Glossary

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Glossary

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3' (3-prime)

A term that identifies one end of a single-stranded nucleic acid molecule. The 3' end is that end of the molecule which terminates in a 3' phosphate group. The 3' direction is the direction toward the 3' end. Nucleic acid sequences are written with the 5' end to the left and the 3' end to the right, in reference to the direction of DNA synthesis during replication (from 5' to 3'), RNA synthesis during transcription (from 5' to 3'), and the reading of mRNA sequence (from 5' to 3') during translation.

For more detail, please see the entries on nucleosides and nucleic acids at Wikipedia.

See also:

5' (5-prime)
central dogma

3' UTR

3' Untranslated Region. That portion of an mRNA from the 3' end to the position of the last codon used in translation.

For more detail, please see the entry on mRNA at Wikipedia.

See also:

3' (3-prime)
central dogma

5' UTR

5' Untranslated Region. That portion of an mRNA from the 5' end to the position of the first codon used in translation.

For more detail, please see the entry on mRNA at Wikipedia.

See also:

amino acid
carboxy-terminal
central dogma

anaphase

That part of M phase (either mitosis or meiosis) of the cell cycle when condensed chromosomes aligned at the metaphase plate separate and progress toward opposite poles of the spindle apparatus.

aneuploid

Not euploid.

asexual reproduction

Any method of producing offspring that does not involve the production of gametes. In eukaryotes, asexual reproduction is accomplished through mitosis.

backcross

A type of genetic cross in which a hybrid is crossed to one of the two parental strains.

See also:

incross
intercross
outcross
testcross

base

One of a set of nitrogenous compounds attached to the sugar-phosphate backbone in a nucleic acid. In DNA, the purine bases are adenine (A) and guanine (G), while the pyrimidine bases are cytosine (C) and thymine (T). In RNA, the purine bases are adenine (A) and guanine (G), while the pyrimidine bases are cytosine (C) and uracil (U). Although formally incorrect (the nitrogenous base that gives each nucleotide its name is only part of the nucleotide), this is often used as a synonym for nucleotide.

For more detail, please see the entries on nucleosides and nucleic acids at Wikipedia.

base pair (base pairing)

The hydrogen bonding of one of the bases (A, C, G, T, U) with another, as dictated by the optimization of hydrogen bond formation in DNA (A-T and C-G) or in RNA (A-U and C-G). Two polynucleotide strands, or regions thereof, in which all the nucleotides form such base pairs are said to be complementary. In achieving complementarity, each strand of DNA can serve as a template for synthesis of its partner strand.

For more detail, please see the entries on nucleosides and nucleic acids at Wikipedia.

bivalent

A set of replicated, paired homologous chromosomes in prophase or metaphase of meiosis I.

Please see the figure at Scitable.

C-terminal

Refers to the end of a protein that contains the carboxylic group -COOH, corresponding to the 3' end of the encoding gene. Also called carboxy-terminal.

For more detail, please see the entry on protein at Wikipedia.

See also:

amino acid
amino-terminal
central dogma

carboxy-terminal

Refers to the end of a protein that contains the carboxylic group -COOH, corresponding to the 3' end of the encoding gene. Also called C-terminal.

For more detail, please see the entry on protein at Wikipedia.

See also:

amino acid
amino-terminal
central dogma

cDNA

"Complementary DNA," a double-stranded DNA molecule prepared in vitro by copying an RNA molecule back into DNA using reverse transcriptase. The RNA component of the resulting RNA-DNA hybrid is then destroyed by alkali, and the complementary strand to the remaining DNA strand synthesized by DNA polymerase. The resulting double-stranded DNA can be used for cloning and analysis.

CDS

Coding sequence, the part of the DNA sequence of a gene that is translated into protein.

For more detail, please see the entry on mRNA at Wikipedia.

Please see the visual guide to terms associated with parts of a typical eukaryotic gene, below.

cell cycle

The cycle of alternating interphase and M phase (either mitosis or meiosis) during the growth and division of cells.

central dogma

The principal statement of the molecular basis of inheritance. In its simplest form:

"DNA makes RNA makes protein."

