Introduction to Proteins

What are proteins made of?

Amino acids linked by peptide bonds.

What determines protein function?

Amino acid sequence and resulting 3D conformation.

What is a ligand?

A molecule that binds to a protein with specificity and affinity.

What are enzymes?

Proteins that catalyse biochemical reactions with high specificity.

What are glycoproteins?

Proteins modified with carbohydrates.

What are lipoproteins?

Proteins modified with lipids.

How many standard amino acids exist?

Twenty.

What is the general structure of an amino acid?

Central carbon with amino group

What makes glycine unique?

Its R group is hydrogen

What makes proline unique?

Its R group bonds to the amino group

What is chirality in amino acids?

Existence of L‑ and D‑enantiomers; proteins use L‑amino acids.

What determines amino acid classification?

Side chain properties such as charge

What are hydrophobic amino acids?

Non‑polar residues that cluster inside proteins.

What are hydrophilic amino acids?

Polar or charged residues that interact with water.

What is a zwitterion?

An amino acid with both positive and negative charges at physiological pH.

What is a peptide bond?

A covalent bond between the amino group of one amino acid and the carboxyl group of another.

Why is the peptide bond rigid?

It has partial double‑bond character due to resonance.

What are phi (φ) and psi (ψ) angles?

Rotation angles around the Cα–N and Cα–C bonds that determine backbone conformation.

What is primary protein structure?

The linear sequence of amino acids.

What is secondary protein structure?

Local folding patterns such as α‑helices and β‑sheets.

What is tertiary protein structure?

The overall 3D shape of a single polypeptide.

What is quaternary protein structure?

Association of multiple polypeptide chains into a complex.

What stabilises protein structure?

Hydrogen bonds

What is an α‑helix?

A right‑handed helix stabilised by hydrogen bonds every four residues.

Why does proline break α‑helices?

Its rigid structure disrupts hydrogen bonding.

What is a β‑sheet?

A structure formed by hydrogen bonding between adjacent polypeptide strands.

What is the difference between parallel and antiparallel β‑sheets?

Parallel strands run in the same direction; antiparallel run in opposite directions.

What are loops or coils?

Non‑repetitive connecting regions between secondary structures.

What are protein domains?

Independently folding regions with specific structural or functional roles.

What are structural motifs?

Super‑secondary structures such as helix‑turn‑helix or β‑hairpins.

What is a functional domain?

A region responsible for a specific activity

What is a structural domain?

A stable folding unit of ~40+ amino acids.

What are globular proteins?

Compact

What are fibrous proteins?

Elongated

What is collagen?

A triple‑helix protein with repeating Gly‑Pro‑X sequences.

What are integral membrane proteins?

Proteins embedded in membranes

What determines protein folding?

Amino acid sequence and thermodynamic stability.

What are chaperones?

Proteins that assist in correct folding of other proteins.

What diseases involve misfolded proteins?

Alzheimer’s disease (amyloid plaques).

Where are hydrophobic residues usually found?

Buried in the protein core.

Where are polar and charged residues usually found?

On the protein surface exposed to water.

What are disulphide bonds?

Covalent bonds between cysteine residues that stabilise protein structure.

Where do disulphide bonds form?

In the oxidising environment of the endoplasmic reticulum.

What is haemagglutinin?

A viral protein with multiple domains

What is myosin?

A motor protein functioning as a dimer.

Why are domains important?

They allow modular function and independent folding.

What are protein families?

Groups of evolutionarily related proteins with similar structure and function.

Why is protein structure important for drug development?

Drugs bind specific protein structures; understanding structure enables rational drug design.

How does aspirin work?

It covalently modifies cyclooxygenase enzymes to reduce prostaglandin production.

How are proteins degraded?

Via the ubiquitin‑proteasome pathway.

What is ubiquitination?

Attachment of multiple ubiquitin molecules to a protein to target it for degradation.

What is the proteasome?

A large complex that degrades ubiquitinated proteins into peptides.

What biomarkers indicate myocardial infarction?

Creatine kinase and troponin released from damaged cardiac muscle.