BIOC*2580 Midterm: Amino Acids, Proteins, Ionization, Chromatography & Catalysis

Vocabulary practice cards covering biochemical concepts, amino acid side chains and classifications, ionization principles, chromatography techniques, reagents, and enzymatic catalytic mechanisms.

Ninhydrin

A chemical reagent that detects free amino groups, producing a purple colour with most amino acids and a yellow colour with proline.

Cyanogen bromide

A chemical reagent that specifically cleaves peptide bonds at the carboxyl side of methionine residues.

Urea

A chemical denaturant that unfolds proteins by weakening the hydrophobic effect.

2-Mercaptoethanol

A reducing agent that breaks and reduces disulfide ($S-S$) bonds in proteins.

PITC (Phenylisothiocyanate)

Edman's reagent, used in Edman degradation to identify the N-terminal amino acid during protein sequencing.

Trypsin

A proteolytic enzyme that cleaves peptide bonds after lysine (Lys, K) and arginine (Arg, R) residues.

Peptide bond

A covalent amide bond ($-C(=O)-NH-$) formed between the carboxyl group of one amino acid and the amino group of another.

Condensation reaction

A dehydration reaction that joins two molecules together with the loss of $H_2O$, such as the formation of a peptide bond.

Hydrolysis reaction

A cleavage reaction that breaks a covalent bond using a molecule of $H_2O$, regenerating free amino and carboxyl groups.

Primary structure

The linear sequence of amino acids in a polypeptide chain, read from the N-terminus to the C-terminus.

Secondary structure

Local conformations of the polypeptide backbone, predominantly forming regular repeating structures such as $\alpha$-helices and $\beta$-sheets.

Tertiary structure

The overall three-dimensional spatial arrangement and fold of a single polypeptide chain.

Quaternary structure

The three-dimensional spatial arrangement and subunit association of multiple folded polypeptide chains.

$\beta$-barrel

A protein structural fold in which multiple $\beta$-strands curve around into a closed barrel-like structure.

$\alpha/\beta$ fold

A three-dimensional protein fold containing an arrangement of both $\alpha$-helices and $\beta$-sheets.

Alanine (Ala, A)

A very non-polar amino acid featuring a single methyl side chain ($-CH_3$).

Valine (Val, V)

A very non-polar amino acid containing a branched isopropyl side chain ($-CH(CH_3)_2$).

Leucine (Leu, L)

A very non-polar amino acid with an isobutyl side chain ($-CH_2-CH(CH_3)_2$).

Isoleucine (Ile, I)

A very non-polar amino acid with a sec-butyl side chain ($-CH(CH_3)-CH_2-CH_3$).

Methionine (Met, M)

A very non-polar, sulfur-containing amino acid with a thioether side chain ($-CH_2-CH_2-S-CH_3$).

Phenylalanine (Phe, F)

A very non-polar amino acid possessing a benzyl side chain ($-CH_2-\text{phenyl ring}$).

Glycine (Gly, G)

A moderately non-polar amino acid whose side chain is a single hydrogen atom ($R = H$).

Cysteine (Cys, C)

A moderately non-polar, sulfur-containing amino acid containing an ionizable thiol side chain ($-CH_2-SH$).

Proline (Pro, P)

A moderately non-polar cyclic amino acid whose aliphatic side chain loops back to covalently bond to the backbone $\alpha$-nitrogen.

Tyrosine (Tyr, Y)

A moderately non-polar aromatic amino acid containing a polar, ionizable para-hydroxyl group on its phenol side chain.

Tryptophan (Trp, W)

A moderately non-polar aromatic amino acid containing a bicyclic fused ring system with an indole nitrogen.

Serine (Ser, S)

A polar, uncharged amino acid possessing a primary hydroxyl side chain ($-CH_2-OH$).

Threonine (Thr, T)

A polar, uncharged amino acid possessing a secondary branched hydroxyl side chain ($-CH(OH)-CH_3$).

Asparagine (Asn, N)

A polar, uncharged amino acid containing a terminal carboxamide side chain ($-CH_2-CONH_2$).

Glutamine (Gln, Q)

A polar, uncharged amino acid containing a terminal carboxamide side chain ($-CH_2-CH_2-CONH_2$) with one more carbon than asparagine.

Histidine (His, H)

A basic, positively charged/ionizable amino acid with an imidazole ring side chain; predominantly neutral at physiological $pH = 7$.

Lysine (Lys, K)

A positively charged amino acid containing a primary amino group at the end of an aliphatic four-carbon chain ($-(CH_2)_4-NH_3^+$).

Arginine (Arg, R)

A positively charged amino acid featuring a resonance-stabilized, nitrogen-rich guanidinium group.

Aspartate (Asp, D)

A negatively charged amino acid at neutral pH with a carboxylate side chain ($-CH_2-COO^-$).

Glutamate (Glu, E)

A negatively charged amino acid at neutral pH with a carboxylate side chain containing two methylene groups ($-CH_2-CH_2-COO^-$).

Hydrogen bond

An electrostatic attraction between an electronegative donor covalently bonded to a hydrogen atom and an electronegative acceptor possessing an available lone pair.

pH

A logarithmic measure of hydrogen ion concentration and availability, defined by the formula $pH = -\log_{10}[H^+]$.

pKa

The pH threshold at which a specific ionizable functional group exists in an exact $1:1$ ratio of protonated to deprotonated states ($50\%$ protonated, $50\%$ deprotonated).

Henderson–Hasselbalch equation

The equation used to determine solution pH or the ionization ratio of a buffer: $pH = pKa + \log_{10}\left(\frac{[\text{deprotonated}]}{[\text{protonated}]}\right)$.

Hydrophobic effect

The thermodynamic driving force that directs non-polar side chains into the interior core of a folding water-soluble protein away from aqueous solvent.

Retention factor ($R_f$)

A unitless chromatographic value calculated as $R_f = \frac{\text{distance travelled by compound}}{\text{distance travelled by solvent front}}$.

Cation-exchange chromatography

A charge-based separation method utilizing a negatively charged stationary phase resin to bind positively charged molecules.

Anion-exchange chromatography

A charge-based separation method utilizing a positively charged stationary phase resin to bind negatively charged molecules.

Electrophilic catalysis

A catalytic mechanism wherein the catalyst speeds up a reaction by withdrawing or accepting electron density.

Nucleophilic catalysis

A catalytic mechanism wherein the catalyst donates an electron pair to form a transient covalent bond with the reactant.

General acid catalysis

A catalytic mechanism in which a catalyst enhances the reaction rate by donating a proton ($H^+$).

General base catalysis

A catalytic mechanism in which a catalyst enhances the reaction rate by abstracting or removing a proton ($H^+$).