This means that (generally) genetic information is stored in and transmitted as DNA. Genes are expressed by being copied as RNA ( transcription), which in eukaryotes is processed into mRNA via splicing and polyadenylation. The information in mRNA is translated into a protein sequence using a genetic code to interpret three-base codons as instructions to add one of twenty amino acids or to stop translation.

For more detail, please see the entry on genetic code at Wikipedia.

centriole

Cylindrical structures made of microtubules, found in pairs in the centrosome.

centrosome

The microtubule organizing center of animal cells that organizes the spindle_apparatus. It contains two centrioles.

chiasma (plural: chiasmata)

The cytologically observable consequence of meiotic recombination between homologous chromosomes during meiotic prophase. Sister chromatid cohesion holds sister chromatids together as bivalents progress toward metaphase I. Sites of crossing over (reciprocal recombination) appear as X-shaped points of exchange that hold the bivalent together during metaphase I orientation. The sites of exchange resemble the Greek letter Chi (Χ), hence the name.

Please see the figure at Scitable.

chromatid

One of the two copies of a replicated chromosome that is ready to enter M phase of the cell cycle. The two identical chromatids are also referred to as sister chromatids.

chromatin

The nuclear material that makes up chromosomes, consisting of DNA and protein.

See also:

euchromatin
heterochromatin

chromosome

1. In eukaryotes, one of the "colored bodies" into which the nuclear material resolves itself during mitosis and meiosis.

2. One molecule of double-stranded DNA, carrying an arrangements of genes interspersed with other sequences. In prokaryotes the chromosome is often a circle of DNA, while in eukaryotes chromosomes are typically linear, extending from one end, a telomere, through the centromere to the other telomere.

coding exon

In a gene, any exon that contains some part of the CDS; in contrast, an exon that has no part translated into protein is called a "non-coding exon."

Please see the visual guide to terms associated with parts of a typical eukaryotic gene, below.

codominant

One of a series of terms applied to the phenotypic effect of a particular allele in reference to another allele (usually the standard wild-type allele) with respect to a given trait. An allele "a" is said to be codominant with respect to the allele "A" if the A/a heterozygote fully expresses both of the phenotypes associated with the A/A and a/a homozygotes. An example of codominance is the ABO blood type antigens in humans, where AA individuals are type A, BB individuals are type B, and AB individuals are type AB.

See also:

dominant
recessive
semidominant

codon

The sequence of three nucleotides in DNA or RNA that specifies a particular amino acid. For more detail, please see the entry on genetic code at Wikipedia.

complement

The nucleotide sequence of the nucleic acid strand that would form a double-stranded molecule with the nucleic acid strand in question, using standard base-pairing rules.

compound heterozygosity

The state of being heterozygous for two different variant alleles, each different from the wild-type allele.

compound heterozygote

An individual that is heterozygous for two different variant alleles, each different from the wild-type allele.

coupling

In linkage analysis, the presence of two specified alleles (typically the recessive alleles) on the same chromosome, with the other two alleles on the homolog.

cross

An experimental mating of two genetically distinct sexually reproducing organisms.

See also:

backcross
incross
intercross
outcross
testcross

cross-fertilization

Producing offspring from crosses in which the two gamete types come from the different individuals, typically from different pure-breeding lines.

crossing over

The precise breakage and reunion of non-sister chromatids belonging to homologous chromosomes during meiotic prophase, leading to the formation of chiasmata. Crossovers are observable as reciprocal recombination events in genetic experiments, leading to the formation of nonparental genotypes among progeny.

database

A data structure that stores metadata, i.e. data about data. More generally, an organized collection of information.

degenerate sequence

A sequence in which one symbol can represent multiple possibilities. The genetic code is said to be degenerate because most amino acids are encoded by multiple codons. For more detail, please see the entry on genetic code at Wikipedia.

In DNA sequence a degenerate code allows for a single symbol to designate more than one possible base, e.g. B stands for C, G or T.

deletion

The removal of some part of a nucleic acid or protein sequence.

dihybrid

A type of cross in which individuals from two different true-breeding lines differing with respect to two traits are crossed. The hybrids from this cross may be further used for an intercross or testcross.

diploid

Having two copies of each homologous chromosome. The two homologous chromosomes are typically derived from separate parents, and may carry different alleles of the same gene.

