Proteins and Peptide Bonds – Lecture Review

These flashcards review key points on peptide bonds, protein structure levels, classifications, folding forces, examples of functional proteins, and analytical methods, providing a comprehensive study aid for the protein lecture.

What type of reaction links two amino acids to form a peptide bond?

A condensation (dehydration) reaction that releases water.

During peptide bond formation, which groups of adjacent amino acids react?

The α-carboxyl group of one amino acid reacts with the α-amino group of the next.

In a polypeptide chain, what do the N-terminus and C-terminus represent?

The free α-amino end (N-terminus) and the free α-carboxyl end (C-terminus), respectively.

Why is rotation around the C–N peptide bond restricted?

Resonance gives the C–N bond partial double-bond character, making it rigid.

What are the φ (phi) and ψ (psi) angles in proteins?

They are the angles of rotation around the N–Cα (φ) and Cα–C (ψ) single bonds.

Name the three broad size categories of amino-acid chains.

Peptide (≈3–20 aa), polypeptide (≈20–1000 aa), and protein (>1000 aa or functional chain).

Which 20 stereochemical form of amino acids is used in proteins?

The α-L-amino acids.

What are the three chemical classes of proteins based on composition?

Simple proteins, conjugated (compound) proteins, and derived proteins.

Give an example of a conjugated protein and its prosthetic group.

Hemoglobin; its prosthetic group is heme.

How do fibrous and globular proteins differ in solubility?

Fibrous proteins are generally insoluble; globular proteins are usually soluble in aqueous fluids.

Provide two examples of fibrous proteins.

Collagen and keratin.

Provide two examples of globular proteins.

Hemoglobin and egg albumin.

Which covalent cross-link stabilizes many proteins, and between which residue(s) does it form?

A disulfide bond forms between two cysteine residues.

Define a native protein.

A protein in its original, fully folded, biologically active conformation.

List three common agents that can denature proteins.

Heat, extreme pH (acids or bases), and chemical solvents (e.g., urea, SDS).

Does denaturation break peptide bonds?

No; primary structure remains intact, but non-covalent interactions (and sometimes disulfides) are disrupted.

What drives proper protein folding into its lowest free-energy conformation?

Many weak non-covalent interactions such as hydrogen bonds, hydrophobic interactions, electrostatic forces, and van der Waals forces.

What is the main stabilizing interaction of an α-helix?

Hydrogen bonds between the carbonyl oxygen of residue n and the amide hydrogen of residue n+4.

Why are proline and glycine often helix breakers?

Proline’s rigid ring prevents φ rotation and its N lacks a hydrogen for H-bonding; glycine’s high flexibility destabilizes helix geometry.

How do β-sheets differ from α-helices in hydrogen-bond pattern?

β-sheets form H-bonds between adjacent strands, whereas α-helices form H-bonds within a single coil.

Differentiate parallel and antiparallel β-sheets.

Parallel strands run N→C in the same direction; antiparallel strands run in opposite directions (N→C vs C→N).

Which three amino acids play key roles in tertiary structure and why?

Cysteine (forms disulfide bridges), proline (induces bends), glycine (adds flexibility).

Name four interactions stabilizing tertiary structure.

Hydrophobic interactions, hydrogen bonds, electrostatic (salt-bridge) interactions, and disulfide bonds.

Define quaternary structure.

The arrangement and interaction of multiple polypeptide subunits in a multi-chain protein.

How many subunits compose adult hemoglobin and of what types?

Four subunits: two α-globin and two β-globin chains.

What is a protein domain?

An independently folding, structurally distinct region of a polypeptide that often confers a specific function.

What structure results when a protein has two identical subunits?

A homodimer.

Give an example of a protein assembly that forms long helical fibers in muscle.

Actin filaments.

What genetic mutation causes sickle-cell anemia?

A single amino acid change (Glu→Val) at position 6 of the β-globin chain of hemoglobin.

Why do sickled red blood cells cause organ damage?

They polymerize under low O₂, become rigid, block capillaries, and impede blood flow.

Name the six major functional classes of proteins highlighted in the notes.

Enzymic, structural, transport, storage, regulatory (signal), and defense proteins.

Provide two examples of transport proteins and their cargo.

Hemoglobin (oxygen) and transferrin (iron).

Which storage protein stores iron inside cells?

Ferritin.

Give two peptide hormones that regulate blood glucose.

Insulin and glucagon.

What class of proteins includes antibodies?

Defense proteins (immunoglobulins).

Which vitamin acts as a cofactor to prevent scurvy by aiding collagen maturation?

Vitamin C (ascorbic acid).

What laboratory technique separates proteins by size to estimate molecular weight and detect quaternary structure?

SDS-PAGE (polyacrylamide gel electrophoresis in the presence of SDS).

Which physical method can directly visualize large protein complexes at up to 100,000× magnification?

Electron microscopy.

Why is rotation around the φ and ψ angles important?

It permits the polypeptide backbone to fold into α-helices, β-sheets, and other conformations critical for function.