Term Definition

abasic site a site on DNA which has lost the base portion of the nucleotide, while retaining the
sugar-phosphate backbone
acetyl CoA a molecule consisting of an acetyl group attached to coenzyme A
acids substances that release hydrogen ions into solution (decrease pH)
adipocytes fat cells; cells that form the adipose tissue
affinity chromatography a type of chromatography in which a particular ligand is bound to the resin; only
proteins that will bind that ligand will stick to the column
aldolase an enzyme in glycolysis that cleaves fructose 1,6-bisphosphate to yield one
molecule of dihydroxyacetone phosphate and one molecule of glyceraldehyde 3-
phosphate
aldol linkage a chemical structure in which an alcohol is attached to a carbon at the beta
position relative to a carbonyl (e.g., ...-CO-CH2-CHOH-...)
aldose a monosaccharide containing an aldehyde group in the straight-chain form
allosteric regulation regulation of enzyme activity that occurs when a small molecule interacts non-
covalently with a regulatory site distinct from the active site
alpha-keto acid a molecule containing a ketone direclty adjacent to a carboxylic acid
alpha carbon the carbon atom of an amino acid or amino acid residue to which the side chain is
attached
alternative splicing variations in splicing of a particular pre-mRNA, resulting in differential retention of
exons and introns; also called differential splicing
Alu repeats repeating, non-coding DNA sequences of about 300 base pairs found in the
human genome that were originally characterized by the restriction enzyme Alu I
amino acid a class of organic compounds in which an amino group and a carboxyl group are
linked to a central carbon atom to which a variable side chain is also bound
amino acid activation the process of attaching an amino acid to its tRNA by aminoacyltransferase
amino acid residue
the remaining portion of an amino acid after it has been incorporated into a
polypeptide chain; the free amino acid loses a water molecule when the peptide
bond is formed
amphipathic describes a molecule that is hydrophobic on one side or end, and hydrophilic on
the other
anabolism the set of metabolic processes by which small molecules are combined into larger
ones
ngstrom a unit of length. One ngstrom is equal to 1 E-10 metres, or 0.1 nanometres
annealing the process of allowing single-stranded DNA or RNA to hybridize to a
complementary polynucleotide sequence
anomeric carbon in a linear monosaccharide, the carbon atom of the carbonyl group; in a cyclized
monosaccharide, the orientation of the hydroxyl at this carbon distinguishes
anomers from one another
apoenzyme an enzyme that is missing a subunit or cofactor required for full function
apurinic site a position in a DNA strand at which the sugar-phosphate backbone is intact but a
purine base is missing
automated thermocyclers machines used for polymerase chain reactions; the cycler automatically changes
the temperature of the reaction to allow the cycles of PCR to take place
bases substances that acquire protons from solution (increase pH)
base excision repair repair of damaged DNA that is initiated by the removal of the damaged base
(except for repair of abasic sites) and involves synthesis of one (short-patch BER)
or 2-10 (long-patch BER) new nucleotides
beta-oxidation of fatty acids degradation of fatty acids into two-carbon units, accomplished by oxidizing the
carbon beta to the carboxylic acid group
biochemistry the study, primarily at the molecular level, of the chemical and physical processes
that go on in the cell
Bradford method a colorimetric assay for measuring the total amount of protein present in a
solution, done using a dye that binds to certain common amino acid side chains
carboxymethyl (CM)
cellulose beads to which a carboxymethyl group has been added. The
cellulose carboxymethyl group is negatively charged at neutral pH, allowing it to interact
with positively charged proteins during ion exchange chromatography.
