Glossary
Excerpted with modification from the Glossary in Genes V
by Benjamin Lewin published by Oxford University Press, 1994.
This material is limited exculsively to enrolled students in BB4592/5592!
Active site is
the restricted part of a protein to which a substrate binds.
Allele is one of several alternative
forms of a gene occupying a given locus on a chromosome.
Allosteric control refers to
the ability of an interaction at one site of a protein to influence
the activity of another site.
Amber codon is the nucleotide
triplet UAG, one of three codons that cause termination of protein
synthesis.
Amber mutation describes any
change in DNA that creates an amber codon at a site previously
occupied by a codon representing an amino acid in a protein.
Amber suppressors are mutant
genes that code for tRNAs whose anticodons have been altered so
that they can respond to UAG codons as well as or instead of to
their previous codons.
Aminoacyl tRNA is transfer RNA
carrying an amino acid; the covalent linkage is between the amino
group of the amino acid and either the 3' or 2'OH group of the
terminal base of the tRNA.
Aminoacyl tRNA synthetases are
enzymes responsible for covalently linking amino acids to the
2' or 3'OH position of tRNA.
Annealing is the pairing of complementary
single strands of DNA to form a double helix.
Antiparallel strands of the double
helix are organized in opposite orientation, so that the 5' end
of one strand is aligned with the 3' end of the other strand.
Antitermination proteins allow
RNA polymerase to transcribe through certain terminator sites.
Apoinducer is a protein that
binds to DNA to switch on transcription by RNA polymerase.
Attenuation describes the regulation
of termination of transcription that is involved in controlling
the expression of some bacterial operons.
Attenuator is the terminator
sequence at which attenuation occurs.
Autoradiography detects radioactively
labeled molecules by their effect in creating an image on photographic
film.
Back mutation reverses the effect
of a mutation that had inactivated a gene; thus it restores wildtype.
Bacteriophages are viruses that
infect bacteria; often abbreviated as phages.
Base pair (bp) is a partnership
of A with T or of C with G in a DNA double helix; other pairs
can be formed in RNA under certain circumstances.
Bidirectional replication is
accomplished when two replication forks move away from the same
origin in different directions.
Blocked reading frame cannot
be translated into protein because it is interrupted by termination
codons.
Blunt cuts in duplex DNA are
made when two strands are cleaved opposite each other.
Blunt-end ligation is a reaction
that joins two DNA duplex molecules directly at their ends.
bp is an abbreviation for base pairs; distance along DNA is measured
in bp.
Buoyant density measures the
ability of a substance to float in some standard fluid, for example,
CsCl.
CAP (CRP) is a positive regulator
protein activated by cyclic AMP. It is needed for RNA polymerase
to initiate transcription of certain (catabolite-sensitive) operons
of E. coli.
Capsid is the external protein
coat of a virus particle.
Catabolite repression describes
the decreased expression of many bacterial operons that results
from addition of glucose. It is caused by a decrease in the level
of cyclic AMP, which in turn is needed to activate the CAP (CRP)
regulator.
cis-acting locus affects
the activity only of DNA sequences on its own molecule of DNA;
this property usually implies that the locus does not code for
protein.
cis configuration describes
two sites on the same molecule of DNA.
cis/trans test assays
the effect of relative configuration on expression of two mutations.
In a double heterozygote, two mutations in the same gene show
mutant phenotype in trans configuration, wildtype in cis
configuration.
Cistron is the genetic unit defined
by the cis/trans test; equivalent to gene in comprising
a unit of DNA representing a protein.
Clone describes a large number
of cells or molecules identical with a single ancestral cell or
molecule.
Closed reading frame contains
termination codons that prevent its translation into protein.
Coding strand of DNA has the
same sequence as mRNA.
Codominant alleles both contribute
to the phenotype; neither is dominant over the other.
Codon is a triplet of nucleotides
that represents an amino acid or a termination signal.
Cognate tRNAs are those recognized
by a particular aminoacyl tRNA synthetase.
Cold-sensitive mutant is defective
at low temperature but functional at normal temperature.
