Glossary | Molecular Biology (2022)

Glossary of Terms for Molecular Technology

Last Updated on Monday, 02 November 2009 16:34Written by PatrickMonday, 26 October 2009 10:51

Active siteThe part of protein that must be maintained in a specific shape if the protein is to be functional.

AlleleOne of two copies of a gene.

Amino acidA peptide; the basic building block of proteins.

AmpliconReplicated target molecules created by polymerase chain reaction or other nucleic acid amplification methods.

AmplificationIncreasing the number of copies of a desired DNA segment. The amplified regions are called amplicons.

Aneuploid cellA cell having a chromosome number that differs from the normal chromosome number for the species by a small number of chromosomes.

AnnealingSpontaneous alignment of two single DNA strands to form a double helix.

AntibodyA protein molecule, produced by the immune system, that recognizes a particular substance and binds to it.

AnticodonA nucleotide triplet in a tRNA molecule that aligns with a particular codon in mRNA under the influence of the ribosome so that the amino acid carried by the tRNA is inserted in a growing protein chain.

AntiparallelA term used to describe the opposite orientations of the two strands of a DNA double helix; the 5’ end of one strand aligns with the 3’ end of the other strand.

AvidinA protein that specifically binds to biotin with usually high affinity.

AutoradiographyThe exposure of roentgenographic film to a blot or membrane containing a radiolabeled probe, used to locate the labeled probe

BacteriophageA virus that infects bacteria

BaseOne nucleotide consisting of a nucleoside, pentose sugar and triphosphate; building blocks for either DNA or RNA

Base analogA chemical whose molecular structure mimics that of a DNA base; because of the mimicry, the analog may act as a mutagen.

Base pair (bp)One pair of complementary nucleotides (e.g. adenine to thymine or guanine to cytosine) on opposite sides of the duplex strands

Cell cycleThe set of events that take place in the divisions of mitotic cells. The cell cycle oscillates between mitosis (M phase) and interphase. Interphase can be subdivided in order into G1, S phase and G2. DNA synthesis takes place during S phase. The length of the cell cycle is regulated through a special option in G1, in which G1 cells can enter a resting phase call G0

ChromosomeStructure of DNA and associated proteins that contain the hereditary material within the cell. Genes are organized in linear arrangement in the chromosome.

CistronSegments of DNA corresponding to one polypeptide chain, plus transcriptional start and stops signs.

CloningThe process of generating a large number of identical DNA fragments, typically to produce a probe for a specific gene.

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CodominanceThe situation in which a heterozygote shows the phenotypic effects of both alleles.

CodonA sequence of three nucleotides that specifies a particular amino acid

CompetentAble to take up exogenous DNA and thereby be transformed.

ComplementarityThe specific binding of adenine to thymidine (or uracil in RNA) and cytosine to guanine on opposite strands of DNA or RNA.

Complementary DNA or Copy DNA(cDNA)DNA generated form mRNA by the use of reverse transcriptase.

Complementary RNASynthetic RNA produced by transcription from a specific DNA single-stranded template.

ComplementationThe production of a wild-type phenotype when two different mutations are combined in a diploid or a heterokaryon.

CosmidA genetically engineered construct containing sites from lambda phage that allow for insertion of large pieces of DNA (30-50 kb). Recombinant cosmids can then be replicated in bacterial hosts.

Degenerate codeA genetic code in which some amino acids may be encoded by more than one codon each.

DegradationDue to physical shearing or exposure to endogenous or exogenously added nucleases, DNA and RNA can become hydrolyzed or degraded to the oligonucleotide or single-nucleotide level.

DenaturationThe process of making double-stranded DNA single stranded.

Dideoxy sequencingA method of DNA sequencing in which dideoxynucleotide triphosphates (ddNTPs) are used in the growing oligonucleotide chains synthesized from the DNA template, thereby terminating elongation.

DNADeoxyribonucleic acid

DNAaseDeoxyribonuclease, an endonuclease that randomly hydrolyzes (nicks) DNA at single sites on either strand of the DNA

DNA ligaseAn enzyme that covalently joins two pieces of double stranded DNA.

DNA polymeraseThe enzymes(s) that make DNA by the addition of bases to the end of the replicating DNA strand.Also has an editing function that can repair nicked DNA by removal of old nucleotides and replacement with new (e.g. labelled) nucleotides.

Dominant alleleAn allele that expresses its phenotypic effect even when heterozygous with a recessive allele; thus if A is a dominant over a, then A/A and A/a have the same phenotype.

Dominant phenotypeThe phenotype of a genotype containing the dominant allele; the parental phenotype that is expressed in a heterozygote.

Dot (slot) blotThe immobilization of DNA or RNA to a sample spot (slot) on a filter that will be subsequently probed by hybridization. Usually many samples are applied, each to a different location on the same filter, for mass screening.

dsDouble stranded

End-labelingThe incorporation of nucleotides at the 5‘ end of a strand of DNA by the use of specific enzymes as one means of making labeled probes.