catabolism the set of metabolic processes by which large molecules are broken down into
smaller ones
catabolite repression the process by which certain genes are not expressed when a particular catabolite
(substrate for catabolism) is present in the media
central dogma a phrase used to describe how genetic make-up determines the properties of an
organism, based on flow of information from DNA to RNA to proteins
centrifugation a purification method in which a sample is fractionated based on density by
spinning it at high speed
chaperone a protein that binds to unfolded or misfolded proteins, and promotes normal folding
and formation of native three-dimensional structure
chemiosmotic hypothesis the idea that ATP synthesis is driven by movement of ions across a membrane
and down an electrochemical gradient
chimeric protein a protein that results when genes encoding two or more distinct proteins (or parts
of proteins) are fused to express a single polypeptide chain
chiral carbon a carbon molecule that has four non-identical groups attached to it
chromatin the complex of DNA and protein that comprises the eukaryotic chromosomes
coding strand the DNA strand which has the same base sequence as the RNA transcript
produced; also called the sense strand or non-template strand
coenzyme a small organic molecule that is essential for particular enzymatic activities;
vitamins are often converted to coenzymes
coiled coil an arrangement of polypeptide chains in which several (usually two) alpha-helices
wind around each other, as in alpha-keratin
collagen the protein substance of the white fibres of connective tissue
competitive inhibitor an enzyme inhibitor that competes with substrate for binding to the active site of
the enzyme
complementary DNA a DNA molecule, usually synthesized by the action of reverse transcriptase, that is
(cDNA) complementary to an mRNA molecule
consensus sequence
a sequence that is representative of a group of related sequences that have
similar functions. The consensus sequence is obtained by compiling the most
common base or amino acid at each position within the group of sequences.
cytochrome b-c1 complex Complex III of the electron transport chain, which accepts electrons from
uibquinone and transfers them to cytochrome c via the Q cycle
cytochrome oxidase Complex IV of the electron transport chain, which accepts electrons from
complex cytochrome c and transfers them to oxygen
cytoplasm everything inside the plasma membrane of the cell and outside the nucleus
cytosol the aqueous solution inside the cytoplasm, excluding membrane-bound organelles
deamination the spontaneous loss of an amine group from a nitrogenous base. When cytosine
is deaminated it is coverted to uracil.
dehydrogenase an enzyme that catalyzes a redox reaction; electron carriers are reduced, and the
substrate is oxidized
denaturation Separation of a DNA double helix into single strands, OR unfolding of a protein or
RNA molecule from its native structure
diabetes mellitus a condition characterized by a failure of the body to respond to high blood glucose
dialysis
a procedure in which solvent molecules and solutes smaller than the pores in a
semipermeable membrane freely exchange between a sample and a larger
volume of medium, while larger solutes are retained. This process changes the
buffer in which the larger molecules are dissolved

a type of local protein structure that permits binding to DNA, commonly through
DNA binding motif interactions with the major groove
DNA polymerase an enzyme responsible for DNA chain elongation
domain a functional unit of a protein; can be either a single polypeptide chain or multiple
chains
downstream on a DNA molecule, towards the 3' end (usually to the right, depending on how the
molecule is written)
enantiomers molecules that are nonsuperimposable mirror images of one another; a type of
stereoisomer
endonuclease an enzyme that cleaves at internal sites in DNA or RNA
enzyme a protein that catalyzes a chemical reaction
enzyme assay a way of detecting enzyme activity; specific assays vary
epimers isomeric structures with more than one chiral centre that only differ in the
configuration of a single carbon atom
exonuclease an enzyme that removes nucleotides from the end of a DNA or RNA chain
extrinisic factors factors that are related to the environmental conditions; for example, salt
concentration or solvent composition
facultative anaerobe
FAD
FADH2
feedback inhibition
feedforward activation
fermentation
flux
free energy (G), also Gibbs
free energy
French pressure cell
furanose
gene disruption
gene-specific regulatory
proteins
genetic instability
genome
