Molecular Terms: Considerations and Examples
15.10.2 Molecular Terms: Considerations and Examples
Molecular terms often are more familiar in unexpanded form; their expansions may be obscure. Molecular terms often mix numbers, letters, and cases. They may be abbreviations or abbreviations within abbreviations (for instance, see TAF and subsequent entries in Table 13). Molecular terms differ from standard abbreviations, which typically are uppercase initialisms (eg, premature ventricular contraction, PVC). In contrast, many molecular terms are (or incorporate) contractions of single words, using all lowercase letters or mixing capital and lowercase letters (eg, apo, apolipoprotein; Hb, hemoglobin).
Table 13. Molecular Terms
Term |
Explanation |
Suggested Usage at First Mention |
|---|---|---|
Aβ peptide, Aβ42 |
amyloid-β peptide |
amyloid-β peptide (Aβ), Aβ42 peptide, or 42-residue form of Aβ |
Aβ*56 |
56-kDa Aβ fragment |
56-kDa Aβ fragment |
Ach |
acetylcholine |
acetylcholine |
Acrp30 (or adiponectin) |
adipocyte-complement related 30 kDa-protein |
the protein Acrp30 or adiponectin |
acyl coenzyme A (CoA) |
acyl derivatives of coenzyme A |
acyl coenzyme A |
sulfonated acyl coenzyme A (CoA) |
sulfonated acyl-CoA |
sulfonated acyl-CoA |
ADAMTS [see Apte3] |
a disintegrinlike and metalloprotease domain (reprolysin-type) with thrombospondin type 1 motifs |
ADAMTS protease |
specific ADAMTS, eg, ADAMTS-13 |
ADAMTS-13; trivial name von Willebrand factor (vWF) protease (see also 15.7, Hemostasis) |
ADAMTS-13 and/or vWF protease |
adoHcy |
S-adenosylhomocysteine |
S-adenosylhomocysteine |
adoMet (also SAM) |
S-adenosylmethionine |
S-adenosylmethionine |
Akt |
a serine-threonine kinase, also known as protein kinase B, related to akt oncogene (origin: AKT retrovirus isolated from AKR mouse thymoma) |
Akt or protein kinase B |
allo-SCT |
allogenic stem cell transplantation |
allogenic stem cell transplantation |
ATCase |
aspartate transcarbamoylase |
aspartate transcarbamoylase |
ATPase |
adenosine triphosphatase |
adenosine triphosphatase |
BNP |
brain (or b-type) natriuretic peptide |
brain (or b-type) natriuretic peptide |
1,3-BPG |
1,3-bisphosphoglycerate |
1,3-bisphosphoglycerate |
CAK (=cyclinH/CDK7) |
CDK-activating enzyme |
the CDK-activating enzyme (CAK) cyclinH/CDK7 |
CaM |
calmodulin |
calmodulin |
CDK2, CDK3, CDK7, etc |
cyclin-dependent kinases |
the cyclin-dependent kinase CDK2, etc |
CDKI |
CDK inhibitors (see also INK4 below) |
CDK inhibitors |
coenzyme A (CoA) |
coenzyme A |
coenzyme A |
COX-1, COX-2 |
cyclooxygenases 1 and 2 |
cyclooxygenase 1, cyclooxygenase 2 |
C-reactive protein |
protein reactive to pneumococcal cell wall C polysaccharide |
C-reactive protein (CRP) |
cyclin D/CDK4/CDK6, cyclin E/CDK2 |
cyclin-CDK complexes |
the cyclin D/CDK4/CDK6 complex; the cyclin E/CDK2 complex |
CYP1A2, CYP2C9, CYP2C19, CYP2D6, CYP3A4 |
isoforms of cytochrome P450 enzymes (also cytochrome P450 isozymes) [P: pigment; 450: 450-nm absorbance] |
various, eg, cytochrome P450 1A2 isozyme (CYP1A2); cytochrome P450 3A4 isozyme (CYP3A4 or P450 3A4 or 3A4) |
Dkk-1 |
Dickkopf-1 |
the inhibitor protein Dkk-1 |
F0 (subscript is zero, not capital O) |
portion of mitochondrial ATP synthase (F: energy-coupling factor) |
context, eg, F0 portion of mitochondrial ATP synthase, proton channel portion of ATP synthase, etc |
F0F1 |
complex portion of mitochondrial ATP synthase |
context, eg, F0F1 mitochondrial ATP synthase, F0F1 complex, etc |
F1 |
portion of mitochondrial ATP synthase |
