1. The document discusses organic chemistry concepts including organic molecules, carbon, functional groups, isomers, macromolecules, and the four major types of organic molecules: carbohydrates, lipids, proteins, and nucleic acids. 2. Carbohydrates are composed of carbon, hydrogen, and oxygen and include monosaccharides like glucose and disaccharides formed from monosaccharide units. 3. Proteins are composed of amino acids joined by peptide bonds to form polypeptides or proteins. They have primary, secondary, tertiary, and quaternary structure levels.

1. CHAPTER 3 LECTURE SLIDES Prepared by Brenda Leady University of Toledo To run the animations you must be in Slideshow View. Use the buttons on the animation to play, pause, and turn audio/text on or off. Please note: once you have used any of the animation functions(such as Play or Pause), you must first clickin the white background before you advance the next slide. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

2. 2 Organic Chemistry Organic molecules contain carbon Abundant in living organisms Macromolecules are large, complex organic molecules

3. 3 Carbon Carbon has 4 electrons in its outer shell Needs 4 more electrons to fill the shell It can make up to 4 bonds Usually single or double bonds Carbon can form nonpolar and polar bonds Molecules with nonpolar bonds (like hydrocarbons) are poorly water soluble Molecules with polar bonds are more water soluble

4. 4 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Nucleus First shell is filled with 2 electrons – Spherical s orbital of second shell is filled with 2 electrons – – – – Other energy orbitals of second shell contain 1 or 0 electrons – (a) Orbitals – – – + + + + – – + + – (b) Simplified depiction of energy shells

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6. 6 Functional Groups Groups of atoms with special chemical features that are functionally important Each type of functional group exhibits the same properties in all molecules in which it occurs

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9. 9 Isomers Two structures with an identical molecular formula but different structures and characteristics Structural isomers- contain the same atoms but in different bonding relationships Stereoisomers- identical bonding relationships, but the spatial positioning of the atoms differs in the two isomers cis-trans isomers- positioning around double bond Enantiomers- mirror image of another molecule

10. 10 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H H H H H H H C C C H H C C C OH H H OH H H H Isopropyl alcohol Propyl alcohol (a) Structural isomers H H H H H H H H C C C C H H C C C C H H H H H H trans-butene cis-butene Cis–trans isomers Molecule Mirror image Enantiomers (b) Two types of stereoisomers

11. Macromolecules Condensation or dehydration reaction Links monomers to form polymers Hydrolysis Polymers broken down into monomers 11

12. Figure 3.5 12 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Monomers HO H H HO +

13. Figure 3.5 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H2O Monomers H HO HO H H HO + 13

14. Figure 3.5 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H2O H2O Monomers HO H H H H HO HO HO + H HO 14

15. Figure 3.5 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H2O H2O H2O Monomers + HO H H H H H HO HO HO HO H HO H HO 15

16. Figure 3.5 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H HO 16

17. Figure 3.5 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H HO H H HO HO H2O 17

18. Figure 3.5 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H H HO HO H H H HO HO HO H2O H2O 18

19. Figure 3.5 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H H HO HO H H H HO H H + HO HO HO HO H2O H2O H2O 19

20. Figure 3.5 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H2O H2O H2O Monomers HO H H H H + HO HO HO H HO H HO H HO (a) Polymer formation by dehydration reactions H H HO HO H H H HO H H + HO HO HO HO H2O H2O H2O (b) Breakdown of a polymer by hydrolysis reactions 20

21. 21 Four major types of organic molecules and macromolecules Carbohydrates Lipids Proteins Nucleic acids

22. 22 Carbohydrates Composed of carbon, hydrogen, and oxygen atoms Cn(H2O)n Most of the carbon atoms in a carbohydrate are linked to a hydrogen atom and a hydroxyl group

23. 23 Monosaccharides Simplest sugars Most common are 5 or 6 carbons Pentoses- ribose (C5H10O5), deoxyribose (C5H10O4) Hexose- glucose (C6H12O6) Different ways to depict structures Ring or linear

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25. 25 Glucose isomers Structural isomers- different arrangement of same elements Glucose and galactose Stereoisomers α- and β-glucose Hydroxyl group of carbon 1 above or below ring D- and L-glucose Enantiomers- mirror image

27. 27 Disaccharides Carbohydrates composed of two monosaccharides Joined by dehydration or condensation reaction Glycosidic bond Broken apart by hydrolysis Examples − sucrose, maltose, lactose

28. 28 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CH2OH CH2OH OH O O H H H H HO H OH + CH2OH H HO O H OH H H OH Glucose Fructose

29. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CH2OH CH2OH OH O O H H H Glucose + Fructose H HO H OH + CH2OH H HO O H OH H H OH Glucose Fructose CH2OH H H O Glycosidic bond H H OH HO OH H Sucrose + Water + H2O O CH2OH O H HO CH2OH H 29 H OH Sucrose

30. 30 Polysaccharides Many monosaccharides linked together to form long polymers Examples Energy storage – starch, glycogen Structural role – cellulose, chitin, glycosaminoglycans