genomic library
globular protein
glycosylation
an organism that can survive in the absence of oxygen but can use oxidative
phosphorylation to make ATP when oxygen is present
flavin adenine dinucleotide (oxidized form)
flavin adenine dinucleotide (reduced form)
the inhibition of an earlier step in a reaction sequence by the product of a later
step
the activation of a later step in a reaction sequence by the product of an earlier
step
a process by which ATP is generated through a series of reactions involving no
net change in the overall oxidation state of the atoms of the substrate
the rate at which molecules flow through a metabolic pathway
a thermodynamic quantity, the change of which for a reaction at constant pressure
indicates the spontaneity of the reaction; for a spontaneous reaction, delta G is
negative
a piece of equipment commonly used to shear cells, in which the cells are forced
through a small opening at high pressure
a monosaccharide that exists as a five-membered ring in the cyclic form
replacing a large part of a gene (or the entire gene) with other DNA, often acquired
by homologous recombination. This technique is usually used to knock out a
particular gene and introduce markers in its place that can be followed to ensure
that the resulting strain is now missing the targeted gene
proteins that regulate the transcription of one specific gene, as opposed to a group
of related genes
a general term that refers to a variety of phenomena, including DNA
rearrangements, which all result in changes in the genomic DNA
the complete set of genetic instructions in an organism
a set of cloned DNA fragments representing an organism's entire genome
a water-soluble protein characterized by a compact, highly folded structure
the attachment of carbohydrate chains to a protein through N- or O-glycosidic
linkages
helicase an enzyme responsible for the unwinding of the template DNA double helix at the
replication fork
helix-turn-helix motif a protein motif that forms two alpha-helices that cross; this motif binds in DNA's
major groove to specific base sequences
heterodimer a dimer that consists of two non-identical subunits
"high energy" molecule a molecule that releases a lot of free energy when hydrolyzed
hinge region of an IgG; a region that allows for the Fab and Fc regions to move more or less
independently
histones highly conserved basic proteins that constitute the protein core to which DNA is
bound to form a nucleosome core particle and a 30-nm chromatin fibre
holoenzyme a complete and active enzyme that includes all subunits and bound cofactors
homologous recombination
a process in which similar sequences of DNA from different chromosomes
exchange places; also describes DNA repair in which DNA from one chromosome
is used as a template to regenerate the analogous sequence on the damaged
sister chromosome
homodimer a dimer which consists of two identical subunits
hot probe a probe labeled with a radioactive element (has nothing to do with temperature)
housekeeping genes genes that are expressed in all cells and that encode proteins necessary for
maintenance and essential cellular functions
hybridization annealing of two nucleic acid strands
hydrogen bond an electrostatic interaction between a weakly acidic donor group such as O--H or
N--H and a weakly basic acceptor atom such as O or N
hydrophobic column a type of chromatography in which the column resin has hydrophobic groups stuck
chromatography to it; therefore, proteins with exposed hydrophobic areas will bind to the resin
hydrophobic/hydrophilic
interactions non-covalent attractions between molecules; not types of bond
hydroxyapatite deposition when calcium is deposited as a brittle substance which forms bone
hydroxyproline/hydoxylysine in the formation of collagen, these molecules both stabilize the collagen fibrils
through aldol crosslinks between the collagen fibers
hypervariable when referring to a region of DNA, means that this region can be quite different
from one individual to the next
imino acid a molecule like an amino acid except that the nitrogen is bound to two carbon
atoms and only one hydrogen; for example, proline
immunodetection detection of a protein using an antibody that binds to that protein
induced fit model of enzyme a model that states that the active site of an enzyme undergoes conformational
function change to adapt to the binding of a substrate
integral membrane protein a protein that interacts with the hydrophobic centre of a lipid bilayer, either directly
or via a covalently attached lipid. Integral membrane proteins cannot be removed
from a membrane without disrupting the membrane.