context, eg, F1 portion of mitochondrial ATP synthase, catalytic portion of ATP synthase, etc |
F1P, F6P |
fructose 1-phosphate, fructose 6-phosphate |
fructose 1-phosphate, fructose 6-phosphate |
FAD |
flavin adenine dinucleotide |
flavin adenine dinucleotide |
FADH2 |
reduced (hydrogenated) FAD |
FADH2 or reduced (or hydrogenated) FAD |
FBPase-1, FBPase-2 |
fructose 1,6-bisphosphatase, fructose 2, 6-bisphosphatase |
fructose 1,6-bisphosphatase, fructose 2,6-bisphosphatase |
Fd |
ferredoxin |
ferredoxin |
Fhit |
fragile histidine triad protein |
fragile histidine triad protein |
FMN |
flavin mononucleotide |
flavin mononucleotide |
FMNH2 |
reduced (hydrogenated) FMN |
FMNH2 or reduced (or hydrogenated) FMN |
Fp |
flavoprotein |
flavoprotein (Fp) |
G0 |
quiescent state of cell cycle |
G0 phase |
G1 |
growth or gap 1 phase of cell cycle |
G1 phase |
G2 |
growth or gap 2 phase of cell cycle |
G2 phase |
G protein |
guanine triphosphate (GTP)-binding protein |
G protein |
Gα, Gβ, Gγ |
G protein families |
Gα, Gβ, Gγ protein or family |
Gα12, Gα13 |
members of Gα |
Gα12, Gα13 protein |
Gβγ, βγ |
Gβ subunit or complex |
Gβγ, βγ subunit or complex |
G1P, G6P |
glucose 1-phosphate, glucose 6-phosphate |
glucose 1-phosphate, glucose 6-phosphate |
GalN |
d-galactosamine |
d-galactosamine |
GalNAc |
N-acetyl-d-galactosamine |
N-acetyl-d-galactosamine |
Gi |
inhibitory G protein |
inhibitory G protein |
Glc or d-Glc |
d-glucose |
glucose or d-glucose |
Gq, Gq/11 |
classes of G protein |
Gq, Gq/11 protein |
Gs |
stimulatory G protein |
stimulatory G protein |
GlcA |
d-gluconic acid |
gluconic acid or d-gluconic acid |
GlcNAc (also NAG) |
N-acetyl-d-glucosamine |
N-acetyl-d-glucosamine GlcNAc |
GlcUA |
d-glucuronic acid |
d-glucuronic acid |
Grb2 |
growth factor receptor-bound protein 2 |
the protein Grb2 |
H2F (also DHF) |
dihydrofolate or 7,8-dihydrofolate |
dihydrofolate (H2F or DHF) or 7,8-dihydrofolate (H2F or DHF) |
H4F (also THF) |
tetrahydrofolate or 5,6,7,8-tetrahydrofolate |
tetrahydrofolate or 5,6,7,8-tetrahydrofolate |
Hb |
hemoglobin |
hemoglobin |
HbA1a, HbA1b, HbA1c |
glycated (not glycosylated4-7) hemoglobin fractions |
preferred: glycated hemoglobin A1c, etc (also: glycohemoglobin A1c) |
HbCO |
carbon monoxyhemoglobin, carboxyhemoglobin |
carbon monoxyhemoglobin |
HbO2 |
oxyhemoglobin |
oxyhemoglobin |
HER2/neu |
from human epidermal growth factor receptor 2; preferred term is now ERBB2; see also 15.6.3, Genetics, Oncogenes and Tumor Suppressor Genes |
ERBB2 (formerly HER2 or HER2/neu) |
β-hydroxy-β-methylglutaryl–coenzyme A (CoA) |
β-hydroxy-β-methylglutaryl-CoA |
β-hydroxy-β-methylglutaryl-CoA |
IKKβ |
IκB kinase β (I: inhibitor) |
IκB kinase β |
INK4 |
inhibitors of CDK4 (see also CDKI above and p16Ink4, etc, below) |
inhibitors of CDK4 |
IGF-1, IGF-2 |
insulinlike growth factor, type 1 and type 2 |
insulinlike growth factor 1, insulinlike growth factor 2 |
IGF-R1, IGF-R2 |
IGF-1 receptor, IGF-2 receptor |
IGF-1 receptor, IGF-2 receptor |
IP3 |
inositol 1,4,5-triphosphate |
inositol 1,4,5-triphosphate |
α-KG |
α-ketoglutarate |
α-ketoglutarate |
lac |
lactose |
lactose |
M |
mitosis (phase of cell cycle) |
M phase |
Man |
d-mannose |
d-mannose |
Mb |
myoglobin (don't confuse with Mb, megabase, or MB, megabyte) |
myoglobin |
MbO2 |
oxymyoglobin |
oxymyoglobin |
M-CDK |
M-cyclin-CDK complex |
M-phase CDK |
Mcm proteins |
minichromosome maintenance proteins |
Mcm proteins |
M-cyclin |
M-kinase-cyclin complex |
M-cyclin |
M-kinase |
mitosis-phase kinase |
M-kinase |
Mur |
muramic acid |
