OH -

1. Charge: -1 Charge: +1 Pka=2 H 2 OH- Pka=10 OH- Charge: 0 (When aa have a net charged of zero its called a Zwitterion) PH=7 PH=1 PH=12 Adding a base Low PH High PH

2. 9.60 X X PH/ increasing OH Pka (Low will lose first) Pka1 (for carboxyl H 2.34), Pka2 (for amino group H 9.60) PI is PH when aa is neutral PI (isoelectric point)= (Pka1+PKa2)/2 2.34

3. 9.60 2.34

4. Calculate the pI of methionine. Methionine has Ka values pKaC = 2.1 and pKaN = 9.3. pI = 1/2(pKaC + pKaN) pI = 1/2(2.1 + 9.3) pI = 5.7

5. WHAT ABOUT THE R Groups?

6. Pka: 2.19 Pka: 6.97 X X PH Pka (Low will lose first) Pk1 (for carboxyl H 2.19), Pk2 (for amino group H 9.67), PKR (for R group H 4.25). PH< PK1 (All Protonated) PH> PK1 COOH COO- PH> PKR COOHR COO- 4. PH>PK2 H3N+ H2N Pka: 4.25

7. Write equations for the dissociation of aspartate and calculate its pI. A zwitterion is a molecule with both positive and negative charges, but with a net charge of zero. The isoelectric form is found after the first dissociation, between pKaC and pKaR pI = 1/2(pKaC + pKaR) pI = 1/2(2.1 + 3.9) pI = 3.0 Pka: 9.8 Pka: 2.1 Pka: 3.9 pH = 3.0 • If the pH is less than the pI, the amino acid will have a net positive charge. • If the pH is greater than the pI, the amino acid will have a net negative charge. • If the pH equals the pI, the amino acid will have no net charge (this is the definition of pI.)

8. Pka=6 H+ H+ Histidine: side chain can be a proton donor and a proton acceptor Histidine: weakly basic, but uncharged at physiological PH (7.4) PH> Pka , Lose the proton!

9. Protein Structure

10. Peptide:A short chain of amino acids. • Polypeptides:A long chain of amino acids. • Protein: A protein is a biological polymer of amino acids bonded together by peptide bonds between the carboxyl (-COOH) and amino (-NH2) groups of adjacent amino acid residues and folds into a defined three dimensional structure. peptide bond

11. Protein Structure: The different levels……………. Primary Secondary Tertiary Quaternary Assembly Folding Packing Interaction S T R U C T U R E P R O C E S S

12. The Primary Structure: Amino acids joined by peptide bonds!

13. Defining the primary structure of a protein The primary structure of a designated protein is the amino acid sequence of the protein!

14. Chemistry of peptide bond formation • α-carboxyl of one amino acid is joined to α -amino of a second amino acid (with removal of water). • Peptide bond has a partial double bond character. • It is a rigid bond that is shorter than a single bond. R groups are not involved in forming peptide bonds!

15. Protein Structure: The different levels……………. Primary Secondary Tertiary Quaternary Assembly Folding Packing Interaction S T R U C T U R E P R O C E S S

16. Defining the secondary structure of a protein local sub-structures in a polypeptide chain predominantly formed by the participation of hydrogen-bond

17. Understanding the H-bond A hydrogen bond is the interaction of a hydrogen atom with an electronegative atom. Ex: nitrogen, oxygen etc.

18. α-Helix • α-helix is a right-handed spiral conformation • Every N-H group of the amino group forms a hydrogen bond with the C=Ogroup of the carboxylic acid group of an amino acid four residues earlier

19. Short peptides do not form α-helix • The side chains of the amino acids face outward! • Formed by the same groups that are involved in the formation of peptide bond (Amino group and carboxylic acid group)!. peptide bond

20. Some amino acids can disrupt the α-helix structure: • Proline: Insert a Kink in the chain. • Large numbers of charge amino acids (Glutamate, aspartate, histadine, Lysine and arginine) can also disrupt the helix by forming ionic bonds!

21. Keratin……………….. • Keratin structure is nearly entirely α-Helical • Major component of tissue • Such as hair and skin.

22. β-sheet • β-strands connected by hydrogen bond to form a β-sheet. • Less common than α-helix

23. Types of β-sheet