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32. 32 Lipids Composed predominantly of hydrogen and carbon atoms Defining feature of lipids is that they are nonpolar and therefore very insoluble in water

33. 33 Fats Also known as triglycerides or triacylglycerols Formed by bonding glycerol to three fatty acids Joined by dehydration or condensation reaction Broken apart by hydrolysis

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35. 35 Fatty acids Saturated- all carbons are linked by single covalent bonds Tend to be solid at room temperature Unsaturated- contain one or more double bonds Tend to be liquid at room temperature (oils) cis forms naturally trans formed by synthetic process – disease link

36. 36 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. O CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH3 C HO Saturated fatty acid (Stearic acid) O CH C CH2 CH2 CH2 CH2 CH2 CH2 CH2 HO CH CH2 CH CH CH2 CH2 CH3 CH2 CH2 Unsaturated fatty acid (Linoleic acid)

37. 37 Fats are important for energy storage 1 gram of fat stores more energy than 1 gram of glycogen or starch Fats can also be structural in providing cushioning and insulation

38. 38 Phospholipids Glycerol, 2 fatty acids and a phosphate group Amphipathic molecule Phosphate region- polar, hydrophillic, head Fatty acid chains- nonpolar, hydrophobic, tail

39. 39 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Charged nitrogen- containing region CH3 CH3 CH3 N+ CH2 CH2 O Polar head (hydrophilic) – O O P Phosphate O Glycerol backbone H Polar heads CH2 C H2C Schematic drawing of a phospholipid O O Ends of fatty acids C C O O H2C H2C CH2 CH 2 H2C H2C Nonpolar tails Membrane bilayer CH2 CH 2 H2C H2C CH2 CH 2 H2C H2C Polar heads CH2 Nonpolar tail (hydrophobic) CH 2 H2C H2C CH2 CH 2 H2C H2C Nonpolar fatty acid tails CH2 CH 2 H2C H2C CH2 CH 2 H3C H3C Polar heads Space-filling model Chemical structure (a) Structure and model of a phospholipid (b) Arrangement of phospholipids in a bilayer

40. 40 Steroids Four interconnected rings of carbon atoms Usually not very water soluble Cholesterol Tiny differences in chemical structure can lead to profoundly different biological properties Estrogen vs. testosterone

41. 41 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CH3 CH2 CH CH2 H3C CH3 CH CH2 CH H 3 CH3 H H 3 Cholesterol HO

42. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CH3 CH2 CH CH2 H3C CH3 CH CH2 CH H 3 CH3 H H 3 Cholesterol HO OH H3C OH H3C H CH3 H H H H H HO O Testosterone Estrogen 42 Female cardinal Male cardinal b: © Adam Jones/Photo Researchers; c: © Adam Jones/Photo Researchers

43. 43 Proteins Composed of carbon, hydrogen, oxygen, nitrogen, and small amounts of other elements, notably sulfur Amino acids are the monomers Common structure with variable R-group 20 amino acids Side-chain determines structure and function

44. 44 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. R H O C H N+ C O– H H -carbon

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46. 46 Joined by dehydration or condensation reaction Peptide bond Forms polypeptides Proteins are made up of 1 or more polypeptides Broken apart by hydrolysis

47. 47 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Glycine H H O N+ C H C O– H H Carboxylgroup

48. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Alanine Glycine H H H CH3 O O + H N+ C H N+ C C C O– O– H H H H Aminogroup Carboxylgroup 48

49. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Alanine Glycine H H H H CH3 O H CH3 O O O + H N+ C H H N+ C N+ C C N C C C C Peptide bond O– O– O– H H H H H H H H Aminogroup Carboxylgroup 49

50. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Alanine Glycine H H H H CH3 O H CH3 O O O H2O + + H N+ C H H C N+ C C N+ C C N C C Peptide bond O– O– O– H H H H H H H H Aminogroup Carboxylgroup (a) Formation of a peptide bond between 2 amino acids OH O O– C SH OH H3C CH3 O H H O O O O CH3 CH2 O O CH2 CH2 CH2 CH2 CH O N+ C N N H C C C C N C C C C N N C C N N C C C C C O– H H H H H H H H H H H H H H H H Free carboxyl group Free aminogroup (b) Polypeptide—a linear chain of amino acids N-terminus C-terminus 1 2 3 4 5 6 7 8 H3N+ COO– Gly Ala Ser Asp Phe V al T yr Cys 50 (c) Numbering system of amino acids in a polypeptide

51. 51 Protein Structure Primary Secondary Tertiary Quaternary

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53. 53 Primary structure Amino acid sequence Determined by genes

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55. 55 Secondary Structure Chemical and physical interactions cause folding Repeating patterns αhelices and β pleated sheets Key determinants of a protein’s characteristics “Random coiled regions” Not αhelix or β pleated sheet Shape is specific and important to function

56. 56 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. NH3+ O C CH2 + NH3 O– CH2 CH2 CH2 O H CH2 H COO– O CH3 HC CH3 H CH2 CH2 CH2 O CH3 CH2 H N CH2 OH CH2 CH CH3 CH3 O H NH2 C CH2 N CH 2 CH3 CH3 H CH3 CH2 CH3 OH CH CH2 CH3 CH S S CH2 CH2 CH3

