1. Chapter 3. Amino Acids and Peptides

2. Amino Acids and Peptides
Chapter 3
Amino Acids and Peptides
Amino Acids Exist in a Three-Dimensional World
- All the amino acids have a carboxyl group and an amino group bonded to the same carbon atom.
- They differ from each other in their side chains (R groups) which vary in structure, size, and electric charge, and which influence the solubility of the amino acids in water.
- The amino acids have been assigned three-letter abbreviations and one-letter symbols.

3. Amino Acids and Peptides
Chapter 3
Amino Acids and Peptides

4. Amino Acids and Peptides
Chapter 3
Amino Acids and Peptides
- For all the amino acids except glycine, the  carbon is bonded to four different groups: a carboxyl group, an amino group, and R group, and a hydrogen atom
 A chiral center: the two forms represent a class of stereoisomers (enantiomers)
- Special nomenclature has been developed to specify the absolute configuration:
D, L system  Most protein molecules have L stereoisomers

5. Individual Amino Acids: Structure & Properties
Chapter 3
Individual Amino Acids: Structure & Properties
, 2
, 3
, 4
, 5
, 6 1
Amino Acids Share Common Structural Features
- Two conventions are used to identify the carbons in an amino acid
1) The additional carbons in an R group are designated , , , , proceeding out from the  carbon
2) Carbon atoms are simply numbered from one end, giving highest priority (C-1) to the carbon with the substituent containing the atom of highest atomic number

6. Individual Amino Acids: Structure & Properties
Chapter 3
Individual Amino Acids: Structure & Properties
Amino Acids Can Be Classified by R Group
- Nonpolar, Aliphatic R Groups
They tend to cluster together within proteins, stabilizing protein structure by means of hydrophobic interactions
Methionine: One of the two sulfur-containing amino acids
Proline: The secondary amino group reduces the structural flexibility of polypeptide regions

7. Individual Amino Acids: Structure & Properties
Chapter 3
Individual Amino Acids: Structure & Properties
- Aromatic R Groups
They are relatively nonpolar (hydrophobic) and can participate in hydrophobic interactions
Tryptophan and tyrosine absorb ultraviolet light, which account for the characteristic strong absorbance by most proteins at a wavelength of 280 nm

8. Individual Amino Acids: Structure & Properties
Chapter 3
Individual Amino Acids: Structure & Properties
The measured absorbance of tryptophan is as much as four times that of tyrosine

9. Individual Amino Acids: Structure & Properties
Chapter 3
Individual Amino Acids: Structure & Properties
- Polar, Uncharged R Groups
They are hydrophilic because they contain functional groups forming hydrogen bonds with water
Cystein is readily oxidized to form a covalently linked dimeric amino acid called cystine; the disulfide-linked residues are strongly hydrophobic

10. Individual Amino Acids: Structure & Properties
Chapter 3
Individual Amino Acids: Structure & Properties
- Positively Charged (Basic) R Groups
The most hydrophilic R groups are those that are either positively charged or negatively charged
Histidine is the only common amino acid having an ionizable side chain with a pKa near neutrality (6.0)

11. Individual Amino Acids: Structure & Properties
Chapter 3
Individual Amino Acids: Structure & Properties
- Negatively Charged (Acidic) R Groups
Asparagine and glutamine are easily hydrolyzed by acid or base to aspartate and glutamate, respectively
Uncommon Amino Acids also have important functions
- Proteins may contain residues created by modification of common residues already incorporated into a polypeptide

12. Individual Amino Acids: Structure & Properties
Chapter 3
Individual Amino Acids: Structure & Properties
Uncommon Amino Acids Also Have Important Functions
Found in prothrombin
Found in plant cell wall and collagen
Found in collagen
Found in elastin
Introduced during protein synthesis
Found in myosin, a contractile protein of muscle

13. Amino Acids Can Act as Both Acids and Bases
Chapter 3
Amino Acids Can Act as Both Acids and Bases
What happens when we titrate an amino acid?
- An amino acid exists in solution as the dipolar ion, or zwitterion
 A zwitterion can act as either and acid (proton donor) or a base (proton acceptor)
Acid
Neutral
base

14. Amino Acids Can Act as Both Acids and Bases
Chapter 3
Amino Acids Can Act as Both Acids and Bases
What happens when we titrate an amino acid?
Inflection point
Isoelectric pH

15. Amino Acids Can Act as Both Acids and Bases

16. Amino Acids Can Act as Both Acids and Bases
Chapter 3
Amino Acids Can Act as Both Acids and Bases
- The relationship between its net electric charge and the pH
 At pH 5.97, glycine is present as its dipolar from
(no net electric charge)
 Isoelectric point or isoelectric pH, called “pI”
 At any pH below its pI, glycine has a net
positive charge
- Amino acids with an ionizable R groups have more complex titration curves with the three pKa values
 The pIs reflect the nature of the ionizable groups present
e.g., glutamate (pI: 3.22), histidine (pI: 7.59)

17. Chapter 3
The Peptide Bond
Which groups on amino acids react to form a peptide bond?
- Peptide bond: α-carboxyl group + α-amino group
- Peptides: Small numbers of Amino Acids
- Proteins: Many Amino Acids (> 100)

18. Chapter 3
The Peptide Bond
The Peptide Bond is Rigid and Planar

19. Chapter 3
Proteins
- Proteins are the most abundant biological macromolecules in all cells.
- Proteins exhibit enormous diversity of biological function and the molecular instruments through which genetic information is expressed.
- All proteins are constructed from the same set of 20 amino acids.
- Cells can produce proteins with strikingly different properties and activities by joining the same 20 amino acids in many different combinations and sequences.
Luciferin (firefly)
Hemoglobin
Keratin (rhinoceros)

20. Small Peptides with Physiological Activity
Chapter 3
Small Peptides with Physiological Activity
What are some biological functions of small peptide?
- Amino acids are joined through a peptide bond
 dipeptide, tripeptide, tetrapeptides, pentapetides, and so on
- L-Aspartyl-L-phenylalanine (methyl ester):
 200 times sweeter than sugar
 Marketed as a sugar substitute useful for controlling obesity and diabetes.

21. Chapter 3
Summary

22. Chapter 3
Summary