP 28 abbr. for channel-forming integral membrane protein 28;
`also called AQP 1 (see aquaporin).
`chiral describing a chemical compound that displays chirality.
`chiral drug a single pure enantiomer of a specified drug rather than
`the racemate; the enantiomers may have very different pharmaco-
`logical effects, e.g. in the case of propoxyphene and levo-
`propoxyphene.
`chirality topological handedness; the property of nonidentity of an
`object with its mirror image. A chiral chemical compound, i.e. one
`that possesses chirality, is one that cannot be superimposed on its
`mirror image, either as a result of simple reflection or after rotation
`and reflection. If superposition can be achieved then the molecule is
`said to be achiral. Chirality is most commonly due to the presence
`of one or more chiral centres (formerly referred to as asymmetric
`carbon atoms) or the presence of a chiral axis (as in allene struc-
`tures, some of which are found in natural products). Rarely, chiral-
`ity may also result from the presence of a chiral plane. See also
`prochiral. [From Greek kheir, hand.]
`chiral methyl a carbon atom carrying the three hydrogen isotopes,
`i.e. -C1H2H3H.
`chiral recognition the differentiation of the enantiomers of a com-
`pound. This can be achieved by living organisms, chiral molecules,
`enzymes, drug receptors, etc.
`chiroid (rare) any molecule that has chirality.
`chiroptical describing any of the phenomena that depend on the
`ability of chiral and other intrinsically asymmetric molecules to ro-
`tate the plane of polarized light, known collectively as optical activ-
`ity. Such phenomena include optical rotation, optical rotatory disper-
`sion, and circular dichroism. The term is also applied to any of the
`techniques used for investigating these phenomena.
`chi sequence or chi site a sequence of base pairs first discovered in
`a phage lambda mutant, called chi. These mutants were found to
`have single base pair changes creating sites that stimulate recombi-
`nation. Characteristic of chi sites is a nonsymmetrical sequence of
`eight base pairs, consensus sequence:
`5′ GCTGGTGG 3′.
`
`strate to an enzyme by 50%, to the dissociation constant, Ki, of the
`enzyme–inhibitor complex; it is:
`I50 = Ki (1 + S/Km),
`where S is the substrate concentration and Km the Michaelis con-
`stant for the enzyme–substrate complex.
`chenodeoxycholate or chenodiol the anion of (3a,5b,7a)-3,7-dihy-
`droxycholan-24-oic acid; a major component of bile in some species
`(hens, geese) but a minor component in humans. It is used thera-
`peutically to decrease the synthesis of cholesterol and to help dis-
`solve cholesterol gallstones.
`
`H3C
`CH3
`
`H
`OH
`
`H3C
`
`H
`
`H
`
`H
`
`HO
`
`O
`
`OH
`
`Cherenkov counter or Cerenkov counter a device for counting
`charged particles, or radionuclides emitting them, that depends on
`Cherenkov radiation.
`Cherenkov radiation or Cerenkov radiation a radiation of bluish
`light, consisting of photons, emitted when charged particles, espe-
`cially high-energy beta particles, pass through either a solid or liq-
`uid medium at velocities greater than that at which light passes
`through the same medium. The effect is analogous to the creation
`of a sonic boom that occurs when an object exceeds the speed of
`sound
`in a medium.
`[After Pavel Alekseyevich Cherenkov
`(1904–1990), Russian-born Soviet physicist.]
`Ches abbr. for 2-(cyclohexylamino)ethanesulfonic acid; a compound
`with similar properties to a Good buffer substance; pKa (25°C) = 9.3.
`
`SO3H
`
`NH
`
`chewing gum see chicle.
`chi symbol: v (lower case) or V (upper case); the twenty-second letter
`of the Greek alphabet. For uses see Appendix A.
`chiasma (pl. chiasmata) 1 (in genetics) a connection formed be-
`tween chromatids, visible during meiosis, thought to be the point of
`the interchange involved in crossing-over. 2 or (esp. US) chiasm (pl.
`chiasms) (in anatomy) a decussation or intersection, as of two
`nerves; e.g. optic chiasma.
`chicle a mixture of cis- and trans-1,4-polyprenoids obtained from
`the evergreen tree, Achras sapota; the original chewing gum base.
