1. Lecture 3-Amino Acid & Protein
Ahmad Razali Ishak
Department of Environmental Health
Faculty of Health Sciences
UiTM Puncak Alam

2. Function of Protein Catalysts- enzymes for metabolic pathway
Storage and transport- myoglobin and hemoglobin
Structural- actin, myosin
Decoding information- translation and gene expression
Hormones and hormone receptors
Specialized functions-antibodies

3. Amino Acids- Primary structure of protein
Amino acid: a compound that contains both an amino group and a carboxyl group
 -Amino acid has an amino group attached to the carbon adjacent to the carboxyl group
-carbon also bound to side chain group, R
R gives identity to amino acid

4. Cont..
The  - carbon is chiral/asymmetric (4 different groups are attached to the carbon: exception is glycine )- mirror image, non super imposable
AA exist as stereoisomer (same molecular formula, but differ in arrangement of groups) – designated D (right) or L (Left)
Vast majority of  -amino acids have the L- configuration at the  -carbon (Proline is usually D)

6. -amino group orientation determines L or D
NH3+ on left = L
NH3+ on right = D
Carboxylate group at top- point away side chain at the bottom

7. AA structure and properties
AA are grouped based upon the properties and structures of side chains
Aliphatic (R groups consist of carbons and hydrogens)- Glycine, Alanine, Valine, Leucine, Isoleucine, Proline

8. Sulfur containing R group- methionine, cysteine

9. Aromatic (R group have phenyl ring)- Phenylalanine, tyrosine

10. Polar R group - Ser, Thr, Tyr, Cys, Glu

11. Non Polar R group - Ala, Val, Leu, Ile, Pro. Phe, Trp, Met.

12. Cont.. Basic R group- Histidine, lysine, arginine
Acidic R group - Glutamate, Aspartate
Side chain with alcohols – Serine, threonine

13. Ionization of Simple Amino Acids
Amino acids are more complicated than simple weak acids since amino acids have at least 2 ionizing groups.
Glycine (abbrevation is Gly), for example, has both a carboxylic acid and an amino group that can ionize:

14. If we dissolve the free base of Gly in pure water (ie neutral pH),
it will ionize.
The equilibrium is far to the right so most of the Gly is in the
charged form called the Zwitterion and Gly is still neutral
because the + charge is neutralized by the - charge.
Gly is always in the Zwitterion form at neutral pH.

15. Ionization of Amino Acids
• Remember, amino acids without charged groups on side chain exist in neutral solution as zwitterions with no net charge

16. If one aa being titrated from acidic condition, you will get this titration curve
E.g. Titration curve for glycine

17. At given pH, amino acid have different net charge
The isoelectric point (pI) is the pH at which the amino acid has no net charge = zwitterion
If pH > pI, amino acid would be –ve charged
If pH < pI, amino acid would be positively charged

18. Isoelectric pH
Isoelectric pH, pI: the pH at which the majority of molecules of a compound in solution have no net charge
the pI for glycine, for example, falls midway between the pKa values for the carboxyl and amino groups
Isoelectric pH values for the 20 protein-derived amino acids are given in Table 3.2

20. Protein Structure
Four Levels of Protein Structure: 1. Primary Structure- Polypeptide backbone- Linear sequence of amino acid 2. Secondary Structure- regular patterns formed by primary structure folding-Local Hydrogen bonds along the backbone 3. Tertiary structure- Completely folded polypeptide with one or more domains. Long distance bonding involving the AA side chains 4. Quaternary structure- Association of multiple polypeptides. Protein interactions leading to formation of dimers, tetramers, etc.

21. Protein Covalent Structure (Protein Primary Structure)
I. Peptide Bonds, Peptides and Proteins
Proteins are sometimes called Polypeptides, since they contain many Peptide Bonds

22. The peptide bond is an amide bond
Water is lost in forming an amide bond.

23. Comparison of an amino acid, a dipeptide and a tripeptide

24. Peptides = Mini-Proteins
A pentapeptide -- GlyAlaSerPheGln
1st amino acid is always written on the left and called the Amino
terminal, since it is always the only amino acid of the peptide with a
free alpha-amino group. Last amino acid is always written on the right
and called the Carboxyl terminus, since it is always the only amino
acid of the peptide with a free alpha-carboxylic acid group.

25. SECONDARY STRUCTURE OF PROTEINS
In 1950's, Linus Pauling named the first structures he found by X-ray diffraction, the Alpha Helix and the second structure he found was called Beta Sheet
The 2 COMMON Types of Protein Secondary Structure:
Alpha-helix
Beta-sheet

26. -Helix Coil of the helix is clockwise or right-handed
There are 3.6 amino acids per turn
Repeat distance is 5.4Å
Each peptide bond is s-trans and planar
C=O of each peptide bond is hydrogen bonded to the N-H of the fourth amino acid away
C=O----H-N hydrogen bonds are parallel to helical axis
All R groups point outward from helix

27. -Helix (Cont’d)

28. -Pleated Sheet
Polypeptide chains lie adjacent to one another; may be parallel or antiparallel
R groups alternate, first above and then below plane
Each peptide bond is s-trans and planar
C=O and N-H groups of each peptide bond are perpendicular to axis of the sheet
C=O---H-N hydrogen bonds are between adjacent sheets and perpendicular to the direction of the sheet

29. -Pleated Sheet (Cont’d)

30. -Pleated Sheet (Cont’d)
-bulge- a common nonrepetive irregular 2˚ motif in anti-parallel structure

31. Myoglobin A single polypeptide chain of 153 amino acids
A single heme group in a hydrophobic pocket
8 regions of -helix; no regions of -sheet

32. Quaternary Structure
Quaternary (4°) structure: the association of polypepetide monomers into multisubunit proteins
dimers
trimers
tetramers
Noncovalent interactions
electrostatics, hydrogen bonds, hydrophobic

33. Hemoglobin (Hb)
A tetramer of two -chains (141 amino acids each) and two -chains (153 amino acids each); a2b2

34. Homework
Describe the difference between alpha-helix and beta- sheet protein structures.
Describe the metabolic disorder of protein- phenylketonuria
Please upload the answer in the i-discuss before next seminar