Biochemistry: Proteins - Their Primary Structure and Biological Functions

Vocabulary practice flashcards covering protein structures, analytical separation techniques, sequencing methods, mass spectrometry, homologous alignments, chemical synthesis, and ligand-binding kinetics from Chapter 5 of Garrett and Grisham's Biochemistry.

Fibrous proteins

Proteins characterized by relatively simple, regular, linear structures that typically serve structural roles in cells and are often insoluble in water.

Globular proteins

Proteins that are folded into compact, roughly spherical shapes and are typically soluble in aqueous solution.

Membrane proteins

Proteins associated with cellular membranes that fold so that their hydrophobic amino acid side chains are exposed in the membrane-embedded regions.

Primary structure ($1^\circ$)

The first level of protein structure, defined as the specific linear sequence of amino acid residues in a polypeptide chain.

Secondary structure ($2^\circ$)

Local backbone structural arrangements in a protein that are stabilized by hydrogen bonds, most notably the $\alpha$-helix and $\beta$-pleated strand.

Tertiary structure ($3^\circ$)

The overall three-dimensional arrangement formed when a polypeptide chain folds into a compact, distinct conformation.

Quaternary structure ($4^\circ$)

The organization and spatial arrangement of multiple individual polypeptide subunits within an oligomeric protein complex.

Conformation

The overall three-dimensional shape of a molecule that can be altered by rotation around single bonds without breaking any chemical bonds.

Configuration

The geometric arrangement of atoms in a molecule that cannot be altered without breaking and remaking covalent bonds.

Isoelectric point ($\text{pI}$)

The pH value at which a protein carries no net electrical charge, representing the pH condition where the protein is typically least soluble.

Salting-in

The phenomenon in which the addition of low concentrations of salt increases the solubility of a protein by stabilizing ionic charges.

Salting-out

The precipitation of proteins from solution that occurs at high salt concentrations due to competition between protein molecules and excess salt ions for solvating water.

Specific activity

The total catalytic activity of an enzyme per milligram of total protein, serving as a measure of enzyme purity during purification.

Dialysis

A separation procedure in which a macromolecular solution is placed inside a semipermeable bag bathed in solvent, allowing small diffusible solutes to equilibrate across the membrane while retaining large proteins.

Ion exchange chromatography

A chromatographic method used to fractionate proteins based on differences in their net electrical surface charge at a chosen pH.

Gel filtration chromatography

A size-exclusion separation method wherein larger molecules are excluded from porous resin beads and elute sooner, whereas smaller molecules enter the pores and are retarded.

Sodium dodecyl sulfate (SDS)

An anionic surfactant that binds to and denatures proteins, imparting a uniform negative charge-to-mass ratio to enable electrophoretic separation based strictly on molecular weight.

Isoelectric focusing (IEF)

An electrophoresis technique that separates proteins by charge within a stable pH gradient gel until each species reaches the pH where its net charge is zero.

Two-dimensional gel electrophoresis

A protein separation technique coupling isoelectric focusing in the first dimension (charge separation) with SDS-PAGE in the second dimension (size separation).

Affinity chromatography

A high-resolution purification method that utilizes the specific, noncovalent binding interaction between a target protein and a small ligand molecule covalently attached to an insoluble column matrix.

Performic acid oxidation

A chemical reaction that cleaves disulfide ($\text{S}-\text{S}$) cross-bridges oxidatively to generate stable, negatively charged cysteic acid residues.

Edman degradation

A sequential sequencing technique using phenylisothiocyanate to covalently label and cleave the N-terminal amino acid as a phenylthiohydantoin (PTH) derivative without hydrolyzing other peptide bonds.

Carboxypeptidase A

An exopeptidase used for C-terminal sequencing that hydrolyzes the C-terminal amino acid from a polypeptide chain, but cannot cleave proline, arginine, or lysine.

Carboxypeptidase B

An exopeptidase isolated from hog pancreas that specifically cleaves only basic C-terminal residues (arginine and lysine).

Trypsin

An endopeptidase that selectively cleaves peptide bonds on the carboxyl side of positively charged lysine and arginine residues, provided the following residue is not proline.

Chymotrypsin

An endopeptidase that hydrolyzes peptide bonds on the carboxyl side of bulky aromatic residues (phenylalanine, tryptophan, and tyrosine) as well as leucine.

Cyanogen bromide ($\text{CNBr}$)

A chemical reagent that specifically cleaves peptide chains on the carboxyl side of methionine residues, converting each cleaved methionine into a C-terminal homoserine lactone residue.

Electrospray ionization mass spectrometry (ESI-MS)

A soft ionization mass spectrometry method in which macromolecular solutions are dispersed through an electric field to create highly charged intact gaseous ions differing by single proton additions.

MALDI-TOF MS

Matrix-Assisted Laser Desorption Ionization-Time of Flight mass spectrometry, a sensitive technique that uses laser excitation of a matrix-embedded protein to produce singly protonated gas-phase ions.

Tandem mass spectrometry (MS/MS)

A two-stage mass spectrometry method where a specific precursor ion is isolated in MS-1, fragmented by collision-induced dissociation in a collision cell, and analyzed in MS-2 to deduce amino acid sequence.

BLOSUM62

A scoring matrix commonly used with BLAST that assigns probability log-odds scores for all possible amino acid substitutions based on observed substitution frequencies in blocks of related proteins.

Orthologous proteins

Homologous proteins in different species that perform identical biological functions and evolved from a common ancestral gene via speciation.

Solid-phase peptide synthesis (SPPS)

A laboratory method developed by R. Bruce Merrifield where polypeptides are synthesized in a $C\rightarrow N$ direction while the growing chain is anchored to an insoluble resin support.

Prosthetic group

A tightly bound non-amino acid chemical group permanently attached to a conjugated protein that is required for the protein to carry out its biological activity.

Post-translational modifications (PTMs)

Covalent chemical alterations introduced into specific amino acid side chains or terminal groups of a protein following its ribosomal translation.

Dissociation constant ($K_D$)

An equilibrium constant quantifying binding affinity, equivalent to the free ligand concentration ($[L]$) required to achieve half-maximal saturation of the protein ($\nu = 0.5$).

Proteome

The entire complement of proteins expressed by a cell, tissue, or organism at a specific point in time under designated environmental conditions.