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Ch. 3 - Organic Molecules

Inorganic – Chemistry of elements other than carbon Organic – Carbon-based chemistry. Ch. 3 - Organic Molecules. p. 36 text. Inorganic. Organic. Usually with + & - ions. Always contain carbon and hydrogen. Usually ionic bonding. Always covalent bonding. Always with few atoms.

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Ch. 3 - Organic Molecules

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  1. Inorganic – Chemistry of elements other than carbon Organic – Carbon-based chemistry Ch. 3 - Organic Molecules p. 36 text • 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

  2. Carbohydrates as structural materials

  3. 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

  4. Octane & Cyclohexane

  5. 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

  6. Biologically ImportantFunctional Groups (Fig. 3.2) R R SH OH O O R R C C OH H O R R C H R N H O R OH P 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 • Sulfhydryl • Thiols • Disulfide Bonds; some amino acidsExample: Ethanethiol • Polar, basic; amino acidsExample: Tryptophan • OrganicPhosphates • Disulfide Bonds; some amino acidsExample: Ethanethiol • Polar, acidic; some amino acidsExample: Adenosine triphosphate • Phosphate

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

  8. 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

  9. Common Foods

  10. Dehydration and Hydrolysis • Dehydration (condensation) - Removal of water molecule • Connects monomers together to make polymers • Glucose monomers condense to make starch • Hydrolysis - Addition of water molecule • Disassembles polymers into monomer parts • Digestion of starch into glucose monomers • Specific enzymes required for each reaction • Accelerate reaction • Are not used in the reaction

  11. Synthesis and Degradationof Polymers

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

  13. Popular Models for RepresentingGlucose Molecules

  14. Synthesis and Degradationof Maltose, a Disaccharide

  15. 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

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

  17. 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

  18. Carbohydrates Examples:Polysaccharides (2) • More polysaccharide examples • Cellulose • Long, coiled polymer of glucose • Structural element for plants • Indigestible by most animals • Chitin • Polymer of glucose • Very resistant to wear and digestion • Arthropod exoskeletons, cell walls of fungi

  19. StarchStructure and Function

  20. GlycogenStructure and Function

  21. CelluloseStructure and Function

  22. 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

  23. Blubber

  24. Types of Lipids:Triglycerides

  25. Types of Lipids:Triglycerides (1) • Triglycerides (Fats) • Long-term energy storage • Backbone of one glycerol molecule • 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

  26. Dehydration Synthesis of Triglyceridefrom Glycerol and Three Fatty Acids

  27. 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

  28. Phospholipids Form Membranes

  29. 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

  30. Steroid Diversity

  31. Waxes

  32. 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

  33. Protein Subunits:The Amino Acids • Proteins are polymers of amino acids • Each amino acid has a central carbon atom 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

  34. Structural Formulas for the20 Amino Acids

  35. 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

  36. Synthesis and Degradation of a Peptide

  37. Protein Molecules:Levels of Structure • Primary: • Literally, the sequence of amino acids • Secondary: • The way the amino acid chain coils or folds • Tertiary: • Overall three-dimensional shape of a polypeptide • Quaternary: • Consists of more than one polypeptide

  38. Levels of Protein Organization

  39. Examples of Fibrous Proteins

  40. 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

  41. 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) • Single-stranded • Serves primarily in assembly of proteins • In nucleus and cytoplasm of cell

  42. The Nucleotides ofNucleic Acids • Three components: • A phosphate group, • A pentose sugar (ribose or deoxyribose), and • A nitrogenous base (4 kinds in DNA, 4 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

  43. Nucleotides

  44. DNA Structure

  45. RNA Structure

  46. 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 • Single stranded • Helix • Yes • No • Function • Heredity; cellular control center • Interprets genetic info; protein synthesis • Where • Chromosomes of cell nucleus • Cell nucleus and cytoplasm

  47. 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

  48. ATP

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