Glossary

2-micron plasmid A naturally occurring

Saccharomyces cerevisae plasmid (circumference
:
2 pm) that has been engineered to work as a vector
in yeast.
3' polyadenylation (3' poly-A tailing) During
eukaryotic pre-mRNA processing, an enzyme-driven
modification that removes the 3' end of the pre-
mRNA and adds numerous adenines.
3'splice site In eukaryotic pre-mRNA processing,
the location of cleavage at the 3' end of an intron.
Contains an AG dinucleotide in a consensus sequence.
3'to 5'exonuclease activity DNA- and RNA-
digesting activity that progresses in the 3' to 5'
direction to remove nucleotides. See also DNA
proofreading.
3' untranslated region (3' UTR) The untranslated
segment of mRNA between the stop codon and the 3'
end of the transcript.
5'capping In eukaryotic pre-mRNA processing, the
addition of 7-methylguanosine to the nucleotide at
the 5' end of pre-mRNA by a triphosphate bridge.
Methylation of adjacent nucleotides may also occur.
5'splice site In mRNA processing, the location of
cleavage at the 5' end of an intron. Contains a GU
dinucleotide in a consensus sequence.
5'to 3'exonuclease activity DNA- or RNA-
digesting activity that progresses in the 5' to 3'
direction to remove nucleotides.
5'to 3'polymerase activity DNA synthesizing
activity of DNA polymerases that progresses in the
5' to 3' direction to add new nucleotides to a growing
DNA strand. Requires a template strand.
5' untranslated region (5' UTR) The untranslated
segment of mRNA between the 5'end of the tran-
script and the start codon.
5-4 photoproduct A DNA lesion and potential
mutagenic event caused by exposure to ultraviolet
(UV) irradiation.
-10
consensus sequence See Pribnow box.
1O-nm fiber The "beads-on-a-string" form of
chromatin, in which DNA is wrapped around
nucleosomes.
3o-nm fiber A structure of chromatin in which his-
tone 1 (H1) partially condenses chromatin fibers into
a coiled form. Also known as solenoid or solenoid
structure.
30S initiation complex In bacterial translation, the
complex formed by a small ribosomal subunit,
mRNA, and the tRNA carrying fMet.
-35
consensus sequence A specifi.c consensus
sequence of the bacterial promoter at which RNA
polymerase is bound.
7OS initiation complex The fully assembled bacte-
rial ribosome that is prepared to initiate translation.
300-nm fiber A structural state of chromatin
in which chromatin fibers are looped and
condensed.
a-globin gene A gene belonging to a family of
closely related genes that encode a globin polypep-
tide that is part of hemoglobin.
cr-proteobacteria Lineage of bacteria that are the
closest extant relatives of the lineage that gave rise to
mitochondria.
pA allele The common (wild-type) allele of the
human
B-globin
gene.
B-globin
gene A gene belonging to a family of
closely related genes that encode a globin polypep-
tide that is part of hemoglobin.
ps allele A specific mutant allele of the human
B-globin
gene that produces sickle cell disease in
homozygous individuals.
e (theta) structure In bacterial DNA replication, the
name given to an intermediate structure of DNA
replication of a circular molecule with a single origin
of bidirectional replication.
e (theta) value A variable indicating a recombination
distance between genes. Used in lod score analysis.
aberrant ratio In fungi, a ratio of haploid spore geno-
types within a single ascus indicating gene conversion.
acentric fragment (acentric chromosome) A chro-
mosome fragment without a centromere.
acrocentric chromosome A eukaryotic chromo-
some in which the centromere is very near one end.
Forms a chromosome with long and short arms of
distinctly different lengths.
activator (Ac)element In transposition, a transpos-
able genetic element containing a transposase gene.
activator binding site DNA sequence to which an
activator protein binds to regulate gene expression.
Term refers to regulatory sites in bacteria; in eukary-
otes, the equivalent sequence would be called an
enhancer element.
activator protein A transcription factor that binds
to regulatory sequences associated with a gene and
upregulates that gene's expression.
addition rule See sum rule,
additive genes Genes contributing to a polygenic
trait and producing their effect by their cumulative
contributions that are approximately equal for
each gene.
additive variance (Va) For quantitative traits, the
component of genetic variance contributed by genes
having an additive effect on phenotypic variance.
adenine (A) One of four nitrogenous nucleotide
bases in DNA and RNA; one of the two types of
purine nucleotides in DNA and RNA.
adjacent-l segregation A pattern of chromosome
segregation that can occur following reciprocal bal-
anced translocation. Leads to gametes carrying gene
duplications and deletions.
admixed population A population whose members
are a blend of formerly distinct populations.
agarose An inert material derived from agar that is
mixed with buffer and used to form gels for gel
electrophoresis.
allele An alternative form of a gene.
allele-counting method A method for determining
allele frequency in a sample by tabulating the number
of alleles of each type.
allelic phase Describing the cis and trans arrange-
ments of alleles of linked genes on homologous
copies of a chromosome pair.
allelic series A group of alleles of a gene that display
a hierarchy of dominance relationship among them.
allolactose A modified from of lactose that binds
to the lac repressor protein, inducing an allosteric
change that reduces the DNA binding ability of the
complex.
allopatric speciation The development of new
species in geographic isolation.
allopolyploidy A polyploidy organism arising
through the union of chromosome sets from differ-
ent species.
allosteric domain Domain of a protein that allows
the protein to change shape when it binds to a spe-
cific molecule; the protein in the new shape is altered
in its ability to bind to a second molecule (e.g., DNA).
Also known as allostery,
allosteric effector compound Molecule that binds
to the allosteric protein domain and subsequently
induces a change in the bound protein.
allostery Reversible interactions of a small molecule
with a protein that lead to changes in the shape of the
protein and to a change in the interaction of the
protein with a third molecule.
alternate segregation A pattern of chromosome
segregation that can occur following reciprocal bal-
anced translocation that leads to the production of
viable gametes.
alternative mRNA processing (alternative intron
splicing, promoters, polyadenylation) In eukary-
otic pre-mRNA processing, alternative processes
by which different mRNAs can be produced from
the same gene using different promoters, polyadeny-
lation sites, or by removal of different exon
elements.
alternative sigma (o) factor Different forms of the
sigma subunit of bacterial RNA polymerase that
induce distinct conformational changes to the RNA
polymerase core and to the recognition of distinct
promoters.
Ames test A laboratory method commonly used to
determine whether a compound or one of its break-
down products is mutagenic.
amino acid An aminocarboxylic acid that is a com-
ponent of a polypeptide or protein.
aminoacyl site (A site) The site on a ribosome at
which incoming charged tRNAs match their anti-
codon sequence with mRNA codons.
aminoacyl-tRNA synthetase (IRNA synthetase)
A group of enzymes whose specific functions are to
identify particular tRNAs and catalyze the attachment
of the appropriate amino acid at the 3'terminus.
amorphic mutation See null mutation.
anagenesis Phylogenetic evolution of a new species
from an ancestral species without branching.
anaphase The phase of mitosis during which sister
chromatids separate (anaphase A) and move to
opposite poles (anaphase B).
G-1
G.2 GLOSSARY
aneuploid An uneven number of chromosomes.
Usually the result of the gain or loss of a
chromosome-that is,2n + 1 (trisomy) or 2n
-
|
(monosomy).
annotation (gene annotation, genome annota-
tion) The process of attaching biological functions
to DNA sequences. Genome annotation is the
process of identifying the location of genes and other
functional sequences within the genome sequence;
gene annotation defines the biochemical, cellular, and
biological function of each gene product the genome
encodes.
Antennapedia complex One of two homeotic gene
clusters in Drosophila consisting of five genes (labial,
Deformed, Sex combs reduced, proboscipedia, and
Antennapedia) that act in combination to specify the
cephalic and thoracic parasegments.
anticodon The nucleotide triplet sequence of trans-
fer RNA that pairs with an mRNA codon sequence in
translation.
antiparallel Opposite 5'and 3'orientations of two
complementary nucleic acid strands.
antisense RNA An RNA molecule that is comple-
mentary to a portion of a specific mRNA.
antitermination stem loop A stem loop that allows
RNA polymerase to continue transcription through
the leader region of bacterial attenuator controlled
operons and into the structural genes of an operon
(e,g.,the2-3 stem loop in trp operon regulation).
apurinic site The location of a nucleotide that has
lost its purine base.
arabinose(ara) operon An inducible operon consist-
ing of genes encoding enzymes allowing the use of ara-
binose as a carbon source. The operon is controlled by
a single regulatory protein, which carries out both
positive and negative transcriptional regulation.
Archaea One of the three domains of life; separate
from Bacteria and Eukarya.
Argonaute Protein subunit of RISC (RNA-induced
silencing complex) that binds small RNA molecules
and provides either the catalytic "slicer" activity or
the translational repressor activity.
artificial cross-fertilization A controlled cross
between plants made by an investigator who trans'
fers pollen from one plant to fertilize the other plant.
ascus The spore sac formed by fungi containing four
(tetrad) or eight (octad) haploid spores. Also called
spores.
aster The structure forming during cell division
that contains microtubules emanating from
centrosomes.
attachment site (att site) Identical or nearly identi-
cal sequences on the bacterial and bacteriophage
chromosomes that are cut and used to integrate or to
excise the bacteriophage chromosome from the
bacterial chromosome.
attenuation A gene regulatory mechanism that
fine-tunes transcription to match the momentary
requirements of the cell, achieving a more or less
steady state of compound availability.
attenuator region A regulatory region downstream
of the promoter of repressible amino acid operons
that exerts transcriptional control (in the form of I
transcription termination) based on the translation of
a leader peptide, the efficiency of which is deter-
mined by the availability of specific amino acids.
autonomous transposable element A transposable
genetic element that encodes transposase and can
initiate its own transposition.
autopolyploidy A pattern of polyploidy produced
by the duplication of chromosomes from a single
genome.
autoradiograph A photographic image obtained by
exposure of X-ray film to the radioactive decay of
isotopes attached to molecular probes. Used in the
analysis of gel electrophoresis,
autosgmal dominant inheritance A pattern of
hereditary transmission in which the dominant allele
of an autosomal gene results in the appearance of the
dominant phenotype.
autosomal inheritance Hereditary transmission of
genes carried on autosomes.
autosomal recessive inheritance A pattern of
hereditary transmission in which the recessive allele
of an autosomal gene results in the appearance of the
recessive phenotype.
Bacteria One of the three domains of life; separate
from Archaea and Eukarya.
bacterial artificial chromosome (BAC) Cloning vec,
tor used in bacteria that utilizes the F plasmid origin of
replication; can accept DNA inserts up to 500 kb.
bacterial chromosome The main, usually singular,
chromosome encoding the genome of a bacterium.
bacteriophage (phage) A virus whose host is a
bacterium.
balanced polymorphism A genetic polymorphism
maintained in a population because organisms with
the heterozygous genotype have higher relative
fitness than do organisms with either of the homozy-
gous genotypes.
balancer chromosome A chromosome with
inversions used to maintain specific allele combina-
tions (u.9., recessive lethal alleles) in genetic stocks.
band (in electrophoresis gel) A region in an elec-
trophoresis gel or in an autoradiograph where a pro-
tein of nucleic acid congregates. Usually visualized
using a stain or molecular probe.
barcode Short DNA sequences that identify specific
strains in knockout libraries.
Barr body The darkly staining inactive X chromo-
some visible in mammalian female nuclei. The result
of random X inactivation.
base analog A compound with structure similar to
a naturally occurring nucleotide base that can substi-
tute for the base in DNA.
base-pair substitution mutation A DNA sequence
change resulting in the substitution of one base pair
for another.
base stacking A phenomenon of DNA base-pair
interaction that rotates the base pairs around a cen-
tral axis of symmetry and imparts twisting to the
double helix.
basic local alignment search tool (BLAST) A com-
puter program designed to search for homologous
sequences in databases.
bidirectional DNA replication The standard
method of DNA replication that synthesizes new
DNA in both directions from a replication origin.
binomial probability A probability function using
two coefficients, a and b, whose sum equals 1 and
whose products predict the probability of events.
bioinformatics The use of computational
approaches to decipher DNA-sequence information.
biosynthetic pathway A multistep biochemical
pathway that synthesizes an end product or
compound.
biparental inheritance Condition in organellar
inheritance where both parental gametes make con-
tributions of cytoplasmic organelles to the zygote;
contributions are often unequal because one gamete
contributes more of the cytoplasm and the other
gamete makes a smaller contribution.
bithoraxcomplex One of two homeotic gene
clusters in Drosophila consisting of three genes
(U lt r ab ith o r A n, ab d o m in al - A, and Ab d o m i n al - B)
that act in combination to specify the thoracic and
abdominal parasegments.
blending theory of heredity An obsolete theory of
heredity proposing that the traits of offspring are the
average of parental traits.
blotting (in gel electrophoresis) The process of
transferring proteins or nucleic acids from an elec-
trophoresis gel to a permanent membrane or filter.
blunt ends 5' or 3' ends of double-stranded DNA
lacking any single-stranded overhangs.
branch point adenine In intron splicing, an adenine
nucleotide near the 3' splice site of an intron that
joins with a guanine located at the 5' splice site by a
2'-to-S' phosphodiester bond to form a lariat intron.
BRCAl -associated genome surveillance complex
(BASC) A multiprotein complex that surveys the
genome for mutations at the G1- to S-phase cell cycle
checkpoint.
broad sense heritability (H2l The proportion of
total phenotypic variance that is contributed by total
genetic variance.
bulky adduct Large chemical groups added to
nucleotides by alkylating agents.
bypass polymerase A group of DNA polymerases
that are unstable and synthesize short regions of
DNA under conditions in which the main DNA poly-
merase is unable to function, such as when faced
with DNA lesions that block replication. Also called
translesion DNA poly merase.
CAAT box A common consensus sequence compo-
nent of eukaryotic promoters.
CAP (catabolite activator protein) In bacterial
transcription regulation, binds cAMP (cyclic AMP)
at low glucose concentrations to positively regulate
the transcription of operons that allow the use of
alternative carbon sources.
CAP binding site A bacterial DNA regulatory
sequence to which the CAP-cAMP complex binds to
positively regulate gene expression. See also
CAP-cAMP complex,
CAP-cAMP complex Formed by joining catabolite
activator protein to cAMB the complex binds to the
CAP binding site of the bacterial lac promoter to reg-
ulate gene expression.
catabolite repression Situation where the presence
of the preferred catabolite (e.g., glucose) represses
the transcription of genes for an alternative catabolite
(e.9., lactose).
Cdks (cyclin-dependent kinases) A group of
multimeric proteins whose levels fluctuate during the
cell cycle. Composed of cyclin proteins and protein
kinases, Cdks control entry and progression through
mitosis.
cell cycle Consisting of interphase (G1phase,
S phase, and G2phase) and M phase (mitosis or
meiosis) in cells. The transition from one phase to
the next is controlled by protein-based interactions.
cellular blastoderm Stage of Drosophila
embryogenesis in which the nuclei are located at the
periphery of the embryo and are enclosed by cell
membranes.
central dogma of biology The description of the
functional relationship between DNA, RNA and pro-
teins (DNA to RNA to protein).
centromere A specialized DNA sequence on
eukaryotic chromosomes that is the site of kineto-
chore protein and microtubule binding.
Gentrosome A cytoplasmic region, containing a pair
of centrioles in many eukaryotic species, from which
the growth of microtubules forms the spindle appara-
tus during cell division.
chaperone A category of eukaryotic proteins that
assist with the folding or movement of other
polypeptides.