`Chico an insulin receptor substrate-like protein in Drosophilia that
`links the insulin receptor to phosphatidylinositol 3-kinase and then
`protein kinase B and protein synthesis. A mutation of the corre-
`sponding gene results in fruit flies less than half the normal size.
`chimera or (esp. Brit.) chimaera (in genetics) an organism compris-
`ing tissues of two or more genotypes. Chimeras can occur as a result
`of mutation, abnormal distribution of chromosomes, grafting, or
`genetic manipulation. For example, a chimera can be created by
`mixing the cells from embryos of two different animal species at the
`blastocyst stage of development and implanting the chimeric em-
`bryo in a surrogate mother to continue development. When the
`species are sheep and goats, the resulting chimeric progeny are
`called ‘geep’, or ‘shoats’. Alternatively, in mice, genetically manipu-
`lated mouse embryonic stem (ES) cells are injected into the blasto-
`coel of a blastocyst. Later stages of development are completed in
`the reproductive tract of a surrogate mother to produce chimeric
`mice. These are readily identified if the strain from which the ES
`5
`115
`
`

`

`cytes from small volumes of blood by centrifugation. It is also used
`as a radiopaque material.
`
`diazotize
`
`O
`
`-
`
`O
`
`CH3
`
`O
`
`I
`
`NH
`
`I
`
`I
`
`NH
`
`O
`
`H3C
`
`diaphragm
`
`diaphragm 1 (in chemistry) a semipermeable membrane, or porous
`plate, used to separate two solutions in dialysis or osmosis. 2 (in
`anatomy) any separating membrane, especially the thin, domed fi-
`bromuscular partition separating the thorax from the abdomen.
`Flattening of the diaphragm, accompanied by expansion of the rib
`cage, causes air to be sucked into the lungs. 3 (in optics) any device,
`sometimes adjustable (e.g. iris diaphragm), that can limit or vary
`the aperture of a lens or optical system. 4 any other thin dividing
`membrane.
`diarylpropane peroxidase see ligninase.
`diasolysis a membrane permeation process for the separation of
`organophilic from hydrophilic solutes, akin to dialysis but differing
`in that separation depends primarily on the relative solubilities of
`the solutes in the membrane rather than on their molecular dimen-
`sions. Such a process may play a part in the selective passage of
`solutes through membranes of living cells.
`diastase 1 obsolete name for a-amylase (EC 3.2.1.1). 2 the crude
`mixture of amylases obtained commercially as a yellowish white
`amorphous powder from malt. [From Greek diastasis, a separa-
`tion.] —diastatic adj.
`diastatic activity the enzymic activity of a-amylase.
`diastereoisomer or diastereomer any stereoisomer that is not enan-
`tiomeric; it may be either chiral or achiral. The term includes
`cis–trans isomer, configurational isomer, conformational isomer, and
`epimer. —diastereoisomeric or diastereomeric adj.; diastereoiso-
`merism or diastereomerism n.
`diastereotopic 1 chemically-like ligands in constitutionally equiva-
`lent locations that are not symmetry related (cannot be inter-
`changed by rotation about an axis (Cn) or alternating axis (Sn) of
`symmetry) are diastereotopic; the two ligands are in a stereochemi-
`cally different, nonmirror-image environment. Separate replace-
`ment of each ligand by a different achiral ligand yields two products
`that are in a diastereoisomeric relationship. Example: replacement
`hydrogen
`of
`the methylene
`group
`in
`of
`the HR
`(R)–CH3–CH2–CHBr–CH3 with chlorine yields (2R,3R)-2-bromo-
`3-chlorobutane; the similar replacement of the HS hydrogen yields
`the diastereoisomeric (2R,3S)-2-bromo-3-chlorobutane. A bio-
`chemically important example is that both of the methylene groups
`of citric acid have diastereotopic hydrogens. 2 the two faces of a
`double bond or of a planar cyclic ring system that are not related by
`any symmetry operation (axis, plane, centre, or alternating axis) are
`diastereotopic; the two faces show stereochemically different, non-
`mirror-image environments. Separate addition of an achiral reagent
`to each face yields two diastereoisomeric products. Example: hy-
`(3S)–CH3–CH2–
`drogenation
`of
`the C=O
`bond
`in
`CH(CH3)–CO–COOH (in absence of any chiral influence such as a
`chiral catalyst) yields the two diastereoisomers, (2R,3S)-2-hydroxy-
`3-methylpentanoic acid and (2S,3S)-2-hydroxy-3-methylpentanoic
`acid. A biochemical example is the two diastereotopic faces, A and
`B, of the (dihydro)pyridine ring of nicotinamide-adenine coen-
`zymes (see nicotinamide-adenine dinucleotide (reduced)). Compare
`enantiotopic.