DNA

Deoxyribonucleic acid. The nucleic acid of which genes are made. For more detail, please see the entry on DNA at Wikipedia.

See also:

central dogma
nucleic acid
RNA

DNA Gyrase

An enzyme necessary for DNA replication that relieves the supercoiling introduced by unwinding the DNA double helix; it is a special form of topoisomerase.

DNA Helicase

An enzyme necessary for DNA replication that unwinds the DNA double helix at the replication fork.

DNA Ligase

An enzyme necessary for DNA replication that repairs missing phosphodiester bonds, resulting in the joining of Okazaki fragments.

DNA Polymerase

An enzyme necessary for DNA replication that synthesizes a new DNA strand on the template strand, adding nucleotides in the 5' to 3' direction. There is also a 3' to 5' exonuclease activity for proofreading and error correction.

DNA replication

The process of producing two DNA molecules from one. During replication, the two strands of the parent helix separate and DNA Polymerase synthesizes a new, complementary strand for each parental strand, following the rules of base pairing (A-T and G-C).

For more detail, please see the entry on DNA replication at Wikipedia.

dominant

One of a series of terms applied to the phenotypic effect of a particular allele in reference to another allele (usually the standard wild-type allele) with respect to a given trait. An allele "A" is said to be dominant with respect to the allele "a" if the A/A homozygote and the A/a heterozygote are phenotypically identical and different from the a/a homozygote. For example, in humans, the wild-type allele of the gene encoding tyrosinase is dominant to the recessive variant allele that causes albinism.

See also:

codominant
recessive
semidominant

donor site

Splicing donor site. The boundary between an intron and the exon immediately upstream (i.e. on the 5' side of the intron).

For more information, please see the entry on mRNA splicing at Wikipedia.

downstream

Toward the 3' end of a single stranded DNA molecule or gene of interest. "Upstream" similarly refers to something closer to the 5' end.

duplication

1. A class of chromosome rearrangement in which a chromosomal segment is present elsewhere in the genome in addition to the original location.

2. A second copy of a sequence in a genome. A duplicate copy of a gene may be mutated without affecting the viability of the organism, so gene duplication is thought to be a significant factor in the evolution of genomic diversity.

electrophoresis

A procedure to separate molecules in an electric field. DNA migration takes place through a gel matrix (agarose or polyacrylamide) that acts as a molecular sieve. Since DNA is negatively charged, when placed in an electric field, it is attracted toward the positive electrode. Because the negative charges are uniformly distributed along the DNA, molecules separate in the field based on their sizes.

endonuclease

An enzyme that cleaves phosphodiester bonds within a nucleic acid chain. A particular endonuclease may be specific for RNA or for single-stranded or double-stranded DNA. Restriction enzymes are endonucleases that cut double-stranded DNA at or near a specific target sequence, such as CGCG.

enhancer

A eukaryotic DNA sequence located outside of the promoter region, where an activator of transcription ( protein) may bind.

enzyme

Enzymes are proteins that serve as biological catalysts. Only proteins were once thought to be enzymes; now, catalytic RNAs called ribozymes are known.

epistasis

Masking of a phenotypic trait through the action of a mutant allele. For example, albinism (absence of pigment) is epistatic to coat color genes that determine black vs. brown fur in mice.

equational division

The second division of meiosis, because, like mitosis, it produces cells that have the same number of chromosomes as the parent cell.

euchromatin

Those regions of the genome that do not remain condensed throughout the cell cycle. Euchromatic regions are typically enriched for genes, show significantly higher levels of recombination and lower levels of repeats than heterochromatic regions.

See also:

chromatin
heterochromatin

eukaryote

The class of organisms composed of one or more cells, each of which contains a membrane-enclosed nucleus and packages its DNA with histones in a nucleosome array. Eukaryotic cells typically have other complex organelles, such as mitochondria.

euploid

Having a chromosome number that is an integral multiple of the haploid number without segmental duplications or deletions.

exon

An exon is a contiguous segment of eukaryotic DNA that corresponds to a portion of the mature (processed) RNA product of that gene. Exons are found only in eukaryotic genomes, and are separated by introns. Although the introns are transcribed with the exons, the latter are spliced out and discarded during RNA processing.