Chargaff's rule The observation that the percentage
of adenine equals that of thymine and that guanine
percentage equals cytosine percentage in DNA.
charged IRNA A IRNA to which the correct amino
acid has been attached.
chiasma (plural: chiasmata) Points of contact
between homologous chromosomes that are coinci-
dent with crossover locations between the homologs.
chi-square test (X2 test) A statistical test to compare
the observed results of an experiment with the
results predicted by chance.
chloroplast An organelle, bounded by a double
membrane, where photosynthetic reactions convert
light energy and CO2 into fixed organic carbon.
chromatin The complex of nucleic acids and pro-
teins that compose eukaryotic chromosomes.
chromatin modifier Proteins that chemically mod-
ify histone proteins in the nucleosomes by adding
or removing specific chemical groups, thereby
modifying chromatin structure and regulating gene
expression.
chromatin remodeler Proteins that reposition
nucleosomes within chromatin in such a way as to
open or close promoters and other regulatory
sequences or that change the composition of
nucleosomes, altering their biological activity
(e.9., S!flIlSNF, IS'W.I, S\)fRl).
chromatin remodeling Processes that modify the
structure or composition of chromatin. Usually asso-
ciated with alterations of nucleosome binding to DNA
and affecting the regulation of gene transcription.
chromatography A technique for separating the
components of a molecular mixture by their similari-
ties and differences.
chromosome A structure composed of DNA and
associated proteins that in total contain the genome
of an organism.
chromosome aberration An abnormality of chro-
mosome number or structure.
chromosome arms fiong arm (q arm), short arm
(p arm)] The segments of eukaryotic chromosomes
between the centromere and the telomeres.
chromosome banding A group of laboratory
methods that stain eukaryotic chromosomes to
reveal distinctive patterns of light and dark bands.
Chromosome banding by Giemsa staining produced
standardized patterns for different chromosome
of selected species. Also known as Giemsa, (G)
banding.
chromosome break point The location of a chro-
mosome break.
chromosome fusion See Robertsonian
translocation,
chromosome inversion (paracentric, pericentric)
A structural alteration of a chromosome in which a
segment breaks away from the chromosome and sub-
sequently reattaches after 180" rotation. See also
inv ersio n heterozygote.
chromosome scaffold Composed of numerous
nonhistone proteins, the superstructure of eukaryotic
chromosomes.
chromosome territory The region within a nucleus
occupied by a particular chromosome during
interphase.
chromosome theory of heredity The theory
developed in the early 20th century that genes are
carried on chromosomes and that the meiotic
behavior of chromosomes is the physical basis of
Mendel's laws.
chromosome translocation The relocation of
a chromosome or chromosome segment to a non-
homologous chromosome.
chromosome walking See positional cloning,
cis-acting Acting on the same chromosome
(e.g., DNA sequences that control expression of
genes encoded on the same piece of DNA).
cis-acting regulatory sequence Sequences to
which proteins bind to regulate transcription of
genes located on the same chromosome as the
sequences.
cis-dominant The principle that the operator
can influence only the transcription of adjacent
downstream genes.
clade In phylogenetics, a group of organisms
defined by characteristics that are unique to the
group and distinguish the group from others.
cladistics The classification of organisms by charac-
teristics that are unique to the group and distinguish
it from other groups. Involves branching of new
species from ancestral species. See also clade.
cladogenesis Phylogenetic evolution by branching
of descendant species from ancestral species.
clamp loader A multiprotein complex that pairs
with DNA polymerase and the sliding clamp during
replication.
clone-by-clone sequencing An approach to
genome sequencing where each chromosome is
first broken into overlapping clones that are then
arranged in linear order to produce a physical map of
the genome. Each clone in the map is then sequenced
separately. Contrast with who le-genome shotgun
sequencing.
closed chromatin Chromatin in which regulatory
DNA is covered by nucleosomes, thus restricting the
access of regulatory proteins to the sequences ren-
dering genes in closed chromatin transcriptionally
silent.
closed promoter complex The initial stage of tran-
scription that forms when RNA polymerase loosely
binds the promoter.
coding strand The nontemplate strand of DNA
that has the same 5'-to-3' polarity as its transcript
and the same sequence, except for t in DNA and
u in RNA.
codominance The equal and detectable expression
of both alleles in a heterozygous organism.
codon The nucleotide triplet of mRNA that encodes
a single amino acid.
(odon
bias The preferential use of specific codons
where there is redundancy in encoding a specific
amino acid.
G LOSSARY G.3
coefficient of coincidence (c) The ratio of the
observed number of double recombinants to the
number of double recombinants expected to occur
by chance.
coefficient of inbreeding (F) The probability that
two alleles carried in an individual are homozygous
identical by descent (IBD).
cohesive (cos) ends Short, single-stranded over-
hangs at 5' and 3' ends produced after digestion with
certain restriction ends. The cohesive ends are termed
compatible if they can base-pair with complementary
single-stranded ends of another DNA molecule.
Compare with cohesive sites.
cohesive (cos) sites The single-stranded ends of
phage lambda that facilitate circularization or con-
catamerization of lambda phage genomes and that
interact with coat proteins during packaging of phage
particles. Compare with cohesive ends.
cointegrate In replicative transposition, the fusion
of two circular transposable elements into a single,
larger circular element.
comparative genomics See evolutionary
genomics.
Gompensatory mutation A second mutation
occurring at another site that fully or partially
restores wild-type function lost when an initial
mutation occurs.
complementary base pairs The specific pattern
of purine-pyrimidine pairing of nucleic acid
strands. In DNA, e with c and A with r; RNA uses u
instead of r.
complementary DNA (cDNA) library Collection of
DNA clones, originally derived via reverse transcrip-
tion of mRNA molecules into DNA (cDNA) and
cloned into a vector.
complementary gene interaction (927 ratio)
A characteristic ratio of phenotypes produced by the
interaction of two complementary genes that control
a trait.
complementation group A group of mutations that
affect the same gene.
complete genetic linkage The absence of crossing
over between linked genes.
complete initiation complex The multisubunit
complex that forms at the promoter immediately
before the onset of transcription.
Gomposite transposon In bacteria, a transposable
element containing multiple genes located between
terminal insertion sequences.
concordance In twin studies, the observation that
both twins exhibit the trait.
conditional probability A probability prediction
that is dependent on another previous event having
taken place.
conjugation The short-term union of two bacterial
cells for the unidirectional transfer of DNA from the
"donor" to the "recipientl'The transferred material
may be plasmid DNA or donor bacterial chromo-
some DNA.
conjugation pilus The hollow filament extending
from the donor bacterium to the recipient bacterium
through which DNA is transferred. Also known as
conjugation tube.
conjugation tube See conjugation pilus.
consanguineous mating See inbreeding,
consensus sequences A nucleotide sequence in a
DNA segment derived by comparing sequences of
similar segments from other genes or organisms.
G-4 GLOSSARY
The most commonly occurring nucleotides at each
position comprise the sequence.
conservative DNA replication A disproven model
of DNA replication positing that one duplex pro-
duced by replication contained the two original
strands and the other two daughter strands.
conservative transposition In transposition,
the removal of a transposable element from one
location followed by insertion into a new location.
conserved noncoding sequence (CNS)
Sequences
that do not code for amino acids and are conserved
across significant phylogenetic distances.
constitutive heterochromatin Chromosome
regions containing chromatin that is always densely
compacted. Usually containing highly repetitive DNA
sequences.
constitutive mutants Mutants in which a gene is
always expressed rather than being under regulatory
control.
constitutive transcription State in which a gene is
continuously transcribed.
contiguous sequence (contig)
Overlapping DNA
clones that together cover an uninterrupted continu-
ous stretch of DNA sequence.
continuous variation In polygenic and multifacto-
rial traits, the observation of phenotypic distribution
over a continuous range.
controlled genetic cross Genetic crosses controlled
by an investigator who usually knows the genotypes
and/or phenotypes of the organisms being crossed.
convergent evolution Processes of independent
evolution of similar structures in unrelated species.
Also known as homoplasmy.
co-option A common theme in the evolutionary
history of genes bywhich genes and genetic modules
are reused in a new manner to direct the patterning or
growth of novel organs.
coordinate genes Genes, often with maternal
effects, that establish the major axes of the embryo,
especially the anterior-posterior and dorsal-ventral
axes; examples include bicoid and nanos.
copy number variant (CNV) A specific type of
structural variant due to insertions or deletions
(indels) greater than 1 kb in length.
core DNA The approximately 146 base pairs of
eukaryotic DNA that wrap each nucleosome.
core element Consensus sequences in the active
regions of promoters recognized by RNA polymerase I.
core enzyme The five-polypeptide component of
bacterial RNA polymerase that actively carries out
transcription.
corepressor An accessory molecule required for a
repressor protein to exert its function.
cosmid vector Cloning vector used in bacteria
that utilizes phage lambda cos sites for packaging of
phage and a bacterial origin of replication for
subsequent maintenance in bacteria; can accept DNA
inserts of up to 40 kb.
cosuppression The silencing, via a small RNA
mediated mechanism, of an endogenous gene due to
the presence of a homologous transgene or virus.
Cosuppression can occur at the transcriptional or
post-transcriptional level.
cotransduction The simultaneous transduction of
two or more genes contained on a donor DNA
fragment into a recipient cell, where it undergoes
homologous recombination to be spliced into the
transductant chromosome.
cotransduction frequency The frequency with
which two genes are transduced.
cotransduction mapping A method of mapping
donor bacterial genes based on their frequency of
cotransduction.
cotransformation Simultaneous transformation of
two or more genes carried on a donor DNA fragment
into a recipient.
covered promoter Promoter in which nucleosomes
are found adjacent to the transcription start site, pre-
venting efficient transcription initiation. This feature
is common at highly regulated genes.
CpG dinucleotide See CpG island.
CpG island Region in which the frequency of CpG
dinucleotides is higher than the average for the
genome; commonly found near the transcription
start sites of animal genes. The cytosines are often
methylated when the gene is inactive and demeth-
ylated when the gene is transcriptionally active.
crossing over The breakage and reunion of
homologous chromosomes that results in reciprocal
recombination.
crossover suppression The significant reduction, or
complete absence, of progeny with recombinant
chromosomes due to duplications and deletions of
genetic material following crossing over within the
inversion loop in organisms that are heterozygous for
an inversion.
cryptic splice site A 5' or 3'splice site that is not nor-
mally used except when a mutation either inactivates
an authentic splice site or creates a new splice site at
the cryptic site location. See also splicing mutation,
cyanobacteria Lineage of photosynthetic bacteria
that are the closest extant relatives of the lineage that
gave rise to the plastids.
cyclin protein A family of proteins whose levels
fluctuate during the cell cycle. Cyclins pair with
protein kinases to form cyclin-dependent kinases
(Cdks) that help regulate the cell cycle.
cytokinesis Part of telophase, the process of cyto-
plasmic division between daughter cells.
cytological markers Structural differences between
homologous chromosomes that serve to differentiate
the chromosomes when they are visualized using
microscopy.
cytoplasmic inheritance (organellar
inheritance)
The transmission of genes on mitochondrial and
chloroplast chromosomes; genes that are located
in the cytoplasmic organelles as opposed to the
nucleus.
cytosine (C) One of four nitrogenous nucleotide
bases in DNA and RNA; one of the two types of
pyrimidine nucleotides in DNA and RNA.
daughter cell The genetically identical cells pro-
duced by mitotic cell division.
daughter strand A newly synthesized strand of
DNA that is complementary to a template strand.
deamination A DNA lesion resulting in the loss of
an amino group (NHr) from a nucleotide base.
degrees of freedom (df) The number of
independent variables in an experiment. In a chi-
square test, most often the number of outcome class
minus l(n-l).
delayed age of onset The appearance of an
abnormal phenotype that is not present at birth but
appears later in life and is caused by an inherited
mutation.
deletion The loss of genetic material (see also
interstitial, microdeletion, partial deletion, partial
deletion heterozygote, terminal deletion),
deletion mapping A,method for mapping genes
utilizing partial chromosome deletions with
known locations to expose recessive mutants by
pseudodominance.
denaturation In DNA, the separation of
complementary strands of nucleic acids by hydrogen
bond breakage. In polypeptides and proteins, the
unfolding of tertiary or quaternary structures.
densitometry A technique for passing Iight through
an electrophoresis gel to detect the presence of a
stained band of protein or nucleic acid.
deoxynucleotide monophosphates (d NMps)
Monophosphate forms of deoxynucleotides.
deoxynucleotide triphosphates (dNTps)
Triphosphate forms of deoxynucleotides.
deoxyribonucleic acid (DNA)
The hereditary mole-
cule of organisms. Composed of two complementary
strands of nucleotides with purine bases adenine (A)
and guanine (G) and pyrimidine bases thymine (T)
and cytosine (C).
depurination A DNA lesion occurring when a
deoryribose molecule loses its purine nucleotide base.
See apurinic site.
dicentric bridge In a dicentric chromosome, the
portion between the two centromeres that are drawn
to opposite poles of the cell during division.
dicentric chromosome A chromosome with two
centromeres.
dicer Ribonuclease that acts on double-stranded
RNA responsible for the generation of small regula-
tory RNA molecules, such as microRNAs and small
interfering RNAs; typically 2L-30 nucleotides in
length.
dideoxy DNA sequencing A method of DNA
sequencing devised by Fred Sanger that uses a
mixture of deoxynucleotide and dideoxynucleotide
triphosphates to selectively block DNA replication,
producing a ladder of partially synthesized DNA
strands of different lengths. Also known as the
Sanger method.
dideoxynucleotide triphosphates (ddNTps)
Rare
DNA nucleotides absent oxygen molecules at the 2'
and the 3'carbons that are most commonly used in
dideoxynucleotide DNA sequencing.
differential reproductive fitness. See relative
fitness.
differentiation Process by which cells become
restricted in their developmental potential and take
on specialized morphologies and physiological
activities.
dihybrid cross A cross between organisms that are
heterczygous for two loci.
diploid number of chromosomes (2n) The
characteristic number of chromosomes in somatic
cell nuclei of diploid species. Equal to twice the
haploid (n) number of chromosomes found in the
nuclei of gametes of sexually reproducing diploid
species.
direct repeat Identical or nearly identical DNA
sequences in the same orientation that are separated
by intervening DNA.
directionalcloning Technique whereby a DNA inser!
is cloned with a specific directionality with respect to
/
sequences of the cloning vector; usually accomplished
by using two different restriction enzymes.
directional natural selection See directional
selection,
directional selection Natural or artificial selection
that continuously changes the frequency of an allele
in a direction toward fixation (frequency
-
1.0) or
toward elimination (frequency :
0.0).
discontinuous variation A phenotype distribution
containing discrete or separable categories.
discordance In twin studies, the observation that
the traits exhibited by the twins are different.
disjunction The normal process separation of
homologous chromosomes or of sister chromatids
during cell division.
dispersive DNA replication A disproven model of
DNA replication positing that each strand of daugh-
ter duplexes is composed of segments of original
DNA and segments of newly synthesized DNA.
displacement loop (D loop) During DNA damage
repair and homologous recombination, the displace-
ment of a single strand of DNA by strand invasion.
disruptive selection Natural or artificial selection of
phenotypic extremes in a population, leading eventu-
ally to two strains with distinctive phenotypes.
dissociation (Ds) element In transposition, a non-
autonomous genetic element that is incapable of
transposing on its own.
DNA-binding protein A general term for a protein
that binds to DNA; the interaction can be either
DNA-sequence specific (most regulatory proteins) or
DNA-sequence nonspecific (e.g., structural proteins
such as histones).
DNA clone A fragment of DNA that is inserted into
a vector, such as a plasmid, cosmid, or artificial
chromosome.