EndonucleaseEnzyme that hydrolyzes dsDNA at internal locations

EnhancerA regulatory sequence that can elevate levels of transcription from an adjacent promoter. Many tissue-specific enhancers can determine patterns of gene expression in higher eukaryotes. Enhancers can act on promoters over many tens of kilobases of DNA and be 5’ or 3’ to the promoter that they regulate. Generally they are on the same chromosome.

Ethidium bromideA chemical dye that intercalates between the bases in DNA and causes DNA to fluoresce when illuminated with ultraviolet light.

EuploidA cell having any number of complete chromosome sets or an individual composed of such cells.

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ExonThe portion of a gene that is actually translated into protein. [Eukaryotic genes only.]

ExonucleaseEnzyme that hydrolyzes ss or ds NA from the ends

FingerprintThe characteristic spot pattern produced by electrophoresis of the polypeptide fragments obtained through denaturation of a particular protein by a proteolytic enzyme.

FISHFluorescent in situ hybridization. In situ (in the physical location) hybridization using a probe coupled to a fluorescent molecule.

Frame-shift mutationThe insertion or deletion of a nucleotide pair or pairs, causing a disruption of the translational reading frame.

Functional genomicsThe study of patterns of gene expression and interaction in the genome as a whole.

GeneA sequence of nucleotides that code for a protein product.

Gene doseThe number of copies of a particular gene present in the genome.

Gene locusThe specific place on a chromosome where a gene is located.

Gene therapyThe correction of a genetic deficiency in a cell by the addition of new DNA with or without its insertion into the genome.

Genetic codeThe set of correspondences between nucleotide pair triplets in DNA and amino acids in proteins.

GeneticsThe study of genes.

GenomeThe complete set of hereditary factors of an organism, contained in the chromosome.

Genomic libraryCollection of DNA fragments (library) whose sum represents the entire genomic DNA of an organism.

GenotypeThe specific genes that are present in an individual; they may or may not be expressed.

Germ lineThe cell lineage in a multi-tissued eukaryote from which the gametes derive.

Growth factorSignaling molecules, usually secreted polypeptides, that induce cell division in cells receiving theses signals. Signals can be autocrine (self derived), paracrine (from another cell but local in origin), endocrine (from a distant cell/organ) or neurocrine (from nerve cells).

HaploidA cell having one chromosome set or an organism composed of such cells.

HeteroduplexA DNA double helix formed by annealing single strands of a heteroduplex DNA.

HeterozygoteAn individual having a heterozygous gene pair.

HomologySimilarity between two distinct genes in their nucleotide sequence.

HybridizationThe process of complementary base pairing between two single strands of DNA, DNA and RNA, or sense and anti-sense RNA.

InhibitorAs it pertains to DNA manipulation in vitro, contamination in the preparation or sample can inhibit the biochemical processes involved in the manipulation, generally polymerases. Can be endogenous (from the sample matrix) or exogenous.

In situ hybridizationUse of labeled DNA or RNA probes to localize complementary sequences within a cell.
Intron A portion of a gene not translated into protein, even though it is transcribed into RNA. A splicing event removes it from the primary RNA transcript leaving only the exons in the mRNA. [Eukaryotes only.]

Inverted repeat sequenceA sequence found in identical form, but inverted. Commonly found in transposons and viruses.

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Kilobase (kb)Unit of 1000 base pairs of DNA or 1000 bases of RNA.

LabelingThe process of marking a DNA molecule using radioactive or non-radioactive labels.

LigaseAn enzyme that can rejoin a broken phosphodiester bond in a nucleic acid.

Ligase chain reaction (LCR)An in vitro nucleic acid amplification method that uses DNA ligase, an enzyme that joins two pieces of DNA together.

Lagging strandIn DNA replication, the strand that is synthesized apparently in the 3’ to 5’ direction, by ligating short fragments synthesized individually in the 5’ to 3’ direction. The short fragments called Okazaki fragments are primed using snRNAs.

LocusThe site on the chromosome where a gene is located.

Missense mutationA mutation that alters a codon so that it encodes a different amino acid.
mtDNa Mitochondria DNA.

MutationThe process that produces a gene or a chromosomal set differing from the wild type.

Nick translationA means of incorporating labelled nucleotides into a segment of nucleic acid by displacing random nicks (introduced by DNAase) through the use of DNA polymerase.

Nonsense codonA codon for which no normal tRNA molecule exists; the presence of a nonsense codon causes termination of translation (ending of the polypeptide chain). The three nonsense codons are called amber, ocher, and opal.

Nonsense mutationA mutation that alters a gene so as to produce a nonsense codon.

Northern blotRNA immobilized on a solid support after separation according to size by electrophoresis.

