Biochemistry: Amino Acids and Peptide Bonds

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Questions and Answers

What type of glycosylation involves the -OH of Thr and Ser?

Phosphorylation

O-linked (correct)

C-linked

N-linked

What is the primary structure of a protein?

The sequence of amino acids in a peptide chain (correct)

The folding of a peptide chain into a β-pleated sheet

The quaternary structure of a protein

The 3D structure of a protein

What is the function of hydrogen bonds in an α-helix?

To form disulphide bridges

To stabilise the α-helix structure (correct)

To hold the peptide chain in a β-pleated sheet

To form an electrostatic interaction

What type of β-sheet structure is widespread in globular proteins?

β-Hairpin bend Signup and view all the answers

What is the function of collagen triple helix?

To provide tensile strength to connective tissue Signup and view all the answers

What is the quaternary structure of haemoglobin?

α2β2 Signup and view all the answers

What is the percentage of α-helix structure in haemoglobin?

60% Signup and view all the answers

What is the type of protein that has a high percentage of β-sheet structure?

Fibrillar protein Signup and view all the answers

What is the primary function of the peptide bond in proteins?

To provide a covalent linkage between amino acids Signup and view all the answers

What type of bond is involved in the interaction between the δ– and δ+ charges?

Van der Waals force Signup and view all the answers

What is the role of the nitrogen and oxygen atoms in the peptide bond?

They form hydrogen bonds with other peptide units Signup and view all the answers

What is the main structural feature of an α-helix?

A spiral, helical structure Signup and view all the answers

Which of the following is an example of a hydrogen bond acceptor?

C=O carbonyl (peptide bond) Signup and view all the answers

What type of interactions are responsible for maintaining the tertiary structure of proteins?

Both covalent and non-covalent interactions Signup and view all the answers

What is the approximate energy of a hydrogen bond?

12 kJ mol-1 Signup and view all the answers

Which of the following is an example of an electrostatic interaction?

Attraction between COO- and NH3+ Signup and view all the answers

What is the significance of conformation in determining the biological functions of proteins?

Conformation determines biological function in all proteins Signup and view all the answers

What is the result of defects in amino acid metabolism and mis-folding?

Disease Signup and view all the answers

What is the primary reason for hydrophobic regions of a protein folding in a particular way?

To minimize contact with the aqueous environment Signup and view all the answers

What is the distance at which Van der Waals forces operate?

Equal to 0.28 nm Signup and view all the answers

What is the function of the NH3⁺ group in a polypeptide?

To mark the N-terminal end of the polypeptide Signup and view all the answers

Which of the following is NOT an example of a hydrogen bond donor?

C=O (peptide bond) Signup and view all the answers

What type of modification is involved in the formation of disulphide bridges?

Post-translational modification Signup and view all the answers

What is the term for the unequal distribution of electrons in a covalent bond?

Dipole effect Signup and view all the answers

What is the primary reason for the sensitivity of proteins to denaturation?

Their sensitivity to changes in pH, temperature, and ionic strength Signup and view all the answers

What is the main factor that determines the final structure of a protein?

The sequence of amino acids Signup and view all the answers

Why is misfolding of proteins associated with disease?

Because it disrupts the normal function of the protein Signup and view all the answers

What is the primary reason for the stability of proteins?

The stabilization energy provided by the environment Signup and view all the answers

What is the main consequence of denaturation of proteins?

A loss of function of the protein Signup and view all the answers

What is the primary role of the amino acid sequence in protein folding?

To encode the final structure and the pathway to that structure Signup and view all the answers

Study Notes

Protein Structure and Function

Proteins perform various biological functions, including structural, movement, enzymatic, transport, membrane transport, hormonal, receptor, defense, and gene regulation.
Examples of proteins and their functions:
- Structural: collagen, keratin
- Movement: actin, myosin
- Enzymes: trypsin, DNA polymerase
- Transport: haemoglobin, transferrin
- Membrane transport: Na+/K+ pump
- Hormones: insulin
- Receptors: acetyl choline receptor
- Defence: antibodies, clotting factors
- Gene regulation: histones
- Chromosome separation: tubulin

Amino Acids and Polypeptides

Amino acids have a specific structure, with a NH3+ group at the N-terminal end and a COO- group at the C-terminal end.
Amino acid side chains can form various interactions, including hydrogen bonds, ionic, van der Waals, and hydrophobic interactions.
Disulphide (S-S) bridges can form between two cysteine residues, joining subunits together (e.g., insulin).
Glycosylation can occur, with O-linked and N-linked modifications.

Protein Structure

3D structure has four levels: primary, secondary, tertiary, and quaternary.
Primary structure: sequence of amino acids in the peptide chain.
Secondary structure: folding/coiling of the peptide chain, often into α-helix or β-pleated sheet.
Tertiary structure: peptide chain folds upon itself, forming a 3D structure.
Quaternary structure: folded peptide chains join together to form a functional protein.

α-Helix

Formed by hydrogen bonds between peptide bonds in the same polypeptide chain.
Hydrogen bonds formed between peptide bond carbonyl-O and H of N-H every 4th peptide.
Regular right-handed helix, with 3.6 residues per turn, stabilized by hydrogen bonds.
R groups on the outside, forming a rigid cylinder shape that provides architectural support for the protein.

β-Pleated Sheets

Linear peptide chains held together by hydrogen bonds between peptide chains.
Side chains in each strand alternate above and below the plane of the sheet.
Antiparallel and parallel β sheet structures exist.

Collagen Triple Helix

Three chains held together by hydrogen bonds between chains.
Found in collagen, with a left-handed helix and 3 residues per turn.
Gly-X-Y-Gly-X-Y-Gly sequence, with X mainly proline and Y mainly hydroxy-proline.

Tertiary and Quaternary Structure

Tertiary structure: how the whole polypeptide (subunit) is folded in 3D, consisting of different supersecondary structures (domains).
Quaternary structure: how the whole functional protein is formed in 3D, possibly consisting of multiple subunits (e.g., haemoglobin α2β2).

Forces that Stabilize Protein Structure

Covalent: disulphide bridges.
Non-covalent: hydrogen bonds, electrostatic interactions, van der Waals forces, and the hydrophobic effect.

Hydrogen Bonds

Formed between two electronegative atoms competing for the same H atom.
Hydrogen bond donors (D): O, N, and NH3+.
Hydrogen bond acceptors (A): O, N, and =N-.

Electrostatic Interactions

Between charged side chains: Asp/Glu carboxyl groups (COO-) and Lys/Arg amino groups (NH3+).

Van der Waals Forces

The sum of attractive or repulsive forces between molecules, excluding covalent bonds, hydrogen bonds, and electrostatic interactions.
Dependent on dipole effects caused by the unequal distribution of electrons.

Hydrophobic Effects

Hydrophobic regions of a protein fold to minimize contact with the aqueous environment, unable to form hydrogen bonds.

Protein Structure and Folding

The amount of stabilization energy in a protein is quite small, making them sensitive to denaturation by pH, temperature, and ionic strength.
Amino acid sequence encodes the final structure and the pathway that leads to that structure.
Misfolding can cause disease.

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Description

This quiz covers the foundational principles of biochemistry, focusing on the structures and functions of amino acids, peptide bonds, and their importance in protein structure.