Polar &/or Charged Carbon-Containing Molecules/Groups

Biochem Outcome 2 Cluster

bicarbonate

derived from carbon dioxide via the carbon anhydrase reaction & functions both as a potential proton-absorbing buffer compound & as a source of carbon for metabolic carboxylation reactions

formate

important single-carbon anion, being the deprotonated conjugate base of formic acid (H₂CO₂)

formyl group

derived from formate, also common

carbonyl group

any carbon atom double-bonded to an oxygen atom; carbonyl groups may be found in either a ketone or aldehyde form

carobonyls

are also often found within other groups, e.g., carboxyl & carboxamide groups

carbonyl (aldehyde)

carbonyl (ketone)

carboxyl groups

the most common ionizable weak acid group found in biomolecules & can reversibly interconvert between a polar, protonated form & a charged (anionic) deprotonated conjugate base form

deprotonated (anionic) form

the predominant form at neutral or near-neutral pH

many key metabolic intermediates are

carboxylic acids (or more precisely carboxylates, when in their deprotonated conjugate base forms, that would predominate in biological aqueous solutions)

α-ketoglutarate & oxaloacetate

also contain additional ketone carbonyl groups

α-ketoglutarate

citrate

malate

oxaloacetate

acetic acid

2-carbon compound that acts as a weak acid & will be predominantly deprotonated to the anionic conjugate base acetate at neutral or near-neutral pH; acetyl groups are also derived from acetate

acetyl coenzyme A (acetyl CoA)

metabolically most important form of acetate/acetyl, which features an acetyl group joined in a thioester linkage to coenzyme A

Coenzyme A

the thioester S atom + everything else to the right

thioester group

essentially a substituted form of the much more common ester groups, with the sulfur replacing an oxygen in the ester

“thio-”

refers to sulfur

ethers

closely related to ethers

thioester linkage or group (R₁-CO-S-R₂)

ester linkage or group (R₁-CO-O-R₂)

phosphate ester

another important substituted ester

phospho-monoester

phospho-diester

thioether linkage or group (R₁-S-R₂)

ether linkage or group (R₁-O-R₂)

acetyl group