Complementation refers to the
ability of independent (nonallelic) genes to provide diffusible
products that produce normal (wildtype) phenotype when two mutants
are tested in trans configuration in a heterozygote.
In vitro complementation assay
consists of identifying a component of a wildtype cell that can
confer activity on an extract prepared from a mutant cell. The
assay identifies the component rendered inactive by the mutation.
Complementation group is a series
of mutations unable to complement when tested in pairwise combinations
in trans; defines a genetic unit (the cistron) that might
better be called a noncomplementation group.
Conditional lethal mutations
kill a cell or virus under certain (nonpermissive) conditions,
but allow it to survive under other (permissive) conditions.
Conjugation describes 'mating'
between two bacterial cells, when (part of) the chromosome is
transferred from one to the other.
Consensus sequence is an idealized
sequence in which each position represents the base (nucleotide)
most often found when many actual sequences are compared.
Constitutive genes are
expressed as a function of the interaction of RNA polymerase with
the promoter, without additional regulation; sometimes also called
household genes in the context of describing functions expressed
in all cells at a low level.
Constitutive mutations cause
genes that usually are regulated to be expressed without regulation.
Coordinate regulation refers
to the common control of a group of genes.
Corepressor is a small molecule
that triggers repression of transcription by binding to a regulator
protein.
Cyclic AMP (cAMP) is a molecule
of AMP in which the phosphate group is joined to both the 3' and
5' positions of the ribose; its binding activates the CAP (CRP),
a positive regulator of prokaryotic transcription.
Degeneracy in the genetic code
refers to the lack of an effect of many changes in the third base
of the codon on the amino acid that is represented; that is, many
different codons specify the same amino acid.
Deletions are generated by removal
of a sequence of DNA, the regions on either side being joined
together.
Denaturation of DNA or RNA describes
its conversion from the double-stranded to the single-stranded
state; separation of the strands is most often accomplished by
heating .
Derepressed state describes a
gene that is turned on. It is synonymous with induced when describing
the normal state of a gene; it has the same meaning as constitutive
in describing the effect of mutation.
Discontinuous replication refers
to the synthesis of DNA in short (Okazaki) fragments that are
later joined into a continuous strand.
Divergence is the percent difference
in nucleotide sequence between two related DNA sequences or in
amino acid sequences between two proteins.
Divergent transcription refers
to the initiation of transcription at two promoters facing in
the opposite direction, so that transcription proceeds away in
both directions from a central region.
dna mutants of bacteria
are temperaturesensitive; they cannot synthesize DNA at 42 degrees
C, but can do so at 37 degrees C.
DNAase is an enzyme that breaks
bonds in DNA.
DNA polymerase is an enzyme that
synthesizes a daughter strand(s) of DNA (under direction from
a DNA template). May be involved in repair or replication.
DNA replicase is a DNA synthesizing
enzyme required specifically for replication.
Dominant allele determines the
phenotype displayed in a heterozygote with another (recessive)
allele.
Down promoter mutations decrease
the frequency of initiation of transcription.
Downstream identifies sequences
proceeding farther in the direction of expression, for example,
the coding region is downstream of the initiation codon.
Elongation factors (EF in prokaryotes)
are proteins that associate with ribosomes cyclically, during
addition of each amino acid to the growing polypeptide chain.
End product inhibition describes
the ability of a product of a metabolic pathway to inhibit the
activity of an enzyme that catalyzes an early step in the pathway.
Endonucleases cleave bonds within
a nucleic acid chain; they may be specific for RNA or for single-stranded
or double-stranded DNA.
Essential gene is one whose deletion
is lethal to the organism (see also lethal locus).
Exonucleases cleave nucleotides
one at a time from the end of a polynucleotide chain; they may
be specific for either the 5' or 3' end of DNA or RNA.
F factor is a bacterial sex or
fertility plasmid.
Footprinting is a technique for
identifying the site on DNA bound by some protein by virtue of
the protection of bonds in this region against attack by nucleases.
Forward mutations inactivate
a wildtype gene.
Frameshift mutations arise by
deletions or insertions that are not a multiple of 3 bp; they
change the frame in which triplets are translated into protein.
