Proteins 1: Amino Acids, Ionization, and Chirality

These vocabulary flashcards cover the fundamental concepts of protein biochemistry, including amino acid structure, chemical groupings, ionization states based on pH and pKa values, and the principles of chirality.

Biochemistry

The scientific discipline that seeks to explain life at the molecular level, focusing on carbohydrates, proteins, nucleic acids, and lipids.

Proteins

True polymers comprised of amino acids, which serve as the protein monomers.

Enzymes

Protein molecules that serve as catalysts to enhance the rate of chemical reactions without being permanently affected or changed by the reaction.

Alpha carbon ($\alpha$ carbon)

The central carbon atom in the general anatomy of an amino acid to which the carboxyl group, amine group, hydrogen atom, and side chain are attached.

Standard proteinogenic amino acids

The $20$ different amino acids that differ by their side chains ($R$) and whether humans can synthesize them.

Hydrophobic amino acids

A group of $10$ amino acids with nonpolar $R$ groups consisting mainly of hydrocarbon side chains that are overall neutral at physiological $pH$ (approximately $7.4$).

Polar amino acids

Amino acids with neutral overall charges but uneven electron distribution in their $R$ groups; examples include serine, threonine, and tyrosine.

Cysteine

A polar amino acid containing a thiol ($SH$) group that can form covalent disulfide bonds to stabilize protein structure.

Positively-charged (basic) amino acids

Hydrophilic amino acids with side chains containing an amine group that retain a charge at physiological $pH$.

Negatively-charged (acidic) amino acids

Hydrophilic amino acids with side chains containing a carboxyl group that retain a charge at physiological $pH$, typically only charged when $pH$ is approximately $6.1$ or below.

Zwitterion

The dipolar, neutral ionic form of an amino acid existing at $pH\,7$ where the amine group is protonated ($NH_3^+$) and the carboxyl group is deprotonated ($COO^-$).

Cationic form

The ionic form of an amino acid at $pH\,1$ where the net charge is $+1$ due to protonation.

Anionic form

The ionic form of an amino acid at $pH\,13$ where the net charge is $-1$ due to deprotonation.

$$pKa$$

The negative base-$10$ logarithm of the acid dissociation constant ($K_a$) of a solution, defined as $pKa = -\log_{10}K_a$.

$$pH = pKa$$

The point at which $50\%$ of a functional group exists in the acid form and $50\%$ exists in the conjugate base form.

Peptide bond

A covalent bond formed via a condensation reaction by a ribosome that links amino acids together.

Polypeptide

A long linear chain made of many amino acids, specifically consisting of $50$ or more amino acid residues.

N-terminus

The beginning of a polypeptide chain, characterized by a free $\alpha$-amine group.

C-terminus

The end of a polypeptide chain, characterized by a free $\alpha$-carboxyl group.

Histones

Highly positively-charged proteins (approximately $24\%$ lysine and arginine) that interact with negatively-charged DNA.

L amino acids

The specific configurational isomer of amino acids that are the exclusive constituents of proteins and are recognized by eukaryotic enzymes.

Chiral

A property of a molecule that is asymmetric, meaning its structure and mirror image are not superimposable.

Glycine

The only standard proteinogenic amino acid that is achiral rather than chiral.