Transcript Lab 1 activity, AMINO ACIDS - Cal State LA

On a FREE AMINO ACID, what functional groups will accept or donate
protons at pH 7, and hence are normally charged in water?
side chain groups
-OH
-CH3
-C
O
-NH2
-COOH
AA’s are zwitterions at pH 7, because they have oppositely charged groups
the group “COOH” would be a
very strong acid
in fact, this group is always
deprotonated, and thus exists
as a weak base, COO-
amino acids are salts with high melting points, because as they crystallize,
ionic interactions stabilize the crystal lattice
Titration curve for alanine
pK1 = 2.4
pK2 = 9.9
pIAla = isoelectric point
pKa values
of
amino acid
ionizable
groups
Which amino acid side chains are positively charged at pH 7?
Which amino acid side chains are negatively charged at pH 7?
Which amino acid side chains can act as H-bond donors?
Which amino acid side chains can act as H-bond acceptors?
Aliphatic side chains
Aromatic side chains
Proline has a nitrogen in an
aliphatic ring system
• Proline (Pro, P) - has a three
carbon side chain bonded to
the a-amino nitrogen
• The heterocyclic pyrrolidine
ring restricts the geometry of
polypeptides
Methionine and cysteine
Cys can participate in S-S bonds that covalently link different parts of
a polypeptide chain to stabilize the 3D structure of a protein
Side Chains with Alcohol Groups
- can donate & accept H-bonds, but are NOT charged!
- can be phosphorylated by kinase enzymes
Acidic or polar side chains
Basic amino acids
Side chain of arginine
Due to resonance, all lone pairs are partially occupied by the
proton in its normal, positively charged state
Peptide bond between two amino acids
Peptide bond shown as a C-N
single bond
Peptide bond shown as a
double bond
Actual structure is a hybrid of
the two resonance forms
w/ delocalized electrons
Planar peptide groups in a protein
• Rotation around C-N bond is restricted due to 40% double-bond
nature of the resonance hybrid form
• Peptide groups (blue planes) are therefore planar; restrict
conformations possible in protein chains
features of the peptide backbone
What parts of this polypeptide are charged at pH 7 ?
What groups can accept H-bonds?
What groups can donate H-bonds?
[ Hint: what is different for a peptide versus a free amino acid? ]
draw your amino acids as part of a peptide backbone, not as free aa’s,
on your homework and quizzes!!
Both backbone and side chain groups participate in important intra- and intermolecular binding interactions
- some are responsible for folding
protein into correct 2D and 3D
shape
- others bind to small molecules
like enzyme cofactors & substrates
Features of protein secondary structure (commonly encountered folding patterns)
like b-sheets are due to repeated H-bonding between backbone groups of a protein