Gene (cistron) is the segment
of DNA involved in producing a polypeptide chain; it includes
regions preceding and following the coding region (leader and
trailer).
Gene family consists of a set
of related genes; the members were derived by duplication and
variation from some ancestral gene.
Gene cluster is a group of adjacent
genes that are identical or related.
Genetic code is the correspondence
between triplets in DNA (or RNA) and amino acids in protein.
Gyrase is a type II topoisomerase
of E. coli with the ability to introduce negative supercoils
into DNA.
Housekeeping (constitutive) genes
are those (theoretically) expressed in all cells because they
provide basic functions needed for sustenance of all cell types.
Hyperchromicity is the increase
in optical density at 260 nm that occurs when DNA is denatured.
Inducer is a small molecule that
triggers gene transcription by binding to a regulator protein.
Induction refers to the ability
of bacteria to synthesize certain enzymes only when their substrates
are present; applied to gene expression, refers to switching on
transcription as a result of interaction of the inducer with the
regulator protein.
Initiation factors (IF in prokaryotes)
are proteins that associate with the small subunit of the ribosome
specifically at the stage of initiation of protein synthesis.
Insertions are identified by
the presence of an additional stretch of base pairs in DNA.
Interallelic complementation
describes the change in the properties of a heteromultimeric protein
brought about by the interaction of subunits coded by two different
mutant alleles; the mixed protein may be more or less active than
the protein consisting of subunits only of one or the other type.
Inversion is a chromosomal change
in which a segment has been rotated by 180° relative to the
regions on either side and reinserted.
kb (kilobases or kilobase pairs)
is an abbreviation for 1000 base pairs of DNA or 1000 bases of
RNA.
Kinase is an enzyme that phosphorylates
(adds a phosphate group) to a substrate.
Lagging strand of DNA must grow
overall in the 3' to 5' direction and is synthesized discontinuously
(5' to 3') in the form of short fragments (Okazaki fragments)
that are later joined (ligated) together covalently.
Leader is the nontranslated sequence
at the 5' end of mRNA that precedes the initiation codon.
Leading strand of DNA is synthesized
continuously in the 5' to 3' direction.
Leaky mutations allow some residual
level of gene expression.
Lethal locus is any gene in which
a lethal mutation can be obtained (usually by deletion of the
gene).
Ligation is the formation of a
phosphodiester bond to link two adjacent bases separated by a
nick in one strand of a double helix of DNA.
Linkage describes the tendency
of genes to be inherited together as a result of their location
on the same chromosome; measured by percent recombination between
loci.
Linkage group includes all loci
that can be connected (directly or indirectly) by linkage relationships;
equivalent to a chromosome.
Linking number is the number
of times the two strands of a closed DNA duplex cross over each
other.
Locus is the position on a chromosome
at which the gene for a particular trait resides; locus may be
occupied by any one of the alleles for the gene.
Lysis describes the death of
bacteria at the end of a phage infective cycle when they burst
open to release the progeny of an infecting phage.
Marker (genetic) is any allele
of interest in an experiment.
Melting of DNA means its denaturation.
Melting temperature (Tm) is the
midpoint of the temperature range over which DNA is denatured.
Modifled bases are all those
except the usual four from which DNA (T, C, A, G) or RNA (U, C,
A, G) are synthesized; they result from postsynthetic changes
in the nucleic acid.
Multiforked chromosome (in bacterium)
has more than one replication fork, because a second initiation
has occurred before the first cycle of replication has been completed.
Multimeric proteins consist of
more than one subunit.
Mutagens increase the rate of
mutation by inducing changes in DNA.
Mutation describes any change
in the sequence of genomic DNA.
Mutation frequency is the frequency
at which a particular mutant is found in the population.
Mutation rate is the rate at
which a particular mutation occurs, usually given as the number
of events per gene per generation.
Negative complementation occurs
when interallelic complementation allows a mutant subunit to suppress
the activity of a wildtype subunit in a multimeric protein.
Negative regulators function
by switching off transcription or translation.
Negative supercoiling comprises
the twisting of a duplex of DNA in space in the opposite sense
to the turns of the strands in the double helix.
