BIOCHEMISTRY COURSE – PHARMACY BIOMEDICAL PREVIEW PROGRAM, SUMMER 2016

1. BIOCHEMISTRY COURSE – PHARMACY BIOMEDICAL PREVIEW PROGRAM, SUMMER 2016 Ginika Ezeude, B.A. Biochemistry Barnard College of Columbia University 2nd Year Pharmacy Student Contact: ginika.ezeude@gmail.com

2. 1. LEVELS OF PROTEIN STRUCTURE Primary, Secondary, Tertiary, Quaternary

3. BUILDING BLOCKS OF BIOLOGICAL MACROMOLECULES

4. PROTEINS: NATURE’S LEGOS • Structure • Muscle, collagen, hair • Movement • Muscles (Actin, Myosin) • Enzymes • Molecular Machines • Promote chemical reactions in Anabolism and Catabolism • Life

5. WHAT ARE PROTEINS MADE OF? Proteins are chains of Amino Acids • About Amino Acids: • 20 Amino Acids exist (normally) • We produce 11 of them in our bodies • anabolism and catabolism • 9 are considered “essential” and must be obtained via our diet • All AA have the same basic structure

7. PEPTIDES AND PROTEINS Proteins play a significant role in biological pathways and thus the preservation of life. • Proteins and peptides are polymers of amino acids C-terminal of one aa interact with the N-terminal of another amino acid, looses water molecule to form an amide bond (peptide bond).

8. PEPTIDES AND PROTEINS Oligopeptide Polypeptide

9. PEPTIDE BOND C-terminus slight –ve charge Rigid peptide bonds are unable to rotate freely thereby limiting the range of conformations Ф – phi (N-Cα ) Ѱ – psi angle (Cα–C) N-terminus slight +ve charge

10. 3-D STRUCTURE OF PROTEINS Secondary structures of a protein

11. α – HELIX Ramachandran Plot 3.6 residues 5.4Å • α – helix • ѱ = -45° to -50° • Ф = -60° H-bond the helix has 3.6 residues per turn wenxiang diagram

12. α – HELIX Factors affecting the Stability of the α - helices The electrostatic repulsion or attraction between successive amino acid residues with charged R groups. The bulkiness of the adjacent R groups The interactions between R groups spaced 3 or 4 residues apart. The occurrence of Pro and Gly residues The interaction between amino acid residues at the ends of helical segment and the electric dipole inherent in the α – helix What do you think would happen if there was stretch of Glu residues present ? Repulsion

13. α – HELIX What do you think would happen if Pro residues present ? Non-polar bulky group does not participate in H-bond interaction and will introduce a kink in the α – helix structure Pro What do you think would happen if Gly residues present ? To much conformational flexibility Gly

14. α – HELIX Recall: A net dipole extends along the helix structure What do you think would happen if a positively charged residue was present at the amino end or vise versa ? Positively charged amino acid at the amino terminus is destabilizing

15. β – SHEETS H-bond formed between adjacent segments of the polypeptide chain. The adjacent polypeptide chains can orient themselves to have the same amino-to-carboxyl orientation (Parallel) or opposite orientation (Antiparallel). • β – sheets • ѱ = 140° • Ф = -130°

16. β – SHEETS • 180° turn involving four amino acid residues. • Carbonyl oxygen of the first residue forming a hydrogen bond with the amino-group hydrogen of the fourth. Pro Gly and Pro residues often occur in turns, why? Gly

17. PROTEIN TERTIARY AND QUATERNARY STRUCTURES Classify proteins into two major groups: Fibrous proteins, having polypeptide chains arranged in long strands or sheets 2. Globular proteins, having polypeptide chains folded into a spherical or globular shape.

18. FIBROUS PROTEIN Cross section of a strand of hair containing the α keratin protein intermediate filament

19. GLOBULAR PROTEIN Quaternary Protein Structure of Human Hemoglobin Red Molecules represent α-globinBlue molecules represent β-globinGreen molecules symbolize heme Globular proteins include enzymes, transport proteins, motor proteins, regulatory proteins, immunoglobulins, and proteins with many other functions. • Differences between fibrous and globular proteins; • Typically fibrous proteins consist largely of a single type of secondary structure. • Globular proteins often contain several types of secondary structure. • The two groups differ functionally in that the structures that provide support, shape, and external protection to vertebrates are made of fibrous proteins, whereas most enzymes and regulatory proteins are globular proteins.

20. HEMOGLOBIN • Hemoglobin • Four polypeptide units • “tetramer” • 2 identical alpha chains • 2 identical beta chains • “hetero” • Often referred to as a “dimer of dimers” because it has 2 alpha chains and 2 beta chains • If Hemoglobin had four identical units… • homo-tetramer

21. HEMOGLOBIN VS. MYOGLOBIN • Myoglobin is like 1 of hemoglobin’s 4 subunits • Similar functions • O2 binding • Hg: binds 4 O2 • O2 transport • Mg: binds 1 O2 • O2 “storage”

22. PROTEIN STRUCTURE: KEY POINTS • Tertiary Structure is determined by hydrophillic/hydrophobic interactions • Nearly impossible to predict • Quaternary Structure is determined by DNA sequence (again) • alpha, beta, delta, gamma chains/units link together... • Primary Structure is determined by DNA sequence • Easy to predict (read the DNA) • Secondary Structure is determined by hydrogen bonds • Alpha-helixes and Beta-sheets have predictable motifs

25. 2. MECHANISM OF PROTEIN FOLDING Why do they fold? What stabilizes them in their conformation?

26. WHY DO PROTEINS FOLD? • To facilitate specific reactions that are necessary for specific physiological function. • Failure of protein to fold or mis-fold results in the disruption of pathophysiological pathways. Allergies Parkinson’s disease

27. STABILIZATION OF PROTEIN CONFORMERS Protein Conformation- spatial arrangement of atoms in a protein Native Conformation –proteins in their functional, folded conformation. It is the typically the most thermodynamically most stable conformer, having the lowest Gibbs free energy (G). Stability – the tendency of a protein to maintain a native conformation ∆G = ∆H - T∆S Betz, S. F. Disulfide bonds and the stability of globular proteins. Protein Sci. 1993, 2, 1551-1558. Forces Contributing to the Stability of Proteins • Intramolecular interactions • Stabilization of dipoles of α helices. • Solvent environment

28. MECHANISMS OF PROTEIN FOLDING Radford, S. E. Protein folding: progress made and promises ahead. Trends Biochem. Sci. 2000, 25, 611-618.

29. THANK YOU!