1. PROTEINS BIT 230 Biochemistry Purification Characterization

2. Review (familiar material) zReview of Central Dogma zReview of Translation zClasses of proteins zAmino Acid Characteristics zProtein Structures zSequencing

3. Fig 13.3 The four levels of organization in proteins. © 2003 John Wiley and Sons Publishers

4. Fig 13.1 Structures of the 20 amino acids commonly found in proteins. © 2003 John Wiley and Sons Publishers

5. 20 amino acids (residues) R groups 1. Hydrophobic, nonpolar aliphatic (side chain only has C H) met is non reactive-often a part of this group pro R group covalently bond to amino group tend to interact non-covalently found in membranes or inside the 3D structure 2. Hydrophilic, polar, non-charged, aromatic cysteine -sulfur group MOST reactive disulfide bonds (intra and inter) Aspargine and Glutamine can deaminate to Aspartic acid and glutamic acid 3. Negatively charged 4. Positively charged Phe, Tyr Trp are aromatic - absorb UV light (280 nm) Bulky R groups

6. p. 304 – All the amino acids except proline contain a free amino group and a free carboxyl group. © 2003 John Wiley and Sons Publishers

7. Fig 13.2 The formation of a peptide bond between two amino acids by the removal of water. © 2003 John Wiley and Sons Publishers

9. Fig 13.4 Secondary structure in proteins. © 2003 John Wiley and Sons Publishers

10. Fig 13.5 The five types of molecular interactions that determine the tertiary structure. © 2003 John Wiley and Sons Publishers

11. Features Denaturation Structure and Function Classes Fibrous simple, elongated, structural, protective Globular complex, spherical Transmembrane proteins Signal Sequence (N terminal region)

12. Simple vs Conjugated Conjugated prosthetic groups (non-peptide) Glycoproteins phosphoproteins flavoproteins metalloproteins

13. Sequencing Amino Acids Edman Degradation http://www.cartage.org.lb/en/themes/R eference/dictionary/Biologie/E/11.htmlhttp://www.cartage.org.lb/en/themes/R eference/dictionary/Biologie/E/11.html Mass Spectrometry http://chipo.chem.uic.edu/web1/ocol/sp ec/MS1.htmhttp://chipo.chem.uic.edu/web1/ocol/sp ec/MS1.htm Swiss Prot Database

14. Secondary Structures Alpha Helix Ala, Leu, Met, Glutamate why would proline and trp not be found here? Beta Sheets zigzag Loops outside of protein (hydrophilic) active sites of enzymes antigen binding region of Ab susceptible to proteolytic cleavage B turn Glycine at bend (small side) and proline (induces kink)

15. Tertiary Structures Domains structural subunits within a single polypeptide intracellular region TMR extracellular domain

16. Post Translational Modifications FUNCTION Proteolytic Processing Pro form (zymogen, inactive) cleave some amino acids- ACTIVE clotting factors, digestive enzymes Glycosylation p 30 O linked serine threonine N linked asparagine

17. PTM Continued Phosphorylation activate or inactivate donor often ATP kinase adds PO3 phosphorylase removes PO3 Acetylation add acetyl group Acylation add fatty acid

18. Inhibition of protein synthesis Antibiotics Cycloheximide -inhibits tranlocation Erythromycin- binds ribosome inhibits tranlocation Streptomycin - inhibits initiation of translation Tetracycline - blocks aminoacyl tRNA from binding to ribosome Antimicrobials Triclosan disrupts membrane of bacteria non-specific? No tolerance developed? Inhibits a reductase (synthesis of fats)