Neutral substitutions in a protein
are those changes of amino acids that do not affect activity.
Nick in duplex DNA is the absence
of a phosphodiester bond between two adjacent nucleotides on one
strand.
Nick translation describes the
ability of E. coli DNA polymerase I to use a nick as a
starting point from which one strand of a duplex DNA can be degraded
and replaced by resynthesis of new material; is used to introduce
radioactively labeled nucleotides into DNA in vitro.
Nonsense codon is any one of
three triplets (UAG, UAA, UGA) that cause termination of protein
synthesis. (UAG is known as amber; UAA as ochre.)
Nonsense mutation is any change
in DNA that causes a (termination) codon to replace a codon representing
an amino acid.
Nonsense suppressor is a gene
coding for a mutant tRNA able to respond to one or more of the
termination codons.
Nonpermissive conditions do not
allow conditional lethal mutants to survive.
Nontranscribed spacer is the
region between transcription units in a tandem gene cluster.
Nucleolytic reactions involve
the hydrolysis of a phosphodiester bond in a nucleic acid.
Null mutation completely eliminates
the function of a gene, usually because it has been physically
deleted.
Ochre codon is the triplet UAA,
one of three codons that cause termination of protein synthesis.
Ochre mutation is any change
in DNA that creates a UAA codon at a site previously occupied
by another codon.
Ochre suppressor is a gene coding
for a mutant tRNA able to respond to the UAA codon to allow continuation
of protein synthesis; ochre suppressors also suppress amber codons.
Okazaki fragments are the short
stretches of 1000 to 2000 bases produced during discontinuous
replication; they are later joined into a covalently intact strand.
Open reading frame (ORF) contains
a series of triplets coding for amino acids without any termination
codons; sequence is (potentially) translatable into protein.
Operator is the site on DNA at
which a repressor protein binds to prevent transcription from
initiating at the adjacent promoter.
Operon is a unit of bacterial
gene expression and regulation, including structural genes and
control elements in DNA recognized by regulator gene product(s).
Origin (ori) is a sequence
of DNA at which replication is initiated.
Overwinding of DNA is caused
by positive supercoiling (which applies further tension in the
direction of winding of the two strands about each other in the
duplex).
Palindrome is a sequence of DNA
that is the same when one strand is read left to right or the
other is read right to left; consists of adjacent inverted repeats.
Permissive conditions allow conditional
lethal mutants to survive.
Phenotype is the appearance or
other characteristics of an organism, resulting from the interaction
of its genetic constitution with the environment.
Phosphatase is an enzyme that
removes phosphate groups from substrates.
Plectonemic winding describes
the intertwining of the two strands in the classical double helix
of DNA; the strands are wound around each other.
Pleiotropic gene affects more
than one (apparently unrelated) characteristic of the phenotype.
Point mutations are changes involving
single base pairs.
Polarity of a nucleic acid chain
(polynucleotide) is 5' to 3'.
Polycistronic mRNA includes coding
regions representing more than one gene.
Polysome (polyribosome) is an
mRNA associated with a series of ribosomes engaged in translation.
Positive regulator proteins are
required for the activation of a transcription unit.
Positive supercoiling describes
the coiling of the double helix in space in the same direction
as the winding of the two strands of the double helix itself.
Primary structure of DNA refers
to the 5' to 3' phosphodiester covalent bonding of nucleotides
together in a chain or strand.
Primary transcript is the original
unmodified RNA product corresponding to a transcription unit.
Primer is a short sequence (often
of RNA) that is paired with one strand of DNA and provides a free
3' OH end at which a DNA polymerase starts synthesis of a deoxyribonucleotide
chain.
Primosome describes the complex
of proteins involved in the priming action that initiates synthesis
of each Okazaki fragment during discontinuous DNA replication;
the primosome may move along DNA to engage in successive priming
events.
Prokaryotic organisms (bacteria)
lack nuclei.
Promoter is a region of DNA involved
in binding of RNA polymerase to initiate transcription.
-10 sequence is the consensus
sequence TATAATG centered about 10 bp before the startpoint of
a bacterial gene. It is involved in the initial melting of DNA
by RNA polymerase.