Nucleotide (nt)The structural unit of nucleic acid consisting of phosphate, sugar and purine or pyrimidine base.

N-Terminus and C-TerminusThe two ends of a protein/polypeptide chain. Protein sequences are given N?C in direction.

OligonucleotideA short (10-100 nt) stretch of ssDNA usually prepared by a series of chemical reaction following a known sequence.

OncogeneA type of gene associated with cancer production.

OperonA set of adjacent structural genes (prokaryotic) whose mRNA is synthesized in one piece, plus the adjacent regulatory signals that affect transcription of the structural genes. Regulation can be postive (turn it on when needed) or negative (keep it off until needed).

ORF (open reading frame)A section of a sequenced piece of DNA that begins with a start codon and ends with a stop codon; it is presumed to be the coding sequence of a gene.

PhenotypeThe form or expression taken by some character or gene in a specific individual. Genotype is not always reflected in the phenotype.

Point mutationA mutation that can be mapped to one specific locus.

Polymerase chain reaction (PCR)Enzymatic technique to create multiple copies of one sequence of DNA

PlasmidA small, circular, extrachromosomal, self-replicating piece of DNA found in some bacteria (e.g. pBR322). Used in cloning (cloning plasmid = vector).

Poly(A)tailA string of adenine nucleotides added to mRNA after transcription.

Polycistronic mRNAAn mRNA that encodes more than one protein (prokaryotes and viruses).

PolymorphismThe occurrence in a population of several phenotypic forms associated with alleles of one gene or homologs of one chromosome

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PrimerA short single-stranded DNA or RNA that can act as a start site for 3’ chain growth when bound to a single-stranded template.

ProbeA fragment or sequence of ssDNA, dsDNA or RNA that will be hybridized to a complementary sequence of nucleotides in another single-strand nucleic acid (target). Probes are labeled in some what to make the reaction visible.

PromoterA regulator region a short distance from the 5’ end (transcription start site) of a gene that acts as the binding site for RNA polymerase.

Reading frameThe codon sequence that is determined by reading nucleotides in groups of three from some specific start codon.

Recombinant DNAThe DNA molecule produced from inserting DNA from one organism into another piece of DNA by using genetic engineering techniques.

Regulatory genesGenes that have roles in turning on or off the transcription of other genes.

ReplicationThe process of making DNA.

Replication forkThe point at which the two strands of DNA are separated to allow replication of each strand.

Restriction enzymeAnother name for restriction endonuclease.

Reverse TranscriptaseAn enzyme capable of synthesizing ssDNA from RNA. From retroviruses.

Ribosomal RNA (rRNA)A class of RNA molecules that have an integral role in ribosome structure and function.

RNARibonucleic acid, the single stranded nucleic acid of three types; mRNA (messenger RNA), tRNA (transfer RNA) and rRNA (ribosomal RNA)

RNA polymeraseA DNA directed RNA polymerase that creates a strand of RNA complementary to one strand of the dsDNA template.

RNasesUbiquitous enzymes that degrade RNA

SequencingA method that determines the actual sequence of the nucleotide bases in DNA or protein.

Signal sequenceThe N-terminal sequence of a secreted protein, which is required for transport through the cell membrane.

Southern blotDNA that has been separated by gel electrophoresis, transferred from the gel to an immobile support (e.g. nitrocellulose or nylon), and bonded onto the support in single-stranded form ready for hybridization
ss Single stranded

Staggered cutsThe cleavage of two opposite strands of duplex DNA at points near one another.

StreptavidinA bacterial form of avidin that has a slightly stronger affinity for biotin than does avidin form egg white.

StringencyThe conditions of hybridization that increase the base-pairing of binding between two single strand portions of nucleic acid.

SupercoilA closed, double-stranded DNA molecule that is twisted on itself.

Target nucleic acidDNA or RNA to be hybridized with the labelled probe.

Tissue-specific gene expressionThe expression of a gene in a specific and reproducible subset of tissues and cells during the development of a higher eukaryote.

TranscriptionThe process of producing an RNA copy from a DNA template.

TranslationThe production of protein from messenger RNA.

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Uracil-N-glycosylaseAn enzyme that digests DNA that was replicated using dUTP instead of dTTP and is used to prevent amplicon carry over contamination.

VectorA plasmid, bacteriophage, cosmid or virus that carries foreign DNA into a host organism.

Western blotProteins that have been separated by acrylamid electrophoresis, transferred and immobilized onto a solid support, then probed with labelled antibody.


1. Molecular Biology Techniques
(AJ Keefe)
2. Introduction To Molecular Biology
(Easy Peasy)
3. Molecular Biology #2 2020
4. Chapter 10 Molecular Biology
(Dr. Julie Wells)
5. DNA Structure and Replication: Crash Course Biology #10
6. Alternative Approaches to Molecular Biology | MIT 7.01SC Fundamentals of Biology
(MIT OpenCourseWare)

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