BIOC192 Lecture 5 - Elements of Protein Structure

Question 1

what is the primary structure of a protein?

Answer 1

the amino acid sequence of a protein

Question 2

what is the secondary structure of a protein?

Answer 2

3D arrangement of a protein chain over a short stretch of adjacent amino acid residues

Question 3

what is the tertiary structure of a protein?

Answer 3

3D structure of a complete protein chain

Question 4

what is the quaternary structure of a protein?

Answer 4

interchain packing and structure for a protein that contains multiple protein chains

Question 5

what are the main chain atoms in a protein?

Answer 5

1) N
2) alpha C
3) C’ (carbonyl carbon)

Question 6

what is the range for bond angles?

Answer 6

+/- 180 degrees

Question 7

what are the 3 main chain bond angles?

Answer 7

1) Ф = phi
2) Ψ = psi
3) ω = omega

Question 8

what is the phi angle?

Answer 8

rotation angle around the N-C𝞪 (alpha carbon) bond

Question 9

what is the psi angle?

Answer 9

rotation angle around the C𝞪 (alpha carbon)-C’ (carbonyl carbon) bond

Question 10

what is the omega angle?

Answer 10

rotation angle around the peptide bond

Question 11

what is phi-psi restrictions?

Answer 11

steric hinderance restricts the values of phi-psi angles

Question 12

what is the result of phi-rotation restriction?

Answer 12

phi rotation can lead to O-O collision

Question 13

what is the result of psi-rotation restriction?

Answer 13

psi rotation can lead to NH-NH collisions

Question 14

what are the key properties of an 𝞪-helix?

Answer 14

• spiral is “right handed”
• side chains point out from the helix
• dipole present
• 3.6 residues in a 1 full turn at 5.4 Å per turn
• each residue goes up 1.5 Å

Question 15

what are the key properties of a β structure?

Answer 15

• H-bonding occurs between adjacent chains
• often form a β sheet instead of 2 β-strands
• each strand may have up to 15 residues
• typically 2-10 strands per sheet
• side chains point above and below the sheet
• usually forms an alternating NP-P-NP-P stretch of residues

Question 16

what are the 2 types of interactions in a β sheet?

Answer 16

1) parallel

2) antiparallel

Question 17

what are the key properties of turns?

Answer 17

• usually involve 3-4 residues
• high Gly, Pro content
• almost 30% of residues involved in turns
• hydrogen bond across the turn is common

Question 18

what are helices shown as in drawing protein structures?

Answer 18

shown as spirals or cylinders

Question 19

what are strands shown as in drawing protein structures?

Answer 19

shown as arrows pointing from N to C

Question 20

what are turns and random coils shown as in drawing protein structures?

Answer 20

shown as loops or rope-like stretches

Question 21

how would you orientate a protein?

Answer 21

start by finding the N and then find the alpha carbon and repeat