1. Amino Acids (Foundation Block) 1 Lecture Dr. Usman Ghani
What are amino acids?
Structure
Types
Peptide bond
Non-standard amino acids
Derivatives of amino acids

2. What are amino acids?
Amino acids are composed of Ca, carboxylic group, amino group, a side chain (R)
Side chain groups (R) are variable
Building blocks of proteins
Amino acids are joined together by peptide bond like a chain in a protein
Amino acids can act as both acid and base

3. General structural formula for a-amino acids
Page 65
© 2004 John Wiley & Sons, Inc.
Voet Biochemistry 3e
General structural formula for a-amino acids

4. There are 20 “standard” amino acids present in proteins

5. The amino and carboxylic groups of aa can ionize

6. Page 65
© 2004 John Wiley & Sons, Inc.
Voet Biochemistry 3e

7. Isoelectric Point The pH at which the molecule carries no net charge
In acidic solution-cationic
In alkaline solution- anionic

8. pK Value It is the ability of an acid to donate a proton (dissociate)
Also known as pKa or acid dissociation constant

9. The pK values of a-carboxylic group is in the range of 2.2
The pK values of a-amino group is in the range of 9.4

10. Titration curve of glycine
pK1- The pH at which 50% of molecules are in cation form and 50% are in zwitterion form
pK2- The pH at which 50% of molecules are in anion form and 50% are in zwitterion form
Buffering action is maximum around pK values and minimum at pI
Page 70
© 2004 John Wiley & Sons, Inc.
Voet Biochemistry 3e
Titration curve of glycine

11. Zwitterions An amino acid contains both:
Basic amino group and
Acidic carboxylic group
Creating a negative and a positive charge
Amino groups are protonated
Carboxylic groups are unprotonated

12. Page 65
© 2004 John Wiley & Sons, Inc.
Voet Biochemistry 3e
Zwitterionic form of the a-amino acids that occur at physiological pH values

13. An amino acid can therefore act as both an acid and a base
At physiological pH, amino acids contain both positive and negative charges with a net charge of zero
Equal number of positive and negative charges

14. Types There are 20 “standard” amino acids found in proteins
All have Ca, carboxylic and amino groups
All have different side chains (R groups)

15. Three major types of amino acids:
Nonpolar
Uncharged polar
Charged polar

16. Nonpolar: Glycine Alanine Valine Leucine Isoleucine Methionine
Proline Phenylalanine
Tryptophan

17. Proline
It is an imino acid
It has a secondary amino group

18. Amino acids with nonpolar side chains
Page 66
© 2004 John Wiley & Sons, Inc.
Voet Biochemistry 3e

19. Uncharged polar: Serine Threonine Asparagine Glutamine
Tyrosine Cysteine

20. Amino acids with uncharged polar side chains
Page 67
© 2004 John Wiley & Sons, Inc.
Voet Biochemistry 3e

21. Charged polar:
Lysine, Arginine
Aspartic acid, Glutamic acid
Histidine

22. Amino acids with charged polar side chains
Page 67
© 2004 John Wiley & Sons, Inc.
Voet Biochemistry 3e
Amino acids with charged polar side chains

23. Peptide bond Amino acids can be polymerized to form chains
Polymers are composed of two, three, few (3-10) or more amino acids known as dipeptides, tripeptides, oligopeptides or polypeptides

24. Condensation of two a-amino acids to form a dipeptide
Page 68
© 2004 John Wiley & Sons, Inc.
Voet Biochemistry 3e
Condensation of two a-amino acids to form a dipeptide

25. Amino acids are joined together in a chain by peptide bond [CO–NH linkage]
Known as peptide bond
Each amino acid in a chain makes two peptide bonds

26. Condensation of two a-amino acids to form a dipeptide
Page 68
© 2004 John Wiley & Sons, Inc.
Voet Biochemistry 3e
Condensation of two a-amino acids to form a dipeptide

27. The amino acids at the two ends of a chain make only one peptide bond
The aa with a free amino group is called amino terminus or N-terminus
The aa with a free carboxylic group is called carboxyl terminus or C-terminus

28. The tetrapeptide Ala-Tyr-Asp-Gly
Page 71
© 2004 John Wiley & Sons, Inc.
Voet Biochemistry 3e
The tetrapeptide Ala-Tyr-Asp-Gly

29. Optical activity All aa are optically active except glycine
They rotate the plane of polarized light in a polarimeter
Optically active molecules are asymmetric:
They are not superimposable on their mirror image
Asymmetric means Ca is bonded to four different groups

30. Glycine contains two hydrogen atoms on Ca
The Ca of glycine is not asymmetric
Therefore glycine is optically inactive

31. Schematic diagram of a polarimeter
Page 72
© 2004 John Wiley & Sons, Inc.
Voet Biochemistry 3e
Schematic diagram of a polarimeter

32. Both L and D forms are chemically same
L-Amino acids rotate polarized light to the left
D-Amino acids rotate polarized light to the right
Both L and D forms are chemically same

33. Non-standard amino acids

34. Page 77
© 2004 John Wiley & Sons, Inc.
Voet Biochemistry 3e
Some uncommon amino acid residues that are components of certain proteins

35. Biologically active amino acids
Neurotransmitters
Hormones

36. Page 77
© 2004 John Wiley & Sons, Inc.
Voet Biochemistry 3e
Some biologically produced derivatives of “standard” amino acids and amino acids that are not components of proteins

37. That’s all folks!