Lecture 5 Protein Structure and Function

Question 1

How does the sequence of amino acids influence protein structure?

Answer 1

The sequence determines the folding pattern, which forms the protein’s structure.

Question 2

What happens at the first level of protein formation?

Answer 2

Linear sequence of amino acids

Question 3

What happens at the second level of protein formation?

Answer 3

⍺-helix, β-strands, and β-turns

Question 4

What happens at the third level of protein formation?

Answer 4

Folded 3D structures of secondary motifs

Question 5

What happens at the fourth level of protein formation?

Answer 5

Assembly of multiple polypeptides

Question 6

What is the N-terminus of a polypeptide?

Answer 6

It begins the polypeptide chain, marked by the free amino group (-NH2).

Question 7

What is the C-terminus of a polypeptide?

Answer 7

It is the end of the polypeptide chain, marked by the free carboxyl group (-COOH).

Question 8

What are the characteristics of peptide bonds? (3)

Answer 8

Polar and uncharged

Rigid and planar due to resonance

Little rotation around the bond

Question 8

What is a peptide bond?

Answer 8

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

Question 9

What is the role of hydrogen bonds in α-helices and how do they form?

Answer 9

They stabilize the helix by forming between the carbonyl oxygen of one amino acid and the amine hydrogen of another four residues away.

Question 10

Why is Proline a helix breaker?

Answer 10

Proline’s rigid structure disrupts the proper angle formation for the α-helix and prevents hydrogen bonding.

Question 11

What are β-sheets, how do they form and what are the different ways the strands of the sheets can be arranged?

Answer 11

β-sheets are formed by hydrogen bonds between the carbonyls and amines of β-strands. These strands can run parallel or antiparallel.

Question 11

What are β-turns, and where are they found?

Answer 11

Short 4-residue segments that allow the polypeptide chain to reverse direction, are often found on the surface of globular proteins.

Question 12

What is a disulfide bond and what are their significance?

Answer 12

A covalent bond between the sulfur atoms of two cysteine residues, stabilizing protein structure.

Question 13

What types of interactions stabilize tertiary structures?

Answer 13

Electrostatic (ionic) interactions
Hydrogen bonds
Hydrophobic interactions
Van der Waals forces

Question 14

What is a quaternary structure in proteins?

Answer 14

The arrangement of multiple polypeptide chains into a multi-subunit structure.

Question 15

What is the role of chaperones in protein folding?

Answer 15

They prevent aggregation of unfolded proteins by binding to exposed hydrophobic regions.

Question 16

What is protein denaturation and what is the significance of this?

Answer 16

The disruption of weak forces maintaining a protein’s structure, leading to loss of function.

Question 17

What is the hydrophobic effect and how does it affect protein folding?

Answer 17

Non-polar amino acids cluster together inside the protein to avoid water, driving folding.

Question 18

How do post-translational modifications (PTMs) affect protein structure?

Answer 18

PTMs can alter interactions between amino acids, changing the tertiary or quaternary structure.