Organic Chemistry

1. Organic Chemistry Ms. Napolitano Honors Biology

3. Introduction to Orgo • Organic chem – the study of C based compounds (must have both C & H) • Why Carbon? • It’s versatile! • 4 valence electrons (4 covalent bonds) • Form simple or complex compounds • C chains form backbone of most biological molecules (straight, bent, double bond, rings)

4. Hydrocarbons • Hydrocarbons ONLY consist of C & H • Importance – store energy • Hydrophobic

5. Organic Shorthand

6. Isomers • Isomers – same number of atoms per element, different arrangement • 3 types: • Structural – differ in covalent partners • Geometric – differ in arrangement around a double bond • Enantiomers – mirror images of each other • Different structure means different function!

7. Isomers Geometric Isomers Structural Isomers cis trans Enantiomers

8. Functional Groups • Functional groups– parts of organic molecules that are most commonly involved in chemical reactions • replace H in hydrocarbons • Most are hydrophilic • Variation of life is due to molecular variation

9. Functional Groups

10. Macromolecules • Huge biological molecules! • 4 classes: • Carbohydrates • Lipids • Proteins • Nucleic Acids • Polymers – long molecule made of monomers

11. Polymerization • Building dimers or polymers • Condensation rxn AKA dehydration synthesis: • Monomer-OH + monomer-H  dimer + H2O • Breaking down dimers or polymers • Reverse rxn called hydrolysis • Dimer + H2O monomer-OH + monomer-H

13. Carbohydrates • Cells get most of their energy from carbs • Carbs are sugars, most end in “-ose” • Multiple of molecular formula: CH2O • Glucose: C6H12O6 • Carbonyl group • Multiple hydroxyl groups

14. Carbohydrates • Monosaccharides • Monomers: simple sugars w/ 3-7 carbons • Ex. (C6H12O6): Glucose, Fructose, Galactose • Disaccharide – formed by 2 monosaccharides forming a glycosidic linkage by dehydration synthesis • Ex: • glucose + glucose  maltose + H2O • glucose + fructose  sucrose + H2O • glucose + galactose  lactose + H2O

15. Carbohydrates

16. Carbohydrates • Polysaccharides: 100’s – 1000’s of monosaccharides joined by glycosidic linkages • Storage polysaccharides • Starch • Plants – stored in plastids • Made entirely of glucose - helical • Glycogen • Animals – stored in liver & muscle (in vertebrates) • Made entirely of glucose - branched • Structural polysaccharides • Cellulose – plant cell walls • Made of glucose – linear • Chitin • Exoskeleton of arthropods & fungi cell walls

17. Lipids • No polymers! • Hydrophobic (mostly hydrocarbons) • Store energy efficiently (2x more than carbs!) • Types : • Fats & oils • Phospholipids • Steroids • Waxes

18. Fats & Oils • Fat = dehydration synthesis of: • Glycerol C3H5(OH)3 • Fatty acid: 16 or 18 carbon hydrocarbon chain w/ carboxyl group • Glycerol + 3 fatty acid chains = triglyceride + 3 H2O • Function: • Energy storage • Insulation • Protective cushioning around organs

19. Saturated Fats • No double bonds between carbons • Saturated with hydrogens • Solid at room temperature • Mostly animal fat • Ex: butter, lard, adipose

20. Unsaturated Fats • 1 or more double bonds between carbons • Bent or kinked chains • Liquid at room temperature • Mostly plant or fish fat • Ex: olive oil, cod liver oil, corn oil

21. Phospholipids • Glycerol + 2 fatty acids + phosphate • Phosphate head = hydrophilic • Fatty acid tails = hydrophobic • Form a bilayer in water • Makes up cell membranes

22. Phospholipids

23. Steroids • 4 fused carbon rings with various functional groups • Ex: cholesterol • Component of cell membrane & many hormones

24. Proteins • Functions: enzymes, structural support, storage, transport, cellular communication, movement, defense • Monomer = amino acid • Short C chain • Amino group • Carboxylic acid group • “R” group determines type • Cells use 20 different amino acids to build 1000’s of different proteins • Amino acids linked by peptide bonds via dehydration synthesis to form polymers – polypeptides • Chaperonins assist in protein folding

26. Protein Structure • 10 Structure - Sequence of amino acids (length vary) - Determined by genes • 20 Structure • How polypeptide folds or coils • Α helix • β pleats • 30 Structure - 3D (fold onto itself) • H bonds • Hydrophobic interaction • Disulfide bridges • 40 Structure – bonds to other polypeptides • 2 or more polypeptide chains bonded together

28. Protein Conformation • Structure of a protein is directly related to function • Protein conformation is determined when it is synthesized, and it is maintained by chemical interactions • Protein conformation also depends on environmental factors: pH, salt concentration, temp…etc • Protein can be denatured – unravel and lose conformation, therefore biologically inactive. • When conditions change again, protein can be renatured(restored to normal)

29. Nucleic Acids • 2 types: • DNA (deoxyribonucleic acid) • Found in nucleus of eukarya • Double stranded helix • Provides directions for its own replication • Also directs RNA synthesis • Though RNA controls 10 structure of proteins • RNA (ribonucleic acid) • Single stranded, variety of shapes • Transfers information from nucleus to cytoplasm (where proteins are made) DNA RNA Proteins

30. Structure of Nucleic Acids • Monomers – nucleotides composed of 3 parts: • Pentose (ribose or deoxyribose) • Phosphate group • Nitrogenous base • Pyrimidines – 6 membered rings of C & N • Cytosine (C) • Thymine (T)….DNA only • Uracil (U)… RNA only • Purines – 6 membered ring fused to 5 membered ring of C & N • Adenine (A) • Guanine (G)

31. Nucleotide Structure

32. Bonding of Nucleotides

33. ATP • Not a macromolecule, but still important for life! • Adenosine Triphosphate (ATP) – primary energy transferring molecule in the cell • ATP   ADP + Pi + Energy