peptide stuctures

Question 1

How many amino acid chains make aup a protein

Answer 1

normally 1 however can be many (these make up at Quaternary strcture)

Question 2

Define the 4 stages of protein structures

Answer 2

Primary - the aminoa acid sequence
secodary - The short stuctures formed by adjacent sections of amino acids
tertiary - the 3d sturcture of an amino acid chain
Quatinary - the interchain packing of multiple proteins

Question 2

what are the three parts of the main chain amino acid + properties within these sections

Answer 2

Amino N, alpha carbon Ca, Carboxy carbon C’
flexibilty between bonds
between N + Ca = Phi (Φ)
between Ca and C’ = Psi (Ψ)
Between C’ -> N (peptide) = omega (ω)

Question 3

What are the bond angle posibilitys of psi phi and omega

Answer 3

Phi and Psi = +,- 180 degrees
Omega = 0 (cis), 180 (trans) due to planar config of peptide

Question 4

Why is rotation around phi and psi bonds restricted

Answer 4

Steric hinderance
Phi can cause O-O collision
Psi can cause NH-NH collisions

Question 5

name the characteristics of the peptude bond

Answer 5

• trans config
• planar sp2 max pi bond
• dipoled (+NH, -Ve C=O)
• 80Kj/mol rot barrier
• 40% double bond characteriest

Question 6

When is it a peptide bond more linkly to be cis than normal

Answer 6

Bonds preceeding a proline have a 10 % chance to be cis

Question 7

What are the properties of an alpha helix

Answer 7

• Right handed spiral around central axis, N- > C
• H-Bond stabilised between n, n+4 residues between C=O and N-H
• each H-bond has 12-28Kj/mol every to stabilise
• 3.6 residues per turn rising 5.4A
• side chains point outwards
• dipols act in the same direction in the helix
• Glycine + proline break alpha helix structure

Question 8

What can the helix wheel view help with

Answer 8

Determining the properties of an alpha helix, where groups of particular side chains are located
- each side chain is seperated by 100 degrees

Question 8

What is a beta sheet + properties

Answer 8

Made up from adjacent beta strands which H-bond to one annother
make a beta sheet 2-10 strands thick and 6-15 amino acids long
often have P-NP-P-NP… squence

Question 9

How do beta sheets look

Answer 9

betasheets have a right handed twist,
they are pleated structures
Can run parralel with V shaped H-bonds or
antiparralel with perpendicular H-bonds
they have alternating top bottom side chains

Question 10

What are the key properties of turns

Answer 10

• form globular proteins
• hairpin loops often 3-4 residues
• often contain glycine or proline
• 30% of protein residue
• common to have H-bond across turn

Question 11

What is the acepted 3d structure model for proteins

Answer 11

Ribbon model/ Richardson model

• alpha helix shown as spirals, beta sheets as arrows from N-C, turns + coils shown as loop like structures