Structure of Proteins

Question 1

What weak (non covalent) bonds are there in proteins

Answer 1

-The hydrophobic effect
-Hydrogen bonds
-London dispersion
-Electrostatic interactions

Question 2

Where are hydrogen bonds in protein structure?

Answer 2

Interactions of N-H and C=O of peptide bond leads to local regular structures such as alpha helicies and ß sheets

Question 3

Where does London dispersion effect in proteins?

Answer 3

Medium-range weak attraction between all atoms contributes significantly to the stability in interior of protein

Question 4

Can the C-N bond rotate?

Answer 4

No. Rotation around the C-N bond is restricted due to the double-bond character of the resonance hybrid form - acts as a double bond

Question 5

What are the bonds that can rotate?

Answer 5

Rotation around bonds connected to the alpha carbon are permitted. Not around the peptide bond.

Question 6

What are the angles of rotation around the alpha bonds?

Answer 6

o (phi) is angle around the alpha carbon - amide bond
Y (psi) is angle around the alpha carbon - carbonyl carbon bond

Question 7

Why are some o and Y combinations unfavourable?

Answer 7

Because of steric crowding of backbone atoms with other atoms in the back bone or side chain

Question 8

Why are some o and Y combinations more favourable?

Answer 8

Because of chance to form favorable H-bonding interactions along the backbone

Question 9

What are the 2 regular arrangements in the secondary structure of proteins?

Answer 9

-alpha helix - stabilised by hydrogen bonds between nearby structures
-ß sheet- stabilised by hyfdrogen bonds between adjacent segments that may not be nearby

Question 10

How are alpha helices held together?

Answer 10

By hydrogen bonds between the backbone amides of an n and n+4 amino acid

N-H group of 1 hydrogen bonds with O-C of 4

Question 11

What kind of helix is the alpha helix and how many residues does it have per turn?

Answer 11

A right handed helix with 3.6 residues per turn

Question 12

What are the orientations of the peptide bonds and side chains in alpha helix

Answer 12

-Peptide bonds aligned parallel with helical axis
-Side chains point out and roughly perpendicular w helix

Question 13

What kind of amino acids are strong helix formers?

Answer 13

Small hydrophobic residues like Alanine and Leucine are strong helix formers

Question 14

What amino acids act as helix breakers and why?

Answer 14

Proline acts as a helix breaker because the rotation around the N-C (alpha c) bond is impossible - proline found at bend of alpha helix
Glycine acts as helical breaker because the tiny R group supports other conformations

Question 15

What will affect the formation of alpha helices?

Answer 15

Attractive or repulsive interactions between side chains 3 to 4 amino acids apart

Question 16

What often occur near the positive end of helix dipole?

Answer 16

Negatively charged residues

Question 17

What creates the pleated sheet like structure of ß sheets?

Answer 17

-The planarity of the peptide bond and tetrahedral geometry of the alpha carbon.
-Side chains protrude from the sheet, alternating in an up and down direction

Question 18

How are ß sheets held together?

Answer 18

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

Question 19

Parallel ß sheets VS Antiparallel ß sheets

Answer 19

-In parallel- hydrogen bonded strands are in same direction- h bonds between strands are bent=weaker
-In antiparallel- hydrogen bonded strands are in opposite directions- h bonds between strands are linear=stronger

Question 20

When do ß turns occur? How many amino acids does it take for a 180 turn?

Answer 20

Occur whenever strands in ß sheets change direction
Accomplished over 4 amino acids

Question 21

How is the turn stabilised?

Answer 21

By a hydrogen bond between a carbonyl oxygen and amide proton three residues down the sequence

Question 22

What amino acid is common in i) position 2 and ii) position 3 in ßturns?

Answer 22

Proline in pos 2
Glycine in pos 3

Question 23

What are the 2 major classes of tertiary structure protein?

Answer 23

fibrous and globular

Question 24

What is tertairy protein structure?

Answer 24

Refers to overall 3D spatial arrangement of atoms in a protein

Question 25

How is teriary structue stabilised?

Answer 25

By numerous weak interactions between AA side chains
-Largely hydrophobic and polar interactions
-can be stabilised by disulphide bonds

Question 26

What is collagen a repeat sequence of and what kind of helix is it?

Answer 26

Gly-X-Pro or Gly-X-4-Hyp
Left handed helical structure w 3 residues per turn
3 collagen chains intertwine into a right-handed superhelical triple helix

Question 27

How are collagen fibrils formed?

Answer 27

Crosslinks (covalent bonds between lysine or HyLys hydroxyl lysine or histidine) of triple-helices

Question 28

How does permanent waving of hair work chemically?

Answer 28

Disrupt the disulphide bridges in hair strands with oxidation reduction reaction

Question 29

What is the main protein in silk from moths and spiders? and how is it structured?

Answer 29

Fibroin
-Antiparallel ß sheet struture
-Small side chains of ala and gly allow close packing of sheets

Question 30

What is Quaternary structure?

Answer 30

Formed by the assembly of individual polypeptides into a larger functional cluster

Question 31

What is the role of chaperones?

Answer 31

Prevent misfolding and aggregation of misfolded proteins