3D Structure of Proteins

Question 1

4 Interactions in Proteins

Answer 1

1. Hydrophobic Effect
2. Hydrogen Bonds: lead to alpha helix and beta sheet structures
3. London Dispersion: Weak interactions between atoms contributes to stability of interior of the protein
4. Electrostatic Interactions: Strong interactions

Question 2

What are the repeating atoms in the peptide backbone

Answer 2

N-C-C

Question 3

Characteristics of the peptide bond

Answer 3

• Planar
• Polar
• Rigid
• Limited rotation around peptide bond
• Behaves like a double bond

Question 4

what bond is the peptide bond (atom wise)

Answer 4

C-N bond

Question 5

Why is rotation around the peptide bond not permitted

Answer 5

Due to the resonance structure

Question 6

Rotations around what bonds are permitted

Answer 6

Rotations around bonds connected to the alpha carbon are permitted:
* The alpha carbon - carbon bond (carbonyl carbon bond)
* The alpha carbon - nitrogen bond (amide nitrogen bond)

Question 7

What does secondary structure refer to

Answer 7

1. Local spatial arrangement
2. Interactions within the polypeptide backbone

Question 8

What are both alpha helices and beta sheets stabilised by

Answer 8

hydrogen bonds

Question 9

What is irregular arrangement of the polypeptide chain called

Answer 9

Random coil

Question 10

Which AAs are strong helix formers

Answer 10

Alanine (Ala)
Leucine (Leu)

Question 11

What AAs are helix breakers and why (2)

Answer 11

1. Proline (Pro): the rotation around the alpha carbon - nitrogen bond is impossible
2. Glycine (Gly): the tiny R group supports other conformations (R group = H)

Question 12

What creates a pleated sheet like structure

Answer 12

1. The planarity of the peptide bond
2. The tetrahedral geometry of the alpha carbon

Question 13

What are beta sheets held together by

Answer 13

The hydrogen bonding of amide and carbonyl groups of the peptide bond from opposite strands

Question 14

Characteristic of the h. bonds in parallel beta sheets

Answer 14

The hydrogen bonds between strands are bent and therefore weaker

Question 15

Characteristic of the h. bonds in antiparallel beta sheets

Answer 15

The h. bonds between sheets are linear (straight) and therefore stronger

Question 16

What AAs are common in beta turns

Answer 16

Proline & Glycine

Question 17

What does tertiary structure refer to

Answer 17

the overall 3D spatial arrangement of atoms in a protein

Question 18

what is the tertiary structure stabilised by

Answer 18

Multiple weak interations between AA side chains:
* Mostly hydrophobic and polar interactions
* Can be stabilised by disulphide bonds

Question 19

Structure of collagen (a fibrous protein)

Answer 19

• Triple alpha helix coming together into a collagen fibril
• Triple helices crosslinked to form collagen fibrils
• Triple helix gives rigidity

Question 20

What is the structre of silk fibroin

Answer 20

Antiparallel beta sheet structure results in soft, flexible filaments

Question 21

How is the quaternary structure formed

Answer 21

The assembly of individual polypeptides into a larger functional cluster

Question 22

4 ways proteins can be denatured

Answer 22

1. Heat/cold
2. Extremes of pH
3. Organic solvents
4. Chaotropic agents: e.g: urea

Question 23

Function of chaperones in protein folding

Answer 23

Aid in folding protein into its native conformation.
They prevent misfolding & aggregation of unfolded peptides.
(Disaggregation, remodeling, folding)