Peptide Structure-1 - UCLA Chemistry and Biochemistry

Peptide Structure:
The Building Blocks of Life
Peptides are short polymers of amino acids linked by peptide (amide) bonds.
 What is an amino acid?
o An amino acid is a molecule containing…
 an amine group
 a carboxylic acid
 a side chain (R-varies)
α­carbon
•
There are 20 standard amino acids (standard meaning that they are directly coded for by
DNA)
 All except Proline are primary amines.

All have a stereocenter with R-configuration at the alpha carbon
 Except Cysteine, which has an S- configuration.
 Except Glycine which is achiral (i.e. has no stereocenter).
•
Amino acids have varying side chains (R), and thus are categorized by their side chains.


Hydrophilic vs. Hydrophobic
o This property is determined by the polarity of the side
chain.
 “Like dissolves Like”
• Polar - Hydrophilic
• Non-Polar – Hydrophobic
Acidic vs. Non-acidic vs. Basic
o This property is determined by comparison to water
(pka=15.7)
•
•
•
More acidic than water: Acidic
Lone pairs ready to accept a proton: Basic
Every thing else: Non-acidic
 What is a Peptide bond?
o A Peptide bond links two amino acids together.

Formed when the carboxyl group of one amino acid reacts with the amine
group of another amino acid.
 One molecule of water is released per bond formed.
o Peptide bonds provide stability.
 Torsional Strain: Cis vs. Trans
• Equilibrium favors Trans: The largest
groups are furthest apart.
 Conjugation: Peptide bond
• Creates a Barrier to Rotation
• Every conjugated atom and those
directly bonded to them, stay Planar.
• This creates multiple flat areas (not all in the same plane) within
the peptide molecule, stabilizing the Peptide structure.
 Peptide Structure is classified into four levels:




Primary Structure
Secondary Structure
Tertiary Structure
Quaternary Structure
 Primary Structure:
o Refers to the sequence in which the amino acids are bonded from N-terminus to
C-terminus.
N‐
Terminus
C‐Terminus
Gly
Ser
Val
 Secondary Structure:
o Intramolecular Hydrogen bonds cause three different motifs:
 α-Helix
 β-Sheet
 Coil
• α-Helix

Clockwise spiral down

Hydrogen Bonds between the carboxyl oxygen
and the amine hydrogen 4 residues away.

Side chains point away from the coil
• β-Sheet
C‐Terminus

Hydrogen Bonds not
always
paralle
l to
each
other.

Side chains stick out above
and below the chain.

More rigid and less elastic
than α-Helix.
N‐Terminus
N‐Terminus
N‐Terminus
• Coil
• Not Random, just complicated.
 Tertiary Structure:
o 3D positions of atoms in space.
• Determined by the side chain and how it interacts with the
environment.
 Hydrophilic side chain:
• Polar environment: points out
• Non polar environment: points in
 Hydrophobic side chain:
• Polar environment: points in
• Non polar environment: points out
o Disulfide Bonds impact the 3D structures of proteins.


•
Form a loop in one chain
Bond two separate chains
ONLY CYSTINE forms disulfide bonds because a sulfur-hydrogen bond is
required.
 Quaternary Structure:
o
Association of subunits (i.e. proteins etc.) by
Non covalent Molecular Bonds:
•
•
Hydrogen Bonds
London Forces
References
Chemistry 14C Lecture supplement
Images: Google and ChemDoodle
Wikipedia
http://en.wikipedia.org/wiki/Amino_acid
http://en.wikipedia.org/wiki/Peptide