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Because
of the close relationship between biochemistry and
medicine, I have included in this glossary a collection of prefixes,
suffixes
and root words typically found in medical dictionaries in hopes that
some
words I may have forgotten to define can be figured out. These are in
bold,
with prefixes and suffixes followed or preceded by a hyphen,
respectively.
Roots have no hyphens. I have left words as lower case except in those
cases where capitalization is necessary (named pathways for
example).Glossary
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ab-
- from
- Abbreviated New Drug Application (ANDA)
- a simpler submission permitted for a generic form of
an approved drug
- ad-
- towards
- ADME-
- An anacronism used in drug development, meaning
absorption, distribution, metabolism and excretion.
- a(n)-
- without
- absolute configuration
- The configuration of four different substituent
groups around an asymmetric carbon atom; for historical reasons
molecules in biochemistry are compared to D- and L-glyceraldehyde.
- absorption
- Transport of the products of digestion from the
intestinal tract into the blood.
- acceptor control (Electron transport chain)
- The regulation of the rate of respiration by the
availability of ADP as a phosphate group acceptor.
- accessory pigments
- Visible light-absorbing pigments such as carotenoids
and xanthophyll in green plants and photosynthetic bacteria that trap
energy from sunlight and pass it on to "special
pairs".
- acidosis
- A condition in which blood pH decreases, either for
metabolic or respiratory reasons.
- actin
- A protein (~ kDa) making up the thin filaments of
muscle and cytoskeleton of eukaryotic cells.
- activation energy
- (DGo') The
amount of energy (SI unit of joules) required to convert 1 mole of a
reactant from the ground state to the transition state.
- allosteric activator
- Any molecule which positively modulates the activity
of an allosteric enzyme.
- active pharmaceutical ingredient (API)
- The biologically active compound in a drug
formutation that imparts the desired therapeutic effect.
- active site
- The region of an enzyme that binds a substrate
molecule and catalytically transforms it, usually a small portion of
the total enzyme molecule
- active transport
- Energy-requiring transport of a solute across a
membrane in the direction of increasing concentration. Contrast with passive transport.
- activity
- The true thermodynamic activity of a substance, as
distinct from its molar concentration. Most of the time we call the
activity equal to the molar concentration and ignore it.
- acyl phosphate
- Any molecule with the general chemical form
- adenosine 3',5'-cyclic monophosphate
- cAMP.
- adenosine diphosphate (ADP)
- A ribonucleoside 5'-diphosphate serving as phosphate
group acceptor in the cell energy cycle.
- adenosine triphosphate (ATP)
- A ribonucleoside 5'-triphosphate functioning as a
phosphate group donor in the cell energy cycle.
- adipo
- fat
- adipocyte
- An animal cell specialized for the storage of
triacylglycerols.
- adipose tissue
- Connective tissue specialized for the storage of
large amounts of triacylglycerols.
- ADP
- (adenosine diphosphate) A ribonucleoside
5'-diphosphate serving as phosphate group acceptor in the cell energy
cycle.
- ADME
- Absorption, dilution, metabolism, excretion.
The four steps a drug goes through when administered.
- aerobe
- An organism that uses oxygen as the terminal electron
acceptor in respiration.
- aerobic
- Requiring or occurring in the presence of oxygen.
- albumin
- 66.3 kDa protein comprising most of the protein in
serum and largely responsible for buffering pH and volume of blood.
- alcohol fermentation
- The anaerobic conversion of glucose to ethanol via
anaerobic glycolysis. See also fermentation.
- aldose
- A simple sugar in which the carbonyl carbon atom is
an aldehyde
- alkaloids
- Nitrogen-containing organic compounds of plant
origin. They are usually basic, and often have biological
activity. An example would be caffeine.
- alkalosis
- A metabolic condition in which blood pH decreases,
usually the result of a metabolic condition or vomiting.
- allo-
- other
- allosteric enzyme
- A regulatory enzyme, with catalytic activity
modulated by the noncovalent binding of a specific molecule at a site
other than the active site.
- allosteric site
- The specific site on the surface of an allosteric
enzyme molecule (distinct from the active site) to which a modulator
molecule binds.
- a1-microglobulin
- 26.7 kDa protein
- a1-glycoprotein
- 41 kDa protein
- a1-antitrypsin
- 54 kDa protein
- a helix
- A helical conformation of a polypeptide chain,
predominantly right-handed, with maximal intrachain hydrogen bonding of
the peptide bonds; one of the most common secondary structures in
proteins.
- ambi-
- both
- Ames test
- A simple bacterial test for carcinogens, based on the
assumption that carcinogens are mutagens. Named after its
inventor Bruce Ames. Somewhat less favored than it used to be,
because of the idea that compounds causing cells to grow more rapidly
will also result in some cancer (the more you do something, the more
likely you are to mess up, since accidents sometimes happen).
- amino acid activation
- Enzymatic esterification of the carboxyl group of an
amino acid to the 3'-hydroxyl group of its corresponding tRNA which
requires 2 ATP-equivalents of energy.
- amino acids
- Molecules which serve as the building blocks of
proteins and having the general formula
 .
- amino-terminal residue
- The amino acid residue in a polypeptide chain which
has a free a-amino group.
- aminoacyl-tRNA
- An aminoacyl ester of a tRNA.
- aminoacyl-tRNA synthetases
- Enzymes that catalyze synthesis of an aminoacyl tRNA
at the expense of ATP energy.
- aminotransferases
- Enzymes that catalyze the transfer of amino groups
from a-amino to a-keto
acids; commonly called transaminases.
- ammonotelic
- Organisms which excrete excess nitrogen in the form
of ammonia.
- amphi-
- on both sides
- amphibolic pathway
- A metabolic pathway used in both catabolism and
anabolism.
- amphipathic
- Containing both polar and nonpolar domains.
- amphiprotic
- Capable of donating and accepting protons, thus able
to serve as an acid or a base.
- amylo
- starch
- anabolism
- The phase of intermediary metabolism concerned with
the energy-requiring biosynthesis of cell components from smaller
precursors.
- anaerobe
- An organism that lives without oxygen and uses
another chemical species as a terminal electron acceptor. Obligate
anaerobes die when exposed to oxygen; facultative anaerobes can live in
both aerobic and anaerobic environments.
- anaerobic
- Occurring in the absence of air or oxygen.
- anaplerotic reaction
- An enzyme-catalyzed reaction that can replenish the
supply of intermediates in a metabolic pathway, most commonly the
citric acid cycle.
- angstrom (Å)
- An older unit of length (10-10 cm)
sometimes used to indicate molecular dimensions. In the 21st century it
is preferable to use nm.
- anhydride
- The product of the condensation of two carboxyl or
phosphate groups to form a compound with the general structure
 where X is either
carbon or phosphorus (a phosphoanhydride).
- anion-exchange resin
- A resin with fixed cationic groups which is used in
the chromatographic separation of anions, e.g. DEAE
(diethylaminoethyl)-cellulose.
- anomers
- Two stereoisomers (a and
ß) of a given sugar that differ only in the configuration about
the carbonyl (anomeric) carbon atom (carbon 1 for pyranoses and carbon
2 for furanoses).
- ante-
- before, forwards
- anti-
- against, opposite
- antibiotic
- An organic compound secreted by many species of
microorganisms and fungi which is toxic to other species, e.g.
penicillin.
- antibody
- A defense protein synthesized by the immune system of
vertebrates. See also immunoglobulin.
- anticodon
- A specific sequence of three nucleotides in a tRNA,
complementary to a codon for an amino acid in a mRNA.
- antigen
- Any molecule which causes the synthesis of a specific
antibody in vertebrates.
- antiparallel
- Describing two linear polymers that are opposite in
polarity or orientation.
- antiport
- Cotransport of two solutes across a membrane in
opposite directions.
- Active pharmaceutical ingredient (API)
- is the biologically active compound in a drug
formutation that imparts the desired therapeutic effect.
- apoenzyme
- The protein portion of an enzyme, absent any organic
or inorganic cofactors or prosthetic groups that might be required for
catalytic activity.
- arthro
- joint
- -ase
- enzyme
- asymmetric carbon atom
- A carbon atom that is covalently bonded to four
different groups and thus may exist in two different stereospecific
configurations (D- and L- in biochemistry).
- -ate
- negatively charged form of an acid
- ATP
- (adenosine triphosphate) A ribonucleoside
5'-triphosphate functioning as a phosphate group donor in the cell
energy cycle.
- ATP synthase
- An enzyme complex that forms ATP from ADP and
phosphate during oxidative phosphorylation oin the inner mitochondrial
membrane or the bacterial plasma membrane, and during
photophosphorylation in chloroplasts. Uses a proton gradient to
chemiosmotically drive the synthesis.