-35 sequence is the consensus
sequence centered about 35 bp before the startpoint of a bacterial
gene. It is involved in initial recognition by RNA polymerase.
Proofreading refers to any mechanism
for correcting errors in protein or nucleic acid synthesis that
involves scrutiny of individual units after they have been added
to the chain.
Pulse-chase experiments are performed
by incubating cells very briefly with a radioactively labeled
precursor (of some pathway or macromolecule); then the fate of
the label is followed during a subsequent incubation with a nonlabeled
precursor.
Quaternary structure of a DNA
refers to interlinked circular molecules.
Quickstop dna mutants of
E. coli cease replication immediately when the temperature
is increased to 42 degrees C.
Reading frame is one of three
possible ways of reading a nucleotide sequence as a series of
triplets.
Reassociation of DNA describes
the pairing of complementary single strands to form a double helix.
Recessive allele is obscured
in the phenotype of a heterozygote by the dominant allele, often
due to inactivity or absence of the product of the recessive allele.
Recessive lethal is an allele
that is lethal when the cell is homozygous for it.
Recombinant progeny have a different
genotype from that of either parent.
Regulatory gene codes for an
RNA or protein product whose function is to control the expression
of other genes.
Release (termination) factors
respond to termination codons to cause release of the completed
polypeptide chain and the ribosome from mRNA.
Renaturation is the reassociation
of denatured complementary single strands of a DNA double helix.
Replacement sites in a gene are
those at which mutations alter the amino acid that is coded.
Replication fork is the point
at which strands of parental duplex DNA are separated so that
replication can proceed.
Replicon is a unit of the genome
in which DNA is replicated; contains an origin for initiation
of replication.
Replisome is the multiprotein
structure that assembles at the bacterial replicating fork to
undertake synthesis of DNA. Contains DNA polymerase and other
enzymes.
Repression is the ability of
bacteria to prevent synthesis of certain enzymes when their products
are present; more generally, refers to inhibition of transcription
(or translation) by binding of repressor protein to a specific
site on DNA (or mRNA).
Repressor protein binds to operator
on DNA or RNA to prevent transcription or translation, respectively.
Restriction enzymes (endonucleases)
recognize specific short sequences of (usually) unmethylated DNA
and cleave the duplex (sometimes at target site, sometimes elsewhere,
depending on type).
Restriction fragment length polymorphism
(RFLP) refers to inherited differences in sites for restriction
enzymes (for example, caused by base changes in the target site)
that result in differences in the lengths of the fragments produced
by cleavage with the relevant restriction enzyme. RFLPs are used
for genetic mapping to link the genome directly to a conventional
genetic marker.
Restriction map is a linear array
of sites on DNA cleaved by various restriction enzymes.
Reversion of mutation is a change
in DNA that either reverses the original alteration (true reversion)
or compensates for it (second site reversion in the same gene).
Revertants are derived by reversion
of a mutant cell or organism.
Rho factor is a protein involved
in assisting E. coli RNA polymerase to terminate transcription
at certain (rho-dependent) sites.
Rho-independent terminators are
sequences of DNA that cause E. coli RNA polymerase to terminate
in vitro in the absence of rho factor.
Rifamycins (including rifampicin)
inhibit transcription in bacteria.
RNAase is an enzyme whose substrate
is RNA.
RNA polymerase is an enzyme that
synthesizes RNA using a DNA template (formally described as DNA-dependent
RNA polymerase).
Secondary structure of DNA is
the local folding of the polymer chain which involves non-covalent
bonding; for example, hydrogen bonding between complementary bases
in base pairs.
Selection describes the use of
particular conditions to allow survival only of cells with a particular
phenotype.
Semiconservative replication
is accomplished by separation of the strands of a parental duplex,
each then acting as a template for synthesis of a complementary
strand.
Semidiscontinuous replication
is mode in which one new strand is synthesized continuously while
the other is synthesized discontinuously.
Sequence is the order of nucleotides
along a polynucleotide chain or strand.
Sex plasmid is actually an episome;
it is able to initiate the process of conjugation, by which chromosomal
material is transferred from one bacterium to another.
