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Biomolecules glossary & taxonomy
Evolving terminology for emerging technologies
Comments? Questions? Revisions?
Mary Chitty MSLS firstname.lastname@example.org
July 10, 2019
Biology term index
Related glossaries include: DNA, Glycosciences,
biology, Proteins, RNA,
DNA & beyond
amino acids: Proteins glossary
base, base pair: Sequences, DNA
biological macromolecules: DNA, RNA
and proteins. This term is used
particularly in reference to structural modeling.
Biomolecular interactions, including contacts between
biological macromolecules (protein/protein or protein/nucleic acids) and
protein-ligand interactions are central to biochemistry. This grouping addresses
fundamental questions concerning, for example, the recognition of DNA by
bacterial proteins, the biophysical basis of allostery and the supply of metals
to proteins. Multiple projects aim to identify targets for new antimicrobial
(and antiviral) compounds and typically exploit a wide range of chemical,
biochemical, and biophysical methods.
Narrower terms: Proteomics protein- DNA
interactions, protein- protein interactions, protein- RNA interactions
Related terms: Omes & omics:
interactome, interactomics, kinomics
An organic molecule, part of a living organism.
Includes proteins, DNA,
biomolecules, Wikipedia http://en.wikipedia.org/wiki/List_of_biomolecules
binding proteins CBPs: Proteins
chemical compound: Wikipedia
thing that is composed of two or more separate elements; a mixture.
A substance formed from two or more elements chemically united in fixed
proportions. More definitions at
glycobiology, glycoproteins, glycoscience,
is now clear that most functions in the cell are not carried out by
single protein enzymes, colliding randomly within the cellular
jungle, but by macromolecular complexes containing multiple subunits
with specific functions (Alberts 1998 ).
Many of these complexes are described as "molecular
machines." Indeed, this designation captures many of the aspects
characterizing these biological complexes: modularity, complexity,
cyclic function, and, in most cases, the consumption of energy.
Examples of such molecular machines are the replisome, the
transcriptional machinery, the spliceosome, and the ribosome.
Molecular Machines: Putting the Pieces Together, Eva Nogalesa and
Nikolaus Grigorieffb Journal of Cell Biology, 152 (1): F1-10, January 8, 2001 http://www.jcb.org/cgi/content/full/152/1/F1
Complexes or cellular systems composed
of macromolecules (proteins, DNA,
RNA, polysaccharides, etc.) such as RIBONUCLEOPROTEINS,
CHROMATIN, MULTIENZYME COMPLEXES and other multimeric proteins. MeSH
macromolecule (polymer molecule): A molecule of high relative
molecular mass, the structure of which essentially comprises the multiple
repetition of units derived, actually or conceptually, from molecules of
low relative molecular mass. Notes: 1. In many cases, especially for synthetic polymers, a molecule can be regarded as having a high relative molecular
mass if the addition or removal of one or a few of the units has a negligible
effect on the molecular properties. This statement fails in the case of
certain macromolecules for which the properties may be critically dependent
on fine details of the molecular structure. 2. If a part or the whole of
the molecule has a high relative molecular mass and essentially comprises
the multiple repetition of units derived, actually or conceptually, from
molecules of low relative molecular mass, it may be described as either
macromolecular or polymeric, or by polymer used adjectivally. IUPAC Compendium
A general term to describe a "huge molecule." Although there is no set criteria for macromolecules, they are generally considered to be structures with over 1000 atoms.
DNA and proteins are common examples of macromolecules.
Dictionary of Chemistry
Related terms: large molecules, small molecules
Early biochemists thought small. They knew a lot about
the little molecules in the cells ... Into the nineteen- twenties and after,
many biochemists doubted the reality of very large molecules, even when they
were using the activity of enzymes, unpurified, as practical tools to catalyze
small molecular reactions. There was no way biochemists then could discern
that the molecules in the cell are all either small or very large, with nothing
between - that even small macromolecular chains are forty times or more the size
of even the largest, so to speak, micromolecules. HF Judson Eighth Day if
Creation, Cold Spring Harbor Laboratory Press, 1996 p. 186
"Any type of molecule composed of a relatively small number of atoms.