- ATPase
- An enzyme that hydrolyzes ATP to yield ADP and
phosphate; usually coupled to some process requiring energy such as the
sodium potassium ATPase.
- attenuator
- An RNA sequence involved in regulating the expression
of some prokaryotic genes.
- autotroph
- An organism that can synthesize its own complex
molecules from simple carbon and nitrogen sources, such as CO2
and NH3.
- auxin
- A plant growth hormone.
- auxotrophic mutant
- (auxotroph) A mutant organism defective in the
synthesis of a given biomolecule, which must therefore be supplied for
the organism's growth.
- Avogadro's number
- The number of molecules in one mole of any compound
(6.02 x 1023).
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- back-mutation
- A mutation that causes a mutant gene to revert back
to its
wild-type genotype.
- bacteriophage (phage)
- A virus capable of replicating in a bacterial cell.
- basal metabolic rate
- The rate of oxygen consumption by an animal's body at
complete
rest under
fasting conditions.
- base pair
- Two nucleotides in nucleic acid chains that are
paired by
hydrogen bonding
of their bases; for example, A with T or U, and G with C.
- ß2-microglobulin
- 11.8 kDa protein
- ß conformation
- An extended, zigzag arrangement of a polypeptide
chain
which can
be parallel
or antiparallel. One of the common secondary structure in
proteins.
- ß oxidation
- Oxidative degradation of fatty acids into acetyl-CoA
by
successive oxidation,
reduction and hydrolytic reactions at the ß-carbon atom.
- bilayer
- A double layer of amphipathic lipid molecules which
orient
themselves so
the hydrocarbon tails face inward to form a continuous nonpolar phase
and
the polar head groups face outward. In this way they form the
basic
structure of membranes.
- bile salts
- Amphipathic steroid derivatives with detergent
properties,
participating
in digestion and absorption of lipids.
- Biologics License Application
- application filed with the Center for Biologics
Evaluation and Research (of the FDA) for approval to market a
biological drug (for example, herceptin, a monoclonal antibody used to
treat breast cancer).
- binding energy
- The energy derived from noncovalent interactions
between
enzyme
and substrate
or receptor and ligand, resulting from displacement of water, formation
of hydrogen bonds, etc.
- bio-
- life
- biocytin
- The molecule arising from covalent attachment of
biotin to
a Lys
residue via
an amide linkage.
- biopterin
- An enzymatic cofactor derived from pterin and
involved in
certain
oxidation-reduction
reactions.
- biomarker
- Specific biochemical compounds that are detected
within the body,
and which have a particular molecular feature that makes it useful for
measuring a specific process (flux through a pathway, e.g.), the
progress of a disease, the effects of treatment of a disease, etc.
- biotin
- An enzymatic cofactor involved in carboxylation
reactions,
 .
- bi(s)-
- twice, double
- bond energy
- The energy required to break a bond.
- branch migration
- See Holliday intermediate.
- buffer
- A system capable of resisting changes in pH when
small
amounts of
acid
or base are added. Consists of a conjugate acid-base pair in
which
the ratio of proton acceptor to proton donor is near unity.
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- calorie
- The amount of heat required to raise the temperature
of 1.0 g of water from 14.5 to 15.5°C. One calorie (cal) equals
4.18 joules (J). Contrast with Cal, used in dietary applications,
which is 1,000 cal.
- Calvin cycle
- The cyclic pathway used by plants to fix carbon
dioxide and produce triose phosphates. Named after Melvin Calvin, an
early worker in the field.
- cAMP
- A second messenger within cells; its formation by
adenylate cyclase is stimulated by certain hormones (epinephrine) or
other molecular signals. structure
- cGMP (current Good Manufacturing Practices)
- Refers to the body of regulations that describe the
methods, equipment, facilities, and controls required for producing
human and veterinary products, medical devices, and processed food.
- capsid
- The protein coat of a virus particle.
- carbanion
- A negatively charged carbon atom.
- carbocation (AKA) carbonium ion
- A positively charged carbon atom.
- carbon fixation reactions (dark reactions)
- The light-independent enzymatic reactions involved in
the synthesis of glucose from CO2, ATP, and NADPH.
- carboxyl-terminal residue
- The amino acid residue in a polypeptide chain with a
free a-carboxyl group.
- carotenoids
- Lipid-soluble photosynthetic pigments made up of
isoprene units.
- cata-
- down
- catabolism
- The phase of intermediary metabolism concerned with
the energy-yielding degradation of nutrient molecules.
- catabolite gene activator protein (CAP)
- A specific regulatory protein that controls
initiation of transcription of the genes producing the enzymes required
for a bacterial cell to use some other nutrient when glucose is
lacking.
- catalytic site
- See active site.
- catecholamines
- Hormones, such as epinephrine, that are amino
derivatives of catechol.
- cation-exchange resin
- A polymeric substance with fixed negative charges
used in the chromatographic separation of cationic substances, e.g. CM
(carboxymethyl)-cellulose.
- cDNA (complementary DNA)
- A DNA, usually made by reverse transcriptase, which
is complementary to given mRNA and used in cloning.
- central dogma
- The organizing principle of molecular biology:
genetic information flows from DNA to RNA to protein.
- centromere
- A specialized region of a chromosome which serves as
the attachment point for the mitotic or meiotic spindle.
- cerebroside
- Sphingolipid containing one sugar residue as a head
group, e.g. glucosylceramide.
- cGMP (current Good Manufacturing Practices)
- Refers to the body of regulations that describe the
methods, equipment, facilities, and controls required for producing
human and veterinary products, medical devices, and processed food.
- channeling
- The direct transfer of a reaction product from the
active site of one enzyme directly to the active site of a different
enzyme, where it serves as a substrate.
- chemiosmotic coupling
- Coupling of ATP synthesis to electron transfer via
an electrochemical pH gradient across a membrane (inner mitochondrial
membrane, bacterial plasma membrane, or thylakoid membrane).
- chemotaxis
- A cell's sensing of and movement toward, or away
from, a specific chemical agent.
- chemotroph
- An organism that obtains energy by metabolizing
organic compounds derived from other organisms.
- chiral compound
- A compound that contains an asymmetric (chiral)
center and thus can occur in two nonsuperimposable mirror-image forms
(enantiomers).
- chlorophylls
- A family of green pigments functioning as receptors
of light energy in photosynthesis; magnesium-porphyrin complexes.
- chloroplasts
- Chlorophyll-containing photosynthetic organelles in
some eukaryotic cells.
- chromatin
- A filamentous complex of DNA, histones, and other
proteins, constituting the eukaryotic chromosome.
- chromatography
- A process in which mixtures of molecules are
separated by many repeated partitionings between a mobile phase and a
stationary phase. The major types are size exclusion, ion
exchange and affinity; can be conducted at high or low pressure.
- chromosome
- A single large DNA molecule and its associated
proteins. The function is to store information in genes and transmit
genetic information.
- chylomicron
- A plasma lipoprotein composed of a triacylglycerol
core and a shell of protein and phospholipid. The chylomicron
carries lipid from the intestine to the tissues.
- -cide
- kill
- circum-
- around
- cis and trans isomers
- Isomers related by rotation about a double bond.
- cistron
- A unit of DNA or RNA corresponding to one gene.
- citric acid cycle
- Krebs cycle.
- clinical trial, phase I
- The first trial, designed to determine the safety of
an experimental drug
- clinical trial, phase II
- The second trial, designed to continue to collect
safety data, but adding the assessment of side effects and establish
dosage guidelines
- clinical trial, phase III
- The third phase, designed to verify the safety and
effectiveness of an experimental drug
- clinical trial, phase IV
- Post-approval trials, designed to monitor the safety
and effectiveness of the new drug, as well as examine additional
applications.
clones- The descendants of a single cell. Classically,
this has meant cells, but Dolly the sheep was a clone.
- cloning
- The production of large numbers of identical DNA
molecules or cells (or organisms) from a single ancestral DNA molecule,
nucleus or cell.
- closed system
- A system that exchanges neither matter nor energy
with the surroundings.
- cobalamin
- See coenzyme B12.
- codon
- A sequence of three adjacent nucleotides in a nucleic
acid that codes for a specific amino acid.
- -c(o)ele
- cavity, hollow
- coenzyme
- An organic cofactor required for the action of
certain enzymes; often contains a vitamin as a component. A very
common example is NADH.
- coenzyme A
- A coenzyme serving as an acyl group carrier in
certain enzymatic reactions. Composed of pantothenic acid and
adenine. Structure
- coenzyme B12
- An enzymatic cofactor derived from the vitamin
cobalamin, involved in alkyl group transfers. Structure
- cofactor
- An inorganic ion or a coenzyme required for enzyme
activity.