DNA double helix (DNA duplex) The two
complementary strands of DNA arranged in antipar-
allel orientation.
DNA library Collection of DNA clones in which the
DNA is usually derived from a single source.
DNA ligase An enzyme active in DNA replication
that joins together segments of a DNA strand by
catalyzing formation of a phosphodiester bond.
DNA loop In gene regulation, a condition where the
DNA sequences between regulatory elements form an
extended loop that allows distant regulatory sequences
with associated DNA-binding proteins to interact.
DNA microarray Collections of synthesized DNA
fragments attached to a solid support and represent-
ing sequences present in a genome; can be used to
assess transcription patterns, transcription factor
binding sites, and recombination patterns, among
other uses.
DNA nucleotides DNA building blocks composed
of deoxyribose sugar, a nitrogenous base, and one or
more phosphate groups. See also adenine (A),
thymine (T), cytosine (C), and guanine (G).
DNA polymerase (pol l, pol ll, pol lll) The large
multisubunit complex responsible for the synthesis of
new strands of DNA during DNA replication or
DNA repair.
DNA proofreading The capacity of many types of
DNA polymerase to utilize a 3'to 5'exonuclease
activity to remove and replace mismatched or dam-
aged nucleotides during replication. See also 3'to S'
exonuclease activity.
DNA replication The synthesis of new DNA strands
by complementary base pairing of nucleotides in a
daughter strand to those in a template strand.
DNasel hypersensitive site Regions of chromatin
sensitive to cleavage by DNase I; these often represent
open chromatin that is transcriptionally active.
DNA transposon One type of transposable genetic
element encoding a transposase and capable of
transposition.
DNA triplet Three DNA nucleotides corresponding
to a codon of mRNA.
dominance varianG In polygenic and multifacto-
rial inheritance, the portion of genetic variance
attributed to the dominance effects of contributing
genes.
dominant epistasis (12:3:1 ratio) A characteristic
ratio of phenotypes produced by the interaction of
two genes that control a trait in which a dominant
allele of one gene masks or reduces the expression of
alleles of a second gene.
dominant interaction (9:6:1 ratio) A characteristic
ratio of pheno{pes produced by the interaction of
two genes that control a trait in which the presence
of dominant alleles of both genes produces one phe-
notype, one dominant allele of either gene produces
a second phenotype, and organisms with only
recessive alleles for the interacting genes have a
third phenotype.
dominant negative mutation A dominant muta-
tion that behaves as a loss-of-function, often due to
blocking the formation or normal function of a mul-
timeric protein complex.
dominant phenotype The phenotype observed in
a heterozygous organism that is identical to the phe-
notype observed in a homozygote. The phenotype
produced when an organism is homozygous for the
dominant allele or carries a single copy of the domi-
nant allele in the heterozygous genotype. Compare
with recessive phenotype.
dominant suppression (13:3 ratio) A characteristic
ratio of phenotypes produced by the interaction of
two genes that control a trait in which the dominant
allele of one gene suppresses the expression of the
dominant allele of the second gene.
donor cell (bacterial donor) The bacterial cell
that is the source of DNA transferred to a recipient
cell by either conjugation, transduction, or
transformation.
donor DNA DNA to be used in cloning or other
recombinant DNA technologies.
dosage compensation A mechanism for equalizing
the expression of X-linked genes in males and
females of a species.
double Holliday junction (DHJ) An intermediate
structure temporarily connecting chromatids of
homologous chromosomes that forms during homol-
ogous recombination.
double recombinant (double crossover) The
occurrence of two crossovers between homologous
chromosomes in a particular region. May involve
two, three, or all four chromatids.
double-strand break repair Following phosphodi-
ester bond breakage on both strands of a DNA
duplex, a mechanism of DNA damage repair. Related
to the mechanism for homologous recombination.
downstream Referring to a gene or sequence
location that is toward the 3' direction on the
coding strand.
drosha Ribonuclease that processes pri-microRNA
molecules into pre'microRNA molecules in animals.
duplicate gene action (15:1 ratio) A characteristic
ratio of phenotypes produced by the interaction of
GLOSSARY G-5
two genes that duplicate each other's action due to
genetic redundancy.
duplication The gain of genetic material by the
inclusion of one or more additional copies of a chro-
mosome segment. See also microduplication, partial
dup li c at i o n, and p ar ti al dup lic atio n h eter o zy go te,
early genes The first genes expressed following the
infection of bacterial cells by bacteriophage. The fate
of early gene expression determines whether the
phage undergoes the lytic cycle or the lysogenic cycle.
early promoters Regulatory sequences responsible
for the activation of early genes or operons in
bacteriophage.
East-West (EW) resolution One of the possible pat-
terns for resolving a Holliday junction to separate
homologous chromosomes before meiotic anaphase.
electrophoretic mobility A measurement of (1) the
distance of migration or (2) the speed of migration of
a nucleic acid or protein in gel electrophoresis.
elongation factor (EF) A group of proteins associ-
ated with ribosomes that contribute to the elongation
of the polypeptide product.
embryonic stem cells In vertebrates, totipotent cells
of early embryos that can give rise to any and all cell
types of the organism.
endosymbiont An organism that lives within the
body or cell of another organism.
endosymbiosis An (often) mutually beneficial
relationship between organisms in which one
organism, the endosymbiont, inhabits the body
of the other.
endosymbiosis theory Hypothesis that the
mitochondrion and chloroplast are evolutionarily
derived from bacterial endosymbionts related
to extant u-proteobacteria and cyanobacteria,
respectively.
enhanceosome Protein complex that binds enhancer
elements and directs DNA bending into loops that
bring the protein complex into contact with RNA
polymerase and transcription factors bound at the
core promoter or with protein complexes bound to
proximal promoter elements.
enhancer A eukaryotic cis-acting DNA regulatory
sequence to which trans-acting factors bind
and stimulate transcription. See also enhancer
sequence.
enhancer screen A genetic screen designed to iden-
tify mutations in genes that worsen the phenotypic
effects of mutations in another gene.
enhancer sequence Sets of regulatory sequences
that bind specific transcriptional proteins that can
elevate transcription of targeted eukaryotic genes.
enhancer trap A transgenic construct inserted ran-
domly into the genome that allows identification of
enhancer elements controlling specific patterns of
gene expression.
environmental variance (t/g) For quantitative traits,
the proportion of the total phenotypic variance
contributed by differences in the environment expe-
rienced by population members.
epigenetic Heritable patterns or changes in gene
expression that are not associated with any change in
DNA sequence.
epigenetic marks A collection of chemical marks
and modifications, such as acteylation and methyla-
tion of histone proteins, that are functional in
chromatin remodeling. Also known as epigenetic
modif.cation.
G.6 G LOSSARY
epigenetic modification Chemical modifications of
DNA or associated histones, such as acetylation and
methylation, that alter chromatin structure and influ-
ence gene transcription.
epistasis See epistatic interaction.
epistatic interaction A group of specific patterns of
gene interaction in which an allele of one gene modi-
fies or prevents the expression of alleles of another
gene. Also known as epistasis.
equilibrium frequency The stable frequency of an
allele in a population attained and maintained
through the action of evolutionary processes.
ethidium bromide (EtBr) A compound used to stain
DNA and RNA in electrophoresis gels.
euchromatic region See euchromatin.
euchromatin Chromosome regions containing chro-
matin that is not densely compacted. Most expressed
genes are located within euchromatic regions of chro-
mosomes. Also known as euchromatic region.
Eukarya One of the three domains of life; separate
from Archaea and Bacteria. See also eukaryote.
eukaryote Referring to organisms belonging to the
domain Eukarya.
eukaryotic initiation factor (elF) A group of
eukaryotic proteins that associate with ribosomal
subunits and help initiate translation.
euploid A number of chromosomes that is an exact
multiple of the haploid number.
E(var) mutations Mutations that enhance position
effect variegatio n in Drosophila. Mutated genes
produce proteins that are active in chromatin
remodeling.
evo-devo The study of the evolution of development.
evolution (1) Any change in the genetic characteris-
tics of a population, strain, or species over time.
(2) The theory that all organisms are related by com-
mon ancestry and have diversified from common
ancestors over time.
evolutionary genetics The study of evolution and
evolutionary processes using genetic techniques
and tools.
evolutionary genomics The comparison of
genomes, both within and between species. It illumi-
nates the genetic basis of similarities and differences
between individuals or species.
evolutionary processes Four processes-natural
selection, migration, mutation, and random genetic
drift-that can cause changes in the genetic charac-
teristics of a population or lineage.
exconjugant cell The cell that is the product of con-
jugation between a donor cell and a recipient cell.
exit site (E site) On the ribosome, the site through
which an uncharged tRNA exits.
exon A nonintron segment of the coding sequence
of a gene.
)oined together following intron splicing,
exons correspond to the mRNA sequence that is
translated into a polypeptide.
exonic splicing enhancers (ESEs) Exon sequences
that play a role in intron splicing.
expression array DNA microarray that carries
unique sequences from every annotated gene of the
genome and is used to monitor gene expression
patterns.
expression vector Cloning vector possessing DNA
sequences required for DNA fragments inserted into
the vector to be transcribed and translated. Vectors
with sequences facilitating expression in eukaryotes
are called eukaryotic expression vectors.
F (fertility) factor The plasmid containing genes
that confer the ability to act as a donor cell on a bac-
terium. May be either an extrachromosomal plasmid
or may be incorporated into the donor bacterial
chromosome. Also known as F plasmid,
F' cell (F' donor) An extrachromosomal fertility
plasmid into which a portion of the donor bacterial
chromosome has been incorporated.
F plasmid. See F (fertility)factor.
F*cell (F*donor)
A donor bacterium containing an
extrachromosomal fertility plasmid.
F, generation (first filial generation) The first gen-
eration of offspring. In genetic experiments, usually
the offspring produced by crossing pure-breeding
parents.
F, generation (second
filial generation) The
second generation, produced by crossing F1 organisms.
F, generation (third filial generation) The third
generation, produced by crossing F2 organisms.
facultative heterochromatin Heterochromatic
chromosome regions whose level of compaction can
vary. Often contains repetitive DNA, but may also con-
tain some expressed genes.
first-division segregation In Neurospord, and other
organisms forming an ascus, the separation of alleles
at the first meiotic division due to no crossing over
having occurred.
fluorescent in situ hybridization (FISH) A labora-
tory method for identifying genes or DNA sequences
using molecular probes labeled with a compound
that can emit fluorescent light upon excitation.
forked-line diagram A method for diagramming
the probabilities of outcomes in a branching format.
forward genetic analysis The classical approach to
genetic analysis whereby genes are first identified by
mutant phenotypes caused by mutant alleles and the
gene sequence is subsequently identified by recombi-
nant DNA technologies. AIso known asforward
genetics,
forward genetics See
forward
genetic analysis.
forward mutation A mutation that alters a wild type
and generates a mutant. Also known as mutation.
forward mutation rate (F) The frequency of
mutation from wild-type alleles to mutant alleles.
founder effect The random occurrence of allele and
genotype frequency differences between a new popu-
lation established by a small number of founders and
the larger parental population.
four-strand double crossover Two crossover
events between a pair of homologous chromosomes
that involve all four chromatids.
frameshift mutation The insertion or deletion of
DNA base pairs resulting in translation of mRNA in
an incorrect reading frame.
frequency distribution A visual display or his-
togram of quantitative data.
functional domain A protein region with a specific
function or interaction.
functional genomics Using genomic sequences and
genome-wide patterns of transcripts and protein
expression to understand gene function in an
organism.
functional RNAs Various types of transcripts that
are not translated and are functional as nucleic acids.
See also iRNA, rRNA, snRNA, miRNA, siRNA,
ribozymes.
fusion gene A recombinant gene comprised of
DNA sequences from more than one source (e.g., the
\
codon sequences derive\d from one gene and the
sequences responsible for elpression derived from a
secondgene). \
fusion protein A recombinant protein encoded by
DNA sequences from more than one source; made
by combining the open reading frames of two
unrelated genes.
Go The "G zero" phase of the cell cycle, an alternatiye
to G1 of the cell cycle entered by mature cells that
generally do not divide again until they die. Compare
with G7 and G2phase.
G, phase The "Gap 1" phase of the cell cycle during
which genes are actively transcribed and translated
and cells carcy out their normal functions. Compare
with Gs and G2 phase.
G, phase The "Gap 2" phase of the cell cycle during
which the cell prepares to divide. Compare with
G6 and G
r.
gain-of-function mutation A mutation causing a
gene to be overexpressed, to be expressed at the
wrong time, or to encode a constitutively acting
protein. Usually inherited as a dominant mutation.
gametes The reproductive cells produced by male
and female reproductive structures; sperm or pollen in
male animals and plants, and eggs in females.
gap genes In Drosophila, genes that control
development in large contiguous regions along the
anterior-posterior axis; examples inclu de hunchback,
giant, krilppel, and knirps.
Gaussian distribution See normal distribution.
GC-rich box An occasional upstream consensus
sequence of eukaryotic promoters that is rich in
guanine and cytosine.
gel electrophoresis A laboratory method for
separating proteins or nucleic acid molecules or
fragments using electrical current in a gel matrix.
gene The physical unit of heredity, composed of a
DNA sequence that is transcribed and encodes a
polypeptide or another functional molecule.
gene conversion Repair of mismatched (non-
complementary) DNA nucleotides in heteroduplex
DNA that forms during meiotic recombination. One
allele is switched for another allele already in the
genotype.
gene dosage The number of copies of a gene.
gene-environment interaction Interactions taking
place between particular genes and specific environ-
mental factors.
gene family A group of genes that is evolutionarily
related via successive gene duplication events that are
followed by diversification.
gene interaction Referring to genes that interact
with one another due to their participation in the
production of a particular product or trait.
gene knockout Loss-of-function allele of a gene
usually obtained via a reverse genetic approach.
gene pool The to(al of all alleles present in breeding
members of a population at a given moment.
gene therapy The use of genes as therapeutic agents
to cure or alleviate symptoms of a genetic disease.
generalized transducing phage In transduction, a
bacteriophage that carries a random segment of the
chromosome of a donor cell to the recipient cell.
generalized transduction The transduction of a
random segment of a donor chromosome into a
recipient cell by a transducing phage. See also
general ize d tran s ducing p h age.
genetic bottleneck A period or event character-
izedby a substantial random reduction in popula-
tion size. Loss of genetic diversity and allele
frequency changes usually occur.
genetic chimera A tissue or organism comprised of
cells of two or more distinct genotypes.
genetic Gode The universal set of correspondences
of mRNA codons to amino acids. Used in translation
to synthesize polypeptides.
genetic complementation (1) The observation of a
wild-type phenotype in an organism or cell contain-
ing two different mutations. (2) The cross of two
pure-breeding mutants that yields progeny that are
exclusively wild type.
genetic dissection The use of mutations and
recombinants in genetic analyses to identify and
assemble the genetic components of a biological
property or process.
genetic drift A process of evolution referring to
random changes in allele frequencies that result from
sampling errors. Occurs in all populations but is
strongest in small populations.
genetic fine structure The method of high-
resolution analysis of intragenic recombination to
map genes at the nucleotide level.
genetic heterogeneity The observation of the same
phenotype produced by mutation of any one of two
or more different genes.
genetic liability See threshold of genetic liability.
genetic linkage The result of genes being located so
near one another on a chromosome that their alleles
do not assort independently. Identified by detecting
certain pairs of alleles (parentals) that are transmitted
together significantly more often than expected by
chance and of other pairs of alleles (nonparentals or
recombinants) that are transmitted together signifi-
cantly less often than expected.
genetic linkage mapping Process for creating
maps of genes based on their linkage relationships to
other genes.
genetic markers Alleles of either expressed genes or
non-coding chromosomal regions identifying a spe-
cific region of a chromosome. Can be used to trace or
identify another gene, the chromosome, or a cell,
organ, or individual.
genetic network Set of interacting genes identified
from double mutants or other analyses indicating
gene interaction.
genetic redundancy The situation where the func-
tions of one gene are compensated for by the actions
of another gene.
genetic screen A procedure whereby a population
of organisms is mutagenized and their progeny are
propagated and examined for mutant phenotypes.