... generally ... has a mass less than about 10 kDa. Oxford
Biochemistry Related terms: small molecules,
specificity Compare macromolecules How does this word relate
(if it does) to small molecules?
The mole is the amount of substance of a system which contains as many elementary entities as there are atoms in 0.012 kilogram of carbon 12.
2. When the mole is used, the elementary entities must be specified and may be
atoms, molecules, ions, electrons, other particles, or specified groups of
such particles. NIST Reference
on Constants, Units and Uncertainty
of measurement for amount
of substance in the International
System of Units (SI). The unit is
defined as the amount or sample of a chemical
substance that contains as many
constitutive particles, e.g., atoms, molecules, ions, electrons,
as there are atoms in 12 grams of carbon-12 (12C),
the isotope of carbon with standard
atomic weight 12 by definition. This
number is expressed by the Avogadro
constant, which has a value of
approximately 6.02214076×1023 mol−1. The mole is an SI
base unit, with the unit symbol mol.
Wikipedia accessed 2018 Nov 8
[Bureau International de poids et mesures, SI base units, Système
International d'Unités, (International System of Units)
Narrower terms: Ultrasensitivity attomole, femtomole, picomole, yoctomole, zeptomole
molecular biology: "Molecular biology is an ambiguous
terms," Crick said the first time we [he and author Horace Judson Freeman]
met... "The term is used in two rather different ways. First, in a very
general sense it can mean almost anything - the attempt to understand any
biological problem at the level of atoms and molecules. You could talk about the
molecular biology of animal behavior - and that's not so far-fetched as you
might imagine,; some senior molecular biologists are getting close to that. Second there
is a classical sense of the term, and this is much narrower: classical molecular
biology has been concerned with the very large, long- chain biological molecules
- the nucleic acids and proteins and their synthesis. Biologically, this means
genes and their replication and expression, genes and the
gene products. ...
Several ideas underlay the classical research, Crick said, "The most basic
idea is that biological information is mainly carried by the sequence of side
groups on the regular backbone of a macromolecule. The genetic information is
not conveyed and expressed by a large number of intricate symbols - it's not in
Chinese - but in two very simple and as it were alphabetic languages.
Genetically, the information is carried by nucleic acid, in the sequence of bases; but many such
sequences can be translated into the other language - the
amino - acid sequences of proteins - by special pieces of biochemical machinery.
This machinery is rather elaborate, but the basic biological mechanisms are;
nevertheless, in principle, comparatively simple, and they turn out, with minor
variations, to be the same throughout nature - just as we had assumed. The
simplicity and universality of these mechanisms is, I think, the main reason why
molecular biology has been able to advance so rapidly. Because it is impossible
to deny that molecular biology, since the discovery of the structure of DNA, has
been wildly successful." HJ Freeman Eighth Day of Creation, Cold
Spring Harbor Laboratory Press, 1996 pp. 178-179
Protein based machines that are involved in or cause movement such as the rotary
devices (flagellar motor and the F1 ATPase) or the devices whose movement is
directed along cytoskeletal filaments (myosin, kinesin and dynein motor
families). MeSH, 1999
molecular weight: See relative molecular mass.