- cognate
- Describing two biomolecules that normally interact;
for example, an enzyme and its normal substrate, or a receptor and its
normal ligand.
- cohesive ends
- Two DNA ends in the same DNA molecule, or in
different molecules, with short overhanging single-stranded segments
that are complementary to one another, facilitating ligation of the
ends; also known as sticky ends. Usually generated by the action of
restriction enzymes.
- cointegrate
- An intermediate in the migration of certain DNA
transposons in which the donor DNA and target DNA are covalently
attached.
- colligative properties
- Properties of solutions that depend on the number of
solute particles per unit volume; for example, freezing-point
depression.
- commodity chemicals
- Low-value, high-volume compounds produced in
dedicated plants and used for a wide variety of applications.
- common intermediate
- Referring to a metabolite; A chemical compound common
to two enzymatic reactions, as a product of one and a substrate in the
other.
- competitive inhibition
- A type of enzyme inhibition characterized by the
inhibitor binding to the active site. The inhibition can be reversed by
increasing the concentration of substrate. A competitive inhibitor is
usually a structural analog of the substrate.
- complementary
- Having a molecular surface with chemical groups
arranged to interact specifically with chemical groups on another
molecule.
- con-
- together
- configuration
- The spatial arrangement of an organic molecule that
is conferred by the presence of either a double bond, about which there
is no freedom of rotation, or chiral centers, around which 4 different
substituent groups are arranged in a stereospecific fashion. The
arrangement in either of these cases cannot be changed without breaking
at least one covalent bond.
- conformation
- The spatial arrangement of substituent groups that
are free to assume different positions in space without breaking any
bonds, because of the freedom of single bond to rotate.
- conjugate acid-base pair
- A proton donor and its corresponding deprotonated
species; for example, acetic acid (donor) and acetate (acceptor).
- conjugate redox pair
- An electron donor and its corresponding electron
acceptor form; for example, NADH (donor) and NAD+
(acceptor).
- conjugated protein
- A protein containing one or more prosthetic groups.
- consensus sequence
- A DNA or amino acid sequence consisting of the
residues that occur most commonly at each position within a set of
similar sequences. Example
- conservative substitution
- Replacement of an amino acid residue in a polypeptide
by another residue with similar properties. For example,
substitution of Lys by Arg.
- constitutive enzymes
- Enzymes required at all times by a cell and present
at some constant level; for example, many enzymes of the central
metabolic pathways. Sometimes called "housekeeping" enzymes.
- contra-
- against
- cyte-
- cell
- corticosteroids
- Steroid hormones formed by the adrenal cortex.
- cosmid
- A cloning vector, used for cloning large DNA
fragments; generally contains segments derived from bacteriophages and
various plasmids.
- cotransport
- The simultaneous transport, by a single transporter,
of two solutes across a membrane. Is either antiport or symport,
depending on whether the solutes travel in opposite or the same
direction.
- coupled reactions
- Two chemical reactions that have a common
intermediate and thus a means of energy transfer from one to the other.
Example
- covalent bond
- A chemical bond that involves sharing of electron
pairs.
- cristae
- Infoldings of the inner mitochondrial membrane.
- cyclic electron flow
- In chloroplasts, the light-induced flow of electrons
originating from and returning to photosystem I to produce ATP without
production of NADPH.
- cyclic photophosphorylation
- ATP synthesis driven by cyclic electron flow through
photosystem I (no NADPH produced).
- cytochromes
- Heme proteins serving as electron carriers in
cellular respiration, photosynthesis, or other redox
reactions. Cytochrome c, for example
- cytokinesis
- The final separation of daughter cells following
mitosis.
- cytoplasm
- The portion of a cell's contents outside the nucleus
but within the plasma membrane; includes organelles such as
mitochondria, as well as soluble enzymes and solute particles.
- cytoskeleton
- The filamentous network providing structure,
organization and motion to the cytoplasm: includes actin filaments,
microtubules, and intermediate filaments.
- cytosol
- The aqueous phase of the cytoplasm (including
dissolved solutes and enzymes, but excluding all organelles). It is
most commonly the product of centrifugation at 100,000 xg for 1 h.
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- dalton
- The mass of a single hydrogen atom (1.66 x 1024
g).
- dark reactions
- The light-independent enzymatic reactions involved in
the
synthesis of
glucose from CO2, ATP, and NADPH.
- de-
- from, away from, down from
- de novo pathway
- Pathway for synthesis of a biomolecule from simple
precursors,
such as
synthesis of purine nucleotides from Asp, CO2, Gly, formate
and Glu: Distinguish from a salvage pathway.
- deamination
- The enzymatic removal of amino groups from
biomolecules
such as
amino acids
or nucleotides. q.v. oxidative decarboxylation or
- deca-
- ten
- degenerate code
- A code in which a single element in one language is
specified by
more than
one element in a second language. Example
- dehydrogenases
- Enzymes catalyzing the removal of pairs of hydrogen
atoms
from
their substrates.
Example
- deletion mutation
- A mutation resulting from the deletion of one or more
nucleotides
from
a gene.
- denaturation
- Alteration of the specific native conformation of a
polypeptide
chain,
protein, or nucleic acid.
- deoxyribonucleic acid (DNA)
- A polynucleotide having a defined sequence of
deoxyribonucleotide
units
covalently bonded via 3',5'-phosphodiester bonds. Functions in
the
transmission of genetic information.
- deoxyribonucleotides
- Nucleotides containing 2-deoxy-D-ribose as the
pentose
component.
- desaturases
- Enzymes (dehydrogenases) that catalyze the
introduction of
double
bonds
into the hydrocarbon portion of fatty acids.
- desolvation
- In aqueous solution, the release of bound water
surrounding
a
solute such
as an enzyme.
- dextrorotatory isomer
- A stereoisomer that rotates the plane of
plane-polarized
light
clockwise.
- di(s)-
- two
- dia-
- through, complete
- diabetes mellitus
- A complex endocrine-metabolic disease resulting from
insulin
deficiency;
characterized by a failure in glucose transport from the blood into
cells
at normal glucose concentrations, resulting in hyperglycemia.
- dialysis
- Removal of small molecules from a solution of a
macromolecule by
allowing
them to diffuse through a semipermeable membrane into water or buffer.
- differential centrifugation
- Separation of cell organelles or other particles of
different
density by
their different rates of sedimentation in a centrifugal field.
- differentiation
- Specialization of cell structure and function during
embryonic
growth and
development.
- diffusion
- The net movement of molecules in the direction of
lower
concentration.
- digestion
- Enzymatic hydrolysis of nutrients in the
gastrointestinal
system
to yield
their substituent components.
- diplo-
- double
- diploid
- Having two sets of genetic information; describing a
cell
with
two chromosomes
of each type.
- dipole
- A molecule having both partial positive and partial
negative
charges.
- diprotic acid
- An acid having two dissociable protons, for example H2SO4
or oxalic acid.
- disaccharide
- A carbohydrate consisting of two covalently joined
monosaccharide
units.
Sucrose for example, is composed of glucose and fructose.
- dissociation constant
- An equilibrium constant for the dissociation of one
species
into
two.
Examples would be the dissociation of a complex of two or more
biomolecules
into its components, for example, dissociation of a substrate from an
enzyme,
descibed as a Kd; an acid dissociating into its conjugate base and a
proton,
described as a Ka; the dissociation of water into protons and hydroxide
ions, described as a Kw; or a base dissociating into its conjugate acid
and a hydroxide ion , described as a Kb.
- disulfide bridge
- A covalent cross link between two polypeptide chains
formed
by a
cystine
residue (two Cys residues oxidized together).
- DNA (deoxyribonucleic acid)
- A polynucleotide having a specific sequence of
deoxyribonucleotide units
covalently joined through 3',5'-phosphodiester bonds; serves as the
carrier
of genetic information.
- DNA chimera
- A DNA containing genetic information derived from two
different
DNA molecules.
- DNA cloning
- The production of large numbers of identical DNA
molecules
or
cells from
a single ancestral DNA molecule, nucleus or cell.
- DNA library
- A random collection of cloned DNA fragments designed
to
include
all or
most of the genome of a given organism; also called a genomic library.
- DNA ligase
- An enzyme that creates a phosphodiester bond between
the 3'
end
of one
DNA segment and the 5' end of another.
- DNA polymerase
- An enzyme that catalyzes template-dependent synthesis
of
DNA from
its dNTP
precursors.
- DNA replicase system
- The entire complex of enzymes and specialized
proteins
required
in biological
DNA replication.