Please see the visual guide to terms associated with parts of a typical eukaryotic gene, below.

exonuclease

An enzyme that cleave nucleotides one at a time from the end of a polynucleotide chain. A particular exonuclease may be specific for either the 5' or 3' end of either DNA or RNA. The 3'-to-5' exonuclease activity of DNA pol I and DNA pol III allows these enzymes to excise the nucleotide that they just added if it base pairs incorrectly ("editing").

expressivity

The relative constancy of the phenotype of individuals of a given genotype. Mutations said to have variable expressivity show a relatively large amount of phenotypic variation among individuals having the same genotype.
See also penetrance.

F₁ generation

The "first filial" generation resulting from the cross of two different true-breeding lines.

F₂ generation

The "second filial" generation resulting from the cross of individuals from the F₁ generation to each other.

fertilization

The union of gametes during sexual reproduction.

First Law (Principle of Segregation)

The First Law of Mendelism is that the two different alleles of a gene separate into different gametes during sexual reproduction.

frame

A frame is a single series of adjacent nucleotide triplets in DNA or RNA: one frame would have bases at positions 1, 4, 7, etc. as the first base of sequential codons. There are 3 possible reading frames in an mRNA strand and six in a double stranded DNA molecule due to the two strands from which transcription is possible. Different computer programs number these frames differently, particularly for frames of the negative strand, so care should be taken when comparing designated frames from different programs.

G₀

For cells that will not proceed through cell division, that part of interphase of the cell cycle that immediately follows M phase. Cells that will not proceed through another division are said to be in G₀ indefinitely.

G₁

For cells that will proceed through cell division, that part of interphase of the cell cycle that immediately follows M phase, prior to S phase.

G₂

That part of interphase of the cell cycle that immediately follows S phase, prior to M phase.

gamete

A specialized cell that functions in sexual reproduction. Sexually reproducing animals produce sperm and eggs as gametes; plants produce pollen and eggs. Gametes produced by diploid organisms are haploid.

gene

The basic unit of heredity; a portion of DNA (in most organisms) or RNA (in some viruses) that usually encodes a protein product.

See also:

chromatin
euchromatin

heterozygosity

The state of being heterozygous.

heterozygote

An individual that is heterozygous.

heterozygous

The state of a diploid locus in which different alleles are present at each copy of that locus.

histone

The small, basic proteins used to package the DNA in chromatin in eukaryotes. The core histones (H2A, H2B, H3, and H4) are highly conserved throughout all eucharyotes, while histone H1 is more variable.

homologous

1. The two copies of each chromosome in a diploid cell (one originating from each parent) are said to be homologous even though they might have allelic differences from each other.

2. Nucleic acid and protein sequences are homologous if they have evolved from a common ancestor.

Please see the figure showing homology.

homolog (also homologue)

A specific member of a group of homologous sequences or molecules.

Please see the figure showing homology.

homology

Homology is the state of being homologous. Algorithms such as BLAST identify similarity that is evidence for, but not necessarily proof of, homology.

Please see the figure showing homology.

homozygosity

The state of being homozygous.

homozygote

An individual that is homozygous.

homozygous

The state of a diploid locus in which identical alleles are present at both copies of that locus.

hybridization

The process whereby complementary single strands of DNA come together to form a double helix. If one strand is labeled, it can be used to identify the second, unlabeled strand. For example, in filter hybridization, the labeled probe will hybridize to the unlabeled complementary DNA that is stuck to the filter.

hydrogen bond

A noncovalent bond between an electronegative atom (such as N or O) and a hydrogen atom covalently bonded to another electronegative atom. Hydrogen bonds are individually weak, but collectively contribute significantly to the stabilization of the DNA double helix. The pairing required to form optimal hydrogen bonds between DNA nucleotides underlies the principle of complimentarity.

hypostasis

Masking of a phenotypic trait through the action of a mutant allele. For example, coat color genes that determine black vs. brown fur in mice are hypostatic to albinism (absence of pigment).

imprinting

A phenomenon resulting in differential expression of a gene or group of genes depending on whether they were derived from maternal or paternal transmission.

in-frame

Referring to something (e.g., a deletion) that does not alter the coding frame of a gene.

in situ hybridization

A technique performed by denaturing the DNA of cells or tissue sections and adding a single-stranded DNA probe. The probe is labeled so that the site of hybridization can be detected by autoradiography or other appropriate detection protocols.

in vitro

Performed in the absence of intact cells; "in vitro" literally means "in glass."

