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

2. 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 X X 9.60 2.34

3. 1.pH < pKa C Almost all monopositive formAvg. net charge +1 2.pH = pKa C Half monopositive, half isoelectricAvg. net charge = +0.5 3.pH = 1/2(pKa C + pKa N )All isoelectric formAvg. net charge = 0 4.pH = pKa N Half isoelectric, half mononegative Avg. net charge =  0.5 5.pH > pKa N Almost all mononegative Avg. net charge  1 9.60 2.34

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

5. WHAT ABOUT THE R Groups?

6. 1.PH 2.Pka (Low will lose first) 3.Pk1 (for carboxyl H 2.19), Pk2 (for amino group H 9.67), PK R (for R group H 4.25). 1.PH< PK1 (All Protonated) 2.PH> PK1 COOH  COO- 3.PH> PK R COOH R  COO- 4. PH>PK2 H 3 N+  H 2 N XX Pka: 2.19 Pka: 6.97 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 pKa C and pKa R pI = 1/2(pKa C + pKa R ) pI = 1/2(2.1 + 3.9) pI = 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.) Pka: 2.1 Pka: 3.9 Pka: 9.8 pH = 3.0

8. 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! H+ Pka=6

9. Protein Structure

10.  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: A short chain of amino acids.  Polypeptides : A long chain of amino acids. 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 R groups are not involved in forming peptide bonds! -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.

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=O group 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-strands connected by hydrogen bond to form a β- sheet. Less common than α-helix β-sheet

23. Types of β-sheet