`diastole 1 the passive dilatation of the chambers of the heart that
`occurs between the rhythmical contractions. 2 the rhythmical ex-
`pansion of a pulsating vacuole. Compare systole. — diastolic adj.
`diastrophic dysplasia sulfate transporter abbr.: DTDST; a
`739-residue integral membrane protein that contains 12 transmem-
`brane segments, is produced in many mammalian tissues, and func-
`tions as a sulfate–chloride antiporter. Many mutations in the gene
`at 5q32-q33.1 result in insufficient sulfation of cartilage glycopro-
`teins and are associated with various autosomal recessive skeletal
`dysplasias, some of which are lethal.
`diatomaceous earth or kieselguhr a friable, whitish material con-
`sisting mostly of silica, derived from diatomite, a rock consisting
`largely of the remains of diatoms. It is used as a filter aid and as an
`absorbent in column chromatography. See also Berkefeld filter.
`diatomic (of a molecular entity) composed of only two atoms. —di-
`atomicity n.
`diatrizoate the anion 3,5-diacetamido-2,4,6-triiodobenzoate. Its
`sodium salt forms solutions of low viscosity and high relative den-
`sity. A mixture with Ficoll provides a solution having the optimal
`density and osmolarity for the rapid, one-step isolation of lympho-
`6
`179
`
`diauxy the adaptation of microorganisms to culture media contain-
`ing two different carbohydates. Growth occurs in two phases sepa-
`rated by a period of less rapid or zero growth. In the first phase, the
`organism utilizes the carbohydrate for which it possesses constitu-
`tive enzymes. During the interlude the organism synthesizes the re-
`quired induced enzymes for the metabolism of the other carbohy-
`drate, which it then proceeds to exploit in the second growth phase.
`—diauxic adj.
`diazepam 7-chloro-1,3-dihydro-1-methyl-5-phenyl-2H-1,4-benzo-
`diazepin-2-one; one of the most widely used benzodiazepine drugs,
`noted for its CNS depressant effects. Used as an anti-anxiety–hyp-
`notic agent at subsedative doses, its actions are similar to those of
`chlordiazepoxide, but it has greater potency. One proprietary name
`is Valium.
`
`CH3
`N
`
`O
`
`Cl
`
`N
`
`diazepam binding inhibitor a 10 kDa, 86-residue polypeptide,
`that acts as an endogenous ligand for a mitochondrial receptor (for-
`merly regarded as a peripheral benzodiazepine binding site) in
`steroidogenic cells (i.e., adrenocortical, glial, and Leydig cells), and
`regulates stimulation of steroidogenesis by tropic hormones. It also
`binds to the benzodiazepine binding site on the GABAA receptor,
`and modulates glucose-dependent insulin secretion and synthesis of
`acyl-CoA esters.
`diazo compound any organic compound, other than an azo com-
`pound, that contains the bivalent azo group –N=N– (or =N2) in co-
`valent linkage. It may be (1) any aliphatic compound of general for-
`mula R–CH=N2, in which both nitrogen atoms are linked to the
`same carbon atom by replacing two hydrogen atoms of the parent
`molecule, e.g. diazomethane, CH2=N2; or (2) any aromatic com-
`pound of general formula Ar–N=N–X in which one nitrogen atom
`is linked to a carbon atom of the aromatic ring by replacing one hy-
`drogen atom of the parent molecule, and the other nitrogen atom is
`linked covalently to a group X through an atom other than carbon
`(except when X = CN),
`e.g. benzenediazohydroxide,
`C6H5–N=N–OH.