- DNA supercoiling
- The coiling of DNA upon itself, into a more condensed
structure.
- DNA transposition
- The movement of a gene or set of genes from one site
in the
genome to another.
- dolicho-
- long
- domain
- A distinct structural unit of a polypeptide.
Domains
may
have separate
functions and some are known to fold as independent, compact units,
such
as the Fc and Fab regions of an antibody molecule.
- double helix
- The natural coiled conformation of two complementary,
antiparallel DNA
chains by the formation of A-T and G-C base pairs.
- double-reciprocal plot
- A plot of 1/Vo versus 1/[S], which allows a more
accurate
determination
of Vmax and Km than a plot of Vo versus [S]; also called the
Lineweaver-Burk
plot.
- dur-
- hard, firm
- dys-
- bad, abnormal
A B C
DE
F G HI
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N O PQ
R S TU
V W XY
Z
- e-, ec-
- out, from out of
- Eo'
- The electromotive force exhibited at an electrode by
1 M
concentrations
of a reducing agent and its oxidized form at 25 oC and pH
7.0;
a measure of the relative tendency of the reducing agent to lose
electrons.
- ecto-
- outside, external
- -ectomy
- removal of, cut out
- E. coli (Escherichia coli)
- A common bacterium found in the small intestine of
vertebrates;
the most
well-studied organism.
- electrochemical gradient
- The sum of the gradients of concentration and of
electric
charge
of an
ion across a membrane. Used as the driving force for processes
such
as oxidative phosphorylation and photophosphorylation.
- electrochemical potential
- The energy required to maintain a separation of
charge and
of
concentration
across a membrane.
- electrogenic
- Contributing to the generation of an electrical
potential
across
a membrane.
- electron acceptor
- A substance that receives electrons in a redox
reaction.
- electron carrier
- A protein or other chemical species, such as a
cytochrome
or
coenzyme Q,
that can reversibly gain and lose electrons. They function in the
transfer
of electrons from organic nutrients to oxygen or some other terminal
acceptor
in the case of anaerobes.
- electron donor
- A substance that donates electrons in a redox
reaction.
- electrophile
- An electron-deficient group with a strong tendency to
accept
electrons
from an electron-rich group (nucleophile).
- electrophoresis
- Movement of charged solutes in response to an
electrical
field. Used
experimentally to separate mixtures of electrically charged species
such
as proteins or nucleic acids.
- elongation factors
- Specific proteins required in the elongation of
polypeptide
chains by ribosomes
or DNA strands by replisomes.
- eluate
- The effluent from a chromatographic column.
- em-
- in
- en-
- into
- enantiomers
- Stereoisomers that are nonsuperimposable mirror
images of
each
other.
- end-product inhibition
- Inhibition of an allosteric enzyme at the beginning
of a
metabolic sequence
by the end product of the sequence.
- endergonic reaction
- A chemical reaction that consumes energy (that is,
for
which DG
is positive). These are nonspontaneous processes.
- endo-
- into
- endocrine glands
- Groups of cells specialized to synthesize hormones
and
secrete
them into
the blood to regulate other types of cells. The pancreas, for example.
- endocytosis
- The uptake of extracellular material by its inclusion
within a
vesicle
(endosome) formed by an invagination of the plasma membrane. qv
receptor-mediated
endocytosis
- endonuclease
- An enzyme that hydrolyzes the interior phosphodiester
bonds
of a
nucleic
acid.
- endoplasmic reticulum
- An extensive system of double membranes in the
cytoplasm of
eukaryotic
cells. The two major types are smooth and rough endoplasmic
reticulum.
Functions in calcium storage as well as protein and lipid synthesis.
- endothermic reaction
- A chemical reaction that takes up heat (that is, for
which DH
is positive). These reactions are spontaneous.
- energy charge
- The fractional degree to which the ATP/ADP/AMP system
is
filled
with high-energy
phosphate groups.
- energy coupling
- The transfer of energy from one process to another.
For
example,
the coupling
of ATP hydrolysis with glucose phosphorylation.
- enhancers
- cis-acting DNA sequences that facilitate the
expression of
a given
gene by increasing transcription independent of the enhancer
orientation
or distance relative to the promoter.
- ent-
- within
- enthalpy (H)
- The heat content of a system.
- enthalpy change (DH)
- For a reaction, is approximately equal to the
difference
between
the energy
used to break bonds and the energy gained by the formation of new ones.
- entropy (S)
- The extent of disorder in a system.
- enzyme
- A biomolecule, usually protein but sometimes RNA,
that
catalyzes
a specific
chemical reaction. It does not affect the equilibrium of the catalyzed
reaction; rather, it enhances the rate of a reaction by lowering the
activation
energy.
- epi-
- on, up, against, high
- epimerases
- Enzymes that catalyze the reversible interconversion
of two
epimers.
- epimers
- Two stereoisomers differing in configuration at one
asymmetric
center,
in a compound having two or more asymmetric centers.
- epithelial cell
- Any cell that forms part of the outer covering of an
organism or
organ.
- epitope
- A portion of an antigenic macromolecule recognized
and
bound by a
specific
antibody.
- equilibrium
- The state of a system in which no further net
change is
occurring.
- equilibrium constant (Keq')
- A constant, characteristic for each chemical reaction
relating
the molar
concentrations of all reactants and products at equilibrium at a given
temperature, pressure and pH.
- ERAD
- Endoplasmic reticuluum-associated degradation (of
protein).
Incorrectly formed proteins are destroyed in the ER instead of being
secreted.
- erythrocyte
- A red blood cell containing large amounts of
hemoglobin and
specialized
for oxygen transport.
- Escherichia coli (E. coli.)
- A common bacterium found in the small intestine of
vertebrates;
the most
well-studied organism.
- essential amino acids
- Amino acids that cannot be synthesized by humans (or
other
vertebrates)
and must be obtained from the diet.
- essential fatty acids
- The group of polyunsaturated fatty acids produced by
plants, but
not humans
and are thus required in the human diet: linoleic, linolenic and
arachidonic acids.
- eu-
- true
- euchromatin
- Chromatin which is in an uncondensed form, is more
accessible,
and contains the majority of actively expressed genes. See also
heterochromatin.
- eukaryote
- A unicellular or multicellular organism with cells
having a
membrane-bounded
nucleus. All possess, in addition, multiple chromosomes and
internal
organelles.
- ex-, exo-
- out, from out of
- excited state
- An energy-rich state of an atom or molecule. An
electron
absorbs
electromagnetic energy to be promoted from the ground state to an
excited
state.
- exergonic reaction
- A chemical reaction that proceeds with the release of
free
energy
(that
is, for which DG is negative and the
reaction
spontaneous).
- exocytosis
- The fusion of an intracellular vesicle with the
plasma
membrane,
releasing
the vesicle contents to the extracellular space.
- exon
- The segment of a eukaryotic gene that is transcribed
into a
protein or
incorporated into the structure of an RNA. See also intron.
- exonuclease
- An enzyme that hydrolyzes phosphodiester bonds that
are in
the
terminal
positions of a nucleic acid.
- exothermic reaction
- A chemical reaction that releases heat (that is, for
which DH
is negative).
- extra-
- outside, beyond, in addition
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- facilitated diffusion
- Diffusion of a molecule across a biological membrane via
a protein
transporter down a concentration gradient. Also called passive
diffusion.
- facultative cells
- Cells that can live in the presence or absence of
oxygen.
- FAD (flavin adenine dinucleotide)
- The coenzyme of some redox enzymes; it contains
riboflavin. Structure
- fatty acid
- A long-chain aliphatic carboxylic acid found in fats,
oils,
membrane phospholipids
and glycolipids.
- feedback inhibition
- Inhibition of an allosteric enzyme at the beginning
of a
metabolic sequence
by the end product of the sequence.
- fermentation
- Energy-yielding anaerobic breakdown of a nutrient
molecule,
such
as glucose,
without net oxidation. Most commonly yields lactate in mammals or
ethanol in yeast.
- fibroblast
- A cell of connective tissue that secretes connective
tissue
proteins such
as collagen.
- fibrous proteins
- Water-insoluble proteins that serve in a protective
or
structural
role.
The ratio of length to width generally exceeds 10.
- fine chemicals
- Low-volume, high-value, single-substance chemicals
sold on the basis of specifications (on the basis of what they are, not
what they do).
- fingerprinting
- The characteristic two-dimensional pattern (on paper
or
gel)
formed by
the separation of a mixture of peptides resulting from partial
hydrolysis
of a protein; also known as peptide mapping.
- first law of thermodynamics
- Energy can be neither created nor destroyed, only
converted
to
other forms.