Also known as mutagenesis.
genetic variance (Vc) In polygenic and multifacto-
rial inheritance, the proportion of total phenotypic
variance contributed by genetic variation.
genome The entire complement of DNA sequences
in a chromosome set of an organism.
genome-wide association studies (GWAS)
Association analysis performed using genetic marker
genes distributed throughout the genome. Designed
to locate genes that may influence the variation of
quantitative traits.
genomic imprinting Epigenetic phenomena that
create differential expression of alleles depending
on whether they were maternally or paternally
inherited.
genomic library A set of clones consisting of
the DNA representing the genome of an organism.
genotype (1) The genetic composition of an organ-
ism or a cell (i.e., all the alleles of all the genes).
(2) The alleles of a single gene or a specified set of
genes in a cell or organism.
genotype proportion method A method for
estimating allele frequencies in a population by
manipulation of genotype frequencies.
genotypic ratio (1:2:1 ratio) (1) A ratio or set of rel-
ative proportions between organisms with different
genotypes. (2) The ratio of Il4 : Ll2 :1/4 observed
among the homozygous and heterozygous F2 progeny
of a monohybrid cross.
germinalgene therapy Gene therapy aimed at cor-
recting the genetic defect in the germ cells, such that
progeny would not inherit the genetic defect.
germ-line cell See gametes,
Giemsa (G) banding See chromosome banding.
Goldberg-Hogness box See TATA box.
green fluorescent protein (GFP) A gene, derived
from the jellyfish Aequoria victoria, that is the source
of the natural bioluminescence of this species, fluo-
rescing green (a 509-nm wavelength) when illumi-
nated with UV light (a 395-nm wavelength). When
used as a reporter gene, GFP allows a noninvasive
means of visualizing gene and protein expression
patterns in living organisms.
guanine (G) One of four nitrogenous nucleotide
bases in DNA and RNA; one of the two types of
purine nucleotides in DNA and RNA.
guide RNA (gRNA) In RNA editing, the nucleic acid
that directs the addition or removal of nucleotides
from mRNA. Also known as guide strand.
guide strand See guide RN,4.
gynandromorphy A condition in which the body of
an organism is mosaic, appearing to contain both
male and female features.
hairpin structure See stem-loop.
haploid number of chromosomes (n) One-half the
diploid (2n) number. The number of chromosomes
typically found in nuclei of gametes of diploid species.
haploinsufficient A wild-type allele that is unable
to support wild-type function in a heterozygous
genotype. Classified as a recessive wild-type allele.
Compare with haplosfficient.
haplosufficient A wild-type allele that supports
wild- typ e function in hetero zy gous organisms.
Classified as a dominant wild-type allele. Compare
with haploinsfficient.
haplotype The specific array of alleles encoded by
linked genes in a segment of a single chromosome.
Hardy-Weinberg equilibrium The population
genetic principle that in a population practicing ran-
dom mating and in the absence of natural selection,
mutation, migration, or random genetic drift, allele
frequencies are stable at frequencies p + q: 1.0 for
two alleles and are distributed into genotypes at fre-
quencies p2,2pq, and q2.
helicase In DNA replication, the enzyme
responsible for breaking hydrogen bonds between
complementary nucleotides of a DNA duplex.
Unwinding of the strands occurs ahead of the
advancing replication fork.
helix-turn-helix (HTH) motif A DNA-binding pro-
tein domain consisting of two alpha helices: one helix
binds to a specific DNA sequence, and the second
helix stabilizes the interaction.
G LOSSARY G.7
hemizygous Referring to the genotype of males that
carry a single copy of each X-linked gene.
hemoglobin (Hb) A globin protein composed
of four polypeptides (two o-globin and two p-globin)
found in blood that transports oxygen.
heritability See broad sense heritability and narrow
sense heritability,
heterochromatin A chromosome region containing
densely compacted chromatin and few, if any,
expressed genes. See constitutive heterochromatin
and
facultativ
e hetero chro matin. Also known as
hetero chro matic regio n,
heteroduplex DNA A DNA duplex created during
homologous recombination by combining comple-
mentary strands of DNA from nonsister chromatids.
Also known as heteroduplex region.
heteroplasmic cell or organism A cell or organism
that harbors a mixture of alleles of an organellar
gene. Also known as heteroplasmy.
heteroplasmy See heteroplasmic cell or organism.
heterozygous advantage In evolution, the greater
relative fitness of heterozygous organisms compared
to homozygous organisms in a population. May
result in a balanced polymorphism.
Hfr cellAn abbreviation for "high frequency recom-
bination," pertaining to Hfr chromosomes or to Hfr
donors in bacterial conjugation.
Hfr chromosome See Hfr donor.
Hfr donor A donor bacterial strain containing an
F factor integrated into its chromosome. Also known
as Hfr chromosome.
histone acetyltransferase (HAT) Chromatin-
modifying enzyme that adds acetyl groups to speciflc
positively charged amino acids (e.g., lysine) in the
N-terminal tails of histones.
histone deacetylase (HDAC) Chromatin-modifying
enzyme that removes acetyl groups to specific
positively charged amino acids (e.g., lysine) in the
N-terminal tails of histones.
histone demethylase (HDMT) Chromatin-
modifyingeruzyme that removes methyl groups to
specific positively charged amino acids (e.9., lysine)
in the N-terminal tails of histones.
histone methyltransferase (HMT) Chromatin-
modifyingenzyme that adds methyl groups to specific
positively charged amino acids (e.g., lysine) in the
N-terminal tails of histones.
histone proteins (H1, H2A,H2B, H3, H4) Five
proteins encoded by a gene family that form
octameric nucleosomes (H2A,H2B, H3, and H4) and
adhere to DNA to condense chromatin (H1).
Holliday junction A DNA structure that forms dur-
ing meiotic recombination in which single strands
are crossed over between nonsister chromatids of
homologous chromosomes.
Holliday model Proposed originally by Robin
Holliday; a model intended to explain meiotic recom-
bination at a molecular level.
holoenzyme A fully functional multisubunit protein
complex in bacteria, for example, the RNA poly-
merase holoenzyme.
homeobox A conserved sequence of DNA of 180
nucleotides encoding a homeodomain composed of
three a-helices in a family of transcription factors
found throughout eukaryotes; in metazoans some
genes with homeobox genes are homeotic genes.
homeodomain A 60-amino acid DNA-binding
domain.
G-8 GLOSSARY
homeotic
aene
Gene that controls the developmen-
tal fate of a region of the body of an organism;
examples include the Hox genes in metazoans and the
MADS-bozc genes in flowering plants.
homeotic mutation Mutation in which an
apparently normal organ or body part develops in an
inappropriate location.
homologous chromosomes Chromosomes that
synapse (pair) during meiosis. Chromosomes with
the same genes in the same order. Also known as
homologous p air, homologs,
homologous genes Genes descended from a com-
mon ancestral gene. Also known as homologs.
homologous nucleotides Nucleotides descended
from a common ancestral nucleotide.
homologous recombination Exchange of genetic
information between homologous DNA molecules.
homoplasmic cell or organism A cell or organism
in which all copies (alleles) of a cytoplasmic organelle
gene are the same. Also known as homoplasmy.
hotspot of mutation A location within a gene or
genome at which mutations occur much more often
than average.
housekeeping genes Genes that have essential
cellular or physiological functions.
Hox genes Members of the homeobox gene
clusters found throughout metazoans; the genes
often pattern the anterior-posterior axis and are
homeotic genes.
hybrid dysgenesis In Drosophila,thefailure of F1
progeny of P-cytotype males crossed with M-cytotype
females to develop due to the presence of P elements.
hybrid vigor The greater growth, survival, and
fertility of hybrids produced by crossing highly
inbred lines.
hybridization (of molecular probe) In an elec-
trophoresis gel or in gel blotting, the binding of a
single-stranded nucleic acid probe to a single-stranded
target nucleic acid by complementary base pairing.
hydrogen bond Weak electrostatic attraction
formed by the sharing of a positively charged hydro-
gen atom by negatively charged oxygen and nitrogen
atoms. Hydrogen bonds form between complemen-
tary nucleotides to hold nucleic acid strands together.
hypermorphic mutation A mutant whose pheno-
type is similar to, but greater than, the wild-type
phenotype.
hypomorphic mutation See leaky mutation.
identical by descent (lBD) A homozygous genotype
in an organism in which both copies of the allele in
an individual can be traced back to a common
ancestor.
illegitimate recombination Exchange of genetic
information between non-homologous DNA
molecules.
imprinting control region (lCR) Master regulatory
cis-acting DNA sequences to which trans-acting
factors bind to regulate genomic imprinting.
inbreeding Mating between relatives. Also known
as co nsanguineous mating,
inbreeding depression A reduction in vigor,
survival, or reproductive fitness of offspring due to
inbreeding.
incomplete dominance The observation that the
phenotype occurring in heterozygous organisms is
intermediate between the phenotypes of homozy-
gous organisms, but more similar to one homozygous
phenotype than to the other. Also known as partial
dominance.
incomplete genetic linkage The occurrence of
crossing over between linked genes.
incomplete penetrance The occurrence of
individual organisms that have a particular genotype
or allele but not the corresponding phenotype.
induced mutations Mutations generated by
exposure to physical, chemical, or biological mutagens.
inducer An accessory molecule that binds to a pro-
tein that leads to activation of gene expression. The
inducer can bind to a repressor protein and prevent
its function or bind to an activator protein and stim-
ulate its function.
inducer-repressor complex A molecular complex
consisting of a repressor protein and a bound inducer
molecule.
inducible operon Operon that is not expressed
under one set of environmental conditions, but
whose transcription is activated under an alternative
environmental condition (i.e., the lac operon).
induction Process by which one cell or tissue pro-
motes a particular developmental fate in neighboring
cells or tissues.
inductive signal A molecule that acts non-cell
autonomously to influence cell fate; in C, elegans vulval
development, the lin-3 protein secreted from the
anchor cells acts as an inductive signal to influence the
fate of vulval precursor cells.
informational genes Class of genes that encode pro-
tein products that perform informational processes in
the cell such as DNA replication, packaging of chro-
mosomes, transcription, and translation.
ingroup A species within a clade used to compare to
other members of the clade.
inhibition Process by which one cell or tissue pre-
vents a particular developmental fate in neighboring
cells or tissues.
inhibitor An accessory molecule that converts activa-
tor proteins to an inactive conformation by binding to
an allosteric binding domain of the activator protein.
initial committed complex In eukaryotic transcrip-
tion, a partially completed multiprotein complex that
is preparing to bind RNA polymerase II.
initiation complex In eukaryotic translation, the
complex formed by the small ribosomal subunit,
mRNA, and charged IRNA -carrying methionine.
initiation factor (lf
1 4 group of proteins, associated
with ribosomes, that contribute to ribosome assem-
bly and translation initiation.
initiator IRNA The first charged tRNA associated
with the ribosome.
inosine (l) A modified nucleotide found occasionally
in anticodons that can base-pair with uracil, cytosine,
or adenine.
insertional inactivation A process of mutation in
which the insertion of DNA into a gene renders it
nonfunctional.
in situ hybridization A laboratory method for
hybridizing a molecular probe to a DNA sequence or
a gene on an intact chromosome.
insulator sequence Cis-acting sequences that act to
prevent cross-talk between regulatory elements of an
adjacent gene and are located between enhancers and
promoters of genes that are to be insulated from the
effects of the enhancer.
interactive variance (y,) In polygenic and multifac-
torial inheritance, the proportion of total phenotypic
variance that is due to the interactions of genetic and
environmental factors.
interactome The sum of all of the protein-protein
interactions in an organism.
interchromosomal domain Open spaces between
chromosome domains in the interphase nucleus.
interference (l) Measured on a zero to 1.0 scale,
the measurement of the independence of crossovers.
Expressed as 1.0 minus the cofficient of coincidence.
internal control region (lCR) promoter
consensus
sequences of certain rRNA and IRNA genes that
are downstream of the start of transcription
(i.e., sequences that are internal to the transcriptional
region of the gene).
internal promoter element Promoter consensus
sequences of snRNA and tRNA genes that are down-
stream of the start of transcription (i.e., sequences
that are internal to the transcriptional region of
the gene).
interphase The multiphase period of the cell cycle
between cell divisions. See also G, phase, S phase,
and G2 phase.
interrupted mating A technique used to map
bacterial genes that stops conjugation at timed inter-
vals to determine which genes have transferred from
the donor cell to the recipibnt cell.
interspecific comparison Any comparison between
different species. Compare with intraspecffic
comtrtarison.
interstitial deletion The loss of a portion of a chro-
mosome from within one arm.
intragenic recombination Crossing over within
a gene.
intragenic reversion A reversion produced by a
second site mutation within a single gene.
intraspecific comparison Any comparison between
individuals of the same species. Compare with
interspecific comparison.
intrinsic termination In bacterial transcription,
the DNA sequence-dependent mechanism for
tran s cr ip ti o n ter minati o n. Inverted rep eat DNA
sequences induce formation of 3'mRNA stem-loop
(hairpin) structures that are followed by multiple
uracils (transcribed from adenines).
introgression line Lines of experimental organisms
in which genome segments from two or more
other lines are present due to repeated back
crosses between hybrids and organisms of one
parental line.
intron Intervening sequences between the exons
of many eukaryotic genes. Present in DNA and
pre-mRNA, but spliced out during pre-mRNA
processing.
intron self-splicing The capacity of certain RNA
transcripts to undergo self-generated splicing that
does not require splicing enzymes of the splicosome
complex.
intron splicing The spliceosome complex-driven
process that removes introns from eukaryotic
pre-mRNA and ligates exons to form mature mRNA.
inversion heterozygote Organisms whose
homologous chromosomes have different structural
organization. Most commonly, one has normal struc-
ture whereas the homolog carries an inversion.
inversion loop At homologous chromosome synap-
sis in an inversion heterozygote, the structure that
forms by the looping of one chromosome to align
homologous regions.
inverted repeat (lR) sequence Identical or nearly
identical DNA sequences located on the same mole-
cule but with opposite orientations.
lS (insertion sequence) element Mobile DNA
elements in bacteria that cause mutations by
inactivating the expression of genes into which they
insert.
island model In evolutionary genetics, a model
of species evolution in which new species are repro-
ductively isolated from an ancestral population.
isoaccepting IRNA The group of tRNAs that carry
the same amino acid, but recognize synonymous
codons.
ISWI Imitation switch complex that functions pri-
marily to control the placement of nucleosomes into
an arrangement that causes a region to be transcrip-
tionally silent.
joint probability The likelihood of an outcome
requiring the occurrence of two or more
simultaneous or sequential events.
karyokinesis Part of telophase, the process of
nuclear division between daughter cells.
karyotype A digital of analog photograph of chro-
mosomes arranged by conventional chromosome
numbering.
kilobase (kb) A length of nucleic acid containing
1000 nucleotides.
kinetochore The site of attachment of multiple pro-
teins that connects a spindle fiber microtubule to the
centromeric region of a chromosome. Forms during
M phase of cell division.
knockout library Collections of mutants in which
most or all genes of a particular organism have been
mutated by inactivating (or "knocking out") their
expression.
