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  1. Organic Chemistry

  2. Outline • Organic vs Inorganic • Functional Groups and Isomers • Macromolecules • Carbohydrates • Lipids • Proteins • Nucleic Acids

  3. Inorganic – Chemistry of elements other than carbon Organic – Carbon-based chemistry Organic Molecules • Inorganic • Organic • Usually with+ & - ions • Always containcarbon and hydrogen • Usuallyionic bonding • Alwayscovalent bonding • Always withfew atoms • Often quite large, withmany atoms • Often associated with nonliving matter • Usually associatedliving systems

  4. Carbohydrates as structural materials

  5. Carbon Atom • Carbon atoms: • Contain a total of 6 electrons • Only four electrons in the outer shell • Very diverse as one atom can bond with up to four other atoms • Often bonds with other carbon atoms to make hydrocarbons • Can produce long carbon chains like octane • Can produce ring forms like cyclohexane

  6. Octane & Cyclohexane

  7. Functional Groups and Isomers • Functional groups: • Specific combinations of bonded atoms • Attached as a group to other molecules • Always react in the same manner, regardless of where attached • Determine activity and polarity of large organic molecules • Many functional groups, but only a few are of major biological importance

  8. Biologically ImportantFunctional Groups R R SH OH O O R R C C OH H O R R C H R N H O R R C OH • Group • Structure • Compound • Significance • Hydroxyl • Alcohols • Polar, forms H-bonds; some sugarsand amino acids Example: Ethanol • Polar, forms H-bonds; some sugarsand amino acids; Example: Ethanol • Aldehydes • Polar; some sugarsExample: Formaldehyde • Carbonyl • Polar; some sugarsExample: Formaldehyde • Ketones • Polar; some sugarsExample: Acetone • Polar; some sugarsExample: Acetone • CarboxylicAcids • Polar, acidic; fats and amino acidsExample: Acetic acid • Carboxyl • Polar, acidic; fats and amino acidsExample: Acetic acid • Polar, basic; amino acidsExample: Tryptophan • Amino • Amines • Polar, acidic; some amino acidsExample: Adenosine triphosphate • Polar, basic; amino acidsExample: Tryptophan • Sulfhydryl • Thiols • Disulfide Bonds; some amino acidsExample: Ethanethiol • Disulfide Bonds; some amino acidsExample: Ethanethiol • OrganicPhosphates • Polar, acidic; some amino acidsExample: Adenosine triphosphate • Phosphate

  9. Isomers • Isomers - organic molecules that have: • Identical molecular formulas, but • Differing internal arrangement of atoms

  10. Macromolecules • Some molecules called macromolecules because of their large size • Usually consist of many repeating units • Resulting molecule is a polymer (many parts) • Repeating units are called monomers • Some examples: • Category • Example • Subunit(s) • Lipids • Fat • Glycerol & fatty acids • Carbohydrates • Polysaccharide • Monosaccharide • Proteins • Polypeptide • Amino acid • Nucleic Acids • DNA, RNA • Nucleotide

  11. Common Foods

  12. Dehydration and Hydrolysis • Dehydration - Removal of water molecule • Used to connect monomers together to make polymers • Polymerization of glucose monomers to make starch • Hydrolysis - Addition of water molecule • Used to disassemble polymers into monomer parts • Digestion of starch into glucose monomers • Specific enzymes required for each reaction • Accelerate reaction • Are not used in the reaction

  13. Synthesis and Degradationof Polymers

  14. Four Classes of Organics:1 - Carbohydrates • Monosaccharides: • Single sugar molecule • Glucose, ribose, deoxyribose • Disaccharides: • Contain two monosaccharides joined during dehydration reaction • Sucrose • Polysaccharides: • Polymers of monosaccharides • Starch, cellulose, chitin

  15. Popular Models for RepresentingGlucose Molecules

  16. Synthesis and Degradationof Maltose, a Disaccharide

  17. Carbohydrates Examples:Monosaccharides • Single sugar molecules • Quite soluble and sweet to taste • Examples • Glucose (blood), fructose (fruit) and galactose • Hexoses - Six carbon atoms • Isomers of C6H12O6 • Ribose and deoxyribose (in nucleotides) • Pentoses – Five carbon atoms • C5H10O5 & C5H10O4

  18. Carbohydrates Examples:Disaccharides • Contain two monosaccharides joined by dehydration reaction • Soluble and sweet to taste • Examples • Sucrose • Table sugar, maple sugar • One glucose and one fructose joined by dehydration • Maltose • Malt sugar • Two glucoses joined by dehydration

  19. Carbohydrates Examples:Polysaccharides (1) • Polymers of monosaccharides • Low solubility; not sweet to taste • Examples • Starch • Polymer of glucose • Used for short-term energy storage • Plant starch • Often branched chain • Amylose, corn starch • Animal starch • Unbranched • Glycogen in liver and muscles

  20. Carbohydrates Examples:Polysaccharides (2) • More polysaccharide examples • Cellulose • Long, coiled polymer of glucose • Glucoses connected differently than in starch • Structural element for plants • Main component of wood and many natural fibers • Indigestible by most animals • Chitin • Polymer of glucose • Each glucose with an amino group • Very resistant to wear and digestion • Arthropod exoskeletons, cell walls of fungi