- Fischer projection formulas
- Formulas which, by convention, show bonds coming out
of the
plane
drawn
vertically, and bonds which project behind the plane are drawn
horizontally.
- 5' end
- The end of a nucleic acid that lacks a nucleotide
bound at
the 5'
hydroxyl
group.
- flagellum
- A cell appendage used in propulsion.
- flavin-linked dehydrogenases
- Dehydrogenases requiring one of the riboflavin
coenzymes,
either
FMN or
FAD.
- flavin nucleotides
- Nucleotide coenzymes containing riboflavin, either
FMN or
FAD.
- flavoprotein
- An enzyme containing a FMN or FAD as a tightly bound
prosthetic
group.
- fluid mosaic model
- A model proposed by Singer and Nicholson, describes
biological
membranes
as a fluid lipid bilayer with embedded proteins creating a
mosaic.
Both protein and lipid components of the bilayer are able to move, but
exhibit both structural and functional asymmetry.
- fluorescence
- Instantaneous emission of light by excited molecules
as
they
revert to
the ground state.
- FMN (flavin mononucleotide)
- Riboflavin phosphate, a coenzyme of some redox
enzymes.
- footprinting
- A technique for identifying the nucleic acid sequence
bound
either by a
DNA- or by an RNA-binding protein. This sequence is protected
from
digestion by the protein.
- -form
- shaped like
- frame shift
- A mutation caused by insertion or deletion of one or
more
paired
nucleotides,
changing the reading frame of codons and therefore the amino acids
incorporated
into proteins.
- free energy (G)
- That portion of the total energy of a system that can
do
work at
constant
temperature and pressure.
- free energy of activation (DGdouble daggar)
- q v activation energy.
- free-energy change (DG')
- The amount of free energy released (negative DG)
or absorbed (positive DG) in a reaction at
constant
temperature and pressure.
- free radical
- q v radical.
- functional group
- The specific atom or group of atoms that confers a
particular
chemical
property on a biomolecule.
- furanose
- A simple sugar structurally analogous to the
five-membered
furan
ring.
- fusion protein
- Depending on the context means one of two different
things.
Most
commonly, refers to the protein product of a gene created by the fusion
of two distinct genes, or portions of genes. Less commonly refers
to one of a family of proteins that participate in membrane
fusion
(annexin, e.g.).
- futile cycle
- A set of enzyme-catalyzed cyclic reactions that
results
only in
the net
release of thermal energy by the hydrolysis of ATP. [example]
- DG'°
- standard
free-energy
change.
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- gametes
- Reproductive cells (sperm or egg) which are haploid.
- gangliosides
- Sphingolipids containing complex oligosaccharides as
head
groups.
- GDNF
- glial cell line-derived neurotrophic factor
- gel filtration
- A chromatographic procedure for the separation of a
mixture
of
molecules
on the basis of size.
- gene
- A chromosomal segment that codes for a single
functional
peptide
chain
or RNA molecule.
- gene expression
- The production of a biologically active gene product,
either
constitutive
or regulated.
- gene splicing
- The enzymatic attachment of one exon to another.
- general acid-base catalysis
- Catalysis involving a proton transfer from/to a
molecule
other
than water.
Compare to specific acid-base catalysis.
- genetic code
- The set of triplet code words in mRNA or DNA, coding
for
the
amino acids
of proteins.
- genetic information
- The hereditary information contained in a sequence of
nucleotide
bases.
- genetic map
- A diagram showing the position of specific genes
along a
chromosome relative
to markers.
- genome
- The complete set of genetic information of an
organism (is
a
virus an organism?).
- genotype
- The genetic information of an organism, as distinct
from
its
physical expression
(phenotype).
- germ-line cell
- A class of animal cells formed early in embryogenesis
that
are
set aside
for reproductive function (give rise to gametes). All other cells
are somatic cells.
- globular proteins
- Soluble proteins with a globular (somewhat rounded)
shape.
Their
axial to diameter ratio is less that 10:1, and usually closer to
1:1.
- GLP (Good Laboratory Practices)
- Refers to the body of regulations that govern the
collection of
laboratory data. As two examples, data collected must be tracable
to the exact person who collected the data, and computer files must
have their name changed if the file contents change.
- glucogenic amino acids
- Amino acids with carbon chains that can be
metabolically
converted into
glucose via gluconeogenesis. Contrast with ketogenic
amino
acids.
- gluconeogenesis
- The biosynthesis of a carbohydrate from simpler,
noncarbohydrate
precursors
such as alanine or pyruvate.
- glycan
- A general term for a polymer of monosaccharide units
joined
by
glycosidic
bonds, may or may not have other components, e.g. peptidoglycan.
- glycerophospholipid
- An amphipathic lipid with a glycerol backbone. A
(usually
saturated) fatty
acid is esterified to C-1 and a (usually unsaturated) fatty acid is
esterified
to C-2 of glycerol. A polar alcohol is attached through a
phosphodiester
linkage to C-3.
- glycolipid
- A lipid containing a small amount of carbohydrate.
- glycolysis
- The catabolic pathway by which a molecule of glucose
is
broken
down into
two molecules of pyruvate, which undergoes further metabolism in other
pathways.
- glycoprotein
- A protein containing (a) carbohydrate sidechain(s) in
either an
N- or O-glycosidic
linkage.
- glycosaminoglycan
- A molecule composed of alternating monsaccharide
units. One
is either
GlcNAc or GalNac, the other is a usually glucuronic acid. Formerly
called
mucopolysaccharide.
- glycosidic bonds
- Bonds between a sugar and another molecule (typically
an
alcohol,
purine,
pyrimidine, or a second sugar). Divided into N-glycosidic or
O-glycosidic
linkages, depending on the point of attachment.
- glyoxylate cycle
- A variant of the citric acid cycle present in
bacteria and
some
plant cells
which is used for the net conversion of lipid into carbohydrate.
- glyoxysome
- A specialized peroxisome containing the enzymes of
the
glyoxylate
cycle.
Particularly prevalent and important in germinating seeds.
- Golgi complex
- A complex and dynamic membranous organelle of
eukaryotic
cells. Golgi
bodies function in the posttranslational modification (glycosylation)
and
secretion of proteins or insertion into membranes. Composed
of cis, medial and trans compartments as well as a less well defined
"trans-golgi
network."
- grana
- Stacks of thylakoids in
chloroplasts.
- GPCR
- G-protein (q.v.) coupled receptor. Usually a
serpentine receptor.
- ground state
- The normal, stable form of an atom or molecule.
Contrast
with the
excited
state.
- group transfer potential
- A measure of the ability of a compound to donate an
activated
group (such
as a phosphate group). Computed and expressed from the standard
free
energy of hydrolysis.
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- half-life
- The time required for the disappearance or decay of
one-half of a
given
quantity of substance.
- haplo-
- single
- haploid
- Having a single set of genetic information;
describing a
cell
with one
chromosome of each type; used in reproduction to prevent polyploidy.
- hapto-
- bind to
- haptoglobin
- serum protein which binds free hemoglobin for
transport to
the
liver and
destruction
- Haworth perspective formulas
- A method for representing cyclic chemical structures
(sugars) in
order
to define the configuration around each chiral center. Example
- helicase
- An enzyme that catalyzes the unwinding of strands in
a DNA
molecule before
replication.
- heme
- The iron-porphyrin prosthetic group of heme proteins.
- heme protein
- A protein containing a heme as a prosthetic group.
- hemi-
- half
- hemoglobin
- A heme protein of erythrocytes which functions in
oxygen
transport.
- Henderson-Hasselbalch equation
- An equation relating the pH, the pKa, and the ratio
of the
concentrations
of the proton-acceptor (A-) and proton-donor (HA) species in a
solution.
[equation]
- hepat
- liver
- hepatocyte
- The major cell type of liver tissue, which is
parenchymal
tissue.
Liver also contains fixed macrophages called Kupfer cells and other
cells.
- hept-
- seven
- hetero-
- different
- heterochromatin
- Chromatin which in a condensed, less accessible state
and
are
thus frequently transcriptionally silent. However, some DNA is
constitutive heterochromatin (e.g. the second X chromosome is
inactivated to a Barr body for dosage compensation) whereas other DNA
is facultative heterochromatin. An example might be genes required
under time of stress only, or during a stage of the cell cycle, etc.
- heteroduplex DNA
- Duplex DNA containing complementary strands derived
from
two
different
DNA molecules with similar or partially identical sequences.
Sometimes
from two unmanipulated species, other times a gene has been modified
and
reintroduced.
- heteropolysaccharide
- A polysaccharide containing two or more types of
sugars.
- heterotroph
- An organism that requires complex nutrient molecules,
such
as
glucose,
as an energy source.
