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Contents

Molecular Terms: Considerations and Examples 

Chapter:
Nomenclature
Author(s):

Harriet S. Meyer

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

acyl-S-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

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)

HMG-CoA

β-hydroxy-β-methylglutaryl-CoA

β-hydroxy-β-methylglutaryl–coenzyme A

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 F(6-keto PGF)

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.

HCO3

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.

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