1. الأعمال بالنيات عن أمير المؤمنين أبي حفص عمر بن الخطاب – رضي الله تعالي عنه – قال: سمعت رسول الله – صلي الله تعالي عليه و علي آله و سلم – يقول: "إنما الأعمال بالنيات و إنما لكل امرئ ما نوى، فمن كانت هجرته إلي الله و رسوله، فهجرته إلي الله و رسوله، ومن كانت هجرته لدنيا يصيبها أو امرأة ينكحها فهجرته إلي ما هاجر إليه“ رواه البخاري و مسلم في صحيحيهما

2. Protein Structure and Function Lecture one

3. Objectives To emphasize on the importance of proteins for living systems To understand the structure of amino acids To differentiate between different classes of amino acids according to the side chain

4. Functions of proteins Are So variable although all proteins are linear polymers of Amino Acids ( AA ) Enzymes and polypeptide hormones  metabolism Contractile proteins  movement Structural proteins  form framework (e.g. collagen in bone is a framework for the deposition of Ca 2 PO 3 crystals) Blood proteins  carriers (e.g. Hb, albumin) Blood proteins  protection (e.g. Ig)

5. Structure of AA (fully protonated form) (at physiological pH ~= 7.4) - Depending on to its polarity Lippincott’s Illustrated Reviews, Biochemistry, 3 rd edition, R Harvey & P Champe, 2005 Reem M. Sallam, MD.PhD.

6. Nonpolar vs. Polar = have an even distribution of electrons Do not bind or donate protons Do not participate in H/ionic bonds Promote hydrophobic interactions = have an uneven distribution of electrons NonpolarPolar The reverse of nonpolar Reem M. Sallam, MD.PhD.

7. Location of nonpolar & polar AA in soluble & membrane proteins. The nonpolar “R” is hydrophobic  acts like droplets of oil in H 2 O This  stabilizes protein structure Lippincott’s Illustrated Reviews, Biochemistry, 3 rd edition, R Harvey & P Champe, 2005 Reem M. Sallam, MD.PhD.

8. Classification of the 20 AA According to the properties of (R) AA with Nonpolar side chains The smallest AA The only AA with No asymmetric Carbon Lippincott’s Illustrated Reviews, Biochemistry, 3 rd edition, R Harvey & P Champe, 2005 Reem M. Sallam, MD.PhD.

9. Classification of the 20 AA, contin.. AA with Nonpolar side chains, contin… Branched-chain AA: Lippincott’s Illustrated Reviews, Biochemistry, 3 rd edition, R Harvey & P Champe, 2005 Reem M. Sallam, MD.PhD.

10. Classification of the 20 AA, contin.. AA with Nonpolar side chains, contin… Aromatic AA Benzene ring Indol ring NB. Tyr is also an Aromatic AA but it is Polar Lippincott’s Illustrated Reviews, Biochemistry, 3 rd edition, R Harvey & P Champe, 2005 Reem M. Sallam, MD.PhD.

11. Classification of the 20 AA, contin.. AA with Nonpolar side chains, contin… Imino Acid Rigid “R” Sulfur-containing AA Lippincott’s Illustrated Reviews, Biochemistry, 3 rd edition, R Harvey & P Champe, 2005 Reem M. Sallam, MD.PhD.

12. Comparison of the imino group found in Pro with the  -amino group found in other AA e.g. Ala The “R” of Pro is essential for: The formation of the fibrous structure of collagen The secondary structure of protein (  -helix interruption) Lippincott’s Illustrated Reviews, Biochemistry, 3 rd edition, R Harvey & P Champe, 2005 Reem M. Sallam, MD.PhD.

13. Classification of the 20 AA, contin.. AA with Uncharged Polar side chains 1- AA with OH-containing side chains The polar –OH can be a site of attachment e.g. for PO 4, carbohydrates participate in hydrogen bond formation Aromatic AA Lippincott’s Illustrated Reviews, Biochemistry, 3 rd edition, R Harvey & P Champe, 2005 Reem M. Sallam, MD.PhD.

14. Hydrogen bond between the phenolic –OH group of Tyr & another molecule containing a carbonyl group Lippincott’s Illustrated Reviews, Biochemistry, 3 rd edition, R Harvey & P Champe, 2005 Reem M. Sallam, MD.PhD.

15. Classification of the 20 AA, contin.. AA with Uncharged Polar side chains 2 - AA with carbonyl/amide-containing side chains The polar carbonyl & amide groups can participate in hydrogen bond formation The polar –amide group of Asn can be a site of attachment for carbohydrates  Glycoprotein. Lippincott’s Illustrated Reviews, Biochemistry, 3 rd edition, R Harvey & P Champe, 2005 Reem M. Sallam, MD.PhD.

16. Oligosaccharides can be attached to proteins via: 1- Amide group of Asn 2- (-OH) group of Ser, or Thr Lippincott’s Illustrated Reviews, Biochemistry, 3 rd edition, R Harvey & P Champe, 2005 Reem M. Sallam, MD.PhD.

17. Classification of the 20 AA, contin.. AA with Uncharged Polar side chains: 3- AA with SH-containing side chains Covalent The polar –SH can be oxidized to form a (-S-S-) bond Sulfur-containing AA: Met & Cys Sulfhydryl-containing AA: Cys Lippincott’s Illustrated Reviews, Biochemistry, 3 rd edition, R Harvey & P Champe, 2005 Reem M. Sallam, MD.PhD.

18. Classification of the 20 AA, contin… AA with Acidic side chains 1 2 Lippincott’s Illustrated Reviews, Biochemistry, 3 rd edition, R Harvey & P Champe, 2005 Reem M. Sallam, MD.PhD.

19. Classification of the 20 AA, contin… AA with Acidic side chains, contin…. At physiologic pH, “R” of Asp & Glu are fully ionized i.e. negatively charged  Aspartate & Glutamate - - Aspartate Glutamate Acidic AA are negatively-charged at physiologic pH Lippincott’s Illustrated Reviews, Biochemistry, 3 rd edition, R Harvey & P Champe, 2005 Reem M. Sallam, MD.PhD.

20. AA with Basic side chains Classification of the 20 AA, contin… At physiologic pH, “R” of Lys & Arg are fully ionized 12 Basic AA are positively-charged at physiologic pH Lippincott’s Illustrated Reviews, Biochemistry, 3 rd edition, R Harvey & P Champe, 2005 Reem M. Sallam, MD.PhD.

21. AA with Basic side chains Classification of the 20 AA, contin… At physiologic pH “R” of free His is uncharged Free His If His is within a protein, the “R” can be charged (protonated) OR uncharged (deprotonated) depending on the ionic environment OR His within a protein 3 His is weakly basic His is important in buffering action of hemoglobin Lippincott’s Illustrated Reviews, Biochemistry, 3 rd edition, R Harvey & P Champe, 2005 Reem M. Sallam, MD.PhD.

22. ”و اتقوا الله و يعلمكم الله“