Lecture 2 - Protein Structure

Question 1

What is a polypeptide chain

Answer 1

a series of amino acids joined by peptide bonds

Question 2

What is a peptide bond

Answer 2

linking the carboxyl group of one amino acid to the amino group of another amino acid

Question 3

What is the N-terminus of a protein

Answer 3

Amino side (NH3+)

Question 4

What is the C-terminus of a protein

Answer 4

Carboxyl side (COO-)

Question 5

What is a protein residue

Answer 5

each amino acid unit in a polypeptide chain

Question 6

How many amino acids does an average polypeptide chain contain

Answer 6

50-2000 amino acid residues

Question 7

What is the mass of an amino acid

Answer 7

110 Da (1Da~1g/mol

Question 8

What is the mass of most proteins

Answer 8

5500 Da - 220,000 Da

Question 9

Why are almost all peptide bonds in proteins trans

Answer 9

unfavourable steric clashes in the cis form.

Question 10

What are torsion anvles

Answer 10

Rotation about these bonds can be specified by dihedral angles (torsion angles)

Question 11

What is Phi dihedral angle

Answer 11

𝛟 (Phi) = Angle of rotation about the bond between the nitrogen and the α-carbon atom = -80 degrees

Question 12

What is Psi dihedral angle

Answer 12

ᴪ (Psi) = Angle of rotation about the bond between the α-carbon atom and the carbonyl carbon= +85 degrees

Question 13

How are angles assessed

Answer 13

Ramachadran plot - almost 3/4 of possible dihedral angles are excluded due to steric collisions

Question 14

What are some features of an alpha heliz

Answer 14

• Rod-like structure: inner section = tightly coiled backbone; outer section = side chains in a helical array
• Alpha helices are strongly stabilized by hydrogen bonds
• 3.6 residues per helical turn (13 main chain atoms)
• Rise of 5.4 Å per turn (1.5 Å per residue)

Dihedral Angles in an Alpha Helix:
* 𝛟 (Phi) = -57 °
* ᴪ (Psi) = -47 °
Alpha helices have a dipole moment – which can be functionally relevant
- Eg. When N-terminus binds to negatively charged molecules such as phosphates

Question 15

What are some features of Beta-pleated sheets

Answer 15

• Composed of two or more polypeptide chains called β strands
• While ⍺ helices are tightly compact, β strands are almost fully extended
• Distance between adjacent amino acids = 3.5 Å
• Side chains of adjacent amino acids point in opposite directions

Dihedral angles of amino acids in a β strand ;
* 𝛟 = -120 °
* ᴪ = +120 °
β sheets are formed by linking two or more β strands by hydrogen bonds
- Anti parallel sheet = run in opposite directions
- Parallel Sheet = run in the same direction
* β sheets do not have a dipole as dipoles on adjacent amino acids cancel out

• β sheets are also twisted as a compromise
• A ‘tug of war’ exists between conformational energies of the side chain and maximal H-bonding

Question 16

What are Beta turns/hairpin bend/reverse turn

Answer 16

• Proteins are compact and globular and require reversals in the direction of their polypeptide chains
• Turns/loops invariably lie on the surfaces of proteins and often participate in protein-protein interactions