1. Amino acids
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2. Most amino acids are chiral
All naturally occuring amino acids except Gly are the L isomer
L & D amino acids are stereoisomers
amino acids are zwitterions at neutral pH.
Most amino acids have a chiral center at the α-carbon
Naturally occuring amino acids are the L isomer.
Why are amino acids used in proteins stereospecific? Think ahead to enzyme specificity.

3. Most amino acids are zwitterions
amino acids are zwitterions at neutral pH (contains negative and positive charged groups)
amino acids are zwitterions at neutral pH.
Most amino acids have a chiral center at the α-carbon
Naturally occuring amino acids are the L isomer.
Why are amino acids used in proteins stereospecific? Think ahead to enzyme specificity.

4. Small aliphatic amino acids
Glycine
non-chiral
smallest
most flexible in polypeptides
less hydrophobic
Alanine
chiral
next smallest
Glycine is unique among amino acids. Plays critical role in protein structure because of its flexibility:
More later on restrained conformations of amino acids in polypeptides.
Gly and Ala stand up!
Ala swivel.
Gly turn around.

5. Other aliphatic amino acids
Val, Leu, Ile
Highly hydrophobic
branched side-chains
Important for protein structure because of tendency to cluster away from water.
Val, Leu and Ile stand up.

6. Yet another aliphatic amino acid
Proline
imino acid
rigid ring structure
puts kinks in polypeptides
Pro is another amino acid with unique properties.
Pro stand up!

7. Aromatic amino acids Phenylalanine Tyrosine Tryptophan Absorbs UV
Very hydrophobic
Tyrosine
Absorbs UV
less hydrophobic
H-bonds
OH can ionize
OH can be modified
Tryptophan
Really absorbs UV!
less hydrophobic
H-bonds
Phe Tyr and Trp stand up!

8. Sulfur-containing amino acids
Methionine
highly hydrophobic
initiator amino acid
Cysteine
less hydrophobic
forms disulfide bonds
SH group can ionize
Met and Cys stand up.

9. Oxidation of cysteine to cystine
Disulfide bond formation is reversible
Disulfide bonds form in proteins and help stabilize their structures
Most intracellular proteins do not have disulfide bonds because of the reducing environment inside cells.

10. Alcoholic amino acids Ser, Thr less hydrophobic H-bonding potential
can be modified
Thr is an isostere of Val
Ser and Thr are subject to phosphorylation.
Ser can contribute to an enzymes active site eg. Serine protease
Ser and Thr stand up!

11. Acidic amino acids Asp, Glu highly hydrophilic
negatively charged at neutral pH
Glutamate is the G in MSG. Don’t let this confuse you, though. The single letter code for Glu is E.
Glu an d Asp stant up!

12. Basic amino acids Highly hydrophilic
Lys and Arg are positively charged at neutral pH
His is partially charged at neutral pH
His side chain is an imidazole
Lys side chain has a primary amine
Arg side chain has a guanidinium group

13. Amide-containing amino acids
Asn, Gln
highly hydrophilic
H-bonding potential
isosteres of Asp and Glu
Where would you find these amino acids in protein structure?

14. Peptide bond formation
Primary structure: linear sequence of amino acids in a poly[peptide chain.
Linkage formed between amino acids is a secondary amide bond called a peptide bond.
One water molecule is lost.
Peptide bonds do not carry a charge.
Convention – N-terminus to left, C terminus to right.
N –terminus is the free amine of the first amino acid in a polypeptide.
C terminus is the free carboxyl of the last amino acid in a polypeptide.
Where do most of the ionic charges of a polypeptide come from?

15. The peptide bond is planar
The peptide group is polar.
Peptide bonds have some double bond properties because of resonance stabikization. but rotation can occur around the C-C and C-N bonds – determining the structure of the peptide backbone of proteins. More on this later.
Peptide bond is usually in the trans configuration, but can assume the cis configuration.
Fig. 4.6

16. Aspartame – a dipeptide
200X Sweeter than Sucrose !!!
There are many natural and synthetic peptides.
Natural peptides include some hormones eg endorphins.
Synthetic peptides eg. Aspartame.
Note the nomenclature of this dipeptide. Amino acids end in –yl.
aspartylphenylalanine methyl ester