- heterotropic enzyme
- An allosteric enzyme requiring a molecule other than
its
substrate as a
modulator.
- hex-
- six
- hexose
- A simple sugar with a backbone containing six carbon
atoms.
- high-energy compound
- A compound that on hydrolysis undergoes a large
decrease in
free
energy
under standard conditions.
- high-performance liquid chromatography (HPLC)
- A type of chromatography using relatively high
pressures
and
small diameter
column packings to achieve sharp and highly reproducible elution
profiles.
Used to be called high pressure liquid chromatography.
- histones
- The family of five basic proteins (H1, H2A, H2B, H3
and H4)
that
associate
tightly with DNA in the chromosomes of all eukaryotic cells.
- Holliday intermediate
- An intermediate in genetic recombination in which two
double-stranded DNA
molecules are joined by virtue of a reciprocal crossover involving one
strand of each molecule.
- holoenzyme
- A catalytically active enzyme including all necessary
subunits,
prosthetic
groups, and cofactors.
- homeobox
- A 180 base pair, highly conserved DNA sequence
encoding a
protein
domain
(the homeodomain) found in many proteins that play a regulatory role in
transcription. Particularly important in development.
- homeostasis
- The maintenance of a dynamic steady state by
regulatory
mechanisms that
compensate for changes in circumstances. For example, maintaining
body temperature whether in a 20oC or a 4oC
environment.
- homeotic genes
- Genes originally defined as regulating the
development of
the
pattern of
segments in the Drosophila body plan. Similar genes are now known
to occur in most vertebrates.
- homo-
- same
- homologous genetic recombination
- Recombination between two DNA molecules of similar
sequence,
occurring
in all cells; occurs during meiosis and mitosis in eukaryotes.
- homologous proteins
- Proteins from different species having similar
sequences
and
functions
similar in each. For example the many species which have
hemoglobin
which transports oxygen in all.
- homopolysaccharide
- A polysaccharide made up of only one type of
monosaccharide
unit.
- homotropic enzyme
- An allosteric enzyme that is modulated by its
substrate.
- hormone
- A chemical substance (peptide, steroid) synthesized
in
small
amounts by
an endocrine tissue and carried in the blood to another tissue, where
it
acts as a messenger to regulate the function of the target tissue.
- hormone receptor
- A protein in, or on the surface of the target cells
of a
tissue
that functions
as a sensor for the hormone by binding the hormone and initiating a
cellular
response.
- hydrogen bond
- A weak electrostatic attraction between one
electronegative
atom
(biochemically
oxygen or nitrogen) and a hydrogen atom covalently linked to a second
oxygen
or nitrogen atom.
- hydrolases
- Enzymes that catalyze hydrolysis reactions.
Includes
proteases, lipases,
phosphatases, and nucleases.
- hydrolysis
- Cleavage of a bond, such as a peptide bond, by the
addition
of
the elements
of water, yielding two or more products.
- hydronium ion
- The ion H3O+.
- hydropathy index
- A scale that expresses the relative hydrophobic and
hydrophilic
tendencies
of amino acid R groups. Used to predict membrane-spanning
regions.
- hydrophilic
- Polar or charged molecules that dissolve readily in
water.
- hydrophobic
- Nonpolar molecules that are insoluble in water.
- hydrophobic interactions
- The association of nonpolar groups or compounds with
each
other
in aqueous
systems due to their insolubility in water.
- hyper-
- above, excessive
- hyperchromic effect
- The large increase in light absorption at 260 nm
occurring
as a
double-helical
DNA is melted.
- hypo-
- below, deficient
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- -ia
- got
- -iasis
- full of
- -ile
- little version
- -illa
- little version
- -illus
- little version
- im-, in-
- not
- immune response
- The generation of antibodies to an antigen by a
vertebrate
organism.
- immunoglobulin
- An antibody protein generated against, and
exquisitely
specifically for
an antigen. Composed of two heavy chains (~ kDa) and two light
chains
(~ kDa) which are held together by disulfide bonds.
- -in
- stuff
- in vitro
- Literally, "in glass" meaning in the test tube.
- in vivo
- Literally, "in life" meaning in a living cell or
organism.
- induced fit
- A change in the conformation of an enzyme in response
to
substrate binding
that renders the enzyme catalytically active. It is one of the
models
used to explain substrate specificity.
- inducer
- A signal molecule that, when bound to a regulatory
protein,
produces an
increase in the expression of a given gene.
- induction
- An increase in the expression of a gene in response
to a
change
in the
activity of a regulatory protein.
- informational macromolecules
- Biomolecules containing information in the form of
specific
sequences of
different monomers; for example, many proteins, lipids,
polysaccharides,
and nucleic acids.
- infra-
- below, underneath
- initiation codon
- AUG. Codes for the first amino acid in all
polypeptide
sequences,
which is N-formyl-methionine in prokaryotes and methionine in
eukaryotes.
- initiation complex
- A complex of all ribosomal components, a mRNA and the
initiating
Met-tRNAMet
(eukaryotes) or fMet-tRNAMet (prokaryotes).
- inorganic pyrophosphatase
(pyrophosphatase)
- An enzyme that hydrolyzes a molecule of inorganic
pyrophosphate
to yield
two molecules of phosphate. reaction
- insertion mutation
- A mutation caused by insertion of one or more extra
bases
between
bases
in DNA, or a mutagen which itself is inserted between bases (like
ethidium
bromide).
- insertion sequence
- The specific base sequences at either end of a
transposon
which
allows
for insertion into DNA.
- integral membrane proteins
- Proteins inserted into a membrane by hydrophobic
interactions Contrast
with peripheral proteins.
- inter-
- among, between
- intercalating mutagen
- A mutagen that inserts itself between two successive
bases
in a
nucleic
acid causing a frame-shift mutation.
- intercalation
- Insertion between two stacked aromatic or planar
rings.
Most commonly
refers to the insertion of a planar mutagen between two successive
bases
in a nucleic acid.
- interferons
- A class of glycoproteins with antiviral activities.
- intermediary metabolism
- The enzyme-catalyzed reactions that extract chemical
energy
from
nutrient
molecules and utilize it to synthesize perform cell functions.
- intro-
- inward, during
- intron (intervening sequence)
- A sequence of nucleotides in a gene that is
transcribed but
not
translated.
- IND
- Investigational New Drug. Usually refers to an
application to pursue clinical trials with an experimental drug that
has passed preclinical trials.
- ion channel
- An integral membrane protein that provides for the
regulated
transport
of (a) specific ion(s) across a membrane.
- ion-exchange resin
- A polymeric chromatographic resin that contains fixed
charged
groups and
is used to separate ionic compounds.
- ion product of water (Kw)
- The product of the concentrations of H+
and OH-.
For pure water Kw = [H+][OH-] = 1 x 10-14
at 25 oC.
- ionizing radiation
- Any radiation that causes loss or gain of electrons
from
molecules, thus
making them more reactive.
- ionophore
- A compound that binds metal ions and diffuses across
membranes
carrying
the bound ion. An example is valinomycin, which transports
potassium.
- Institutional Review Board (IRB)
- A committee assigned review of research involving
human subjects.
- iron-sulfur center
- A prosthetic group of some redox proteins involved in
respiration
and other
electron transfers. Fe2+ or Fe3+ is with
Cys
groups in the protein.
- -ism
- theory, characteristic of
- iso-
- equal, same
- isoelectric focusing
- An electrophoretic method for separating
macromolecules on
the
basis of
their pI.
- isoelectric pH (isoelectric point, pI)
- The pH at which a solute has no net electric charge
and
thus does
not move
in an electric field.
- isoenzymes
- isozymes.
- isomerases
- Enzymes that catalyze the transformation of compounds
into
their
positional
isomers.
- isomers
- Any two molecules with the same molecular formula but
a
different
arrangement
of molecular groups: either stereospecific or geometric.
- isoprene
- The hydrocarbon 2-methyl-1,3-butadiene, a recurring
structural
unit of
many lipid molecules.
- isothermal
- Occurring at constant temperature.
- isotopes
- Stable or radioactive forms of an element that differ
in
atomic
weight
but are otherwise chemically identical to the naturally abundant form
of
the element. These properties allow them to be used as tracer
molecules.
- isozymes
- Two or more forms of an enzyme that catalyze the same
reaction
but differ
from each other in their physical properties, such as amino acid
sequence,
substrate affinity, Vmax, tissue expression or regulatory properties.
- -itis
- inflammation
- -ity
- makes a noun of quality
- -ium
- thing
- -ize
- do
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- juxta-
- adjacent to
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- keratins
- Insoluble protective or structural proteins
consisting of
parallel polypeptide
chains in a-helical or ß
conformations.
