1. Organic Chemistry Chapter 03

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

3. Organic Chemistry 3 Organic Molecules Inorganic – Chemistry of elements other than carbon Organic – Carbon-based chemistry Usually associated living systems Often associated with nonliving matter Often quite large, with many atoms Always with few atoms Always covalent bonding Usually ionic bonding Always contain carbon and hydrogen Usually with + & - ions OrganicInorganic

4. 4 Carbohydrates as structural materials

5. Organic Chemistry 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. 6 Octane & Cyclohexane

7. Organic Chemistry 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. Organic Chemistry 8 Polar; some sugars Example: Acetone Polar, forms H-bonds; some sugars and amino acids Example: Ethanol ROH R H C O RR C O R C O R H N H RSH Biologically Important Functional Groups Thiols Phosphate Amines Amino Carboxylic Acids Carboxyl Ketones Aldehydes Carbonyl AlcoholsHydroxyl CompoundStructureGroup Sulfhydryl RR C O OH Organic Phosphates Significance Polar; some sugars Example: Formaldehyde Polar, acidic; fats and amino acids Example: Acetic acid Polar, basic; amino acids Example: Tryptophan Disulfide Bonds; some amino acids Example: Ethanethiol Polar, acidic; some amino acids Example: Adenosine triphosphate Polar, forms H-bonds; some sugars and amino acids; Example: Ethanol Polar; some sugars Example: Formaldehyde Polar; some sugars Example: Acetone Polar, acidic; fats and amino acids Example: Acetic acid Polar, acidic; some amino acids Example: Adenosine triphosphate Disulfide Bonds; some amino acids Example: Ethanethiol Polar, basic; amino acids Example: Tryptophan

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

10. Organic Chemistry 10Macromolecules 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: NucleotideDNA, RNA Nucleic Acids Amino acidPolypeptide Proteins MonosaccharidePolysaccharide Carbohydrates Glycerol & fatty acidsFat Lipids Subunit(s)ExampleCategory

11. 11 Common Foods

12. Organic Chemistry 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. 13 Synthesis and Degradation of Polymers

14. Organic Chemistry 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. 15 Popular Models for Representing Glucose Molecules

16. 16 Synthesis and Degradation of Maltose, a Disaccharide

17. Organic Chemistry 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 C 6 H 12 O 6  Ribose and deoxyribose (in nucleotides) ­Pentoses – Five carbon atoms ­C 5 H 10 O 5 & C 5 H 10 O 4

18. Organic Chemistry 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. Organic Chemistry 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. Organic Chemistry 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. 21 Starch Structure and Function

22. 22 Glycogen Structure and Function

23. 23 Cellulose Structure and Function

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

25. 25 Blubber

26. 26 Types of Lipids: Triglycerides

27. Organic Chemistry 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. 28 Dehydration Synthesis of Triglyceride from Glycerol and Three Fatty Acids

29. Organic Chemistry 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. 30 Phospholipids Form Membranes

31. Organic Chemistry 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. 32 Steroid Diversity

33. 33 Waxes

34. Organic Chemistry 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. Organic Chemistry 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 –NH 2,  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. 36 Structural Formulas for the 20 Amino Acids

37. Organic Chemistry 37 Proteins: The Polypeptide Backbone Amino acids joined together end-to-end  COOH of one AA covalently bonds to the NH 2 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. 38 Synthesis and Degradation of a Peptide

39. Organic Chemistry 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. 40 Levels of Protein Organization

41. 41 Examples of Fibrous Proteins

42. Organic Chemistry 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. Organic Chemistry 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. Organic Chemistry 44 The Nucleotides of Nucleic 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. 45 Nucleotides

46. 46 DNA Structure

47. 47 RNA Structure

48. Organic Chemistry 48NoYes Helix Interprets genetic info; protein synthesis Heredity; cellular control center Function Cell nucleus and cytoplasm Chromosomes of cell nucleus Where Comparison of DNA & RNA Table 3.4 Mostly single stranded Double-stranded; Pairing across strands Strands Cytosine, guanine; adenine, uracil Cytosine, guanine; adenine, thymine Bases RiboseDeoxyribose Sugar RNADNAFeature

49. Organic Chemistry 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 p i  Energy Other energy sources used to put ADP and p i back together again

50. 50 ATP

51. Organic Chemistry 51Review Organic vs Inorganic Functional Groups and Isomers Macromolecules  Carbohydrates  Lipids  Proteins  Nucleic Acids

52. Organic Chemistry Ending Slide Chapter 03