Biochemistry: Carbon Chemistry, Functional Groups, and Amino Acids

Comprehensive vocabulary flashcards covering the chemical structures of organic functional groups, classifications of standard amino acids, stereoisomeric properties, posttranslational modifications, and protein diversity.

Hydroxyl Group

A polar, water-soluble functional group ($R\text{—}OH$) that forms hydrogen bonds; found in carbohydrates and the side chains of serine, threonine, and tyrosine.

Carbonyl Group

A polar functional group consisting of a carbon-oxygen double bond found in aldehydes ($R\text{—}C(=O)\text{—}H$) and ketones ($R\text{—}C(=O)\text{—}R'$); commonly present in sugars.

Carboxyl Group

A weakly acidic functional group ($R\text{—}COOH$) that donates a proton to bear a negative charge ($-COO^-$) at physiological pH; found in amino acids, proteins, and lipids.

Amino Group

A weakly basic functional group ($R\text{—}NH_2$) that accepts a proton to bear a positive charge ($-NH_3^+$) at physiological pH; found in proteins and nucleic acids.

Amido Group

A polar functional group ($R\text{—}C(=O)\text{—}NH_2$) found in amides that does not carry a formal charge; present in the side chains of asparagine and glutamine.

Thiol Group

An easily oxidized functional group ($R\text{—}SH$) found in cysteine that readily reacts to form covalent disulfide ($-S\text{—}S-$) bonds.

Ester

A functional group with the general chemical formula $R\text{—}C(=O)\text{—}O\text{—}R'$, found characteristically in certain lipid molecules.

Alkene

A functional group containing a carbon-carbon double bond ($RCH=CHR'$) that serves as an important structural component of biomolecules such as lipids.

Peptide

A low-molecular-weight amino acid chain typically consisting of fewer than $50$ amino acids.

Polypeptide

A polymer of amino acid residues with molecular weights ranging from several thousand to several million daltons.

Protein

A biological macromolecule consisting of one or more polypeptide chains folded into a specific, biologically functional three-dimensional conformation.

Amphoteric

The property of a molecule that enables it to behave chemically as either an acid or a base, as observed in amino acids containing both carboxyl and amino groups.

Zwitterion

A dipolar molecule carrying both positive and negative charges simultaneously while possessing a net electrical charge of zero, as amino acids do at pH $7$.

Proline

The only standard amino acid with a secondary amino group, formed by a covalent ring closure between its aliphatic hydrocarbon side chain and the amino nitrogen.

Aliphatic Hydrocarbons

Nonaromatic hydrocarbons, such as methane and cyclohexane, that compose the nonpolar side chains of alanine, valine, leucine, isoleucine, and proline.

Aromatic Amino Acids

Amino acids including phenylalanine, tyrosine, and tryptophan that contain cyclic structures with planar conjugated electron clouds.

S-adenosylmethionine (SAM)

A vital metabolic derivative of methionine containing a thioether linkage that functions as a primary methyl donor in biochemical reactions.

Cystine

A covalently linked dimer formed when the sulfhydryl ($-SH$) groups of two cysteine residues oxidize in the extracellular compartment to yield a disulfide bond.

Guanidino Group

The basic functional group found on the arginine side chain with a $pK_a$ range of $11.5$ to $12.5$, rendering it permanently protonated at physiological pH.

Imidazole Group

The aromatic, weakly basic nitrogenous side chain of histidine with a $pK_a$ of approximately $6$, allowing it to reversibly donate or accept protons near physiological pH.

$\gamma$-Carboxyglutamic Acid

A posttranslationally modified, calcium-binding amino acid residue found in the blood-clotting protein prothrombin.

4-Hydroxyproline

A posttranslationally modified amino acid derivative that serves as a vital structural component of collagen, the most abundant protein in connective tissue.

Chiral Carbon (Asymmetric Carbon)

A carbon atom bonded to four different chemical groups; present at the $\alpha$-carbon of $19$ of the $20$ standard amino acids (all except glycine).

Enantiomers

Stereoisomers that are non-superimposable mirror images of each other and exhibit identical physical properties except for the direction in which they rotate plane-polarized light.

Dextrorotatory

The property of an optical isomer that rotates plane-polarized light in a clockwise direction, designated by $(+)$.

Levorotatory

The property of an optical isomer that rotates plane-polarized light in a counterclockwise direction, designated by $(-)$.

GroEL/GroES Chaperonin

A large multi-subunit protein complex found in Escherichia coli that assists and promotes the accurate folding of nascent polypeptides.

Rubisco

The enzyme responsible for fixing atmospheric carbon dioxide by incorporating $CO_2$ into organic molecules.

Cyclooxygenase

An enzyme that catalyzes the initial step in the biochemical pathway responsible for synthesizing fatty acid derivatives such as prostaglandins.

Ionizable Side Chains

Functional groups found on seven standard amino acids (Asp, Glu, His, Lys, Arg, Tyr, and Cys) that transition between charged and uncharged states depending on the ambient pH and their $pK_a$ values.