`diazonium compound any aromatic organic compound of general
`+, containing the univalent cationic diazonium
`formula Ar–N2
`group, –N+≡N, linked to a carbon atom of an aromatic ring sys-
`tem by replacing one hydrogen atom of the parent molecule. The
`positive charge is balanced by an anion to form a diazonium salt,
`+Cl–.
`e.g. benzenediazonium chloride, C6H5–N2
`diazotize or diazotise to cause a primary aromatic amine to form a
`
`

`

`isopeptide bond
`
`structure. 2 describing a type of alternation of generations in which
`morphologically identical generations occur in both diploid and
`haploid phases. It occurs mainly in algae. Compare heteromorphic.
`isomorphism 1 (in biology) similarity of form in organisms of dif-
`ferent ancestry. 2 (in chemistry) similarity of crystalline form and
`structure between substances of similar composition or substances
`that can form a more or less continuous series of solid solutions.
`isomorphous 1 an alternative term for isomorphic (def. 1). 2 display-
`ing isomorphism (esp. def. 2).
`isomorphous replacement method a method used to solve the
`phase problem in X-ray diffraction analysis of macromolecular struc-
`tures. It involves combining one or more heavy atoms (def. 2) (which
`are strong scatterers) in a specific manner with the macromolecule
`in question and investigating their effects on the diffraction pattern.
`The heavy atom must not modify either the conformation or the
`crystal form of the macromolecule, i.e. the replacement must be iso-
`morphous.
`isoniazid 4-pyridinecarboxylic acid hydrazide; an antitubercular
`drug that may act by inhibiting the synthesis of the mycolic acids
`that are vital for the construction of the cell wall of the pathogen,
`Mycobacterium tuberculosis. Like related hydrazides it is highly he-
`patotoxic and no longer used. Its euphoric side effects led to the dis-
`covery of monoamine oxidase inhibitors.
`
`NH2
`
`HN
`
`O
`
`N
`
`isoosmotic a variant spelling of isosmotic.
`isopartitive (in chromatography) describing two or more solvents
`that bring about similar partitions of a given substance between the
`solvent and the stationary phase and hence result in Rf values that
`are the same or nearly so.
`isopentenyl
`3-methylbut-3-enyl,
`for
`name
`the
`trivial
`CH2=C(CH3)–CH2–CH2–, the alkenyl group formally derived
`from isopentenyl alcohol (i.e. 3-methylbut-3-en-1-ol) by loss of its
`hydroxyl group. Compare prenyl.
`isopentenyl diphosphate abbr.: IDP; formerly called D 3-isopen-
`tenyl pyrophosphate (abbr.: IPP); an isomer of dimethylallyl
`diphosphate and the key precursor of all isoprenoids (def. 2). See
`also dimethylallyltranstransferase, isopentenyl-diphosphate D-isomerase,
`isoprene rule.
`
`CH2
`
`CH3
`
`OO
`
`O P O P O
`-
`-
`
`O O
`
`-
`
`isopentenyl-diphosphate D-isomerase EC 5.3.3.2; systematic
`name: isopentenyl diphosphate D3–D2-isomerase; other name: IPP
`isomerase. An enzyme in the pathway for the synthesis of choles-
`terol, terpenes, and prenyl groups; it catalyses the reversible reac-
`tion:
`
`isopentenyl diphosphate = dimethylallyl diphosphate.
`isopeptidase any peptidase catalysing the cleavage of an isopeptide
`bond.
`isopeptide bond any peptide bond other than a eupeptide bond, i.e.
`any amide bond formed between a carboxyl group of one amino-
`acid molecule or residue and an amino group of another, where ei-
`ther group occupies a position other than a (or both do so). Exam-
`ples include peptide bonds formed from the b-carboxyl group of
`aspartic acid, the c-carboxyl group of glutamate from the e-amino
`
`7
`358
`
`isologue
`
`tween two identical protein subunits (i.e., protomers) in which the
`domain of bonding comprises two identical binding sets.
`isologue or (US) isolog any of two or more isologous (def. 1) com-
`pounds.
`isology the state or condition of being isologous (def. 1); chemical
`kinship among molecules or compounds.