interchain bonding bonding between two or more distinct chains
intermediate filaments a family of fibrous protein filaments that provide tensile strength to cells
intrachain bonding bonding within the same polypeptide chain
ion exchange a fractionation procedure in which ions are selectively retained by a matrix bearing
chromatography groups of charge opposite to the bound ions
isoelectric point (pI) the pH at which a molecule has no net charge, and thus does not migrate in an
electric field
ketose a monosaccharide containing a ketone group in the straight-chain form
kinases a family of enzymes that add a phosphate group to a substrate
Km, the Michaelis constant
for an enzyme-catalyzed reaction that obeys Michaelis-Menten kinetics, Km is the
substrate concentration at which reaction velocity equals half the maximum
velocity. Km is an approximate measure of the affinity of the enzyme for the
substrate; low Km means high affinity
lagging strand
a newly synthesized DNA strand for which DNA polymerase travels along the
template strand in the direction opposite to that of the helicase; the lagging strand
is synthesized as a series of discontinuous fragments that are later joined
leading strand
a newly synthesized DNA strand for which DNA polymerase travels along the
template strand in the same direction as the helicase; this strand is synthesized
continuously
ligand any molecule that binds to a specific site on a protein
lipid-linked membrane a protein bearing a covalently attached lipid molecule that is embedded in a lipid
protein bilayer
liposome a lipid bilayer that has closed to form a sphere with an internal aqueous
compartment
Lowry method a colorimetric assy for measuring the total amount of protein present in a solution,
done using a dye that binds to the protein backbone
major groove the wider groove on the surface of a B-DNA double helix, found on the side of the
base pairs where the sugars are farther apart
matrix the region of a mitochondrion enclosed by the inner mitochondrial membrane
membrane-associated a protein that is exposed to the hydrophobic centre of a lipid bilayer, but does not
protein pass all the way through the bilayer
micelle a structure formed by ampiphilic molecules in aqueous solution such that polar
segments form the surface and nonpolar segments form the interior, thereby
avoiding contact with the solvent
minor groove the narrower groove on the surface of a B-DNA double helix, found on the side of
the base pairs where the sugars are closer together
mismatch repair
a postreplication process, in which mispaired nucleotides are excised and
replaced, that distinguishes between the parental (correct) and daughter
(incorrect) strands of DNA
molecular biology the manipulation of genes
NAD+ Nicotinamide adenine dinucleotide (oxidized form)
NADH Nicotinamide adenine dinucleotide (reduced form)
NADH dehydrogenase Complex I of the electron transport chain, which accepts electrons from NADH and
complex transfers them to ubiquinone
NADP+ Nicotinamide adenine dinucleotide phosphate (oxidized form)
NADPH Nicotinamide adenine dinucleotide phosphate (reduced form)
native molecular weight the weight of a protein in its biologically active form
noncoding strand sequence of DNA which is complementary to the mRNA produced; also called the
antisense strand or template strand
non-competitive inhibitor an enzyme inhibitor that binds to a site other than the active site of an enzyme tha
tobeys Michaels-Menten kinetics, and thus changes the conformation of the
enzyme such that the reaction is inhibited
non-covalent force an attractive force between two atoms that do not form a covalent bond; for
example, ionic bonds, hydrogen bonds, and van der Waals forces
nuclear magnetic a method that can be used to determine the three-dimensional structure of a
resonance (NMR)
protein or nucleic acid; this method is based on the signals emitted by
radiofrequency-excited atomic nuclei in a magnetic field
nucleoside a compound consisting of a nitrogenous base joined to a five-carbon sugar by an
N-glycosidic linkage
nucleosome the complex of a histone octamer and approximately 200 base pairs of DNA that
forms the lowest level of DNA organization in the eukaryotic chromosome
nucleosome core particle the complex of a histone octamer and 146 base pairs of DNA in which the DNA
wraps around the outside of the octamer about 1.7 times
nucleotide a compound consisting of a nucleoside attached to one or more phosphate
groups; nucleotides are the monomeric unit of nucleic acids
nucleotide excision repair a multistep process in which a damaged section of DNA is excised and replaced
by normal DNA
obligate aerobe an organism that requires oxygen to survive
obligate anaerobe an organism that can only survive in the absence of oxygen
Okazaki fragments newly synthesized short segments of DNA formed on the discontinuous lagging
strand during DNA replication
oligo-dT column
an affinity column that contains a resin bearing an oligonucleotide with a poly-T
sequence (i.e., TTTTTTT); the poly-A-tail of mRNA will interact with this
oligonucleotide