- ketogenic amino acids
- Amino acids with carbon skeletons that are
metabolized to
ketone
bodies.
Contrast with the glucogenic amino acids.
- ketone bodies
- A group of molecules normally produced in very low
amounts,
but
increased
amounts are found during fasting or in untreated diabetes
mellitus.
The three ketone bodies are acetoacetate, D-ß- hydroxybutyrate,
and
acetone.
- ketose
- A simple monosaccharide in which the carbonyl group
is a
ketone.
- ketosis
- A metabolic condition in which the concentration of
ketone
bodies
in the
blood, tissues, and urine is abnormally high.
- kinases
- Enzymes that catalyze the phosphorylation of certain
molecules
using ATP
as a phosphate source.
- kinetics
- The study of reaction rates.
- Krebs cycle
- A cyclic system of enzymatic reactions for the
oxidation of
acetyl residues
(as acetyl CoA) to carbon dioxide. The formation of citrate is the
first
step. Also called citric acid cycle or tricarboxylic acid (TCA) cycle.
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- lagging strand
- The DNA strand that, during replication, must be
synthesized in
the direction
opposite to that in which the replication fork moves. Synthesized
via
a series of fragments called Okazaki fragments.
- law of mass action
- The law stating that the rate of any given chemical
reaction is
proportional
to the product of the concentrations of the reactants. At
extremely
low concentrations, activities are used.
- leader
- A short sequence near the amino terminus of a protein
or
the 5'
end of
an RNA molecule that has a specialized targeting or regulatory
function.
Often the leader is cleaved after the targeting event.
- leading strand
- The DNA strand that, during replication, is
synthesized in
the
same direction
in which the replication fork moves. Synthesized in a continuous
fashion.
- lethal mutation
- A mutation that inactivates a biological function
essential
to
the life
of the cell or organism.
- leucine zipper
- A protein structural motif involved in
protein-protein
interactions in
many eukaryotic regulatory proteins (C/EBP prototype). Contain a
repeat structure: Leu residues in every seventh position, causes
a large amount of DNA to loop out.
- leukotrienes
- A family of molecules derived from arachidonate
having in
common
3 conjugated
double bonds. In general they cause muscle contractions that
constrict
air passages in the lungs, involved in asthma.
- levorotatory isomer
- A stereoisomer that rotates the plane of
plane-polarized
light
counterclockwise.
- ligand
- A small molecule that binds specifically to a larger
one;
for
example,
a hormone is the ligand for its specific protein receptor.
- light reactions
- The reactions of photosynthesis occuring only in the
light.
- Lineweaver-Burk equation
- An algebraic transformation of the Michaelis-Menten
equation
(plot of 1/V vs.
1/[S]), allowing determination of Vmax and Km by extrapolation of [S]
to
infinity.
- lipases
- Enzymes that catalyze the hydrolysis of
triacylglycerols.
- lipid
- A water-insoluble molecule which is soluble in
nonpolar
solvents
such as
ether. Divided into two classes: Saponifiable and
nonsaponifiable.
- lipoate (lipoic acid)
- A coenzyme involved as a carrier of acyl groups.
- lipoprotein
- A protein-lipid complex that functions in the
transport of
lipids
in the
blood. In cyclical fashion, present as chylomicrons, VLDL, LDL, IDL,
HDL
or chylomicron remnants. The protein component alone is an
apolipoprotein.
- -logy
- study of, reasoning about
- low-energy phosphate compound
- A phosphorylated compound with a relatively small
standard
free
energy
of hydrolysis.
- lyases
- Enzymes that catalyze the removal of a group from a
molecule to
form a
double bond, or the addition of a group to a double bond.
- lymphocytes
- A subclass of leukocytes characterized as
mononuclear, with
a
small amount
of cytoplasm. Involved in the immune response and divided into
two
types: B lymphocytes (synthesize and secrete antibodies) and T
lymphocytes
(participate in cell-mediated immunity).
- lysis
- Destruction of a cell's plasma membrane or of a
bacterial
cell
wall, releasing
the cells contents and killing the cell.
- lysosome
- A membrane-bounded organelle in the cytoplasm of
eukaryotic
cells
whose
function is to degrade and recycle proteins, in particular.
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- macro-
- large
- medi-
- middle
- medulla
- soft inner part
- mega-
- large
- megalo-
- very large
- meso-
- middle
- meta-
- beyond, between
- Michaelis-Menten kinetics
- A kinetic pattern observed in enzyme-catalyzed
reactions when the initial rate (as a function of substrate
concentration) exhibits a hyperbolic shape.
- micro-
- small
- microfilaments
- Thin filaments composed of actin found throughout the
cytoplasm of eukaryotic cells. Their function is give the cell
shape and movement.
- macromolecule
- A molecule having a molecular weight in the range of
a few thousand to many millions: proteins, nucleic acids and
polysaccharides.
- mass-action ratio
- The ratio which describes the kinetics of a reaction,
given as products over reactants. For a hypothetical reaction aA + bB
 cC + dD, the ratio would
be [A]a [B]b/[C]c [D]d
- -megaly
- large
- meiosis
- A type of cell division in which diploid cells give
rise to haploid cells destined to become gametes.
- membrane transport
- Movement of a polar molecule across a membrane via
a specific membrane protein (a transporter).
- messenger RNA (mRNA)
- A class of RNA molecules, each of which is
complementary to one strand of DNA, characterized by a 5'
7-N-methylguanine cap and a 3' polyA tail. Its function is to
carry the genetic message from the chromosome to the ribosomes.
- metabolism
- The sum total of anabolism and catabolism.
- metabolite
- A chemical intermediate in the enzyme-catalyzed
reactions of metabolism.
- metalloprotein
- A protein having a metal ion as its prosthetic group.
- micelle
- An aggregate of amphipathic molecules in water, with
the nonpolar portions in the interior and the polar portions at the
exterior surface, exposed to water.
- Michaelis-Menten constant (Km)
- Practically speaking, the substrate concentration at
which an enzyme-catalyzed reaction proceeds at one-half its maximum
velocity. Rigorously, the ratio k-1·k2/k1.
- Michaelis-Menten equation
- The equation describing the hyperbolic dependence of
the initial reaction velocity, Vo, on substrate concentration, [S], in
many enzyme-catalyzed reactions: Vo=Vmax[S]/Km+[S]
- microsomes
- Membranous vesicles formed by fragmentation of the
endoplasmic reticulum (and probably Golgi) of eukaryotic cells;
recovered by differential centrifugation.
- microtubules
- Thin tubules assembled from two types of globular
tubulin subunits (a and
ß). Found in cilia, flagella, centrosomes, and other
contractile or motile structures.
- mitochondrial matrix
- The aqueous portion of a mitochondrion bounded by the
inner mitochondrial membrane.
- mitochondrion (plural, mitochondria)
- Membrane-bounded organelle in the cytoplasm of
eukaryotes sometimes referred to as powerhouse of the cell because it
contains the enzyme systems required for the citric acid cycle, fatty
acid oxidation, electron transfer chain, and oxidative phosphorylation.
- mitosis
- The multistep process (interphase, prophase,
metaphase, anaphase, telophase) in eukaryotic cells that results in the
replication of chromosomes and cell division.
- mixed-function oxidases (oxygenases)
- Enzymes that use O2 to simultaneously
oxidize a substrate and a cosubstrate (commonly NADH or NADPH).
- modulator
- A metabolite that, when bound to the allosteric site
of an enzyme, alters its kinetic characteristics. Can be
homotropic or heterotropic, inhibitor or activator.
- mole
- One gram molecular weight of a compound, containing
6.02 x 1023 molecules.
- monoclonal antibodies
- Antibodies produced by a cloned hybridoma cell, which
therefore are identical and directed against the same epitope of an
antigen.
- monolayer
- A single layer of oriented lipid molecules or cells.
- monoprotic acid
- An acid having only one dissociable proton.
- monosaccharide
- A carbohydrate consisting of a single sugar unit.
- mRNA
- messenger RNA.
- mucopolysaccharide
- An older name for a glycosaminoglycan.
- multienzyme system
- A group of related enzymes participating in a given
metabolic pathway and often channeling substrates from one to another.
- mutarotation
- The change in specific rotation of a sugar as
equilibrium between its a- and
ß-anomeric and open chain forms occurs.
- mutases
- Enzymes that catalyze the transposition of functional
groups.
- mutation
- An inheritable change in the nucleotide sequence of a
gene.
- myofibril
- A unit of thick and thin filaments of muscle fibers.
- myosin
- The major component of the thick filaments of muscle
and other actin-myosin systems, functioning as a contractile protein.