`isomaltase EC 3.2.1.10; recommended name: oligo-1,6-glucosidase;
`systematic name: dextrin 6-a-D-glucanohydrolase. An enzyme that
`hydrolyses 1,6-a-D-glucosidic bonds in dextrins and isomaltose pro-
`duced after a-amylase degradation of starch and glycogen. The en-
`zyme from intestinal mucosa also catalyses the reaction of EC
`3.2.1.48 (see sucrase).
`isomaltose the disaccharide 6-O-a-D-glucopyranosyl-D-glucose; it
`exists as the branching unit in amylopectin, glycogen, and some bac-
`terial dextrans. Compare maltose.
`
`HOCH2
`
`O
`
`OH
`
`HO
`
`O
`
`CH2
`
`OH
`
`O
`
`OH
`
`OH
`
`HO
`
`OH
`
`isomaltulose the disaccharide 6-O-a-D-glucopyranosyl-D-fructofu-
`ranose.
`isomer 1 (in chemistry) molecular isomer any of two or more com-
`pounds that have identical molecular formulas but differ in the na-
`ture of bonding of their atoms (constitutional isomers) or in the
`arrangement of their atoms in space (stereoisomers). 2 (in physics)
`nuclear isomer any of two or more nuclides that have the same pro-
`ton number and the same mass (nucleon) number but different en-
`ergy states.
`isomerase any enzyme of EC class 5 that catalyses geometric or
`structural changes within one molecule. According to the type of
`isomeric change they catalyse, they may be called racemases or
`epimerases (EC subclass 5.1); cis–trans-isomerases (EC subclass
`5.2); intramolecular oxidoreductases (EC subclass 5.3); intramolec-
`ular transferases (mutases) (EC subclass 5.4); or intramolecular
`lyases (EC subclass 5.5); other isomerases are placed in EC subclass
`5.99.
`isomeric of or pertaining to an isomer; pertaining to the phenome-
`non of, or displaying, isomerism.
`isomeric state any of the states of an atomic nucleus having a dif-
`ferent energy and observable half-life from those of other states of
`the same nucleus; the condition of being an isomer (def. 2).
`isomeric transition abbr.: IT; the change of one nuclear isomer
`(see isomer (def. 2)) into another without change in either proton
`number (atomic number) or nucleon number (mass number), en-
`ergy being lost in the form of gamma radiation; e.g. the decay of the
`metastable nuclide technetium-99m (half-life 6 h) to the unstable
`nuclide technetium-99 (half-life 2.1 × 105 years), which in turn de-
`cays to ruthenium-99 with emission of an electron.
`isomerism the phenomenon of the existence of isomers in general, or
`the occurrence of molecular or nuclear isomers in a particular in-
`stance.
`isomerization or isomerisation the act of changing or the process of
`change of one molecular isomer into another one. —isomerize or
`isomerise vb.
`isometric 1 having identical dimensions. 2 (in physiology) of or per-
`taining to a contraction of a muscle that does not cause shortening
`of the muscle. 3 (in crystallography) having three mutually perpen-
`dicular axes of equal length; cubic.
`isomorph a substance or organism that is isomorphic (def. 1) to an-
`other substance or organism.
`isomorphic 1 or isomorphous of identical or similar form, shape, or
`
`

`

`sequence rule
`
`serine hydroxymethyl transferase
`
`with another kind of ion or molecule to form a firm complex mol-
`ecule with different properties from the original ion. Compare
`chelation. 3 (in cell biology) the intracellular enclosing of material in
`an organelle. —sequester vb.
`Ser symbol for a residue of the a-amino acid L-serine (alternative to
`S).
`SER abbr. for smooth endoplasmic reticulum (see endoplasmic reticu-
`lum).
`sera a plural of serum.
`SERCA abbr. for sarcoplasmic/endoplasmic reticulum calcium-trans-
`porting ATPase, EC 3.6.1.38; a family of Ca2+ pump integral mem-
`brane protein isoforms of sarcoplasmic or endoplasmic reticulum.
`They catalyse the hydrolysis of ATP coupled with Ca2+ transport
`from the cytosol.
