Download Glossary Excerpted with modification from the Glossary in Genes V

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
translation.
function by
switching off transcription or
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
characteristic of the phenotype.
than
one
(apparently
unrelated)
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).