Bioinformatics Glossary

A / B / C / D / E / F / G / H / I / J / K / L / M / N / O / P / Q / R / S / T / U / V / W / X / Y / Z

A

Amino Acid (AA)
A small molecule, chains of which form proteins – a protein is an amino acid polymer. Twenty different amino acids are used to create proteins.

C

Catalytic Activity
The catalytic activity of an enzyme accelerates up to a million times and in an extremely specific way a chemical reaction of the cellular metabolism.

Chromosome
The genome consists of several fragments known as chromosomes. Each contains two strands of DNA consisting of a succession of four nucleotides differentiated by their bases, paired in the shape of a double helix.

Coupled Metabolic Reactions
Set of metabolic chemical reactions linked by a substrate or product. A metabolic reaction is typically catalysed by an enzyme and transforms a substrate into a product.

Covalent Bond
Chemical bond in which each of a pair of linked atoms shares an electron so as to form a pair of electrons that bond the two atoms together.

D

DNA (Deoxyribonucleic Acid)
Biochemical medium for storing the genetic information of all living beings (with the exception of a few viruses that use RNA for this purpose). DNA, as the main component of chromosomes, generally presents in the form of two long filaments (or chains) that are twisted internally and with each other to form the double helix structure. Each of these chains is a polymer formed from an assembly of four different nucleotides, designated by the initial of the nitrogen base that forms part of their composition: A (Adenine), C (Cytosine), G (Guanine) and T (Thymine).

DNA Chip (Microarray or Biochip)
Technology used in the study of the transcriptome and based on the capacity of DNA and RNA molecules to hybridise among themselves. Short, known DNA sequences are fixed on computer chip surfaces measuring about one square centimetre. These are then introduced into the presence of an RNA mixture whose sequences are unknown. The system is designed in such a way that it is only able to detect DNA/RNA that has hybridised. The RNA sequences are deduced from the RNA present in the mixture being studied.

E

Enzyme
A protein whose function is to catalyse, i.e. facilitate and accelerate, biochemical reactions within a cell.

Eucaryotes/Procaryotes
All living organisms fall into three major groups, eucaryotes, eubacteria and archaebacteria. The eucaryotes possess a nucleus inside each of their cells. The nucleus consists of a small sac surrounded by a semi-permeable membrane enclosing the chromosomes. Animals, including humans, as well as plants and fungi, are eucaryotes. Eubacteria and archaebacteria do not possess a true nucleus, but a much more simple structure that is not surrounded by a membrane.

Exon/Intron/Mosaic Gene
In eucaryotes, the genes usually consist of two types of nucleotide sequences. One is known as coding and the other non-coding. The coding sequences, known as exons, carry information that will be used directly to make proteins. Introns are found among the exons but are not “read” during translation. The alternating arrangement of exons and introns has given rise to the expression “genetic mosaic”.

F

Functional Genomics
Study of the gene function through analysing gene sequences and the products through which they express themselves, mRNA (transcriptomes) and proteins (proteomes). It is the study of the way in which genes regulate themselves and how they interact.

G

Gene
Fragment of DNA that contains all of the information needed for manufacturing one or more proteins. A gene consists of a sequence of nucleotides that is transcribed then translated into amino acids, as well as sequences that make it possible to regulate protein manufacture depending on cell conditions. A gene may vary in length  from a few hundred to more than a million nucleotides.

Genetic Code/Codon
The genetic code is the system of correspondence that makes it possible to translate a sequence of nucleic acids into proteins. In this system, a sequence of three nucleotides, known as a codon, designates an amino acid. Since there are 4 nucleotides, this means that there are 4x4x4 = 64 different codons. One particular codon corresponds to a single and unique amino acid. There are only 20 different amino acids in proteins, however, and that is why several codons can represent a single amino acid. The genetic code is thus said to be degenerate or redundant.
Some of these 64 codons do not designate any amino acid. These “senseless” triple codons tell the cell machinery that the reading of the information contained in the genes has ended and causes the manufacture of proteins to cease. These are known as STOP codons.
Almost every living thing possesses the same genetic code, it is universal.

Genetic Regulatory Network
Complex interactions between genes and their products (RNA and proteins) govern cell activity so as to allow them to adapt permanently to variations in their environment. There are true cascades of interactions, often involving positive and negative feedback loops.
As an example, the bacterial genes lacZ lacY and lacA, arranged side by side on the genome, produce coding for the three enzymes involved in transporting and digesting lactose. In the absence of lactose, a repressive protein prevents the synthesis of these three enzymes. In the presence of lactose, a molecule derived from lactose fixes itself on the repressor, activating synthesis of the three genes. The lactose then becomes usable by the cell.

