1. Principles of Biochemistry
Fourth Edition
Chapter 3
Amino Acids and the Primary
Structures of Proteins
Copyright © 2006 Pearson Prentice Hall, Inc.
Horton • Moran • Scrimgeour • Perry • Rawn
Dr. Wisam Alsamah

2. Biological Functions of Proteins
1. As enzymes (catalysts)
2. Storage and transport (hemoglobin)
3. Provide support and shape (collagen)
4. Mechanical work (muscles contraction)
5. Decoding information (translation)
6. As hormones
7. Specialized functions (antibodies)

3. General Structure of Amino Acids

4. General Structure of Amino Acids
Zwitterions
Chiral
Or
Asymmetric

5. General Structure of Amino Acids
Ball-and-stick model of
serine

6. General Structure of Amino Acids
Stereoisomers (enantiomers)

7. General Structure of Amino Acids
The RS system

8. General Structure of Amino Acids
The RS system
Clockwise R configuration
Counterclockwise S configuration

9. Structures of the 20 common Amino Acids
A. Aliphatic R Groups

10. A. Aliphatic R Groups
Structures of the 20 common Amino Acids

11. A. Aliphatic R Groups
Structures of the 20 common Amino Acids
Pyrrolidine ring

12. A. Aliphatic R Groups
Structures of the 20 common Amino Acids
●Valine, Leucine, and isoleucine are known as
branched-chain amino acids
●All three amino acids are highly hydrophobic
●Pyrrolidine ring of proline restricts the geometry
of polypeptides
●Proline is much less hydrophobic than the three
amino acids

13. B. Aromatic R Groups
Structures of the 20 common Amino Acids
(Benzyl) (Phenol) (Indol)
(260 nm) (280 nm) (280 nm)

14. C. Sulfur-Containing R Groups
Structures of the 20 common Amino Acids
Disulfide bond

15. C. Sulfur-Containing R Groups
Structures of the 20 common Amino Acids
Nonpolar
Methyl thioether
Sulfhydryl

16. D. Side Chains with Alcohol Groups
Structures of the 20 common Amino Acids
α- carbon
β- carbon
Stereoisomers

17. E. Basic R Groups
Structures of the 20 common Amino Acids
Imidazole ring
Guanidinium
ion

18. F. Acidic R Groups and Their Amide Derivatives
Structures of the 20 common Amino Acids
Amide

19. F. Acidic R Groups and Their Amide Derivatives
Structures of the 20 common Amino Acids
●Aspartate, and glutamate are dicarboxylic amino acids
and have negatively charged hydrophilic side chains at pH 7.
●These amino acids are often found on the surface of proteins.
●Monosodium glutamate (MSG) is used as a flavor enhancer.
●The polar amide groups of these amino acids can form hydrogen
bonds with atoms in the side chain of other polar amino acids.

20. G. The Hydrophobicity of Amino Acids Chains
Structures of the 20 common Amino Acids
Hydropathy

21. Other Amino Acids and Amino Acid Derivatives
(GABA)

22. Other Amino Acids and Amino Acid Derivatives
(21st
amino acid)
(22nd
amino acid)

23. Ionization of Amino Acids

24. Ionization of Amino Acids

25. Ionization of Amino Acids

26. Ionization of Amino Acids

27. Ionization of Amino Acids

28. Ionization of Amino Acids

29. Peptide Bonds link Amino Acids in Proteins

30. Peptide Bonds link Amino Acids in Proteins
Aspartame
(aspartylphenylalanine methyl ester)

31. Protein Purification Techniques
●Column chromatography /eluate/
●HPLC
●Ion-exchange chromatography
●Gel-filtration chromatography
●Affinity chromatography

32. Column chromatography /eluate/

33. Analytical Techniques
●Polyacrylamide gel electrophoresis (PAGE)
●Mass spectrometry
●Electrospray mass spectrometry
●Matrix-assisted desorption ionization (MALDI)

34. Polyacrylamide gel electrophoresis (PAGE)

35. Matrix-assisted desorption ionization (MALDI)

36. Matrix-assisted desorption ionization (MALDI)
MALDI-TOF

37. Matrix-assisted desorption ionization (MALDI)

38. Amino Acids Composition of Proteins
▪Peptide bonds of the protein are cleaved by acid hydrolysis using
6M HCl.
▪Method of amino acid analysis :
treatment of the protein hydrolysate with PITC at pH 9.0
PTC-amino acid derivatives
HPLC (column of fine silica beads+short hydrocarbon chains)
Detection at 254 nm (peak absorbance of the PTC moiety)
▪1 picomole of a protein that contains about 200 residues
▪Glutamate + glutamine Glx or Z
Aspartate + asparagine Asx or B
▪Side chain of Tryptophan is almost destroyed by acid hydrolysis

39. Amino Acids Composition of Proteins
Acid hydrolysis

40. Amino Acids Composition of Proteins
(phenylisothiocyanate)
(phenylthiocarbomyl)

41. Amino Acids Composition of Proteins

42. Determing the Sequence of Amino Acid Residues
Edman degradation procedure

43. Determing the Sequence of Amino Acid Residues
Entire procedure can be repeated serially
using a sequenator

44. Determing the Sequence of Amino Acid Residues
2-mercaptoethanol

45. Protein Sequencing Strategies
▪Most proteins contain too many residues cleave peptide bonds
proteases (trypsin, staphylococcus aureus V8 protease)
or certain chemical reagents (BrCN)
▪BrCN reacts with Methionine C-terminal homoserine lactone
Residues + new N-terminal residues
▪Trypsin carbonyl side of lysine and Arginine residues
(positively charged side chains)
▪Staphylococcus aureus V8 protease carbonyl side of
glutamate and Aspartate residues (negatively charged side chain)
▪Chymotrypsin carbonyl side of uncharged residues
with aromatic or bulky hydrophobic side chains ( Phe, Tyr, Trp)

46. Protein Sequencing Strategies
▪The amino acid sequence of a protein can be deduced from
the sequence of nucleotides in the corresponding gene.
▪A sequence of three nucleotides specifies one amino acid.

47. Comparisons of the Primary Structures of Proteins
reveal Evolutionary Relationships
▪The protein cytochrome c (single polypeptide chain of about
104 residues) example of evolution at the molecular level
▪Protein sequences from distantly related species are
similar enough proteins are homologous
▪Cytochrome c sequences of humans and chimpanzees are
Identical.

48. Comparisons of the Primary Structures of Proteins
reveal Evolutionary Relationships