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- neo-
- new
- -noid
- mind, spirit
- non-
- not
- noncompetitive inhibition
- A type of enzyme inhibition not reversed by
increasing the
substrate concentration.
The inhibitor binds to a site on the enzyme other than the active site
- noncyclic electron flow
- The light-induced flow of electrons from water to
NADP in
oxygen-evolving
photosynthesis involving both photosystems I and II. Contrat with
cyclic photophosphorylation
- nonessential amino acids
- Amino acids that can be made by humans and other
vertebrates from
simpler
precursors, and thus not required in the diet.
- nucleoside diphosphate sugar
- An activated form of a sugar molecule used in the
enzymatic
synthesis of
polysaccharides and sugar derivatives. The base depends on the
sugar:
for example, UDP-glucose but GDP-fucose.
- nucleoside monophosphate kinase
- An enzyme that catalyzes the transfer of the terminal
phosphate
of ATP
to a nucleoside 5'-monophosphate.
- nucleosome
- Structural unit for packaging DNA into
chromatin. A
nucleosome consists
of a DNA strand wound around an octameric histone core.
- nucleotide
- A nucleoside phosphorylated at one of its pentose
hydroxyl
groups.
- nonheme iron proteins
- Proteins, most often acting in redox reactions, which
contain
iron but
no porphyrin groups.
- nucleus
- In eukaryotes, a membrane-bounded organelle that
contains
chromosomes.
- NAD (nicotinamide adenine dinucleotide)
- Nicotinamide-containing coenzyme functioning as
carriers of
hydrogen atoms
and electrons in some redox reactions, notably carbohydrate and lipid
catabolism.
- NADP (nicotinamide adenine dinucleotide phosphate)
- Nicotinamide-containing coenzyme functioning as
carriers of
hydrogen atoms
and electrons in some redox reactions, notably fatty acid synthesis and
the pentose phosphate shunt.
- native conformation
- The biologically active conformation of a protein.
- negative cooperativity
- A phenomenon of some multisubunit enzymes or proteins
in
which
binding
of a ligand or substrate to one subunit impairs binding of a second
ligand
molecule to another subunit.
- negative feedback
- Regulation of a biochemical pathway achieved when a
reaction
product inhibits
an earlier step in the pathway.
- neuron
- A cell of nervous tissue specialized for transmission
of a
nerve
impulse.
- neurotransmitter
- A low molecular weight compound (usually containing
nitrogen)
secreted
from the terminal of one neuron and bound by a specific receptor in the
next neuron in order to transmit a nerve impulse.
- nicotinamide adenine dinucleotide (NAD)
- Nicotinamide-containing coenzyme functioning as
carriers of
hydrogen atoms
and electrons in some redox reactions, notably carbohydrate and lipid
catabolism.
- nicotinamide adenine dinucleotide phosphate (NADP)
- Nicotinamide-containing coenzyme functioning as
carriers of
hydrogen atoms
and electrons in some redox reactions, notably fatty acid synthesis and
the pentose phosphate shunt.
- ninhydrin reaction
- A color reaction given by free amino groups of amino
acids
and
peptides
on heating with ninhydrin; widely used for their detection and
estimation.
- nitrogen cycle
- The cycling of various forms of biologically
available
nitrogen (N2,
nitrate, nitrite, ammonia, etc.) through the plant, animal, and
microbial
worlds, and through the atmosphere and geosphere.
- nitrogen fixation
- Conversion of atmospheric nitrogen (N2)
into a
reduced, biologically
available form by nitrogen-fixing organisms, often in symbiosis with
legumes.
- nitrogenase complex
- A system of enzymes capable of anaerobic reduction of
atmospheric
nitrogen
(N2) to ammonia in the presence of ATP.
- nonpolar
- Molecules or groups composed of elements not
differing
greatly in
electronegativity
that are poorly soluble in water.
- nonsense codon
- A codon that does not specify an amino acid, but
instead
signals
the termination
of a polypeptide chain (UAA, UAG, UGA).
- nonsense mutation
- A mutation that results in the premature termination
of a
polypeptide chain.
- nonsense suppressor
- A mutation, usually in the gene for a tRNA, that
causes an
amino
acid to
be inserted into a polypeptide in response to a termination codon.
- nucleases
- Enzymes that hydrolyze the phosphodiester linkages of
nucleic
acids.
- nucleic acids
- Biologically occurring polynucleotides in which the
nucleotide
residues
are linked in a specific sequence by phosphodiester bonds, either DNA
and
RNA.
- nucleoid
- In prokaryotes, the nuclear zone that contains the
chromosome but
has no
surrounding membrane.
- nucleolus
- A densely staining structure in the nucleus of
eukaryotic
cells
in interphase.
Contains the machinery involved in rRNA synthesis and ribosome
formation.
- nucleophile
- An electron-rich group with a strong tendency to
donate
electrons
to an
electron-deficient nucleus (electrophile).
- nucleoplasm
- The aqueous portion of a cell's contents enclosed by
the
nuclear
membrane;
also called the nuclear matrix.
- nucleoside
- A compound consisting of a purine or pyrimidine base
covalently
linked
to a pentose, but lacking a phosphate.
- nucleoside diphosphate kinase
- An enzyme that catalyzes the transfer of the terminal
phosphate
of a nucleoside
5'-triphosphate (most often ATP) to a nucleoside 5'-diphosphate (GDP,
e.g.).
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- ob-
- before, against
- octa-
- eight
- octo-
- eight
- -ogen
- precursor
- -oid
- resembling, image of
- Okazaki fragments
- Okazaki fragments
- -ol(e)
- alcohol
- -ole
- little version(usually)
- oligo-
- few
- oligomer
- A short polymer of amino acids, sugars, or
nucleotides. The
definition
of "short" is somewhat arbitrary, but usually less than 50 nucleotides
or amino acids or about a dozen monosaccharides.
- oligomeric protein
- A multisubunit protein having two or more polypeptide
chains.
- oligonucleotide
- A few (usually less than 50) nucleotides joined by
phosphodiester
bonds.
- oligopeptide
- A few amino acids (usually less than 50) joined by
peptide
bonds.
- oligosaccharide
- Several (usually less than a dozen) monosaccharide
groups joined by glycosidic bonds.
- -oma
- tumor
- oncogene
- A gene of cellular or viral origin that causes cells
to
exhibit
rapid,
uncontrolled proliferation. See also proto-oncogene.
- open reading frame (ORF)
- A sequence of nucleotide codons in a DNA or RNA
molecule that does not include a termination codon and thus could code
for a protein.
- open system
- A system that exchanges matter and energy with its
surroundings. See system.
- operator
- A region of DNA that interacts with a regulatory
protein to
control the
expression of a gene or group of genes.
- operon
- A unit of genetic expression in prokaryotes
consisting of
one or
more related
genes and the operator and promoter sequences that regulate their
transcription.
- optical activity
- The capacity of a substance to rotate the plane of
plane-polarized light.
- optimum pH
- The characteristic pH at which an enzyme has maximal
catalytic
activity.
- orphan observation
- A fact that does not fit the model being used
and is therefore ignored.
-
- organelles
- Membrane-bounded structures found in eukaryotic cells
which
contain enzymes
and other components required for specialized cell functions.
- origin
- The nucleotide sequence or site in DNA where DNA
replication is
initiated.
- orosomucoid
- An old term for a1-acid
glycoprotein
- Orphan Drug
- a drug that treats a disease that affects less than
200,000 Americans. This number was chosen because there is no
possibility that the costs of developing a drug for this few patients
could ever earn money. The government then provides incentives for
producers of these drugs.
- -osis
- full of
- osmosis
- Bulk flow of water through a semipermeable membrane
into
another
aqueous
compartment containing solute at a higher concentration.
- osmotic pressure
- The pressure generated by the osmotic flow of water
through
a
semi-permeable
membrane into an aqueous compartment containing solute at a higher
concentration.
- -ostomy
- "mouth-cut"
- oxidation
- The loss of electrons.
- oxidation-reduction reaction
(redox
reaction)
- A reaction in which electrons are transferred from a
donor
(the
reducing
agent) to an acceptor molecule (the oxidizing agent).
- oxidative phosphorylation
- The enzymatic phosphorylation of ADP coupled to
electron
transfer
from
a substrate to molecular oxygen.
- oxidizing agent
- The acceptor of electrons in an redox reaction.
- oxygen debt
- The extra oxygen (above the normal resting level)
consumed
in the
recovery
period after strenuous physical exertion due to the re-oxidation of
lactate.
- oxygenases
- Enzymes that catalyze reactions in which oxygen is
introduced
into an acce
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