See also:

backcross
intercross
outcross
testcross

incomplete dominance

One of a series of terms applied to the phenotypic effect of a particular allele in reference to another allele (usually the standard wild-type allele) with respect to a given trait. An allele "A" is said to show incomplete dominance with respect to the allele "a" if the A/A homozygote has a mutant phenotype, the A/a heterozygote has a less severe phenotype, while the a/a homozygote is wild type. An example is a variant allele of the profillaggrin gene in humans: heterozygotes for the variant allele have the skin disease ichthyosis vulgaris, while homozygotes for the variant allele have a more severe form of ichthyosis vulgaris, and homozygotes for the wild-type allele are unaffected.

See also:

codominant
dominant
semidominant
recessive

indel

Shorthand term to designate a gap in an alignment that designates "either an insertion or deletion." Typically used when the historical event that created the difference between two sequences cannot be determined.

independent

Two events are said to be independent if the probability of one event is not influenced by the outcome of the other event. For example, when a coin is tossed, the probability of heads is always 0.5, regardless of outcome of prior trials. If two coins are tossed at the same time, they do not influence each other.

induced mutation

A change in a DNA sequence caused by exposure of the DNA to a mutagen.

initiation

The process in which DNA or RNA polymerase binds to a DNA strand to begin copying it.

initiation codon

The first codon of a coding sequence. In eukaryotes this is almost always ATG, which codes for methionine.

initiator

A weak consensus sequence [PyPyAN(T/A)PyPyPy] in eukaryotes, found with the A at position +1 of the gene, that serves as a recognition sequence for RNA polymerase II.

insertion

The addition of DNA within a given sequence; this may occur as a result of duplication or insertion of foreign sequences such as transposable elements or viral DNA.

intercross

A cross between two identically hybrid individuals (A/a X A/a).

See also:

backcross
incross
outcross
testcross

interphase

That part of the cell cycle that is not M phase ( mitosis or meiosis). In dividing cells, interphase consists of G₁, S phase, and G₂; cells that are no longer preparing to divide are said to be in G₀.

intron

Non-coding sections of a eukaryotic nucleic acid sequence found between exons. Introns are removed ("spliced out") of mRNA after transcription and before the molecule is exported to the cytoplasm for translation.

See also:

amino acid
carboxy-terminal
central dogma

non-coding RNA

An RNA molecule that functions without being translated into protein for example, transfer RNA and ribosomal RNA; note that this is not the same thing as the "non-coding strand."

nondisjunction

The failure of chromosome segregation. In meiosis, nondisjunction at meiosis I results in one cell with both members of a pair of homologous chromosomes and one cell lacking that chromosome. In meiosis II or mitosis, nondisjunction results in one cell with both copies of one chromosome and one cell lacking that chromosome. Nondisjunction during meiosis produces aneuploid gametes.

nucleic acid

DNA or RNA. Each of these compounds consists of a backbone of sugar molecules ribose for RNA and deoxyribose for DNA linked by single phosphate groups. Attached to the sugars of the backbone are any of four nitrogenous bases, A, T, C or G for DNA and A, U, C or G for RNA.

For more detail, please see the entry on nucleic acids at Wikipedia.

nuclear envelope

The membrane surrounding the nucleus.

nucleoside

A small molecule made up of either a purine or pyrimidine base linked to a pentose (sugar), generally either ribose or deoxyribose.