oligonucleotide a short single stranded man-made piece of DNA; sometimes referred to as a
primer
oncogene a gene capable, under certain conditions, of causing the initial and continuing
conversion of normal cells into cancer cells
open reading frame (ORF) a region of DNA that appears to code for a protein, in that it has a promoter region
with start and stop codons
operator a DNA sequence at or near the transcription start site of a gene, to which
transcription factors can bind to regulate transcription
operon a prokaryotic genetic unit that consists of several genes, encoding proteins with
related functions, that are transcribed as a single mRNA molecule
oxidative phosphorylation phosphorylation of ADP to form ATP driven by a proton gradient that is
established by transferral of electrons from electron donors to molecular oxygen
palindrome a nucleotide sequence that reads the same in the 5' to 3' direction on both strands,
e.g., TTGCAA
pentose phosphate a metabolic pathway for glucose degradation that is a source of ribose-5-
pathway phosphate and NADPH; also called the hexose monophosphate shunt
peripheral membrane a protein that is associated with a lipid bilayer indirectly via interactions with
protein another protein; also called a protein-attached membrane protein
phosphodiester bond a linkage in which a phosphate group is esterified to two alcohol groups; e.g. the
linkages that join adjacent nucleotide residues in a polynucleotide
phosphofructokinase (PFK) an allosteric enzyme in glycolysis that converts fructose-6-phosphate to fructose-
1,6-bisphosphate, consuming ATP
phosphorylation addition of a covalent phosphate group
physiological pH between 7 and 7.5
polycistronic describes a single mRNA molecule that bears two or more different genes
polyribosome a group of ribosomes bound to a single mRNA strand
post-translational a chemical modification to a protein that occurs after the polypeptide chain has
modification synthesized; e.g., phosphorylation of serine, hydroxylation of proline
primer
any oligo nucleotide that enables initiation of DNA synthesis, for example during
PCR, cDNA synthesis by reverse transcription, or DNA replication. Also see RNA
primer.
probe a piece of DNA, usually chemically synthesized and radioactively labelled, which is
used to find complementary sequences
processivity a relative term indicating the number of residues a DNA polymerase adds to a
newly synthesised strand before dissociating
procollagen a form of collagen in which three hydroxylated collagen polypeptides are wrapped
around each other; procollagen is secreted from cells and undergoes proteolysis
to give rise to the more mature tropocollagen molecule
progenitor cell a daughter cell
promoter the DNA sequence, upstream of a gene, at which RNA polymerase and any gene-
specific regulatory proteins bind
proofreading the activity of DNA polymerase by which the enzyme complex detects and
corrects errors made during DNA synthesis
prosthetic group a non-amino acid molecule that is tightly associated with an enzyme, e.g., FAD
protease an enzyme that breaks the peptide backbone of proteins
protein domains a distinct region of a protein, normally folded indepently of other protein regions,
that may have a particular function (e.g., a DNA binding domain)
protein kinase an enzyme that adds a phosphate group to a protein
protein phosphatase an enzyme that removes a phosphate group from a protein
protein subunits distinct polypeptide chains that form part of a larger protein complex (e.g., a dimer
has two subunits)
proto-oncogene
a normal cellular gene that has the potential to become an active oncogene, if
altered; most proto-oncogenes are believed to carry out required functions in cell
growth and differentiation
pyranose a monosaccharide that exists as a six-membered ring in the cyclic form
Q cycle the mechanism by which Complex III of the mitochondrial electron transport chain
transfers electrons from coenzyme Q to cytochrome c, resulting in the transport of
protons out of the matrix
reanneal the process of complementary DNA strands base pairing together again
reducing end an end of a polysaccharide at which the anomeric carbon is not involved in a bond
to a different monosaccaride or other group
replication origin a DNA sequence at which DNA replication is initiated
restriction digest a reaction in which restriction endonucleases are used to cut DNA
restriction enzyme (or
an enzyme that recognizes and cleaves a specific short sequence, the restriction
restriction endonuclease) site, in double-stranded DNA molecules. These enzymes are widespread in
bacteria and are used extensively in recombinant DNA technology.
reverse transcription the process in which an RNA molecule is used as a template for synthesis of a
complementary DNA strand
ribozyme an RNA molecule, or a complex primarily composed of RNA molecules, that has
catalytic activity
RNA primase an enzyme that assembles RNA primers on the separated DNA strand in the 5' to
3' direction
RNA primer a short strand of RNA that is required to begin a newly synthesized DNA strand.