`serglycin a proteoglycan of secretory vesicles of leukocytes. In rat,
`the core protein (104 amino acids) contains a central domain of 49
`alternating Ser and Gly residues. Some 15 chondroitin sulfate/der-
`matan sulfate chains are linked to the Ser residues in this domain.
`serial analysis of gene expression abbr.: SAGE; a method for
`detecting and quantifying gene expression. Short sequence tags
`(10–14bp), each serving as a unique marker for its transcript, are
`extracted from defined locations at the 3′ end of cDNAs, concate-
`nated, inserted into vectors, and cloned in bacteria. The concate-
`mers are sequenced and the tags counted. The relative numbers of
`each tag provide an estimate of the expression level of the corre-
`sponding transcript. Also, tags are matched with their correspond-
`ing genes where the gene sequences are known. SAGE projects usu-
`ally generate an order of magnitude more tags than expressed
`sequence tag (EST) sequencing projects, allowing statistically more
`accurate and more sensitive expression estimates to be made.
`serial dilution a method of achieving dilution of a liquid by se-
`quentially transferring a sample of predetermined volume into an-
`other, empty, vessel (usually a tube), which is then made up with
`diluent to the same total volume as the first. The overall dilution
`achieved is (v/s)x -fold, where v is the chosen total volume in each
`tube, s is the size of the sample, and x is the number of times the
`procedure is repeated.
`serinate 1 serine anion; the anion, HO–CH2–CH(NH2)–COO–, de-
`rived from serine. 2 any salt containing serine anion. 3 any ester of
`serine.
`serine the trivial name for a-amino-b-hydroxypropionic acid; 2-
`amino-3-hydroxypropanoic acid; HO–CH2–CH(NH2)–COOH; a
`chiral a-amino acid. L-Serine (symbol: S or Ser), (S)- 2-amino-3-hy-
`droxypropanoic acid, is a coded amino acid found in peptide link-
`age in proteins; codon: AGC or AGU; UCA, UCC, UCG, or
`UCU. In mammals, it is a non-essential dietary amino acid, and is
`glucogenic. D-Serine (symbol: D-Ser or DSer), (R)-2-amino-3-hy-
`droxypropanoic acid, in both free and combined forms occurs in
`silkworms and earthworms; residues of D-serine occur in certain
`peptide antibiotics, e.g. polymyxins D1 and D2. [Note: the absolute
`configuration of D-serine (and hence that at the a-carbon atom of
`other a-amino acids of the D series) is identical to that of D-glycer-
`aldehyde (and hence to that at the reference carbon atom of other
`monosaccharides of the D series).]
`
`NH2
`OH
`
`H O
`
`HO
`
`L-serine
`
`L-serine dehydratase EC 4.2.1.13; systematic name: L-serine
`hydro-lyase (deaminating); other names: serine deaminase; L-hy-
`droxyaminoacid dehydratase. An enzyme that catalyses a reaction
`between L-serine and water to form pyruvate and ammonium ion.
`It is a pyridoxal-phosphate enzyme. The enzyme for gluconeogene-
`sis from serine in Escherichia coli is a 4Fe–4S protein.
`serine hydroxymethyl transferase see glycine hydroxymethyltrans-
`ferase.