Genome
The set of genetic information contained in an organism. A copy of the genome is present in each of its cells. A  genome is transmitted from generation to generation. By extension, the genome also refers to the physical medium in which this genetic information is held, i.e. the DNA macromolecules.

Genomics
The study of genomes. The objective is to sequence the DNA of an organism and locate all of the genes it carries, then characterise their functions.

Genotype
The genetic information contained in the cells of each individual.

H

Hybridisation
A characteristic and essential property of nucleic acid molecules that gives them their ability to transfer information. Two chains (or strands) tend to pair up to form double strands (DNA/DNA, DNA/RNA or RNA/RNA), using a mechanism resembling that of a zip fastener. In order to be able to perform the transfer, the nucleotides of which they consist need to be complementary, i.e. that a nucleotide (A) must face a (T) or a (U), and a (C) must face a (G), and vice versa.
This property is manifest during replication, transcription and translation. Hybridisation also contains the principles of numerous molecular biology techniques (sequencing, DNA chips, etc.)

I

Interactome/Interactomics
An interactome can be obtained using various techniques, including sequencing. It usually means interaction between proteins, but may also refer to interactions between proteins and DNA, for example. These interactions present in the form of a graph, in which each node represents a biological object (a protein, portion of DNA, portion of RNA, etc.) and each ending signifies the existence the possible interaction between two objects. These graphs typically cover thousands and even tens of thousands of objects. They provide essential information about possible links between biochemical agents.

M

Macromolecule
Giant molecule whose molecular mass consists of several thousand daltons (a dalton is the unit used to describe the mass of a molecule. It corresponds to the mass of a hydrogen atom, i.e. 1.66·10-24 g). Proteins and nucleic acids (DNA and RNA) are macromolecules.

Mass Spectrometry
Mass spectrometry permits the identification of molecules of interest, through the analysis of their various constituents.
A mass spectrometer converts molecules into projectile fragments by ionisation. It subsequently accelerates these ions in a vacuum thanks to an electric and magnetic field. The ions are then classified, depending on their ratio of weight to charge. This filtering is performed either by flight time – the ions arrive at different times depending on their ratio of mass to charge – or by trajectory curve. The point of impact of the ions depends on their ratio of mass to charge. This information is then converted into a mass spectrum.

Maturation (of RNA Messengers)
Set of mRNA modifications prior to their translation. Splicing is one of the maturation processes of mRNA.

Messenger RNA (mRNA)
This carbon copy of the gene is used to transfer genetic information from the place in which it is stored (the chromosome) to the place in which proteins are synthesised (the ribosomes). The mRNA of eucaryote cells must undergo maturation, which often involves a process of excision, of their introns and splicing their exons before they are translated into proteins.

Mutation
An error in the replication of genomic information may escape the correction process and be transmitted to a descendant. The descendant is then said to carry a mutation corresponding to the base, sullied with an error.

N

Nucleic Acid
A polymer created by a chain of nucleotides. Nucleic acids play a fundamental role in the storage, maintenance and transfer of genetic information. There are two types of nucleic acid, ribonucleic acid (RNA) and deoxyribonucleic acid (DNA).

Nucleotide
This is a basic building block (monomer) of nucleic acids, created from an assembly of several molecules, consisting of a sugar (ribose for RNA, deoxyribose for DNA), phosphoric acid and a nitrogenous base (in the case of RNA, this base may be Adenine - A, Cytosine - C, Guanine - G or Uracil - U; the same applies to DNA, except that the Uracil is replaced by Thymine - T).

P

Peptide
Molecule consisting of a chain of a small number (in the order of half a dozen) amino acids, joined together through peptide bonds.

Phenotype
Effective expression of the genetic material in the process of the development of an individual.

Polymer
Macromolecule repeating the same structural pattern known as a monomer. Proteins are polymers of amino acids, nucleic acids are polymers of nucleotides.

Promoter
Short specific DNA sequence, situated at the beginning of the genes, to which the enzyme that performs the transcription (the polymerase RNA) attaches itself. The promoter is necessary for the transcription to start so it is indispensable for the functioning of a gene.

Protein
One of the four basic materials of which all organisms consist, along with carbohydrates, lipids and nucleic acids. Proteins are formed from a specific chain of amino acids (ranging in number from a few tens to a few hundreds).