Kozak sequence A specific consensus sequence of
eukaryotic mRNA that contains the authentic start
codon (nue) sequence.
lac- phenotype Bacteria that are not able to grow
on a medium containing lactose as the only sugar.
Compare with lac+ phenotype,
lac+ phenotype Bacteria that are able to grow on a
medium containing lactose as the only sugar.
Compare with lac- phenotype.
lacAgene A gene of the bacterial lac operon;
encodes lac transacetylase. Compare with lacY gene
and lacZ gene.
lactose (Iac) operon An inducible operon consisting
of genes (lacA, lacY,lacZ) encoding enzymes allow-
ing the use of lactose as a carbon source. The operon
is repressed by the lac repressor regulatory protein
that binds to the lac operator sequence, and is acti-
vated by the CAP-cAMP complex that binds to
sequences of the CAP binding site.
lacY gene A gene of the bacterial lac operon;
encodes lac permease, which facilitates import of
lactose into the cell. Compare with lacZ gene and
lacA gene.
lacZ gene A gene of the bacterial lac operon;
encodes
B-galactosidase,
which breaks down lactose
into glucose and galactose. Compare with lacY gene
and lacA gene,
lagging strand In DNA replication, the discontinu-
ously synthesized strand whose Okazaki fragments
are ligated to complete new strand synthesis.
Compare with leading strand,
large ribosomal subunit The larger of two subunits
of the ribosome.
lariat intron structure During intron splicing, the
structure formed by covalent bonding of the 5' gua-
nine of an intron to the branch point adenine of the
intron.
late genes Bacteriophage genes expressed late in the
lytic cycle. Encode protein products required for
packaging of phage particles and lysis of the host cell.
Late promoters and late operators are the regulatory
sequences responsible for late gene activation.
lateral inhibition Process by which one cell or tissue
prevents neighboring cells or tissues from acquiring a
developmental fate similar its own.
law of independent assortment (Mendel's second
law) The random distribution of alleles of unlinked
genes into gametes.
law of segregation (Mendel's first law) The
separation of alleles of a gene during gamete
formation.
leader region Transcribed region upstream of the
major enzyme encoding genes of repressible amino
acid biosynthesis operons (e.9., trpL). Region encodes
a small peptide whose rate of translation reflects the
concentration of the amino acid (e.g., tryptophan)
in the cells and consequently regulates transcription
of the operon.
leader sequence See signal sequence.
leading strand In DNA replication, the continuously
synthesized strand. Compare with lagging strand.
leaky mutation A mutant whose phenotype is simi-
lar to, but less than, the wild-type phenotype.Also
known as hypomorphic mutation,
lethal allele See lethal mutation.
lethal mutation An allele that results in the prema-
ture death of the organisms that carry it. Lethality
most often affects homozygous organisms. Also
known as lethal allele.
linkage disequilibrium The nonrandom distribu-
tion into gametes of alleles of linked genes.
Iinkage equilibrium The random distribution into
gametes of alleles of linked genes achieved by cross-
ing over between the genes.
linkage group A group of genes displaying genetic
linkage.
linker A short, chemically synthesized oligonu-
cleotide that can be ligated to DNA molecules.
linker DNA DNA between nucleosomes in the
10-nm fiber structure of chromatin.
locus control region (LCR) Specialized enhancer
element that regulates the transcription of multiple
genes, often complexes of closely related genes.
lod score (Iog of the odds ratio) Based on analysis
of transmission in pedigrees, the statistic used to
calculate the likelihood of genetic linkage between
genes.
long terminal repeats (LTRs) Arrays of scores
to hundreds of nucleotides that bracket the ends of
retroviruses integrated into host chromosomes.
loss-of-function mutation A mutant that prevents
the production of the wild-type protein or renders it
inactive. Most commonly a recessive mutation.
lysis See lytic cycle,
lysogenic cycle The Iife cycle of a bacterium
infected by a temperate bacteriophage that
integrates into the host chromosome and replicates
along with it.
GLOSSARY G-9
Iysogeny See lysogenic cycle.
lytic cycle The life cycle of a bacterium infected by a
bacteriophage that replicates within the host cell and
lyses the host to release progeny bacteriophage.
M phase The cell division phase of the cell cycle.
Follows interphase.
macroevolution Evolutionary processes operating
at the species level and higher.
MADS-box A conserved sequence of DNA of
168-180 nucleotides encoding a 56-60 amino acid
DNA-binding domain in a family of transcription
factors found throughout eukaryotes; in flowering
plants, some MADS-box genes are homeotic genes.
major gene A gene that has a substantial effect on
phenotypic variation.
major groove The larger of two grooves formed in
the DNA sugar-phosphate backbone by the helical
twist of the double helix and exposing certain
base pairs.
mapping function Corrective calculations used to
more accurately estimate recombination frequencies
between linked genes. Mapping functions differ
among certain species.
map unit (m.u.), centiMorgan (cM) A theoretical
unit of distance between linked genes on a
chromosome.
maternal effect genes Genes that act in the
mother to impart gene products (RNA or protein)
into the egg and subsequently the embryo. For
maternal effect genes, the embryonic phenotype is
determined by the genotype of the mother rather
than that of the embryo.
maternal inheritance Transmission through the
female (ovule or eggcell). Compare with paternal
inheritance: transmission through the male (sperm).
matrix attachment region (MAR) Portions of the
chromosome scaffold to which loops of chromatin
are attached.
mature mRNA The fully processed product of
eukaryotic transcription that moves to the cytoplasm
for translation.
mean (p) The average value of a group of values.
median In a sample distribution, the middle most
values. Also known as median value.
median value See median,
mediator An enhanceosome complex that forms a
bridge between activator proteins bound to enhancer
elements and the basal transcriptional machinery
bound to the promoter.
meiosis The process of cell division occurring in
germ-line cells. Produces four haploid gametes or
spores through two successive nuclear divisions in
diploid species.
meiosis I First nuclear division characterizedby
homologous chromosomes separating. Compare
with meiosis IL
meiosis ll Second nuclear division characterized
by sister chromatids separating. Compare with
meiosis L
Mendelian genetics Referring to genetic applications
and analyses using the law of segregation and the law
of independent assortment originally described
through experiments and analysis by Gregor Mendel.
meristem Organized groups of pluripotent cells at
the growing tips of plants that both generate organs
and self-maintain to ensure that a pool of stem cells
is always present.
G.lO GLOSSARY
messenger RNA (mRNA) A form of RNA
transcribed from a gene and subsequently trans-
lated to produce a polypeptide or protein.
metacentric chromosome A chromosome with a
centrally located centromere that produces long and
short arms of approximately the same length.
metagenome Sequence derived from whole-
genome shotgun sequencing of DNA from entire nat-
ural communities consisting of a range of organisms.
metaphase The stage of M pha.se during which
chromosomes align in the middle of the cell.
metaphase plate The cell midline along which
chromosomes align during metaphase.
microdeletion A small chromosome deletion
detectable only by using molecular methods of
analysis.
microduplication A small chromosome duplication
detectable only by using molecular methods of
analysis.
microevolution Evolutionary changes at the popula-
tion level.
micro RNA (miRNA)
Small (2I-24 nuts) regulatory
RNAs produced by Dicer and acting in a RISC
complex to either repress translational or cleave
target mRNA molecules. Compare with RNA
interference (RNA|).
microsynteny Conservation of the order of a small
number of genes in the same order in related species.
migration A process of evolution referring to the
movement of organisms and genes between popula-
tions. Also known as geneJlow.
minima! initiation complex In eukaryotic tran-
scription, a partially completed multiprotein complex
that is preparing to bind RNA polymerase II.
minor groove The smaller of two grooves formed in
the sugar-phosphate backbone by the helical twist of
the double helix, exposing certain base pairs.
missense mutation A DNA base-pair substitution
that leads to production of a polypeptide in which
one amino acid substitutes for another.
mitochondrion An organelle, bounded by a double
membrane, encoding polypeptides that interact with
nuclear gene polypeptides in oxidative phosphoryla-
tion to generate ATP. In many species, mitochondria
also participate in other metabolic processes and
biochemical reactions, including ion homeostasis
and biosynthetic pathways.
mitosis The process of cell division in somatic cells
that produces genetically identical daughter cells
through a single nuclear division.
mitosome Double-membrane-bound organelles
that are evolutionarily derived from mitochondria
but have lost all of the ancestral genome; proteins
requiring an anaerobic environment to function are
imported into them.
mitotic crossover Crossing over between
homologous chromosomes during mitosis.
modal value See mode.
mode In a sample distribution, the most commonly
occurring value. Also known as modal value.
modern synthesis of evolution Referring to the
broad-based effort beginning in the middle of the
20th century to unite Mendelian genetics with
Darwin's theory of evolution by natural selection.
modifier gene A gene that modifies the effect of a
major gene.
modifier screen A genetic screen designed to iden-
tify mutations in genes that modify, either enhance
or suppress, the phenotypic effects of mutations in
another gene.
molecular cloning The process whereby a single
DNA molecule is selectively cloned from a mixture of
DNA molecules and then amplified to produce a
large number of identical copies.
molecular genetics The subfield of genetics that
studies hereditary transmission, variation, mutation,
and evolution through the analysis of nucleic acids
and proteins.
molecular probe (probe) A single-stranded nucleic
acid or antibody protein labeled with a detectable
marker that attaches to a specific target molecule,
allowing target molecule detection in subsequent
analysis. Single-stranded nucleic acid probes detect
target nucleic acids, and antibody probes bind specific
target proteins.
monohybrid cross A genetic cross between
organisms that are heterozygous for one gene.
monophyletic group A group of organisms with a
single common ancestor.
monosomy The presence of a single chromosome
instead of a homologous pair, resulting in a chromo-
some number that is 2n
-
L.
morphogen Substance whose presence in different
concentrations directs different developmental fates.
multifactorial inheritance The inheritance of traits
whose phenotypic variation is the result of polygenic
inheritance and environmental influences. See also
multifactorial trait,
multifactorial trait. Traits whose phenotypic varia-
tion is the result of polygenic inheritance and envi-
ronmental influences. See also multifactorial
inheritance.
multiple cloning site (MCS) A vector DNA
sequence containing several unique restriction
enzyme target sequences facilitating cloning of
inserted DNA fragments.
multiple gene hypothesis The hypothesis that alle-
les of multiple genes contribute to the production of
certain traits.
multiplication rule See product rule.
multipoint linkage analysis A statistical method
for testing and mapping alternative orders of multiple
genes linked on a chromosome. Related to lod score
analysis.
mutagen A chemical, physical, or biological agent
capable of damaging DNA and creating a mutation.
mutagenesis A procedure whereby a population of
organisms is mutagenized and their progeny are
propagated and examined for mutant specific pheno-
types.See also genetic screen.
mutation An inherited change in DNA.
mutation frequency The rate at which mutations
occur per gene per unit of time. Most often
expressed per gene per generation.
mutation-selection balance An arithmetic
expression used to determine the equilibrium fre-
quencies of alleles in populations as a result of allele
elimination by natural selection and new allele cre-
ation by mutation.
narrow sense heritability (h2) The proportion of
total phenotypic variance that is contributed by addi-
tive genetic variance.
natural selection The evolutionary process
operating through differences in survival, fecundity,
and relative fitness of organisms with different geno-
types and phenotypes.
negative assortative mating A pattern of preferen-
tial mating based on differences between the mating
individuals.
negative contro! (of transcription) Condition
where binding of a repressor protein to a regulatory
DNA sequence prevents transcription of a gene or a
cluster of genes.
negative interference Occurring when the
cofficient of coincidence is greater than 1.0, the
observation of more double crossovers than expected
between a pair of genes.
negative supercoiling Twisting of the DNA duplex
in the direction opposite to the turns of the double
helix.
neofunctionalization The process, following gene
duplication, whereby a mutation in one of the dupli-
cates provides a function not performed by the
original gene.
neomorphic mutation A mutant expressing a new
or novel function not seen in the wild type.
N-formylmethionine (fMeU
tRNAfMet) A modified
methionine amino acid usually used as the amino
acid that initiates bacterial translation. Carried by a
specialized tRNA.
node An evolutionary branch point in a
phylogenetic tree.
non-autonomous transposable element A trans-
posable genetic element lacking a transposase gene
and incapable of initiating transposition.
nondisjunction The failure of homolog or sister
chromatid separation during cell division. Results in
nuclei with the wrong number of chromosomes.
nonhistone proteins Numerous nuclear proteins
that are not histones associated with chromosomes.
non-homologous end joining (NHEJ) An error-
prone mechanism of double-stranded DNA break
repair in eukaryotic genomes in which damaged
nucleotides are removed and blunt ends of strands
are joined.
noninducible Condition in which transcription of
bacterial genes or operons cannot be activated.
nonparental ditype (NPD) In an ascus, the
occurrence of four haploid spores that are each
recombinant.
nonpenetrant An organism with a genotype corre-
sponding to a mutant phenotype that instead displays
the wild-type phenotype.
nonrecombinant vector Produced in a cloning
experiment when the intended vector does not pick
up a DNA insert.
nonrevertible mutants Mutations caused by partial
deletion of DNA nucleotides that cannot be reverted
to wild type.
nonsense mutation A type of point mutation pro-
ducing a stop codon in mRNA.
nonsister chromatid A chromatid belonging to a
homologous chromosome. Nonsister chromatids of
homologs are involved in crossing over.
non-template strand See coding strand.
normal distribution The continuous distribution of
outcomes predicted by chance. Also known as
G aussian distribution,
northern blotting A method for transferring
mRNA from an electrophoresis gel to a permanent
membrane or filter.
north-south (NS) resolution One possible pattern
for resolving a Holliday junction to separate homolo-
gous chromosomes before meiotic anaphase.
nuclear mitochondria! sequence (NUMTS)
Mitochondrial DNA sequences found in the nucleus
as a result of recent transfer from the mitochondrial
genome to the nuclear genome.
nuclear plastid sequence (NUPTS) Plastid DNA
sequences found in the nucleus as a result of recent
transfer from the plastid genome to the nuclear
genome.
nucleoid The region of bacterial and archaeal cells
(or mitochondria or chloroplasts) where the main
chromosome resides.
nucleolus (plural: nucleoli) Nuclear organelle con-
taining rRNA-encoding genes.
nucleomorph In a secondary endosymbiosis, the
nuclear genome of the secondary endosymbiont.
nucleosome An octameric protein complex com-
posed of two polypeptides each of histones H2A, H2B,
H3, and H4, around which DNA wraps in chromatin.
nucleosome-depleted region (NDR) A 100- to
150-bp region containing few nucleosomes, which lies
immediately upstream of the start of transcription.
nucleotide excision repair A mechanism of DNA
damage repair in which a segment of one strand con-
taining damaged nucleotides is excised and replaced.
null mutation A mutant that produces no func-
tional product. Most commonly a recessive allele.
Also known as amorphic mutation.