`
`8
`610
`
`sequence rule or Cahn–Ingold–Prelog rule or R S convention (of
`configuration specification) a system for specifying the absolute
`molecular chirality of a chemical compound. This system considers
`the sequence of the proton numbers of the atoms directly attached
`to a chiral centre(see chirality); if two or more of these atoms have
`the same proton number, their substituents are then taken into ac-
`count, the group with substituents of highest proton number taking
`precedence. When a multiple bond to a substituent is present, the
`substituent is arbitrarily considered to occur twice, or thrice; an iso-
`tope of higher nucleon number takes precedence over one of lower
`number. For a tetrahedral centre (e.g. a carbon atom) the sub-
`stituent with the lowest priority is placed away from the observer
`(behind the chiral atom) with the other three projecting towards the
`observer; if these three substituents lie in a clockwise (right-handed)
`array of decreasing priority, then the chiral centre is designated
`with the stereochemical descriptor R, denoting Latin rectus, right; if
`the substituents lie in an anticlockwise (left-handed) array of de-
`creasing priority, then the chiral centre is designated with the stere-
`ochemical descriptor S, denoting Latin sinister, left. For the name
`of a compound consisting of molecules with a single chiral centre
`the descriptor R or S, with a preceding locant if needed, is formed
`into a prefix by placing it in parentheses and adding a linking hy-
`phen; a racemate with a single chiral centre in its molecules is la-
`belled with the prefix (RS)-. When a molecule contains more than
`one chiral centre the prefix to the name is composed of multiple de-
`scriptors, each preceded by an appropriate locant; e.g. (2R,3R)-2,3-
`dihydroxybutanedioic acid (= Lg-tartaric acid). If only the relative,
`but not the absolute, configurations of two or more chiral centres in
`a molecule are known, these centres may be designated with the de-
`scriptors R* and S* (spoken as R star, S star), preceded when nec-
`essary by appropriate locants, on the arbitrary assumption that the
`chiral centre first cited (which usually is the one with the lowest lo-
`cant) has an R configuration; for examples, compare the systematic
`names of allothreonine and threonine. See also D/L convention. Exten-
`sions of the sequence rule are the E/Z convention, the pro-E/pro-Z con-
`vention, the pro-R/pro-S convention and the Re/Si convention. [After
`Robert Sidney Cahn
`(1899–1981), British natural-products
`chemist, editor, and scientific semanticist, (Sir) Christopher Kelk
`Ingold (1893–1970), British physical organic chemist, and Vladimir
`Prelog (1906–98), Bosnian-born Swiss organic chemist, who jointly
`developed the system and described it in a series of three papers
`published in 1951, 1956, and 1966.]
`sequence-tagged site abbr.: STS; a unique short, single-copy
`DNA sequence that characterizes a mapping landmark on the
`genome. Such sequences provide unambiguous identification of
`DNA markers generated by the Human Genome Project (see
`HUGO). STSs bind to YACs. If two YACs contain the same STS they
`must overlap. The YACs can be built up into an overlapping series
`of clones (a contig) covering an entire gene.
`sequencing the act, or process, of determining the sequence (def. 1)
`of proteins or nucleic acids. See chain-termination method, chemical
`cleavage method, solid-phase technique.
`sequencing by hybridization see SBH.
`sequencing centre a research institute that provides a major focus
`for genome mapping and sequencing, often also providing genome
`analysis software for free use by the community. Notable examples
`include the Sanger Institute in the UK, and The Institute for
`Genome Research (TIGR) and the Whitehead Institute for Bio-
`medical Research (WIBR) in the USA.
`sequencing gel a polyacrylamide gel run to resolve oligonu-
`cleotides produced in a DNA sequencing procedure. See chain-ter-
`mination method, chemical cleavage method.
`sequential analysis the analysis of a protein or nucleic-acid se-
`quence (def. 1).
`sequential mechanism an enzyme reaction involving two or more
`substrates in such a way that all the substrates must be bound to the
`enzyme to form the central complex before any products can be re-
`leased. A sequential mechanism may be an ordered mechanism or a
`random mechanism.
`sequestering agent see chelating agent.
`sequestration 1 the process of removal or separation. 2 (in chem-
`istry) the effective removal of ions from solution by coordination
`
`

`

`stereoisomer
`
`steroid diabetes
`
`CH3
`
`O O
`
`CH3
`
`H3C
`
`H3C
`
`H
`
`NH HN
`
`H
`
`CH3
`
`NH
`
`HN
`
`CH3
`
`COOH
`
`COOH
`stercobilinogen
`
`ligands (faces) are enantiotopic; if they are diastereoisomers, the
`ligands (faces) are diastereotopic. for more extensive descriptions,
`see diastereotopic, enantiotopic.
`stereoisomer any of two or more isomers that have the same mo-
`lecular constitution and differ only in the three-dimensional
`arrangement of their atomic groupings in space. Stereoisomers may
`be diastereoisomers or enantiomers. Compare constitutional isomer.
`—stereoisomeric adj.; stereoisomerism n.
`stereology the body of mathematical methods dealing with the in-
`terpretation of the structure and dimensions of three-dimensional
`objects from information contained in two-dimensional