Protein Functions
These are the roles fulfilled by proteins. Their functions are very varied and make it possible to classify proteins into “structural proteins”, comparable to cell building blocks (e.g.: collagen),  “carrier proteins” that are responsible for transporting other molecules within the cell or between the cells of an organism (e.g.: haemoglobin transports oxygen); enzymes enable the speeding up of the chemical reactions necessary for life (e.g. glucose 6 phosphatase initiates the breakdown of glucose, our main source of cell energy); immunity proteins  (or antibodies) contributing to our bodies’ defences. The three-dimensional structure of a protein is one of the elements that determines its function.

Protein Structure
Every protein exists in a configuration defined by the various structural levels. The sequence of amino acids linked in the chain of polypeptides constitutes the primary structure of the protein. This sequence is fully defined by the DNA of the cell.
The secondary structure is a first level of folding back on itself adopted by portions of the proteins and resulting from interactions between the neighbouring amino acids in the chain. Two characteristic folds can thus form, in a helix (known as an α-helix) or in pleated sheets (known as beta-pleated sheets), linked by loops or half-turns.
The final structure, i.e. the way in which elements are organised in the secondary structure, is known as the tertiary structure. This is the form adopted by a protein in space. It is due to the interactions between amino acids that are remote on the peptide chain but that are close to this three-dimensional structure.
Certain complex proteins consist of several sub-units (several protein chains). The quaternary structure is the spatial arrangement of these various units that is necessary for the functioning of the whole.

Proteome/Proteomics
A proteome is a set of proteins produced from the genome of an organism. Like the transcriptome, the proteome is not identical in all the cells of a given organism.
Proteomics is the study of proteomes, for the purpose of determining the activity, function and interactions of proteins under diverse conditions.

R

RNA (Ribonucleic Acid)
Several types of RNA are found within the cells, depending on their function. The three main types are messenger RNA, transfer RNA and ribosomal RNA. RNA is a nucleic acid consisting of a single chain of nucleotides with a similar structure to that of DNA. Nevertheless, there are chemical differences between the nucleic acids that give RNA certain special properties. RNA is produced by transcription of the DNA.

RNA Splicing
As applicable to the mosaic genes of eucaryotes, it is a mechanism on messenger RNA that has just been transcribed, used for eliminating (excising) the introns and reuniting (splicing) exons between themselves. The product of this splicing is mature messenger RNA, ready to be translated into protein.

Regulation Signals
Specific nucleotide signals on which proteins fix themselves, thus causing the activation or suppression of the expression of genes.

Replication
Mechanism for synthesising DNA that makes it possible to transmit genetic information from one cell to another or from an organism to its descendants. Each DNA daughter-molecule consists of a strand of the mother-molecule, which serves as a model for a new strand. This leads to the duplication of DNA molecules for the whole genome.

Ribosomal RNA (rRNA)
Main constituent of ribosomes, the cell machinery in which the translation into proteins takes the place of the information contained in the mRNA.

Ribosomes
Cell machinery consisting of proteins and RNA (the rRNA), responsible for the translation of mRNA. A ribosome “reads” each codon of a messenger RNA strand for successive translation and adds the amino acid corresponding to the protein being synthesised.

S

Sequence/Sequencing
A sequence is the linking order for the elements of which nucleic acids or proteins, nucleotides or amino acids consist. The sequence of a protein is dictated by that of its gene.
Sequencing consists in using chemical methods or molecular biology to determine the order of DNA nucleotides or the amino acids of proteins.

T

Transfer RNA (tRNA)
Small RNAs responsible for transporting amino acids to the ribosomes when mRNA is translated. Each tRNA transports an amino acid in a specific way. Its sequence consists of a series of three nucleotides, known as an anticodon, which recognises the codon (see Genetic Code) corresponding to the amino acid it transports.

Translation
A stage in the synthesis (manufacture) of proteins in the course of which the RNA messenger strand obtained during transcription is converted into a chain of amino acids that will produce a protein. Procaryote mRNA is translated as is, but eucaryote mRNA is subject to prior maturation.

Transcription
Manufacturing process of an mRNA from the coding sequence of a gene that serves as the model. The enzyme responsible for this reaction is known as polymerase RNA.

Transcriptome/Transcriptomics
Set of RNA messengers transcribed from the genome. Like the proteome, it varies over time and from one cell to another in an organism. Transcriptomics is the study of this ensemble and makes it possible not only to see the agents of the cell (the genes) but also their level of activity over time and under different conditions (during clinical treatment for example).

Source: Interstices - Revue de culture scientifique en ligne published by INRIA
Access to the original glossary [in French]: https://interstices.info/glossaire-bioinfo