Okazakifragment A short segment of newly
synthesized DNA that is part of a lagging strand and
is ligated to other Okazaki fragments to complete
lagging strand synthesis.
oncogene A mutated form of a proto-oncogene;
frequently associated with cancer development.
one gene-one enzyme hypothesis Proposed by
George Beadle and Edward Tatum in 1941, the
hypothesis proposing that each gene encodes a spe-
cific protein product and controls a distinct function.
open chromatin Chromatin in which the associa-
tion of DNA with nucleosomes is relaxed in regions
containing regulatory sequences, allowing access by
regulatory proteins and giving genes in open chro-
matin the potential to be transcriptionally active.
open promoter Promoters that reside in open chro-
matin, resulting in constitutive transcription. See also
open promoter complex,
open promoter complex At transcription initiation,
the stage at which RNA polymerase is bound and a
short region of DNA opens to allow transcription
from the template strand. See also open promoter.
operationalgenes Class of genes that encode
proteins involved in cellular metabolic processes
(e.g., amino acid biosynthesis, biosynthesis of
cofactors, fatty acid and phospholipid biosynthesis,
intermediary metabolism, energy metabolism,
nucleotide biosynthesis).
operator Regulatory DNA sequences to which
repressor or activator proteins bind. Term used in
bacterial systems.
operon A set of adjacent genes that are transcribed in
a polycistronic mRNA and are thus coordinately regu-
lated; an operon is generally considered to include
associated regulatory sequences (e.g., promoter, opera-
tor, etc.). Primarily found in bacteria and archaea.
ordered ascus The linear sequence in an ascus of
haploid spores whose arrangement allows determina-
tion of the chromatids participating in crossing over.
organizer Groups of cells that possess the ability to
influence the fates of cells in the surrounding tissues
via non-autonomous signals.
origin of migration The starting point of nucleic
acid or protein migration in gel electrophoresis.
origin of replication The specific sequence at which
DNA replication begins.
origin of transfer (oriT) The site within the fertility
(F) factor sequence where transfer to the recipient
cell is initiated.
orthologous genes Genes in different species
whose origin lies in a speciation event and that can
be traced to a single gene in a common ancestor of
the two species. Also known as orthologs,
orthologs See orthologous genes.
outgroup A species related to members of a
clade but outside the clade; used to root
the clade.
P element A specific type of transposable genetic
element prevalent in the Drosophila genome.
Pvalue (probability value) In the chi square
test, the likelihood that a repeat experiment will
produce a result as deviant or more deviant than
expected in comparison to the experimental result
being tested.
paired-end sequencing Sequence generated from
both ends of a DNA clone; provides evidence of
physical linkage of the two paired sequences.
pair-rule genes In Drosophila, genes that delimit
parasegments along the anterior-posterior axis;
examples include even-skipped and odd-skipped,
paracentric inversion A chromosome inversion in
which the inverted segment does not include the
region of the centromere.
paralogous genes Genes whose origin lies in a gene
duplication event within an extant or ancestral
species. Also known as paralogs.
paralogs See paralogous genes.
paraphyletic group A group of organisms which
includes some but not all the members descended
from a common ancestor.
parasegment In Drosophila, the posterior part of
one segment and the anterior part of its neighbor.
The stripes of gene expression of pair-rule genes cor-
respond to parasegments, straddling the boundaries
between segments.
parental (nonrecombinant) chromosome
Chromosomes in gametes produced when crossing
over does not take place between linked genes.
Alleles marking each gene are retained in their initial
(parental) configurations.
parental ditype (PD) In an ascus, the occurrence of
four haploid spores that are each nonrecombinant.
parental generation (P generation) The parents of
F1 progeny. In controlled genetic crosses, the parents
are pure-breeding.
parental strand The DNA strand acting as a tem-
plate to direct the synthesis of a new ("daughter")
strand of DNA.
partial chromosome deletion The loss of a seg-
ment of a chromosome.
partial deletion heterozygote An organism with
one wild-type chromosome and a homolog that is
missing a segment.
partial diploid An exconjugant bacterium that
acquires a second copy of one or more genes by
conjugation with an F'donor cell.
partial dominance See incomplete dominance.
partial duplication The duplication of a segment of
a chromosome.
GLOSSARY G-l 1
part:al duplication heterozygote An organism
with one wild-type chromosome and a homologous
chromosome with a duplicated segment.
particle gun bombardment Technique of using
high pressure to fire microscopic particles coated
with DNA into plant cells. The particles are propelled
with enough force to penetrate the cell wall and
plasma membrane.
particulate inheritance Mendel's theory that
genetic information is transmitted from one genera-
tion to the next as discrete units or elements of
heredity.
Pascal's triangle A diagram listing the coefficients
of a given binomial expansion in which the binomial
expression is expanded n number of times.
PCR primers In polymerase chain reaction, short
single-stranded segments of nucleic acid that bind
template DNA and serve as primers from which
DNA polymerase begins strand synthesis.
pedigree A family tree composed of standard
symbols that depicts relationships in successive
generations and often displays individual
phenotypes.
penetrant Expression of the phenotype corre-
sponding to a particular genotype.
peptide bond A typ. of covalent bond that joins
amino acids in polypeptide chains. Formed between
the amino end of one amino acid and the carboxyl
end of the adjoining amino acid.
peptide fingerprint analysis A form of chromatog-
raphy in which polypeptide fragments are separated
and distinctive patterns revealed.
peptidyl site (P site) The site on the ribosome
where amino acids are joined by a peptide bond.
pericentric inversion A chromosome inversion in
which the inverted segment includes the region of
the centromere.
permissive condition Environmental condition in
which environmentally sensitive (e.9., temperature
sensitive) mutants exhibit the wild-type phenotype
or can survive.
phenocopy A phenotype similar to a phenotype
caused by mutation but that is produced instead by
an environmental condition.
phenotype (1) The observable physical
characteristics or traits of an organism. (2) The physi-
cal manifestation of a specific genotype.
phenotypic ratio (3:1 ratio and 9:3:3:1 ratio)
A ratio or set of relative proportions between
organisms with different phenotypes-e.g., The ratio
of progeny produced by a monohybrid cross (3:1) or a
dihybrid cross (9:3:3:1).
phenotypic variance (t/r) The total variance
observed for a trait.
phosphodiester bond A type of covalent bond
formed between two nucleotides in a nucleic acid
strain. Formed between the 5'phosphate group of
one nucleotide and the 3'OH of the adjacent
nucleotide.
photoproduct A characteristic DNA lesion pro-
duced by exposure to ultraviolet light.
photoreactive repair A mechanism of DNA
damage repair in bacteria that uses visible light
energy to remove the damage done by ultraviolet
irradiation.
phylogenetic footprinting Technique whereby
conserved sequences are identified by searching for
similar sequences in species separated by large evolu-
tionary distances.
G-12 G LOSSARY
phylogenetic shadowing Technique whereby con-
served sequences are identified by first eliminating
sequences that are not conserved in closely related
species.
phylogenetic tree A diagram of evolutionary
relationships among organisms or genes based on
morphological or molecular characteristics.
phylogenomics Method for determining phyloge-
netic relationships of organisms using genomic
DNA sequence information. See also evolutionary
genomics.
physicalgap Sequence gap between scaffolds for
which there is no clone to supply the sequence.
plasmid One of multiple types of extrachromosomal
circular DNA molecules that may be found in bacte-
rial cells.
plastid Organelle, bounded by a double membrane,
descended from the cyanobacterial endosymbiont;
specialized types of plastids include chloroplasts and
chromoplasts.
pleiotropy A single gene mutation that affects
multiple and seemingly unconnected properties of an
organism.
pluripotent State of a cell when it can give rise to
many but not all cell types of an organism.
point mutation A DNA lesion at a defined location.
Usually either a base pair substitution, or the inser-
tion or deletion of one or a small number of base pairs
polyacrylamide A synthetic compound mixed with
buffer and used to form electrophoresis gels.
polyadenylation signal sequence A hexanucleo-
tide sequence of mRNA, usually AAUAAA, that iden-
tifies the location of 3'pre-mRNA cleavage and
polyadenylation.
polycistronic mRNA In bacteria, an mRNA contain-
ing the transcripts of two or more genes.
polygenic inheritance A quantitative trait
dependent on the contributions of multiple genes.
Also known as polygenic trait.
polygenic trait See polygenic inheritance.
polymerase chain reaction (PCR) A laboratory
method for controlled replication of a specific target
sequence of DNA in successive cycles. Using two
short single-stranded primers that bind to sequences
on opposite sides of the target sequence, exponential
replication of the target sequence occurs.
polypeptide A chain of amino acids joined by
peptide bonds. Formed at ribosomes during
translation.
polyploidy The presence of more than two com-
plete sets of chromosomes in a genome. See also
allop olyploidy, autopolyploidy.
polyribosome In translation, the simultaneous
translational activity of multiple ribosomes on a
single mRNA.
population A group of organisms that mate with
one another to establish the next generation.
population genetics The subfield of genetics that
studies the genetic structure and evolution of
populations.
positional cloning The process by which the DNA
sequence of a gene identified only by mutant pheno-
type can be obtained by using genetic and physical
maps. Also known as chromosome walking,
positional information Process by which gene
expression, or other chemical cues, establish geo-
graphical addresses along the axes of a developing
embryo or organ primordium.
position effect variegation (PEV) The observation
in Drosophila of a specific type of mutation produc-
ing variegation of eye color due to the abnormal
positioning of the w (white) gene for eye color.
positive assortative mating A pattern of preferen-
tial mating based on similarity between the mating
individuals.
positive control (of transcription) Condition where
binding of an activator protein to a regulatory DNA
sequence stimulates transcription of a gene or a clus-
ter of genes.
positive-negative selection The use of both nega-
tive and positive selectable markers to follow the fate
of introduced DNA to select for homologous recom-
bination events.
positive supercoiling Superhelical twisting of DNA.
post-translational polypeptide processing In
eukaryotes, modifications to polypeptides in the
endoplasmic reticulum and Golgi apparatus after the
completion of translation.
postzygotic isolation mechanism Mechanisms
operating after mating to reduce or prevent the
possibility of producing hybrids between populations
or species.
precursor microRNA (pre-miRNA) The stem loop
product derived from processing of pri-microRNAs.
The pre-microRNA stem loop is further processed
by Dicer to produce the mature single stranded
microRNA from the double stranded region of the
stem loop.
precursor mRNA (pre-mRNA) The initial transcript
of a eukaryotic gene requiring mRNA processing
prior to translation.
preinitiation complex In eukaryotic transcription, a
large multiprotein complex containing several gen-
eral transcription factors and RNA polymerase II.
prezygotic isolation mechanism Mechanisms
operating before mating to reduce or prevent the
possibility of producing hybrids between populations
or species.
Pribnow box (-10 consensus sequence) A specific
consensus sequence component of the bacterial
promoter with a location centered at approximately
-10
relative to the start of transcription.
primary microRNA (pri-miRNA) The primary tran-
script, with single stranded ends and a stem loop,
from which pre-microRNAs are derived by process-
ing. The single stranded ends of the pri-microRNA
are removed, by Drosha in animals and Dicer in
plants, to produce the pre-microRNA.
primase The specialized RNA polymerase that
synthesizes the RNA primer during DNA
replication.
primer annealing In PCR, the binding by
complementary base pairing of a short single-
stranded primer by complementary base pairing.
primer extension In PCR, the synthesis of DNA by
DNA polymerase beginning at the 3'end of a short
single-stranded primer.
primer walking Technique for sequencing long
DNA molecules where new sequencing primers are
synthesized based on successive DNA sequence
reads. Compare with shotgun sequencing.
primosome In DNA replication, a multisubunit
protein complex whose central component is primase.
product rule The probabiliW of an event requiring
the sequential or simultaneous occurrence of two or
more contributing events. The probabilities of con-
tributing events are multiplied and their product
is the event in question. Also known as the
multiplication rule.
proliferating cell nuclear antigen (PCNA) In
eukaryotic DNA replication, the functional equiva,
lent of the bacterial sliding clamp that adheres DNA
polymerase to the template strand and drives its
progression.
prometaphase In M phase of the cell cycle, some-
times identified as a stage between prophase and
metaphase.
promoter A regulatory sequence of DNA near the 5'
end of a gene that acts as the binding location of
RNA polymerase and directs RNA polymerase to the
start of transcription.
promoter mutation A mutation altering promoter
sequence and function.
promoter-specific element A specific promoter
consensus sequence located upstream of small
nuclear RNA genes.
prophage The designation for bacteriophage that
has integrated into the host bacterial chromosome.
prophase The stage of M phase during which
chromosome condensation occurs.
protein A string of amino acids encoded during
translation of mRNA and linked together by peptide
bonds. See also polypeptide.
protein sorting In eukaryotes, the process using the
polypeptide leader sequence to designate the desti-
nation of polypeptides.
proteome Set of the proteins in a cell, tissue, or
organism.
proteomics The study of all the proteins, collec-
tively known as the proteome, within a cell, tissue, or
organism.
proto-oncogene A broad category of normal genes
p ro duc ing protein whose gener alize d functions
promote cell proliferation. It is often mutated in
carcinogenesis.
pseudoautosomal region (PAR) Homologous
regions on the X and Y chromosomes that synapse
and cross over.
pseudodominance The phenotypic expression of a
recessive allele on one chromosome due to deletion
of a portion of the homologous chromosome con-
taining the dominant allele.
pseudogene Sequences recognizable as mutated
gene sequences often derived from gene duplication
or retrotransposition events.
Punnett square Named in honor of early
20th-century geneticist Reginald Punnett, a checker-
board-like diagram that predicts the genotypes
and genotype frequencies of progeny from a
genetic cross.
pure'breeding A group of genetically identical
homozygous organisms that, when self-fertilized or
intercrossed, only produce offspring that have a
phenotype identical to the parents. Also known as
true-breeding.
pyrimidine dimer The specific type of lesion
formed on DNA due to exposure to ultraviolet irradi-
ation. Also known as thymine dimer.
QTL locus analysis A method for characterizing the
effects of quantitative trait loci on variation.
QTL mapping A method for locating quantitative
trait loci in a genome.
quantitative genetics The subfield of genetics that
studies quantitative traits.
quantitative trait A trait exhibiting polygenic
inheritance and displaying continuous phenotypic
variation.
quantitative trait locus (QTL) A gene contributing
to the phenotypic variation of a quantitative trait.