For more detail, please see the entries on nucleosides and nucleic acids at Wikipedia.

nucleosome

A basic unit of eukaryotic chromatin, consisting of DNA wrapped around a core of eight histone protein molecules.

nucleotide

A nucleoside linked to one or more phosphate groups via an ester bond with the pentose. DNA and RNA are polymers of nucleotides, linked through the 5' and 3' carbons of the sugar.

For more detail, please see the entries on nucleosides and nucleic acids at Wikipedia.

nucleus

The membrane-bound organelle in a eukaryotic cell that contains most of the cell's DNA.

ORF

Open Reading Frame, a long stretch of codons in the same reading frame uninterrupted by stop codons; an ORF may reflect the presence of a gene.

orthologous genes

Genes in different organisms that are direct evolutionary counterparts; that is, they are related by descent from a common ancestor. Orthologous genes normally have the same cellular function.

Please see the figure showing homology.

ortholog (also orthologue)

A specific member of a group of orthologous sequences or molecules.

Please see the figure showing homology.

orthology

Orthology is the state of being orthologous.

Please see the figure showing homology.

outcross

A type of genetic cross in which an organism is crossed to a strain from which it was not recently derived.

See also:

backcross
incross
intercross
testcross

P generation

The parental generation, consisting of two pure-breeding lines differing with respect to one or more traits.

paralogous genes

Genes at different chromosomal locations in the same organism that have structural similarities indicating that they derived from a common ancestral gene and have since diverged from the parent copy by mutation and selection or drift.

Please see the figure showing homology.

paralog (also paralogue)

A specific member of a group of paralogous sequences or molecules.

Please see the figure showing homology.

paralogy

Paralogy is the state of being paralogous.

Please see the figure showing homology.

PCR

Polymerase Chain Reaction. A method of amplifying specific DNA segments based on hybridization to a primer pair. A DNA sample is denatured by heating in the presence of a vast molar excess of short single-stranded DNA primers (around 20 nucleotides) whose sequence is chosen based on the target sequence. The reaction mixture also contains a thermostable DNA polymerase, dNTPs, and buffer. The primer sequences are selected so that they:

are derived from opposite strands of the target sequence,
have their 3' ends facing each other, and
are separated by a length of DNA that can be reliably synthesized in vitro.

The sample is then cooled to a temperature that allows primer annealing and in vitro replication. The sample is subjected to multiple cycles of denaturation and cooling to allow multiple rounds of replication. The quantity of the target sequence doubles during each cycle, causing the target sequence to be amplified, while other DNA sequences in the sample remain unamplified.

penetrance

The fraction of individuals of a given genotype that show a particular phenotype, usually expressed as a percentage.
See also expressivity.

phenotype

A description of the observable state of an individual with respect to one or more inherited traits. Often, individuals with different genotypes display the same phenotype.

phosphodiester bond

A covalent bond in which two hydroxyl groups form ester linkages to the same phosphate group; joins successive nucleotides in DNA or RNA.

plasmid

A small circular DNA molecule that carries genetic elements permitting its autonomous extra-chromosomal replication in bacteria or other single-cell organisms. A plasmid can be used as a recombinant DNA vector, to propagate foreign DNA in a bacterial cell. In addition to the essential origin for replication, plasmids generally carry a variety of marker genes, enabling easy identification of cells harboring the recombinant DNA.

pleiotropy

The production of a phenotype affecting multiple traits by a single mutation.

poly(A) tail

The segment of adenylate residues that is posttranscriptionally added to the 3' end of eukaryotic mRNA. About 250 nucleotides of (A) are added by poly (A) polymerase following cleavage of the newly synthesized RNA about 20 nucleotides downstream of an AAUAAA signal sequence.

polyadenylation

The process by which a series of adenosine (A) ribonucleotides is added to the 3' end of a spliced RNA to make a mature mRNA. This addition to the RNA is sometimes referred to as a poly-A tail, and commonly contains several hundred bases.

polypeptide

An amino acid chain containing hundreds to thousands of amino acids joined together by peptide (amide) bonds.

pre-mRNA

The initial transcript from a protein-coding gene is often called a pre-mRNA and contains both introns and exons. Pre-mRNA requires processing (addition of 5' cap and 3' poly (A) tail, removal of introns) to produce the final mRNA molecule containing only exons.

primary transcript

The immediate product of transcription of a gene, which is often modified before becoming fully functional.