  21. StarchStructure and Function

  22. GlycogenStructure and Function

  23. CelluloseStructure and Function

  24. Four Classes of Organics:2 - Lipids • Insoluble in water • Long chains of repeating CH2 units • Renders molecule nonpolar • Types of Lipids • Type • Organismal Uses • Human Uses • Fats • Long-term energy storage & thermal insulation in animals • Butter, lard • Oils • Long-term energy storage in plants and their seeds • Cooking oils • Phospholipids • Component of plasma membrane • No-stick pan spray • Steroids • Component of plasma membrane; hormones • Medicines • Waxes • Wear resistance; retain water • Candles, polishes

  25. Blubber

  26. Types of Lipids:Triglycerides

  27. Types of Lipids:Triglycerides (1) • Triglycerides (Fats) • Long-term energy storage • Backbone of one glycerol molecule • Three-carbon alcohol • Each has an OH- group • Three fatty acids attached to each glycerol molecule • Long hydrocarbon chain • Saturated - no double bonds between carbons • Unsaturated - 1 double bonds between carbons • Carboxylic acid at one end • Carboxylic acid connects to –OH on glycerol in dehydration reaction

  28. Dehydration Synthesis of Triglyceridefrom Glycerol and Three Fatty Acids

  29. Types of Lipids:Phospholipids (2) • Phospholipids • Derived from triglycerides • Glycerol backbone • Two fatty acids attached instead of three • Third fatty acid replaced by phosphate group • The fatty acids are nonpolar and hydrophobic • The phosphate group is polar and hydrophilic • Molecules self arrange when placed in water • Polar phosphate “heads” next to water • Nonpolar fatty acid “tails” overlap and exclude water • Spontaneously form double layer & a sphere

  30. Phospholipids Form Membranes

  31. Types of Lipids:Steroids & Waxes (3) • Steroids • Cholesterol, testosterone, estrogen • Skeletons of four fused carbon rings • Waxes • Long-chain fatty acid bonded to a long-chain alcohol • High melting point • Waterproof • Resistant to degradation

  32. Steroid Diversity

  33. Waxes

  34. Four Classes of Organics:3 -Proteins • Functions • Support – Collagen • Enzymes – Almost all enzymes are proteins • Transport – Hemoglobin; membrane proteins • Defense – Antibodies • Hormones – Many hormones; insulin • Motion – Muscle proteins, microtubules

  35. Protein Subunits:The Amino Acids • Proteins are polymers of amino acids • Each amino acid has a central carbon atom (the alpha carbon) to which are attached • a hydrogen atom, • an amino group –NH2, • A carboxylic acid group –COOH, • and one of 20 different types of –R (remainder) groups • There are 20 different amino acids that make up proteins • All of them have basically the same structure except for what occurs at the placeholder R

  36. Structural Formulas for the20 Amino Acids

  37. Proteins:The Polypeptide Backbone • Amino acids joined together end-to-end • COOH of one AA covalently bonds to the NH2 of the next AA • Special name for this bond - Peptide Bond • Two AAs bonded together – Dipeptide • Three AAs bonded together – Tripeptide • Many AAs bonded together – Polypeptide • Characteristics of a protein determined by composition and sequence of AA’s • Virtually unlimited number of proteins

  38. Synthesis and Degradation of a Peptide

  39. Protein Molecules:Levels of Structure • Primary: • Literally, the sequence of amino acids • A string of beads (up to 20 different colors) • Secondary: • The way the amino acid chain coils or folds • Describing the way a knot is tied • Tertiary: • Overall three-dimensional shape of a polypeptide • Describing what a knot looks like from the outside • Quaternary: • Consists of more than one polypeptide • Like several completed knots glued together

  40. Levels of Protein Organization

  41. Examples of Fibrous Proteins

  42. Protein-folding Diseases • Assembly of AA’s into protein extremely complex • Process overseen by “chaperone” molecules • Inhibit incorrect interactions between R groups as polypeptide grows • Defects in these chaperones can corrupt the tertiary structure of proteins • Mad cow disease could be due to mis-folded proteins

  43. Four Classes of Organics:4 -Nucleic Acids • Polymers of nucleotides • Very specific cell functions • DNA (deoxyribonucleic acid) • Double-stranded helical spiral (twisted ladder) • Serves as genetic information center • In chromosomes • RNA (ribonucleic acid) • Part single-stranded, part double-stranded • Serves primarily in assembly of proteins • In nucleus and cytoplasm of cell

  44. The Nucleotides ofNucleic Acids • Three components: • A phosphate group, • A pentose sugar (ribose or deoxyribose), and • A nitrogenous base (4 kinds in DNA, 3 kinds in RNA, 3 common to both • Nucleotide subunits connected end-to-end to make nucleic acid • Sugar of one connected to the phosphate of the next • Sugar-phosphate backbone

  45. Nucleotides

  46. DNA Structure

  47. RNA Structure

  48. Comparison of DNA & RNA • Table 3.4 • Feature • DNA • RNA • Sugar • Deoxyribose • Ribose • Bases • Cytosine, guanine;adenine, thymine • Cytosine, guanine; • adenine, uracil • Strands • Double-stranded; Pairing across strands • Mostly single stranded • Helix • Yes • No • Function • Heredity; cellular control center • Interprets genetic info; protein synthesis • Where • Chromosomes of cell nucleus • Cell nucleus and cytoplasm

  49. Other Nucleic Acids • ATP (adenosine triphosphate) is composed of adenine, ribose, and three phosphates • In cells, one phosphate bond is hydrolyzed – Yields: • The molecule ADP (adenosine diphosphate) • An inorganic phosphate molecule pi • Energy • Other energy sources used to put ADP and pi back together again

  50. ATP