R (resistance) plasmid A type of bacterial plasmid
conferring resistance to one or more antibiotic
compounds.
radial loop-scaffold model A model of chromatin
structure that predicts rosettes of looped chromatin
on a chromosome scaffold.
random X-inactivation (Lyon hypothesis)
Proposed by Mary Lyon in the mid-2Oth century,
the process of randomly inactivating one copy of the
X chromosome in each mammalian female nucleus
early in zygotic development.
reading frame The partitioning of sequential sets of
mRNA trinucleotide segments (codons) that are used
in translation to determine amino acid order of a
polypeptide.
realizator genes In Drosophila, the Hox target
genes whose expression contributes to the character-
istic morphology of each segment.
recessive epistasis (9:3:4 ratio) A characteristic
ratio of phenotypes produced by the interaction of
two genes that control a trait in which alleles of one
gene mask or reduce the expression of alleles of a
second gene.
recessive phenotype The phenotype observed in
an organism that is homozygous for the recessive
allele. Compare with dominant phenotype.
recipient cell (F-cell) A bacterial cell that does not
contain fertility factor DNA sequence and can conju-
gate with a donor bacterium.
reciprocal cross Paired crosses involving distinct
parental phenotypes in which the sexes are switched
(i.e., if one cross is d phenotype A X
?
phenotype B,
the reciprocal cross is d
phenotype B X
?
pheno-
type A).
reciprocal translocation (balanced, unbalanced)
Exchange of chromosome segments between non-
homologous chromosomes. If all genes are present,
the translocation is "balancedi' but if genes are miss-
ing, the translocation is "unbalancedl'
recombinant (nonparental) ch romosome
Chromosomes in gametes produced by crossing
over between linked genes. Alleles marking
each gene are rearranged on chromatids by
crossing over.
recombinant clone A combination of DNA mole-
cules from different sources (e.9., vector and insert
DNA), that are joined together using recombinant
DNA technology.
recombinant DNA technology The set of labora-
tory techniques developed for amplifying, maintain-
ing, and manipulating specific DNA sequences in
vitro as well as in vivo.
recombination frequency (r) The rate of occur-
rence of recombination between a pair of linked
genes. Expressed as the number of recombinants
divided by the total number of meioses.
recombination nodule Protein aggregations along
the synaptonemal complex that are thought to play a
role in crossing over.
recombination repair A DNA repair mechanism
that reestablishes normal DNA molecules by
exchanging a damaged strand segment for a normal
strand segment from another chromatid.
reference genome sequence The DNA sequence of
the individual or individuals used to construct the
initial complete genome sequence.
regulated transciption Condition in which gene
expression is controlled at the transcriptional level in
response to changing environmental conditions.
regulatory mutation A mutation altering a regu-
lated attribute of gene expression.
relative fitness (w) In evolutionary genetics, the
measurement of the reproductive fitnesses of organ-
isms in a population relative to one another. The
organism class with greatest fltness has a relative
fitness of w-L.0.
release factor (RF) Molecules that bind mRNA stop
codons and contribute to translation termination.
replicate cross Repeated crosses involving parents
with the same genotypes and phenotypes.
replication bubble A region of active bidirectional
DNA replication containing replication forks on each
end, an origin of replication in the middle, and lead-
ing and lagging strands in each half of the bubble.
replication fork In DNA replication, the site of the
replisome structure, and the site of synthesis of leading
strand and lagging strand DNA.
replicative segregation Random segregation of
organelles during cell division.
replicative transposition Transposition carried out
by replicating a copy of a transposable element and
inserting the copy in a new genome location.
replisome The large molecular machine located at
the replication fork that coordinates multiple reaction
steps during DNA replication.
reporter gene A gene whose expression is easy to
assay phenotypically. Fusion of reporter genes with
heterologous sequences allows both transcriptional
and translational expression patterns to be
visualized.
repressible operon Operon that is expressed under
one set of environmental conditions, but whose tran-
scription is repressed under an alternative environ-
mental condition (i.e., the trp operon).
repressor protein A transcription factor that binds
to regulatory sequences associated with a gene and
represses that gene's expression.
reproductive isolation The absence of interbreed-
ing between populations or species; often involves
geographic, physical, or behavioral mechanisms or
conditions.
response to selection (R) The amount of change
in the phenotype of a trait between parental and
offspring generations as a result of selection on the
parents.
restriction endonuclease One of a large number of
DNA-digesting enzymes, usually of bacterial origin,
that cut DNA at specific recognition sites called
restriction sequences. Each enzyme has its own
particular restriction sequence and generates double-
stranded cleavage of DNA at the restriction se-
quence. Also known as restriction enzyme.
restriction length polymorphism fragment A
fragment of DNA generated by treatment with a
restriction endonuclease.
restriction map A map showing the numbers and
relative positions of target sites for restriction
enzymes of a DNA molecule.
restriction sequence The specific base-pair
sequence recognized by a particular restriction
endonuclease.
GLOSSARY G-l3
restriction-modification system System of a
restriction enzyme with a specific recognition
sequence and a modifyingenzyme that adds methyl
groups to bases of the recognition sequence. The
system protects the bacteria's own DNA from being
digested by endogenous restriction enzymes, but
allows restriction of invading exogenous DNA.
restrictive condition Environmental condition in
which environmentally sensitive (e.9., temperature
sensitive) mutants exhibit the mutant phenotype.
retrotransposon A transposable element that uses
reverse transcriptase to transpose through an RNA
intermediate.
reverse genetic analysis (reverse genetics) Genetic
analysis that begins with a gene sequence, which is
used to identify or introduce mutant alleles and sub-
sequently to identify and evaluate the resulting mu-
tant phenotype. It is the complementary approach to
forward genetics.
reverse mutation rate (r4 The rate at which mutant
alleles are reverted to wild-type alleles. Also known
as reversion rate.
reverse transcriptase Enzyme, derived from
retroviruses or retrotransposons, that catalyzes the
synthesis of a DNA strand (cDNA) from an RNA
template.
reverse transcription The process of DNA
synthesis from an RNA template by the enzyme
reverse transcriptase.
reverse translation The process of using the genetic
code to deduce the possible DNA sequences encod-
ing a specific amino acid sequence.
reversion mutation A mutation that alters a mu-
tant to wild-type sequence and function. Also known
as reversion.
revertible mutant A point mutation caused
by base-pair substitution or deletion of one or a few
base pairs that can be reverted to wild type.
rho-dependent termination
(Rho protein) The
process of bacterial transcription termination involv-
ing rho protein.
rho utilization site (rut site) The site of attachment
of rho protein that aids in rho-protein-driven
bacterial transcription termination.
ribonucleic acid (RNA) A family of polynucleotides
that are transcribed from DNA. RNAs are composed
of nucleotides containing the sugar ribose, one or
more phosphate atoms and one of four nitrogenous
bases (A, G, C, and U).
ribonucleotides Composed of ribose, one or more
phosphate groups, and one of four nitrogenous bases,
the nucleotides that make up RNA. See a\so adenine
(A), uracil (U), guanine (G), and cytosine (C).
ribose The S-carbon sugar molecule in
ribonucleotides.
ribosomal RNA (rRNA) A group of RNA molecules
that compose part of the structure of ribosomes.
ribosome Ribonucleoprotein particles, composed of
rRNAs and numerous proteins, at which translation
takes place.
ribozymes Catalytically active RNAs.
RNA editing The process of post-transcriptional
addition or removal of nucleotide of certain mRNAs.
RNA interference
(RNAi) A regulatory gene-silenc-
ing mechanism based on double-stranded RNA,
which can target complementary sequences for inac-
tivation. The machinery can be harnessed to silence
gene expression in a reverse genetic approach.
G-,14 G LOSSARY
RNA polymerase The enzyme that catalyzes
the synthesis of RNA. See also RN,4 pol, RNA pol I,
RN,4 pol II, and RNA pol III.
RNA polymerase I (RNA pol l) In eukaryotic
transcription, the enzyme that transcribes certain
rRNA genes.
RNA polymerase ll (RNA pol ll) In eukaryotic tran-
scription, the enzyme that transcribes protein-coding
genes to produce mRNA.
RNA polymerase lll (RNA pol lll) In eukaryotic tran-
scription, the enzyme that transcribes tRNA genes.
RNA primer In DNA replication, the short, single-
stranded RNA segment synthesized by primase. The
3' end of the RNA primer is used by DNA poly-
merase to begin synthesis of DNA.
RNA-induced silencing complex (RISC) Complex
containing Argonaute protein that binds small RNA
molecules and targets complementary RNA mole-
cules for degradation or translational repression.
RNA-induced transcription-silencing (RITS)
complex RISC-like complex that mediates small
RNA-induced transcriptional gene silencing.
Robertsonian translocation The fusion of two non-
homologous chromosomes, often with the deletion
of a small amount of nonessential genetic material.
Also known as chromosomefusion.
rolling circle replication A unidirectional mode of
DNA replication used to replicate circular plasmid
molecules in which the replicating circular molecule
appears to reel off its nontemplate DNA strand, using
the other as the template for replication.
S phase The middle phase of interphase, during
which DNA replication takes place.
Sanger method See dideoxy DNA sequencing.
saturation mutagenesis Mutagenesis aimed at
identifying multiple mutant alleles for all loci in the
genome of an experimental organism.
scaffold A set of contigs that are physically linked.
scanning In eukaryotic translation, the process used
by the small ribosomal subunit to locate the authen-
tic start codon.
secondary endosymbiosis (tertiary symbiosis)
Endosymbiotic event where one eukaryotic, usually
photosynthetic, is an endosymbiont within another
eukaryote resulting in an organism with genomes
derived from at least two nuclear genomes and
multiple organellar genomes.
second-division segregation Patterns of haploid
spores in an ascus that indicate the alleles were
separated at the second meiotic division as a result of
crossing over between a gene and the centromere.
second-site reversion A specific type of reversion
taking place at a location separate from the site
altered to generate the original mutation.
segment Division of the body along the anterior-
posterior axis into a series of morphological
similar units.
segment polarity genes ln Drosophila, genes that
delimit the anterior and posterior regions of individ-
ual parasegments along the anterior-posterior axis;
examples include wingless, engrailed, hedgehog, and
gooseberry.
selected marker screen An experimental method
used to detect microorganisms with a specific
genotype.
selection coefficient (s) The value of the
reduction in reproductive fitness for an organism
(i.e., w: 1.0
-
s).
selection differential (5) The difference between
the population mean value for a phenotype and the
phenotype value of population members selected as
parents for the next generation.
selective growth medium The growth medium
used in a selective marker screen.
semiconservative replication The established
method of DNA replication in which each strand of
a parental duplex acts as a template for daughter
strand synthesis, and each daughter duplex is com-
posed of one parental strand and a complementary
daughter strand.
semisterility Reduced fertility, commonly the result
of the occurrence of adjacent segregation during
meiosis in b alanced transloc ation heter ozy gotes.
sequence gap Gap between two contigs for which a
clone is available for further sequencing that could
close the gap.
sex chromosome Homologous chromosomes that
differ between the sexes. Designated X and Y in
species in which females are XX and males XY.
DesignatedZ and'W in species in which females are
Z'W and males are ZZ.
sex determination The genetically controlled
processes that determine the sex of offspring.
sex-influenced trait A gene, usually autosomal,
whose expression differs between males and
females of a species. Also known as sex-influenced
expression.
sex-limited trait A gene or trait expressed
exclusively in one sex. Also known as sex-limited gene.
sex-linked inheritance The inheritance of genes on
the sex chromosomes.
shared derived characteristics Characteristics
or traits of organisms that evolve from more
ancestral characteristics or traits found in ancestral
organisms.
Shine-Dalgarno sequence In bacterial translation,
the 5'UTR mRNA consensus sequence that pairs
with nucleotides near the 3' end of 165 rRNA in the
small ribosomal subunit to orient the start codon on
the ribosome.
shotgun sequencing Method for sequencing large
molecules of DNA that relies on redundant sequenc-
ing of fragmented target DNA in the hope that all
regions will be sequenced at least a few times.
Contrast with primer walking.
shuttle vector A vector that can replicate in two
species and thus can be used to shuttle DNA
sequences between them.
sickle cell disease (SCD) A human autosomal
recessive disorder resulting from homozygosity; a
specific mutant allele (0t) of the
B-globin
gene that is
part of hemoglobin protein.
sigma (o) subunit Accessory protein that changes
the promoter-recognition specificity of the bacterial
RNA polymerase core enzyme.
signal hypothesis The accepted hypothesis propos-
ing that the polypeptide leader sequence identify post-
translational processing and transport.
signal sequence A string of amino acids at the N
terminal and of certain eukaryotic polypeptides
containing information directing post-translational
processing and the extracellular destination of the
polypeptide. Also known as leader sequence,
signal-transduction pathway Pathways through
which cells receive external messages at cell surface
receptors and transmit the messages into the cell to
initiate action or response.
silencer A eukaryotic cis-acting DNA regulatory
sequence to which trans-acting factors bind to
repress transcription.
silencer sequence Regulatory DNA sequences that
can repress transcription of specific genes that may
be located distantly from the sequence. Also known
as silencers.
silent mutation A base substitution mutation that
changes one codon to a synonymous codon and does
not alter the amino acid sequence of a polypeptide.
simple transposon In bacterial transposition, a
transposon containing multiple genes between two
inverted repeats.
single nucleotide polymorphism (SNp) A single
base-pair difference in a specific genome location
detected by comparing individual DNA sequences.
single-stranded binding (SSB) protein In DNA
replication, a protein that adheres to each template
strand following unwinding by helicase to prevent
strand reannealing before the arrival of the
replication fork.
sister chromatid cohesion The protein-based tem-
porary attachment of sister chromatids facilitated by
cohesin protein that resists the pulling forces of spin-
dle fibers in metaphase.
site-directed mutagenesis Introduction of specific
nucleotide changes in a DNA molecule in vitro.
site-specific recombination An exchange between
two DNA molecules that requires specific sequences
in common and that is catalyzed by an enzyme spe-
cific to that recombination (e.g., integration of phage
lambda into the E. coli genome).
sliding clamp In bacterial DNA replication, the
multisubunit protein complex that joins with DNA
polymerase to hold polymerase on the template and
helps drive polymerase along the template.
small interfering RNA (siRNA)
Single-stranded
2L- to 24-nucleotide RNA molecules derived from
either endogenous or exogenous double-stranded
RNA molecules that are incorporated in RISC to
mediate RNAi. Endogenously produced siRNAs are
most often from non-genic regions (e.g., repetitive
RNA or products of an RNA-dependent RNA poly-
merase). Exogenously produced siRNAs are often
derived from invading nucleic acids (e.g., transposons
and viruses).
small nuclear RNA (snRNA)
Regularory RNAs oper-
ating in the nucleus.
small nucleoid-associated proteins In bacterial
DNA, small proteins localized to the nucleoid and
associated with the main chromosome.
small ribosomal subunit The smaller of two sub-
units of the ribosome.
solenoid structure See 30-nmfi,ber.
somatic cell A body cell. All cells of a multicellular
organism excepting those of the germ line.
somatic gene therapy Gene therapy aimed at
correcting a genetic defect in the somatic cells.
Southern blotting A laboratory method devised by
Edwin Southern for transferring DNA from an elec-
trophoresis gel to a permanent membrane or filter.
specialized transduction (specialized transducing
phage) Transduction from a donor cell to a
recipient cell of a few select genes located near the
site of bacteriophage integration.
spindle fiber microtubule (kinetochore, polar, and
astral microtubule) Composed of tubulin proteins,
the fibers emanating from centrosomes that attach to
kinetochore regions (kinetochore), overlap to control
cell shape (polar), or attach to the cell membrane to
stabilize centrosomes (astral).
spliceosome The multiprotein complex that carries
out intron splicing.
splicing mutation A mutation altering the normal
splicing pattern of a pre-mRNA.
spontaneous mutation Mutations occurring due to
spontaneous events or changes involving nucleotides
or nucleotide bases.
square root method A method for estimating allele
frequencies based on manipulation of the frequency
of a homozygous genotype.
5R proteins Proteins rich in serine (S) and arginine
(R); SR proteins are operative in intron splicing.
SRY The sex-determining region of Y gene that initi-
ates male sex development in mammals.
stabilizing selection A pattern of natural or
artificial selection that reduces population variation
by removing organisms with extreme phenotypes.
standard deviation (o) A statistical value that mea-
sures the scatter of outcome values around the mean
or average outcome value. Expressed as the square
root of the sum of squared deviations of each value
from the mean value.
start codon Most commonly AuG, encoding
methionine, the first codon translated in polypeptide
synthesis.
start of transcription The DNA location at which
transcription begins.
stem-loop Short double-stranded segments of RNA
topped by a single-stranded loop containing unpaired
nucleotides. Also known as a hairpin structure,
sticky end Short single-stranded overhangs created
by the cleavage of DNA by specific restriction
endonucleases, which can potentially base-pair with
complementary single-stranded sequences.
stop codon One of three codons that bind a release
factor instead of base-pairing with tRNA to initiate a
series of events that stops translation.
strand invasion During synthesis-dependent strand
annealing and meiotic recombination, the entry of
the 3' end of a displaced DNA into the intact sister
chromatid.
strand polarity (5' and 3') The orientation of a
nucleic acid strand indicating its 5'phosphate and
3'hydroxyl ends.
strand slippage During DNA replication, a muta-
tional event leading to increased or decreased num-
bers of repeating nucleotides in newly synthesized
DNA and caused by slippage of DNA polymerase on
the template strand or slippage of the newly synthe-
sized strand on DNA polymerase.
structural genomics The sequencing of whole
genomes and the catalogin1t ot annotation, of
sequences within a given genome.
structural maintenance of chromosomes
(SMC) A
category of bacterial proteins localized to the nu-
cleoid and associated with the main chromosome.
structural motif The characteristic three dimen-
sional structure of a protein, sometimes obtained
from crystal structure data.
