Biochemistry: Amino Acids, Peptides, and Protein Structure

Flashcards covering key vocabulary, chemical properties, and structural principles of amino acids, peptides, secondary/tertiary/quaternary protein architecture, myoglobin, hemoglobin, and protein folding.

Amino Acid General Structure

A compound containing both an amino group ($\text{--NH}_2$ or $\text{--NH}_3^+$) and a carboxyl group ($\text{--COOH}$ or $\text{--COO}^-$) attached to a central $\alpha$-carbon.

Zwitterion

A dipolar ion carrying spatially separated positive and negative charges resulting in a net electrical charge of zero in neutral solution.

Isoelectric pH ($\text{pI}$)

The specific pH at which the majority of molecules of an amino acid or protein in solution carry no net electrical charge, calculated as $\text{pI} = \frac{1}{2}(\text{pK}_{a1} + \text{pK}_{a2})$.

Guanidine Group

The strongly basic side-chain functional group present in the amino acid arginine.

Imidazole Group

The heterocyclic aromatic amine side-chain functional group present in the amino acid histidine.

Peptide Bond

A covalent amide linkage formed between the $\alpha$-carboxyl group of one amino acid and the $\alpha$-amino group of another with the loss of a water molecule.

Native Conformation

The biologically active three-dimensional spatial structure of a protein under physiological conditions.

Primary Structure ($1^\circ$)

The specific linear sequence of amino acids linked by peptide bonds in a polypeptide chain.

Secondary Structure ($2^\circ$)

The local recurring spatial arrangement of the polypeptide backbone, predominantly stabilized by hydrogen bonds (e.g., $\alpha$-helices and $\beta$-sheets).

$\alpha$-Helix

A common rod-like secondary structure element stabilized by intrachain hydrogen bonds between backbone carbonyl oxygens and amide nitrogens four residues ahead.

$\beta$-Sheet

A secondary structure element composed of extended adjacent polypeptide strands held together by interstrand hydrogen bonds, oriented either parallel or antiparallel.

$\beta$-Bulge

A common non-repetitive irregular secondary structure motif occurring in antiparallel $\beta$-sheets that disrupts regular hydrogen bonding.

Reverse Turn

A secondary structural region that allows a polypeptide chain to abruptly change direction, frequently containing glycine for steric flexibility and proline for its rigid ring structure.

Supersecondary Structure

A recognizable, recurring pattern or arrangement of secondary structure elements connected by loops, such as $\beta\alpha\beta$ units, $\alpha\alpha$ units, $\beta$-meanders, or Greek key motifs.

Collagen Triple Helix

A unique structural motif consisting of three left-handed helical polypeptide chains wrapped around each other in a right-handed superhelix, characterized by repeating $\text{X-Pro-Gly}$ or $\text{X-Hyp-Gly}$ sequences.

Fibrous Proteins

Water-insoluble structural proteins containing polypeptide chains aligned parallel along a single axis to form long fibers or sheets (e.g., keratin, collagen).

Globular Proteins

Water-soluble proteins folded into compact, spherical shapes, displaying polar side chains on the exterior surface and nonpolar side chains buried within the core.

Tertiary Structure ($3^\circ$)

The complete three-dimensional spatial arrangement of all atoms in a single polypeptide chain, stabilized by hydrogen bonds, disulfide bonds, ionic interactions, hydrophobic interactions, and metallic bonds.

Quaternary Structure ($4^\circ$)

The structural arrangement and association of two or more individual polypeptide chains (subunits) into a multi-subunit protein complex.

Oxygen-Binding Curve

A graphical representation of oxygen saturation versus partial pressure ($p\text{O}_2$), which is hyperbolic for myoglobin and sigmoidal for hemoglobin due to cooperative binding.

Denaturation

The unfolding of a protein leading to the loss of its native, biologically active secondary, tertiary, or quaternary structure, caused by agents such as heat, extreme pH, detergents, urea, or guanidine hydrochloride.

Heme

An iron-containing prosthetic group consisting of protoporphyrin IX and a central bound ferrous iron atom ($\text{Fe}^{2+}$) capable of reversibly binding molecular oxygen.

Bohr Effect

The physiological reduction in hemoglobin's oxygen-binding affinity caused by lower pH ($\text{H}^+$ accumulation) and increased $\text{CO}_2$, promoting oxygen release in active tissues.

2,3-Bisphosphoglycerate (BPG)

An allosteric effector that binds to the central cavity of deoxyhemoglobin, stabilizing the T-state and decreasing oxygen affinity.

Molecular Chaperones

Specialized helper proteins (such as Hsp70 and Hsp60) that assist in the correct, timely folding of newly synthesized or unfolded polypeptides and prevent toxic protein aggregation.

Molten Globule

A compact protein folding intermediate characterized by native-like secondary structure but incomplete, dynamic tertiary interactions.

X-ray Crystallography

A structural biology method that determines 3D atomic coordinates from the diffraction patterns of an X-ray beam passed through a protein crystal using Fourier analysis.

Nuclear Magnetic Resonance (NMR) Spectroscopy

A technique used to determine the three-dimensional structures and dynamic behavior of biomolecules in aqueous solution without crystallization.

Alpha Hemoglobin Stabilizing Protein (AHSP)

A specialized molecular chaperone that binds and stabilizes excess free $\alpha$-hemoglobin chains to prevent their precipitation and inclusion body formation during hemoglobin synthesis.