muramic acid |
Mur2Ac (also NAM) |
N-acetylmuramic acid |
N-acetylmuramic acid |
NAD |
nicotinamide adenine dinucleotide |
nicotinamide adenine dinucleotide or the nicotinamide coenzyme NAD |
NAD+ |
oxidized NAD |
NAD+ |
NADH |
reduced (hydrogenated) NAD |
reduced (or hydrogenated) NAD or NADH |
NADH hydrogenase |
NADH hydrogenase |
|
NADP |
NAD phosphate |
NAD phosphate or NADP |
NADPH |
reduced (hydrogenated) NADP |
reduced (or hydrogenated) NADP or NADPH |
NAG |
(see GlcNAc above) |
|
Neu5Ac |
N-acetylneuraminic acid (sialic acid) |
N-acetylneuraminic acid |
NF-κB |
nuclear factor–κB |
nuclear factor–κB |
NMDA |
N-methyl-d-aspartate |
N-methyl-d-aspartate |
NMN |
nicotinamide mononucleotide |
nicotinamide mononucleotide |
NMN+ |
oxidized NMN |
NMN+ |
NMNH |
reduced (hydrogenated) NMN |
reduced or hydrogenated NMN |
NMP |
nucleoside monophosphate |
nucleoside monophosphate |
NOx |
nitrogen oxides, such as nitrate, nitrite, and nitrosothiols; nitric oxide (NO) metabolites |
nitrogen oxides |
NPY |
neuropeptide Y |
neuropeptide Y |
NT-proBNP |
N-terminal fragment of the prohormone brain natriuretic peptide (see 15.6.1, Genetics, Nucleic Acids and Amino Acids under “Amino Acids”) |
N-terminal fragment of the prohormone brain natriuretic peptide |
p16Ink4, p15Ink4B, p18Ink4C, p19Ink4D |
INK4s |
the INK4 p16Ink4, etc |
p21 |
21-kDa protein |
the protein p21 |
p21WAFI/CIP1, p27KIP1, p57KIP2 |
other CDKI; WAFI: wild type p53-activated protein 1; CIP1: CDK-interacting protein 1; KIP: kinase inhibitor protein |
the CDKI p21WAFI/CIP1, etc |
p53 |
53-kDa protein |
the protein p53 (or simply p53 if a similarly named protein has already been introduced) |
p57 |
57-kDa protein |
the protein p57 (or p57) |
PE, PPE |
protein or gene family named for amino acid sequence motif (PE: Pro-Glu, PPE: Pro-Pro-Glu); see 15.6.1, Genetics, Nucleic Acids and Amino Acids |
PE and PPE protein families, PE/PPE gene families, etc |
P-gp |
P-glycoprotein |
P-glycoprotein |
Pi |
inorganic phosphate |
inorganic phosphate |
PI |
phosphatidylinositol |
phosphatidylinositol |
PIP2 |
phosphatidylinositol 4,5-bisphosphate |
phosphatidylinositol 4,5-bisphosphate |
Pol |
polymerase (eg, DNA, RNA) |
polymerase |
PPi |
inorganic pyrophosphate |
inorganic pyrophosphate |
pRb |
retinoblastoma protein |
retinoblastoma protein |
PYY3-36 |
NPY receptor agonist (P: peptide; Y: NPY; Y: Y2 receptor; 3–36: 34 amino acid residue numbers) |
peptide YY3-36, the gut hormone PYY3-36 |
RANKL |
receptor-activated nuclear factor–κB ligand |
receptor-activated nuclear factor–κB ligand |
RecA protein, RecA |
recombinase A |
recombinase A |
RNAi |
RNA interference |
RNA interference |
R point |
restriction point (of cell cycle) |
R point |
RNase |
ribonuclease |
ribonuclease |
rTpo |
recombinant thrombopoietin |
recombinant thrombopoietin |
S |
DNA synthesis phase of cell cycle |
S phase or DNA synthesis phase |
S-cyclin |
S-kinase-cyclin complex |
S-cyclin |
sFlt-1 |
soluble fms-like tyrosine kinase 1 (fms: McDonough feline sarcoma [oncogene]) |
soluble fms-like tyrosine kinase 1 |
S-kinase |
synthesis-phase kinase |
S-kinase |
αSp22 |
22-kDa glycosylated form of α-synuclein |
22-kDa glycosylated α-synuclein |
αSyn |
α-synuclein |
α-synuclein |
TAF |
TBP-associated factor |
TATA-binding protein (TBP)–associated factor |
TAFII |
a class of TAFs |
a class of factors associated with TBP |
TATA box |
a DNA sequence rich in adenine (A) and thymidine (T) |
TATA box |
TBP |
TATA-binding protein |
TATA-binding protein |
TFIID |
complex of TBP and several TAFIIs |
