1. 1 Chapter Outline 13.1 Amino Acid Structures - General structure of the aa; Groups bonded to the alpha carbon; structure of aa in water; zwitterion - Classification of aa’s - D-amino acids and L-amino acids 13.2 The Peptide - Reaction of aa’s to form Peptide, peptide bond - The peptide structure; terms to describe the numbers of aa’s in the peptide (dipeptide, tripeptide, tetrapeptide, … oligopeptide) 13.4 Polypeptide and Protein -Polypeptide -Protein, levels of protein structure, 13.5 Denaturation 13. 6 Enzymes, enzyme reactions, mechanism of enzyme reaction.

2. 2 13.1: Structures of Amino Acids (aa’s) All aa’s have this general structure, except the side chains are different. You need to know the general structure of the aa, but not the side chain structure of each specific aa. What is the name of each group or atom bonded to the alpha C?

3. 3 In water the aa exists as a dipolar ion called Zwitter ion. All aa’s behave like this way.

4. 4

5. 5 The water solubility and the chemistry of amino acids vary to some extent, depending on the makeup of the side chain. It is useful to use side chains to classify each amino acid as being either 1) nonpolar 2) polar-acidic 3) polar-basic 4) polar-neutral. Classifying Amino Acids

6. 6 1) nonpolar - the side chain is usually an alkyl group, an aromatic ring, or a nonpolar collection of atoms. 2) polar-acidic - the side chain contains a carboxyl group. At pH = 7, the carboxyl group is found in its conjugate base form (-COO - ), which means that the side chain carries a negative charge at this pH. 3) polar-basic - the side chain contains an amine group. At pH = 7 the amines exist in their conjugate acid form and therefore carry a positive charge at this pH. 4) polar-neutral - the side chain is usually an alcohol, a phenol, or an amine. They do not carry a charge at pH = 7. Classifying Amino Acids

7. 7 Stereoisomers (remember what enantiomers are?) What is one purpose of amino acids?

8. 8 H2OH2O This bigger molecule is called a Pepetide. Peptide bond formation: Which bond is the amide bond? Or peptide bond? Can you find it?

9. 9 N-terminus C-terminus Dipeptide, tripeptide, oligopeptide Ala-Gly Ala-Gly-Ser Ala-Gly-Ser-Val-Gly

10. 10 Examples of two real peptides in our bodies.

11. 11 13.4: Protein Structure backbone What is a polypeptide?

12. 12 1) Fibrous proteins - These proteins exist as long fibers or strings. These proteins including collagen (in skin) and keratin (in hair), are usually tough and water insoluble. 2) Globular proteins - These proteins are spherical in shape, highly folded, and tend to be water soluble. Protein

13. 13 The structure of proteins is understood in terms of four levels of organization: 1) primary (the aa sequence) 2) secondary 3) tertiary 4) quaternary Protein Structure

14. 14 Secondary Structure: The  -helix.

15. 15 Secondary Structure: The  -sheet; parallel  -sheet and anti-parallel  -sheet.

16. 16 Secondary structures compare to tertiary structure: Tertiary structure

17. 17 Another look at tertiray structure. Where are the aa’s in the protein above? What are we looking at?

18. 18 Non-covalent interactions and –S-S- bond important for maintaining the protein structure: (Can you name each one?)

19. 19 The tertiary structure refers to the overall three- dimensional shape of a protein, including the folding of the  -helices or  -sheets with respect to one another. Of the many folding patterns (conformations) possible for a protein, there is usually only one that leads to a native (biologically active) molecule. The sequence of amino acids (primary structure) ultimately determines which folding pattern is selected, so both secondary and tertiary structure depend on primary structure. Tertiary Structure

20. 20 In an aqueous environment, the native form of a globular protein typically has its nonpolar amino acid side chains folded into the hydrophobic interior and its polar side chains on the hydrophilic surface. This folding rule, known as “nonpolar in, polar out” is the most stable arrangement because it allows polar side chains on the surface of the protein to interact with water molecules and allows nonpolar side chains to avoid water. Tertiary Structure

21. 21 Quarternary Structure of protein:

22. 22 13.5: Denaturation Denaturation is any change in protein conformation caused by disruption of the noncovalent forces responsible for maintaining the native conformation. A loss of biological activity normally accompanies denaturation, and this process is reversible only if minor changes in conformation take place. Denaturation can be caused by: heat, denaturants, extreme pH, sonication, dehydration, …

23. 23

24. 24 13.6 Enzymes Enzymes are often referred to as biological catalysts. Most enzymes are globular proteins. (Enzyme catalysis) Model of enzyme catalysis.

25. 25 Examples of some real enzyme catalyzed reactions : How does maltase cut (hydrolyze) maltose?

26. 26 Examples of other enzyme catalyzed reactions.

27. 27 Real catalytic mechanism of reaction of maltase: How does maltase cut (hydrolyze) maltose? (This is exactly how !)

28. 28 Enzyme Inhibition:

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