57. 57 Tertiary structure Folding gives complex three-dimensional shape Final level of structure for single polypeptide chain

58. 58 Quaternary structure Made up of 2 or more polypeptides Protein subunits – individual polypeptides Multimeric proteins – proteins with multiple parts

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60. 60 5 factors promoting protein folding and stability Hydrogen bonds Ionic bonds and other polar interactions Hydrophobic effects Van der Waals forces Disulfide bridges

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62. 62 Protein-protein interactions Many cellular processes involve steps in which two or more different proteins interact with each other Specific binding at surface Use first 4 factors Hydrogen bonds Ionic bonds and other polar interactions Hydrophobic effects Van der Waals forces

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64. Anfinsen Showed That the Primary Structure of Ribonuclease Determines Its Three-Dimensional Structure Prior to the 1960s, the mechanisms by which proteins assume their three-dimensional structures were not understood. Christian Anfinsen, however, postulated that proteins contain all the information necessary to fold into their proper conformation without the need for organelles or cellular factors He hypothesized that proteins spontaneously assume their most stable conformation based on the laws of chemistry and physics

65. Ribonuclease experimentNobel Prize 1972 In vitro- no other cellular components present Chemicals that disrupt bonds cause the enzyme to lose function Removal of those chemicals restored function Even in the complete absence of any cellular factors or organelles, an unfolded protein can refold into its functional structure We have learned that some proteins do require assistance in folding

66. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. HYPOTHESIS Within their amino acid sequence, proteins contain all the information needed to fold into their correct, 3-dimensional shapes. KEY MATERIALS Purified ribonuclease, RNA, denaturing chemicals, size-exclusion columns. Experimental level Conceptual level Numerous H bonds (not shown) and 4 S—S bonds. Protein is properly folded. Incubate purified ribonuclease in test tube with RNA, and measure its ability to degrade RNA. 1 1 S S S Purified ribonuclease S S S S S -mercaptoethanol No more H bonds, ionic bonds, or S—S bonds. Protein is unfolded. Denature ribonuclease by adding -mercaptoethanol (breaks S—S bonds) and urea (breaks H bonds and ionic bonds). Measure its ability to degrade RNA. 2 + SH Urea SH SH SH SH Denatured ribonuclease SH SH SH -mercaptoethanol Urea Beads have microscopic pores that trap -mercapto- ethanol and urea, but not ribonuclease. Mixture from step 2 containing denatured ribonuclease, -mercaptoethanol, and urea Layer mixture from step 2 atop a chromatography column. Beads in the column allow ribonuclease to escape, while -mercaptoethanol and urea are retained. Collect ribonuclease in a test tube and measure its ability to degrade RNA. 3 Column containing beads suspended in a watery solution Denatured ribonuclease Collection port with filter to prevent beads from escaping Solution of ribonuclease Renatured ribonuclease 4 5 THE D AT A CONCLUSION Certain proteins, like ribonuclease, can spontaneously fold into their final, functionalshapes without assistance from other cellularstructures or factors. (Howeve r , as described in your text, this is not true of many other proteins.) 100 Activity restored 6 SOURCE Habe r , E., and Anfinsen, C.B. 1961. Regeneration of enzyme activity by air oxidation of reduced subtilisin-modified ribonuclease. Journal of Biological Chemistry 236:422–424. Ribonuclease function (%) 50 0 Purified ribonuclease (step 1) Denatured ribonuclease (step 2) Ribonuclease after column chromatography (step 3)

67. Proteins Contain Functional Domains Within Their Structures Module or domains in proteins have distinct structures and function Signal transducer and activator of transcription (STAT) protein example Each domain of this protein is involved in a distinct biological function Proteins that share one of these domains also share that function

68. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. HN3+ STATprotein COO–

69. 69 Nucleic Acids Responsible for the storage, expression, and transmission of genetic information Two classes Deoxyribonucleic acid (DNA) Store genetic information coded in the sequence of their monomer building blocks Ribonucleic acid (RNA) Involved in decoding this information into instructions for linking together a specific sequence of amino acids to form a polypeptide chain

70. 70 Monomer is a nucleotide Made up of phosphate group, a five-carbon sugar (either ribose or deoxyribose), and a single or double ring of carbon and nitrogen atoms known as a base Monomers linked into polymer with a sugar-phosphate backbone

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72. 72 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Bases Backbone Adenine NH2 N N H O– 5 N O O P CH2 N O Guanine 1 Sugar O– 4 H H O H H Phosphate H N 3 2  N H Nucleotide H NH2 N O N 5 O O CH P 2 O Cytosine O– 4 1 NH2 H H H H 2 3 N H N O 5 O O P CH2 O O– 4 1 Thymine H H H H 3 2 H CH3 N O N 5 O O P CH2 O O– 1 4 H H H H 2 3 H OH

73. 73 DNA vs. RNA

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