Download Amino Acids 2

Amino Acids & Side Groups

Polar Charged
◦ ACIDIC negatively charged amino acids
 ASP & GLU
R group with a 2nd COOH that ionizes* above
pH 7.0

Polar Charged
◦ BASIC positively charged amino acids
 LYS, ARG, HIS
 R group with a 2nd amide* that protonates below pH 7.0
Acidic Side Chains
Basic Side Chains
Acidic vs. Basic
Polar Charged
Amino Acids & Side Groups

Polar Uncharged
◦ THR, TYR, ASN, GLN
(cys)
 are soluble in water, i.e., hydrophilic (attract Hbonds)
 Contain hydroxyl or amino functional groups
Polar Uncharged
Hydroxyl
Polar Uncharged II
Amino Functional Groups
Polar Uncharged Amino Acids
Amino Acids & Side Groups

NON-POLAR (aliphatic)
◦ Includes GLY, ALA, VAL, LEU, ILE, PRO
 all contain only hydrocarbons
groups = hydrophobicity

AROMATIC (hydrophobic non-polars)
◦ PHE & TRP
(TYR)
 all contain R groups with
Sulfur*

R groups with sulfur
◦ MET, CYS
ring structures* or
Non-Polar
Hydrocarbon R-Groups
Non-Polar
Aromatic R-Groups
Non-Polar
Sulfur R Groups
Alpha Helix
Beta-pleated sheets

The most common polypeptide helix
•

Stabilized by extensive
hydrogen bonding
•

Hydrogen bonds extend up from the
oxygen from the carbonyl group to
the NH group of a peptide linkage
•
◦ This was shown in class via the visuals


There are approximately 4 peptide
bond links up stream between the
atoms involved in the hydrogen
bonds
Each turn of an alpha helix contains
3.6 amino acids.
•
Unlike the alpha helix, composed
of two or more peptide chains
Polypeptide chains are joined by
hydrogen bonds
When the hydrogen bonds are
formed between the polypeptide
chains they are termed
interchains.
The polypeptide chains can run
parallel to each other or antiparallel
– Recall the “ends” of a polypeptide
chain
• C-terminus
• N-terminus/Amino-terminus
Secondary Protein Structures
Alpha Helix
Beta-pleated sheets
Beta-pleated Sheets and Alzheimer’s
Disease
•
•
The amyloid protein, a class of fibrous
proteins, is deposited in the brain.
Individuals, that have Alzheimer’s Disease,
have the amyloid protein composed of
twisted Beta-pleated sheet fibrils whose
three-dimentional structure is virtually
identical to that of silk fibrils
– Silk
• Contain Beta-pleated sheet protein structures
Tertiary Structure

Interactions stabilizing Tertiary Structures
◦ Four were mentioned in class




Disulfide Bonds
Hydrophobic interactions
Hydrogen bonds
Ionic interactions
Disulfide Bonds
A disulfide bond is a covalent linkage formed by
the sulfhydryl group (-SH) of two cysteine
residues to form cystine
• The folding of the polypeptide chain brings the
cysteine residues near each other
• Disulfide linkage contributes to the stability of the
three-dimensional shape of the protein molecule
• Disulfide bonds are found in proteins that are
secreted by cells
•
– Thought that these strong covalent bonds help
stabilize the structure of proteins and help prevent
them from becoming denatured in the extra-cellular
environment
Hydrophobic Interactions
•
Recall that amino acids with non-polar side
chains tend to be located in the interior of
the polypeptide
– Here, they associate with other hydrophobic
amino acids
•
Special Note
– Proteins located in non-polar (lipid)
environments such as the phopholipid bilayer,
tend to be in an opposite form
• Hydrophobic amino acids are located on the surface
• Hydrophilic amino acids are located on the interior
Ionic Interactions

Negatively charged groups interact with
positively charged groups
◦ Negatively charged groups
 (-COO-) in the side chain of aspartate or glutamate
◦ Positively charged groups
 (-NH3+) in the side chain of lysine
Dipole Moment
Dipole Moment is
the measure of a
molecule’s overall
polarity
 μ=Q*r

◦ μ = Dipole Moment
◦ Q = charge
◦ r = distance between
charges

Measured in debyes
(\də-ˈbī\ )
Van der Waals Forces

A weak attractive
force between atoms
or non-polar
molecules caused by
a temporary change
in dipole moment
◦ Arising from a brief
shift of orbital
electrons to one side
of one atom or
molecule, creating a
similar shift in adjacent
atoms or molecules.