Su(var) mutations Mutations that suppress position
effect variegatio n in D ro s o phil a. Mutated genes
produce proteins that are active in chromatin
remodeling.
subcloning Process by which DNA clones are
further subdivided in order to clone still smaller
fragments for analyses.
subfunctionalization The process, following gene
duplication, whereby mutations in each of the two
copies can result in the two genes having comple-
mentary activities such that their combined activity
is the same as the activity of the gene before
duplication.
submetacentric chromosome A chromosome
with a centromere located near the midpoint that
produces long and short arms of different lengths.
sugar-phosphate backbone The alternating sugar
(deoxyribose or ribose) and phosphate molecule
pattern of nucleic acid strands formed by the forma-
tion of phosphodiester bonds linking nucleotides in
the strand.
sum rule The probability of an event that can result
from two or more equivalent outcomes. The proba-
bilities of the contributing events are added, and their
sum is the probability of the event in question. Also
known as the addition rule,
supercoiled DNA The superhelical twisting of
covalently closed circular DNA. See positive
sup erco iling and negativ e sup erco iling.
suppressor screen A modifier genetic screen
designed to identify mutations in genes that
suppress the phenotypic effects of mutations in
another gene.
SWI/SNF (switch/sucrose nonfermentable) A yeast
chromatin-remodeling complex that modulates
nucleosome positioning in an ATP-dependent
manner.
SWR1 (switch remodeling 1) A chromatin-
remodeling complex responsible for replacing the
common histone 2A protein of nucleosomes with a
variant form known as H2AZ.
sympatric speciation An evolutionary process
in which new species form in overlapping regions.
Reproductive isolation mechanisms accompanying
speciation are usually behavioral or mechanical.
synapsis The close approach and contact between
homologous chromosomes during early prophase I in
meiosis.
synaptonemal complex A specialized three-layer
protein complex, consisting of a central element and
two lateral elements, that forms between homologous
chromosomes at synapsis.
syncitium A multinucleated cell in which the nuclei
are not separated by cell membranes.
syncytial blastoderm Stage of Drosophila
embryogenesis in which the nuclei are located at the
periphery of the embryo but are not separated by cell
membranes.
synonymous codon The groups of codons that
specify the same amino acid.
syntenic genes Genes located on the same
chromosome.
synteny The conserved order ofgenes together on
a chromosome in species that share a common
ancestor.
synthesis-dependent strand annealing (SDSA)
An error-free mechanism for repair of DNA double-
strand breaks occurring after the completion of DNA
replication and utilizing strand invasion to provide
wild-type sequences for repair.
synthetic lethality The situation where a particular
double mutant results in lethality but the two
respective single mutants are viable.
systems biology Prediction of biological functions
of genes based on correlations between different
data sets.
GLOSSARY G.I5
T strand The DNA strand of the T-DNA cleaved to
initiate the transfer of plasmid DNA during rolling
circle replication.
targeted induced local lesions in genomes
(TILLING) A reverse genetic approach in which a
population of organisms of an inbred strain is ran-
domly mutagenized throughout the genome, and this
population is then screened to find mutations in a
gene of interest for which the sequence is known.
TATA-binding protein (TBP) A general transcription
factor protein that binds the TATA box and assists in
binding other transcription factors and RNA
Poly-
merase II to promoters.
TATA box The thymine- and adenine-rich consensus
sequence region found in most eukaryotic promoters.
Also known as Goldberg-Hogness box.
TBP-associated factors (TAF) Specific general tran-
scription factors that associate with TATA-binding
protein.
telocentric chromosome A chromosome with
a centromere located at one end, producing a long
arm only.
telomerase The ribonucleoprotein complex whose
RNA component provides a template used to synthe-
size repeating DNA segments that form chromosome
telomeres.
telomere Repeating DNA sequences, synthesizedby
telomerase, at the ends of linear chromosomes in eu-
karyotes; contain dozens to hundreds of copies of
specific short DNA sequence repeats that buffer the
coding sequence of the chromosome from loss dur-
ing successive cycles of DNA replication.
telophase The last stage of M phase, inwhich the
nuclear contents are divide d (karyokinesis) and the
daughter cells are divided (cytokinesis).
temperate phage A bacteriophage, such as i phage,
that can integrate into the bacterial host chromo-
some and produce either the lytic or lysogenic
life cycle.
temperature-sensitive allele A mutation evident
only at or above a certain temperature due to an
abnormality of the protein product that affects its
stability.
template strand The DNA strand serving as a
template for synthesis of a complementary nucleic
acid strand.
terminal deletion The loss of a chromosome seg-
ment that includes the telomeric region.
termination sequence DNA sequences that serve
to stop transcription. Also known as transcription
termination.
termination stem loop Stem loop of an mRNA
transcript that signals RNA polymerase to terminate
transcription in the leader region of bacterial
attenuator-controlled operons (e.g., trp opeton).
test cross The cross of an organism with the domi-
nant phenotype that may be hetetozygous with an
organism that is homozygous for a recessive allele.
Also known as test-cross analYsis.
tetrad An ascus containing four haploid spores.
tetrad analysis The analysis of genetic linkage by
analysis of different tetrad segregation types.
tetratype
(TT) In an ascus, the occurrence of both
types of parentals and both types of recombinants
among the spores.
third-base wobble The flexibility of purine-
pyrimidine base pairing between the third base of
a codon and the corresponding nucleotide of the
anticodon.
G-l6 GLOSSARY
three-point test-cross analysis A test cross
designed to identify genetic linkage between three
genes and to provide data for determination of
recombination frequency between linked genes.
three-strand double crossover The occurrence
of double crossover involving three of the four
chromatids.
threshold of genetic liability In polygenic and
multifactorial inheritance, a trait with different
phenotypes (i.e., affected and unaffected) that are
determined by whether individual organisms
are above or below a particular critical value on the
phenotypic scale. Also known as threshold trait.
threshold trait See threshold of genetic liability.
thymine (T) One of four nitrogenous nucleotide
bases in DNA; one of the two types of pyrimidine
nucleotides in DNA.
thymine dimer See pyrimidine dimer,
tiling array DNA array that contains all sequences of
the genome or a genomic interval, including introns,
exons, untranslated regions (UTRs), and intergenic
regions.
time-of-entry mapping A method of donor gene
mapping by conjugation that uses interrupted mating
to determine the order and relative timing of gene
transfer.
Ti plasmid A large (200 kb) circular plasmid of
Agrobacterium tumefaciens that harbors genes for
transfer of DNA into plants cells and genes that cause
uncontrolled division of plant cells; hence, the
tumor-inducing (Ti) plasmid. It has been engineered
for the construction of transgenic plants.
topoisomerases Enzyme that relaxes DNA
supercoiling by controlled strand nicking and
rejoining.
totipotency State of a cell when it can give rise to
any and all cell
Wpes
of an organism.
trans-acting Acting between two molecules
(e.g., DNA sequences that control expression
of genes interacting with a diffusible protein
product).
trans-acting regulatory protein Proteins that act in
trans by binding to cis-acting regulatory sequences
and consequently regulating nearby genes, either by
activating or repressing transcription. Often referred
to as transcriptionfactors,
transcription The cellular process that synthesizes
RNA strands from a DNA template strand.
transcription factors (TFs) Proteins that bind
promoters and are functional in transcription.
transcription-terminating factor I (TTFI) A specific
protein that binds a termination sequence to stop
transcription.
transcription termination See termination
sequence.
transcriptome Set of transcripts present in a cel[,
tissue, or organism.
transcriptomics The study of all the transcripts, col-
lectively known as the transcriptome, within a cell,
tissue, or organism.
transductant The bacterium that is the product of
transduction.
transduction In bacterial systems, the process of
transfer of DNA from a donor bacterial cell to a re-
cipient cell using a bacteriophage as a vector. More
generally can refer to the process by which foreign
DNA is introduced into another cell via a viral
vector.
transfer DNA (T-DNA) The portion of the Ti plasmid
that is transferred from the bacterium into the
nucleus of a plant cell.
transfer RNA (IRNA) A family of small RNA mole-
cules that each bind a specific amino acid and convey
it to the ribosome, where the anticodon sequence
undertakes complementary base pairing with an
mRNA codon during translation.
transformant The bacterium that is the product of
transformation.
transformation 1) The bacterial process of gene
transfer in which donated DNA fragments originat-
ing in a dead donor cell, or plasmid DNA, is taken up
across the cell wall and membrane of a recipient cell
and recombined into the transformant genome.
2) More generally refers to the process by which ex-
ogenous DNA is directly taken up by a cell resulting
in a genetic alteration of the cell. 3) The conversion
of animal cells to an abnormal unregulated state by
an oncogenic virus or by transforming DNA.
transgene A gene that has been modified in vitro by
recombinant DNA technology and introduced into the
genome via transformation.
transgenic organism An organism harboring a
transgene.
transition mutation A type of DNA base-pair sub-
stitution in which one purine replaces the other or
one pyrimidine replaces the other.
translation The process taking place at ribosomes to
synthesize polypeptides. Complementary base pairing
between mRNA codons and IRNA anticodons deter-
mines the order of amino acids composing the
polypeptide.
translation repressor protein In bacteria, proteins
that regulate translation by binding mRNA in the
vicinity of the Shine-Dalgarno sequence and thereby
prevent ribosome binding.
translesion DNA synthesis Utilizing a bypass poly-
merase, a mechanism for replicating DNA in the
presence of damage that blocks replication by the
common polymerase.
translocation heterozygote An organism with
chromosome translocation in which chromosome
pairs consist of one normal chromosome and a
homolog carrying a translocation.
transmission genetics The subfield of genetics con-
cerned with assessment and analysis of gene transfer
from parents to offspring. Synonymous with
Mendelian genetics,
transposable genetic element A class of DNA
sequences that can move from one chromosome
location to another, either by excision and
reinsertion or by replication and reinsertion of the
replicated copy.
transposition The process by which mobile genetic
elements move from one portion of a genome to
another. See also transposable genetic element.
transposon tagging Technique used to identify and
clone genes through insertion of a transposon into
the target gene.
transversion mutation A typ. of DNA base substi-
tution mutation in which a purine substitutes for a
pyrimidine, or vice versa.
tree of life The phylogenetic tree depicting the
evolutionary relationships between organisms.
trihybrid cross A genetic cross between organisms
that are heterozygous for three genes.
trinucleotide repeat disorder A hereditary
disorder caused by a mutant gene containing an
increased number of repeats of a DNA trinucleotide
sequence.
trisomy The presence in a genome of three copies
of a chromosome rather than a homologous pair of
chromosomes, and resulting in a number of
chromosomes that is 2n
-
l.
trisomy rescue In a trisomic genome, the random
loss of one extra chromosome to reduce the chromo-
some number to the diploid.
trivalent synaptic structure The specific synaptic
arrangement of three homologous chromosomes in a
trisomic genome.
true-breeding See pure-breeding.
true reversion A type of reversion that exactly
reverses the original mutation.
tumor suppressor gene A broad category of
normal genes whose generalized functions slow,
pause, or stop cell proliferation. It is often mutated in
carcinogenesis.
two-hybrid system A method for discovering
whether two proteins interact using the GAL4 pro-
tein of yeast, which is separated into a DNA-binding
domain and a transcriptional activation domain. The
two GAL4 domains are fused with the two proteins
of interest respectively, and the resultant fusion pro-
teins are assayed for their ability to activate transcrip-
tion, which indicates interaction of the two proteins
of interest.
two-point test-cross analysis A test cross designed
to identify genetic linkage between two genes and to
provide data for determination of recombination
frequency between linked genes.
two-strand double crossover The occurrence of a
double crossover involving trvo of the four chromatids.
ultraviolet (UV) repair A multiprotein DNA
damage repair system that corrects lesions caused by
exposure to ultraviolet irradiation.
uncharged tRNA A tRNA not carrying an
amino acid.
unequal crossover Resulting from the improper
synaptic pairing of homologous chromosomes and
crossing over between the mispaired chromosomes.
A source of duplication and deletion of genetic material.
uniparental disomy In a genome, the presence of a
pair of homologous chromosomes that originate
from a single parent.
uniparental inheritance Condition in organellar
inheritance whereby just one parental gamete-
often the maternal gamete-contributes all of the
cytoplasmic organelles.
unordered tetrad Haploid spores in an ascus that
are arranged in random order.
unpaired loop At synapsis involving partial deletion
or partial duplication of one chromosome of a
homologous pair, the "extra" genetic material that
does not have a homolog on the paired chromosome.
unselected marker screen An experimental
technique used to screen microbial genotypes.
Commonly used following selected marker screening.
unstable mutant phenotype A mutation with an
unusually high frequency of reversion.
upstream Referring to a gene or sequence
location that is toward the 5' direction of a coding
strand.
upstream activator sequence (UAS) An enhancer-
like sequence in yeast, located just upstream of the
genes they regulate.
upstream control element An upstream consensus
sequence found in certain eukaryotic gene
promoters.
uracil (U) One of four nitrogenous nucleotide bases
in RNA; one of the two types of pyrimidine
nucleotides in RNA.
variable expressivity Variation in the degree,
magnitude, or intensity of expression of a
phenotype.
variance (S2) A statistical measurement of
the variation of sample values around the
mean value.
vector A DNA fragment with attributes that will
allow its amplification (origin of replication) in a bio-
logical system and serves as a carrier for foreign
DNA inserted into it. Vectors usually also possess
genes (e.g., encoding resistance to an antibiotic) that
allow selection of hosts carrying the vector.
western blotting A method for transferring protein
from an electrophoresis gel to a permanent mem-
brane or filter.
whole-genome shotgun
(WGS) sequencing An
approach to genome sequencing whereby DNA
representing the entire genome is fragmented into
smaller pieces, and a large number of fragments
are chosen at random and sequenced with the
aim that all genomic regions will be sequenced
multiple times. Compare with clone-by-clone
sequencing.
whole-genome tiling array A microarray on
which sequences representing the entire genome are
present.
X/autosome ratio (X/A ratio) The ratio of X chro-
mosomes to a pair of autosomes. Used in Drosophila
as the mechanism of sex determination.
X-linked dominant A pattern of inheritance consis-
tent with the transmission of a dominant allele of a
gene on the X chromosome. Compare with X-linked
recessive.
X-linked inheritance The pattern of inheritance
characteristic of genes located on the X chromosome.
X-linked recessive A pattern of inheritance consis-
tent with the transmission of a recessive allele of a
GLOSSARY G.17
gene on the X chromosome. Compare with X-linked
dominant.
yeast artificial chromosome
(YAC) Cloning vector
used in yeast that utilizes an endogenous yeast origin
of replication, centromere, and telomere; can accept
DNA inserts in excess of 1 megabase.
Y-linked inheritance The exclusively male-to-male
transmission of genes on the Y chromosome.
2,,'"* The most likely recombination distance (theta
[0]
value) between genes as determined by lod score
analysis.
zone of polarizingactivity (ZPA) The posterior side
of the limb bud that acts as an organizer, secreting
Sonic hedgehog (Shh) protein that acts to pattern the
developing limb.
ZfiN system The sex chromosome inheritance
system in species in which the male is homogametic
(ZZ) and the female is heterogametic (ZW).
zygotic genes Genes that are active only in the
zygote or embryo. For zygotic genes, the genotype of
the embryo determines the phenotype.