See also primer.
riboflavin also called viatmin B2, riboflavin consists of a flavin group attached to the sugar-
like molecule ribitol. Riboflavin is joined to adenosine to make FAD.
salt bridge an attractive electrostatic interaction formed between oppositely charged ions; i.e.,
Ionic bonds
salt stabilization of DNA, refers to the fact that salt shields the repulsive electrostatic interactions
between the negative phosphate groups, and thus salt stabilizes DNA
SDS-PAGE
polyacrylamide gel electrophoresis (PAGE) in the presence of the detergent
sodium dodecyl sulfate (SDS), which denatures and imparts a uniform charge
density to polypeptides and thereby permits them to be fractionated on the basis
of size, regardless of inherent charge
self-complementary DNA DNA having sections that are complementary to each other, and therefore the
DNA molecule will bind to itself
sequence contig an DNA sequence representing an uninterrupted portion of the genome
sigma factor a component of the bacterial RNA polymerase holoenzyme that recognizes a
gene's promoter and is released once chain initiation has occurred
single-strand binding a protein that binds to single stranded DNA during replication to prevent formation
protein of double stranded DNA
site-directed mutagenesis a method to create a mutation at a specific site on a molecule of DNA
spliceosome a multicomponent complex containing protein and RNA that is involved in the
splicing phase of mRNA processing
stereoisomers chiral molecules with different configurations about at least one of their
asymmetric centers but which are otherwise identical
substrate-level phosphoryation involving direct transfer of a phosphate group from a
phosphorylation phosphorylated intermediate metabolic compound to an acceptor compound
succinate dehydrogenase
an enzyme in the citric acid cycle that is also Complex II of the electron transport
chain, which accepts electrons from succinate and passes them, via FAD, to
ubiquinone
supercoiling the coiling of a double helix around itself, such as is found in the packing and
arrangement of the DNA within the chromosome
synthase an enzyme that catalyzes a synthesis reaction without use of a high energy
molecule
synthetase an enzyme that catalyses a synthesis reaction using a high energy molecule such
as ATP
TATA box a eukaryotic promoter element with the consensus sequence TATAAAA, located
upstream from the transcription start site
telomere a protein-DNA complex found the end of a linear eukaryotic chromosome,
containing many repeats of a short nucleotide sequence and an overhanging 3'-
end
toposiomerase
an enzyme that alters the superhelical structure of a double-stranded DNA
molecule by catalyzing breaks in one or both strands, passing DNA through the
break and resealing the break
transcription copying of DNA into RNA, part of gene expression
transgenic organism a genetically altered organism
transient complex a short-lived intermediate complex made of two or more reactants, that resolves to
form products
transition state during the conversion of reactant to product, the point at which the substrate is in
its highest energy conformation
translation the process of decoding an RNA to synthesize protein, part of gene expression
translocation during translation, the shift of the tRNAs to the E and P sites from the P and A
sites of the ribosome
transmembrane protein a protein that passes through a lipid bilayer, such that parts of the protein are
exposed to the aqueous environment on each side of the membrane
transposons mobile pieces of DNA that can move from one site to another, often leaving behind
an inverted repeat
tropocollagen a triple helix of collagen polypeptide chains with the propeptide ends trimmed off
upstream on a DNA molecule, towards the 5' end (usually left, depending on how the
molecule is written)
Van der Waals forces attractive forces between hydrophobic molecules caused by formation of transient
dipoles
variable number of tandem a section of DNA featuring repeats of a certain sequence; often used in forensics
repeats (VNTR) to identify people because the number of repeats vary from person to person
Vmax the maximum velocity of an enzyme-catalyzed reaction; occurs at infinite substrate
concentration and depends on the concentration of enzyme
wobble the phenomenon that at the third anticodon position, base-pairing can disobey the
Watson-Crick rules; this allows many tRNAs to recognize two or three codons
Xeroderma Pigmentosa an inherited dysfunction of the nucleotide excision repair pathway that makes a
person unable to repair UV-damaged DNA
zwitterion a compound bearing spatially separated, oppositely charged groups; also called a
dipolar ion