Please see the visual guide to terms associated with parts of a typical eukaryotic gene, below.

Primase

An enzyme necessary for DNA replication that synthesizes an RNA primer to allow the synthesis of the discontinuous strand by DNA polymerase.

primer

A single-stranded nucleic acid that can "prime" replication of a template. More specifically, a single-stranded nucleic acid capable of hybridizing to a template single-stranded nucleic acid in such a way as to leave part of the template to the 3' end of the primer single-stranded. DNA polymerase can then synthesize a new strand starting from the 3' end of the primer and adding nucleotides to the growing strand by base complementarity to the template.

See also:

codominant
dominant
semidominant

recombination

1. The appearance of nonparental types among the progeny of a dihybrid cross.
2. Any exchange of information between DNA molecules, whether or not it is reciprocal.

reductional division

The first division of meiosis, because it reduces the chromosome number from diploid to haploid.

regulatory elements

DNA sequences that control expression of a gene by binding to proteins that increase or decrease synthesis of the gene product.

repetitious DNA

See repetitive DNA sequence.

repetitive DNA sequence

A DNA sequence that is repeated multiple times in the genome; such sequences can vary considerably in length and number of copies per genome.

replication

The process of producing two DNA molecules from one. During replication, the two strands of the parent helix separate and DNA polymerase synthesizes a new, complementary strand for each parental strand, following the rules of base pairing (A-T and G-C).

repulsion

In linkage analysis, the presence of two specified alleles (typically the recessive alleles) on homologous chromosomes, rather than on the same chromosome.

retrotransposon

These are transposable DNA elements (transposons) that employ retroviral-like reverse transcription during the process of transposition: retrotransposon DNA is first transcribed into an RNA template which is then reverse-transcribed into a DNA copy that is inserted into a new genomic site.

RNA

Ribonucleic acid. A nucleic acid that is the primary product of gene expression. Chemically, it differs from DNA by the substitution of ribose for deoxyribose in the sugar-phosphate backbone and by the substitution of the base uracil for thymine.

See also:

Central Dogma
DNA
nucleic acid

RNA polymerase

An enzyme that synthesizes a strand of RNA by adding successive ribonucleotides in the order dictated by a template strand of DNA.

rRNA

Ribosomal RNA, RNA molecules that are components of the ribosome. rRNA forms the structural scaffold for assembly of the ribosome, and plays a critical role in catalyzing peptide bond formation.

S phase

That part of interphase of the cell cycle in which DNA replication takes place.

satellite DNA/simple sequence DNA

Highly repetitious DNA sequence; generally based on a short sequence (7-20 nucleotides) repeated up to a million times in the haploid genome. Usually found in heterochromatic regions, often associated with the centromere.

Second Law (Principle of Independent Assortment)

segregation

1. Separation of paired homologous chromosomes from each other at meiosis I or separation of sister chromatids from each other at mitosis or meiosis II.

2. The separation of the two alleles of a gene into different gametes during sexual reproduction ( Mendel's First Law).

self-fertilization

Producing offspring from crosses in which both gamete types come from the same individual. This is possible for many plants and some animals.

semidominant

One of a series of terms applied to the phenotypic effect of a particular allele in reference to another allele (usually the standard wild-type allele) with respect to a given trait. An allele "A" is said to be semidominant with respect to the allele "a" if the A/A homozygote has a mutant phenotype, the A/a heterozygote has a less severe phenotype, while the a/a homozygote is wild type. An example is a variant allele of the profillaggrin gene in humans: heterozygotes for the variant allele have the skin disease ichthyosis vulgaris, while homozygotes for the variant allele have a more severe form of ichthyosis vulgaris, and homozygotes for the wild-type allele are unaffected.

