Lecture 5

Question 1

What ae amino acid residues?

Answer 1

When amino acids are bonded together in a peptide or protein they are referred to as amino acid residues

Question 2

How do polypeptide chains occur in proteins?

Answer 2

Each protein is made up of at least one polypeptide chain, they can have several chain but proteins with one are the most common variety.

Question 3

What does proteins being globular mean?

Answer 3

The main chain. has to double back and form a more complex shape

Question 4

What structures are proteins mostly comprised of?

Answer 4

a-helix B-structure and turns

Question 5

What are the four levels of protein structure?

Answer 5

Primary, secondary, tertiary and quaternary

Question 6

What is the primary structure of a protein?

Answer 6

Amino acid sequence of protein

Question 7

What is the secondary structure of a protein?

Answer 7

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

Question 8

What is the tertiary structure of a protein?

Answer 8

3D structure of a complete protein chain

Question 9

What is the quaternary structure of proteins?

Answer 9

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

Question 10

describe the bonds associated with main and side chains in proteins?

Answer 10

Able to rotate and are somewhat flexible

Question 11

What are the main chain atoms in proteins?

Answer 11

N, Ca, C’

Question 12

What is the bond angle between N and Ca called ?

Answer 12

Phi

Question 13

What is the bond angle between Ca and C’ called?

Answer 13

Psi

Question 14

What is the range in which the atoms bond gle can be?

Answer 14

0 to +/- 180

Question 15

What is the chain angle between C’ and N (peptide bond), name and value?

Answer 15

Omega

Very close to either 180 or 0

Question 16

What causes restriction in Phi and Psi bond angles?

Answer 16

Steric Hindrance, for example…
Phi rotation can lead to O-O collision
Psi rotation an lead to NH-NH collisions

Question 17

Describe features of trans peptide bonds?

Answer 17

Most peptide bonds are trans.
-180 angle
Ca atoms are found on opposite sides of the peptide bond

Question 18

Describe features of. cis peptide bonds?

Answer 18

-0 angle
Ca atoms are found on the same side of peptide bond.
Steric crowding s increased

Question 19

How do rotations and turns effect protein shape?

Answer 19

The combination of all the rotations and twists
around all the bonds in a protein leads to its
overall three-dimensional structure, which in turn,
leads to the arrangement of all the side chains in
the protein, which in turn leads to its function.

Question 20

What two canonical structures are involved in secondary space?

Answer 20

a-helix and B-strand or B-sheet

Question 21

Structure of a-helix?

Answer 21

The main chain spirals around the central axis like a right handed spiral staircase

Question 22

What makes the a-helix structure stable?

Answer 22

Non-covalent interaction called a hydrogen bond between the amide hydrogen which has a partial positive charge and the carbonyl oxygen which has a partial negative charge

Question 23

Properties if a-helix?

Answer 23

3.6 residues per turn
5.4A rise per turn
Each residue us 1.5A
Side chains point out from the helix axis; help stabilise the a-helix
Stabilising hydrogen bonds, 3-7 kcal/mol or 12-28 kJ/mol
Phi/psi angles tend to cluster around -57
Some residues are “helix breakers” eg glycine & Proline
Helix itself has a dipole (positive at N terminus)