Shine-Dalgarno sequence is part
or all of the polypurine sequence AGGAGG located on bacterial
mRNA just prior to an AUG initiation codon; is complementary to
the sequence at the 3' end of 16S rRNA; involved in binding of
ribosome to mRNA.
Sigma factor is the subunit of
bacterial RNA polymerase needed for initiation; is the major influence
on selection of binding sites (promoters).
Silent mutations do not change
the product of a gene.
Silent sites in a gene describe
those positions at which mutations do not alter the product.
Slowstop dna mutants of
E. coli complete the current round of bacterial replication
but cannot initiate another at 42 degrees C.
Spontaneous mutations are those
that occur in the absence of any added reagent to increase the
mutation rate.
SSB is the single-strand binding
protein of E. coli, a protein that binds to single-stranded
DNA.
Staggered cuts in duplex DNA
are made when two strands are cleaved at different points near
each other.
Startpoint (startsite) refers
to the position on DNA corresponding to the first base incorporated
into RNA.
Stop codons are the three triplets
(UAA, UAG, UGA) which terminate protein synthesis.
Streptolydigins inhibit the elongation
of transcription by bacterial RNA polymerase.
Structural gene codes for any
RNA or protein product other than a regulator.
Suppression describes the occurrence
of changes that eliminate the effects of a mutation without reversing
the original change in DNA.
Suppressor (extragenic) is usually
a gene coding a mutant tRNA that reads the mutated codon either
in the sense of the original codon or to give an acceptable substitute
for the original meaning.
Suppressor (intragenic) is a
compensating mutation that restores the original reading frame
after a frame shift.
Tm is the abbreviation for melting
temperature.
Temperature-sensitive mutation
creates a gene product that is functional at low temperature but
inactive at higher temperature (the reverse relationship is usually
called cold-sensitive).
Template is a nucleic acid
strand that acts as a surface upon which the assembly of nucleotides
into a polynucleotide occurs. The order of the new nucleotides
is specified by base pairing with the template.
Termination codon is one of three
triplet sequences, UAG (amber), UAA (ochre), or UGA that cause
termination of protein synthesis; they are also celled 'nonsense'
codons.
Terminator is a sequence of DNA,
represented at the end of the transcript, that causes RNA polymerase
to terminate transcription.
Tertiary structure is supercoiling
of double-stranded, covalently closed, circular DNA molecules.
Topoisomerase is an enzyme that
can change the linking number of DNA (in steps of 1 by type I;
in steps of 2 by type II).
Topological isomers are molecules
of DNA that are identical except for a difference in linking number.
Trailer is a nontranslated sequence
at the 3' end of an mRNA following the termination codon.
Trans configuration of
two sites refers to their presence on two different molecules
of DNA (chromosomes).
Transcribed spacer is the part
of an rRNA transcription unit that is transcribed but discarded
during maturation; that is, it does not give rise to part of rRNA.
Transcription is synthesis of
RNA on a DNA template.
Transcription unit is the distance
between sites of initiation and termination by RNA polymerase;
may include more than one gene.
Translation is synthesis of protein
on the mRNA template.
Translocation of the ribosome
is its movement one codon along mRNA after the addition of each
amino acid to the polypeptide chain.
Twisting number of a DNA is the
number of base pairs divided by the number of base pairs per turn
of the double helix.
Underwinding of DNA is produced
by negative supercoiling (because the double helix is itself coiled
in the opposite sense from the intertwining of the strands).
Unidirectional replication refers
to the movement of a single replication fork from a given origin.
Uninducible mutants cannot be
induced.
Upstream identifies sequences
proceeding in the opposite direction from expression; for example,
the bacterial promoter is upstream from the transcription unit,
the initiation codon is upstream of the coding region.
URF is an open (unidentified)
reading frame, presumed to code for protein, but for which no
product has been found.
Wildtype is the normal (that
is, non-mutant) state of a gene .
Wobble hypothesis accounts for
the ability of a tRNA to recognize more than one codon by unusual
(that is, neither GC nor AU) pairing with the third base of a
codon.
Writhing number is the number
of times a duplex axis crosses over itself in space (superhelical
coiling).