An electrically neutral entity consisting of more than one
atom (n > 1). Rigorously, a molecule, in which n > 1 must correspond to a
depression on the potential energy surface that is deep enough to confine at
least one vibrational state. See also molecular entity. IUPAC Compendium 1998
A group of atoms arranged to interact in a particular way; one molecule of
any substance is the smallest physical unit of that particular substance. ORD
A chemical made up of two or more atoms. The atoms in a molecule can be the
same (an oxygen molecule has two oxygen atoms) or different (a water molecule
has two hydrogen atoms and one oxygen atom). Biological molecules, such as
proteins and DNA, can be made up of many thousands of atoms. CancerNet
Smallest particle of a compound that has all the
chemical properties of that compound. A single atom is usually not
referred to as a molecule, and ionic compounds such as common salt are not
made up of molecules. Unlike ions, molecules carry no electrical charge
multimer: A protein made up of more than one peptide chain. FAO
A macromolecule composed of linear sequences of
nucleotides that perform several functions in living cells, e.g., the storage
of genetic information and its transfer from one generation to the next DNA
(deoxyribonucleic acid), the expression of this information in protein
synthesis (mRNA, tRNA) and may act as functional components of subcellular
units such as ribosomes (rRNA). [IUPAC Medicinal Chemistry]
Either of two kinds of molecules (DNA and RNA) formed
by chains of nucleotides, that carry genetic information. NIGMS
Nucleosides with one or more phosphate groups esterified mainly to the 3'- or the 5'- position of the sugar moiety. Nucleotides found in cells are
adenylic acid, guanylic acid, uridylic acid, cytidylic acid, deoxyadenylic acid, deoxyguanylic acid, deoxycytidylic acid and thymidylic acid.
The building block of DNA or RNA. Each nucleotide
consists of a sugar component, a phosphate group, and an organic base.
Four organic bases exist in DNA (adenine, cytosine, guanine, and
and in RNA (adenine, cytosine, guanine, and uracil). NHLBI
Half a "rung" on the DNA ladder.
oligo: A prefix meaning "a few" and used for compounds with a
number of repeating units…The limits are not precisely defined, and in
practice vary with the type of structure being considered, but are generally
from 3 to 10. IUPAC Compendium
A shortened form of oligonucleotide.
A molecule of intermediate relative molecular mass,
the structure of which essentially comprises a small plurality of units derived,
actually or conceptually, from molecules of lower relative molecular
mass. IUPAC Compendium 1998] Related terms: molecular weight, relative molecular mass
An oligomer resulting from a linear sequences
of nucleotides. [IUPAC Medicinal Chemistry] Macromolecules composed of
short sequences of nucleotides that are usually synthetically prepared
and used e.g. in
site directed mutagenesis.
Up to 20 nucleotides \King, Lackie 2-10 nucleotides Oxford Biochem
Related terms: oligos, probe
A fatty compound that contains phosphate. Phospholipids make up much of the outer membranes of
cells and organelles.
Compounds formed by the joining of smaller, usually
repeating, units linked by covalent bonds. These compounds often form large
macromolecules (e.g., polypeptides, proteins, plastics).
polypeptides: Protein categories
proteins: Naturally occurring and synthetic polypeptides having
molecular weights greater than about 10,000 (the limit is not precise).
IUPAC Compendium Related terms Proteins. Narrower term: peptides
purine: The bases adenine and guanine in DNA and
pyrimidine: The bases cytosine, thymine and uracil
in DNA and RNA.
relative molecular mass
Ratio of the mass of a molecule to the unified atomic mass unit. Sometimes called the
molecular weight or relative molar mass.
Discovery & Development
sugar amino acid hybrids SAAHs: Glycosciences
Composed of more than one molecule, more complex than
IUPAC Biotechnology] International
Union of Pure and Applied Chemistry, Glossary for Chemists of terms used
in biotechnology. Recommendations, Pure & Applied Chemistry 64 (1):
143-168, 1992. 200 + definitions. Included in IUPAC Compendium] International
Union of Pure and Applied Chemistry, Compendium of Chemical Terminology:
Recommendations, compiled by Alan D. McNaught and Andrew Wilkinson,
Blackwell Science, 1997. "Gold Book" 6500+ definitions. http://www.chemsoc.org/chembytes/goldbook/
Does not include Glossary of Bioinorganic Chemistry (1997) or Glossary
of Medicinal Chemistry (1998).
to look for other unfamiliar terms
IUPAC definitions are reprinted with the permission of the International
Union of Pure and Applied Chemistry.