BCH 201: Introductory Chemistry, Classification, Biological Functions, and Purification of Proteins

Comprehensive vocabulary flashcards covering the introductory chemistry, structural levels, functional classes, biological roles, and laboratory isolation, purification, and identification techniques of proteins.

Peptide Bond Formation

The condensation reaction between the $\alpha$-amino group of one amino acid (or imino group of proline) and the $\alpha$-carboxyl group of another, accompanied by the concomitant loss of a water molecule ($-H_2O$) to form a rigid, planar covalent bond.

Four Levels of Protein Structure

The structural hierarchy describing protein architecture: Primary (linear amino acid sequence), Secondary (local folding like $\alpha$-helices and $\beta$-pleated sheets), Tertiary (overall three-dimensional conformation of a single chain), and Quaternary (assembly of two or more polypeptide subunits).

Protein Isolation, Purification, and Identification Stages

The multistep process of obtaining characterized proteins, consisting of: 1. Protein Isolation (sample preparation, cell lysis, clarification, and crude extraction), 2. Protein Purification (precipitation, chromatography, and pooling/concentration), and 3. Protein Identification (determining molecular weight, obtaining sequence information, searching databases, and confirming identity).

Conjugated Proteins

Proteins containing an amino acid component (apoprotein) linked to a non-protein prosthetic group, classified into categories such as glycoproteins, lipoproteins, phosphoproteins, metalloproteins, haemoproteins/chromoproteins, flavoproteins, and nucleoproteins.

Protein

A high-molecular-weight biological macromolecule consisting of one or more polypeptide chains composed of amino acid residues linked by peptide bonds, typically containing more than 50 amino acid residues.

Primary Structure

The specific linear sequence of amino acid residues in a polypeptide chain, dictated by the base sequence of corresponding genes and stabilized by covalent peptide bonds and optional disulfide linkages.

Secondary Structure

Regular local folding patterns of the polypeptide backbone, predominantly $\alpha$-helices and $\beta$-pleated sheets, stabilized by hydrogen bonds between backbone carbonyl ($C=O$) and amide ($N-H$) groups.

Tertiary Structure

The overall three-dimensional arrangement of a single polypeptide chain, stabilized by hydrophobic interactions, hydrogen bonds, ionic interactions/salt bridges, van der Waals forces, and covalent disulfide bridges ($-S-S-$).

Quaternary Structure

The arrangement and non-covalent (and occasionally disulfide) interactions of two or more distinct polypeptide chains (subunits) into a functional oligomeric protein complex.

Simple Proteins

Proteins that yield mainly amino acids upon complete hydrolysis; examples include albumins, globulins, prolamins, glutelins, scleroproteins, histones, and protamines.

Derived Proteins

Modification products formed from native proteins via physical or chemical treatments or enzymatic cleavage, categorized into primary derived proteins (proteans, metaproteins, coagulated proteins) and secondary derived proteins (proteoses, peptones, peptides).

Fibrous Proteins

Water-insoluble structural proteins consisting of elongated cable-like arrangements formed completely from helical or sheet structures, exhibiting high mechanical strength (e.g., collagen, keratin, and elastin).

Globular Proteins

Compact, approximately spherical, water-soluble proteins that contain mixtures of secondary structures and perform dynamic functions (e.g., enzymes, haemoglobin, myoglobin, and antibodies).

Protein Denaturation

The unfolding and loss of organized three-dimensional native structure, leading to decreased aqueous solubility, increased proteolytic susceptibility, and loss of biological activity due to heat, extreme $pH$, detergents, or heavy-metal ions.

Salting Out

A classical fractionation procedure in which high concentrations of a neutral salt (commonly ammonium sulphate) decrease protein solubility by competing for water, causing proteins to selectively precipitate.

Isoelectric Point ($pI$)

The specific $pH$ value at which an amino acid or protein possesses zero net electrical charge, characterized by minimized electrostatic repulsion and lowest aqueous solubility.

Dialysis

A separation method utilizing a semipermeable membrane that retains large macromolecules while allowing small solutes (salts, metabolites, buffer components) to diffuse out across a concentration gradient.

Ultrafiltration

A pressure-driven or centrifugal membrane separation method using defined molecular-weight cutoffs to rapidly concentrate protein solutions and exchange buffers.

Ion-Exchange Chromatography

A chromatographic technique that separates proteins on the basis of differences in their net surface electrical charge at a selected $pH$.

Size-Exclusion Chromatography

A chromatographic method separating proteins based on molecular size and hydrodynamic volume using porous beads; larger proteins bypass pores to elute first, while smaller proteins enter pores and elute later.

Affinity Chromatography

A high-resolution purification method that exploits the unique, reversible biological binding interaction between a target protein and a stationary-phase ligand or substrate analogue.

Hydrophobic-Interaction Chromatography (HIC)

A separation method based on differences in exposed non-polar patches on proteins; binding is promoted at high salt concentrations and elution is carried out by decreasing ionic strength.

SDS-PAGE

Sodium dodecyl sulphate-polyacrylamide gel electrophoresis; a technique where proteins are denatured and given a uniform negative charge by SDS, allowing electrophoretic separation strictly by molecular weight.

Isoelectric Focusing (IEF)

An electrophoretic method separating proteins along an established $pH$ gradient according to their individual isoelectric points ($pI$), where migration halts as net electrical charge reaches zero.

Two-Dimensional Electrophoresis

A high-resolution analytical tool combining isoelectric focusing in the first dimension (separation by $pI$) with SDS-PAGE in the second dimension (separation by molecular weight).

Biuret Test

A colorimetric chemical assay wherein peptide bonds coordinate with cupric ($Cu^{2+}$) ions in alkaline medium to generate a characteristic violet or purple complex.

Ninhydrin Test

A chemical reaction detecting free $\alpha$-amino acids by producing a purple/blue compound, while producing a distinct colour with cyclic imino acids such as proline.

Xanthoproteic Test

A biochemical test detecting aromatic amino acid residues (tyrosine, tryptophan, phenylalanine) through the nitration of benzene rings with concentrated acid to produce yellow/orange coloured derivatives.

Millon's Test

A specific colorimetric assay detecting the phenolic hydroxyl group of tyrosine residues, yielding a characteristic red-coloured product.

Hopkins-Cole Test

A qualitative biochemical test for identifying tryptophan residues through a specific reaction involving the indole ring under strongly acidic conditions.

Bradford Assay

A spectrophotometric method for protein quantification that relies on the absorbance shift of Coomassie Brilliant Blue dye upon binding to basic and aromatic amino acid residues.

Edman Degradation

A chemical protein-sequencing procedure that sequentially labels and cleaves the $N$-terminal amino acid residue one at a time without hydrolysing the remaining polypeptide chain.

Specific Activity

The ratio of total enzyme catalytic activity units to the total mass of protein in a sample ($\text{units/mg protein}$), used as the key index to measure purity and purification fold.