TBP-TAFII complex |
UCP-1, UCP-2, UCP-3 |
uncoupling proteins |
uncoupling protein 1, etc |
UDP-Gal |
uridine diphosphate galactose |
UDP-galactose |
UDP-Glc |
UDP-glucose |
UDP-glucose |
uE3 |
unconjugated estriol |
unconjugated E3 |
Wnt |
named for Drosophila melanogaster wingless mutant integration site |
the developmental protein Wnt, the Wnt signaling pathway, etc |
Letter prefixes (including Greek letters) and numeric prefixes are linked to the main term by hyphens.
α1-antitrypsin
β-catenin
γ-tubulin
glucose 6-phosphate
However, these terms are not hyphenated:
α helix
β sheet
Hyphens are added in adjectival usages, eg:
β-pleated sheet
glucose-6-phosphate dehydrogenase
Hyphens are used as follows in numbers that interrupt a word:
propan-1,2-diol (propanol)
flavan-3-ol
For letter or number suffixes, hyphens typically are not used with expanded terms but are handled in various ways with abbreviated terms (see examples in sections cited in Table 13):
interleukin 1 (IL-1)
phosphodiesterase 3A (PDE3A)
6-keto prostaglandin F1α(6-keto PGF1α)
The chemical prefixes d and l are small capitals when referring to biomolecules, such as amino acids and carbohydrates, in the d/l system of configuration:
l-folinic acid
d-glyceraldehyde
Element symbols in chemical names, such as S (sulfur) and N (nitrogen), are italicized. Other capital letters are not italicized.
N-acetyl-d-glucosamine
cytochrome P450
N-terminal, C-terminal
A subscript letter indicates a modifier of the main term.
Pi(inorganic phosphate)
Plus signs and minus signs indicating charges are set superscript. Numerals indicating quantities of an element within a molecule are set subscript. Numerals indicating a charge are superscript.
Fe3+
Proteins are often expressed as p plus a numeral signifying the atomic weight in kilodaltons, eg, p53, a 53-kDa protein. Affixes, such as superscripts, further specify the protein (important because different proteins may have the same weight). See the examples in Table 13. Although the gene symbols for such proteins are often given as the same term italicized, eg, the tumor suppressor gene p53, the correct gene symbols should be used, eg, in humans TP53; in mice, Tp53. Use the search feature at the HUGO Gene Nomenclature Committee website (http://www.gene.ucl.ac.uk/nomenclature/; see also 15.6, Genetics).
The term stem cell has the general meaning of a precursor, pluripotent, or progenitor cell. Research articles should specify the type(s) of stem cell referred to, eg, adult, embryonic, germline, hematopoietic, mesenchymal, neural, peripheral blood, somatic, umbilical cord–derived, unrestricted somatic, and so forth. (The preceding terms are not all mutually exclusive.)
Terms in Table 13 are included as a reference. Some context or explanation of such terms is desirable at first mention, but, in contrast to abbreviations (see 14.0, Abbreviations), first mention need not be a literal expansion and the term may be stated as an appositive, rather than in parentheses, eg:
the cyclin-dependent kinase CDK2
When an abbreviation is used in the Suggested Usage at First Mention column, it is assumed that in the article the abbreviated term has already been introduced and defined or expanded; eg, if INK4 is defined as “inhibitors of CDK4” at first mention, it is assumed that CDK4 was previously defined or expanded. Providing more information is often helpful. For instance, at first mention, p21 may be referred to as “the protein p21” or “the CDKI protein p21” or given additional context.