1. Molecular Structures

2. Classes of Biomolecules Proteins –polymers of amino acids –alias: polypeptides, peptides, enzymes Nucleic Acids –polymers of nucleotides –alias: DNA, RNA Lipids –long chain hydrocarbons tails with carboxylic end –alias: fatty acids, triglycerides, phosphoglycerides, phospholipids, steroids Carbohydrates –3-6 carbon polyhydroxyl compounds –monosaccharides, disaccharides, polysaccharides, starches, glycogen

3. Proteins & Amino Acids Amino Acid Properties

4. Proteins & Amino Acids Common modifications to amino acids in proteins in cells –phosphorylation (kinasing) – signaling, activation/inactivation –acetylation - histones –disulfide bridges – protein folding –hydroxylation – collagen polymerization –glycosylation (see carbohydrates)

5. Protein Structure Peptide bond PEPTIDE Fig 5-1 Essential Cell Biology, Alberts et al A.K.A Amide Bond

6. Protein Structure Backbone –amide nitrogen -  -carbon - carbonyl carbon Side chains –R-groups of each amino acid on  -carbon Peptide bond is planar giving rigidity to backbone Primary Structure Amino Acid Sequence Fig 3-4

7. Protein Structure Secondary Structure intramolecular folding of backbone  -helix  -sheet Fig 3-8

8. Alpha-helix Fig. 3-8 Copyright 2008 by Saunders/Elsevier. All rights reserved.

9. Coiled-coil of two parallel alpha-helices Fig. 3-10 Copyright 2008 by Saunders/Elsevier. All rights reserved.

10. Coiled-coil of two parallel alpha-helices Fig. 3-10 Copyright 2008 by Saunders/Elsevier. All rights reserved.

11. Beta-sheets Fig. 3-8 Copyright 2008 by Saunders/Elsevier. All rights reserved.

12. Protein Structure Tertiary structures –Proteins can have any combination of secondary structures Fig 3-9

13. Protein Structure Modeling protein structures X-ray crystallography Ribbon Space-filling Fig 2-9

14. Protein Structure Panel 5-2 Essential Cell Biology, Alberts et al Backbone Ribbon Wire Space-filling

15. Protein Structures Structural & Functional Domains FN – fibronectin Ig – immunoglobulin SH – src homology Fig 3-13

16. Nucleic Acids Nucleotides –Nitrogenous base Purine –Adenine –Guanine Pyrimidine –Cytosine –Thymine –Uracil –Pentose sugar 2’-deoxyribose Ribose –Phosphate 1-3 (mono, di, tri- phosphate)

17. Nucleic Acids Nitrogenous bases

18. Pentose sugar Nucleic Acids

19. Nucleoside Base + Sugar –Adenosine –Guanosine –Thymidine –Cytosine –Uridine

20. Phosphate –1-3 (mono, di, tri-phosphate) Nucleic Acids

21. Polymerization of nucleotides –Phosphodiester bond 3'-OH of added nucleotide SN2 attack on  phosphate –DNA polymerase –RNA polymerase

22. Nucleic Acid Structure The Double Helix –Watson-Crick base pairs A-T G-C

23. Nucleic Acid Structure RNA secondary structure –Intermolecular base pairing –Stems & loops 16S rRNAPhe tRNA

24. Simple sugars –Monosaccharides Glucose Fructose Galactose Mannose Ribose Arabinose Carbohydrates 6-carbon 5-carbon

25. Carbohydrates Important modificationsGlycosidic bonds glcNAc glcUA

26. Carbohydrates Glycoconjugates (polysaccharides, complex carbos) –Starch (plants) –Glycogen (animals) Branched polymers of glucose –Cellulose Unbranched polymers

27. Carbohydrates Important attachments to amino acid residue side chains

28. Carbohydrates Glycosaminoglycans (GAGs, mucopolysaccharidse) –Polymer of disaccharide units –Sulfate common modification –Linked to protein by O- or N- linkage to S/T or N residues respectively

29. Carbohydrates Proteoglycans –Proteins with attached glycosaminoglycans –Cell surface proteins –ECM