See also:

codominant
dominant
recessive

sexual reproduction

Producing offspring through the fusion of gametes derived from meiosis.

shotgun sequencing

A strategy for sequencing whole genomes, it was pioneered by the for-profit company Celera. Genomes are cut into very small pieces, cloned into plasmids, sequenced, and then assembled into whole chromosomes or genomes. This method is faster than hierarchical shotgun sequencing but more prone to assembly errors.

simple repeat

A nucleotide repeat with one or a small number of bases, such as AAAAAAAAAAAA or CACACACACA.

sister chromatids

The two copies of a replicated chromosome prior to entry into M phase of the cell cycle.

sister chromatid cohesion

The holding together of sister chromatids during M phase of the cell cycle; the loss of sister chromatid cohesion triggers anaphase. In mitosis and meiosis II, sister chromatid cohesion is confined to the region around the centromere, while in meiosis I, sister chromatid cohesion occurs along the entire length of the chromosome.

Please see the figure at Scitable.

SNP

Single-nucleotide polymorphism; a difference in DNA sequence at a single base between two sequences.

somatic cell

Cells in the body of an animal that do not give rise to gametes.

spindle apparatus

The complex assembly of microtubules, centrosomes, and other components that moves chromosomes during M phase. The shape resembles the part of a spinning wheel upon which yarn is wound (the spindle), hence the name.

splicing

The process by which introns are removed and exons are joined to produce a mature, functional RNA from a primary transcript. Some RNAs are self-splicing, but most require a specific ribonucleoprotein complex to catalyze the reaction.

For more information, please see the entry on mRNA splicing at Wikipedia.

Please see the visual guide to terms associated with parts of a typical eukaryotic gene, below.

splicing acceptor site

The boundary between an intron and the exon immediately downstream (i.e. on the 3' side of the intron).

For more information, please see the entry on mRNA splicing at Wikipedia.

See also:

backcross
incross
intercross
outcross

topoisomerase

An enzyme that removes supercoiling or catenation of DNA molecules. Topoisomerase I binds double-standed DNA, cutting and resealing the phosphodiester bond on one strand to allow relaxtion of supercoiled DNA molecules. Topoisomerase II binds double-standed DNA, cutting and resealing the phosphodiester bonds on both stands to allow another DNA double helix to pass through the first.

trait

A specific inherited characteristic that exhibits variation between individuals. The phenotype of an individual with respect to an inherited characteristic will consist of one or more traits.

transcript

An RNA molecule (or species of RNA molecule) that is the product of transcription.

transcription

The process of copying one strand of a DNA double helix by RNA polymerase, creating a complimentary strand of RNA called the transcript.

transcription terminator

Also called simply a terminator, it is a section of genomic DNA that marks the end of gene or operon, where transcription should stop.

translation

The process by which codons in an mRNA are used by the ribosome to direct protein synthesis. For more detail, please see the entry on translation at Wikipedia.

translational start

The first codon of a coding sequence. In eukaryotes this is almost always ATG, which codes for methionine.

translocation

Literally "a change in location." In translocations part of a chromosome is transferred to another position in the genome. In a reciprocal translocation, two nonhomologous chromosomes exchange chromosome segments ending in a telomere. In an insertional translocation, a segment of one chromosome not ending in a telomere is inserted into a location on a nonhomologous chromosome.

transposable genetic element

A genetic element that can insert into (and exit from) a chromosome, and may therefore relocate in the genome; this class includes insertion sequences, transposons, retrotransposons, some phages, and controlling elements. Much of the middle repetitious DNA in eukaryotic genomes is made up of damaged transposable elements.

transposons

Segments of DNA that can move around to different positions in the genome of a single cell. In the process, they may cause mutations or increase (or decrease) the amount of DNA in the genome.

trihybrid

A type of cross in which individuals from two different true-breeding lines differing with respect to three traits are crossed. The hybrids from this cross may be further used for an intercross or testcross.

tRNA

Transfer RNA, small (~75 bp) L-shaped RNA molecules that deliver specific amino acids to ribosomes according to the sequence of a bound mRNA. The proper tRNA is selected through the complementary base pairing of its three-nucleotide anticodon with the mRNA's codon, and its amino acid group is transferred to the growing polypeptide.

true-breeding

A line of plants or animals that produces offspring identical to the parents with respect to some trait when propagated through self-fertilization or by breeding within the line.

upstream

Toward the 5' end of a single stranded lenth of DNA or gene of interest.