1. Chapter 2 Organic Compounds

2. Biochemistry: Essentials for Life Inorganic compounds Lack carbon w/ H & O Tend to be simpler compounds Example: H 2 O (water), CO 2

3. Important Inorganic Compounds Water

4. Water 60%–80% of the volume of living cells Most important inorganic compound in living organisms because of its properties

5. Figure 2.8b

6. Hydrogen Bonds Attractive force between electropositive hydrogen of one molecule and an electronegative atom of another molecule PLAY Animation: Hydrogen Bonds

8. Figure 2.10b (b) A water strider can walk on a pond because of the high surface tension of water, a result of the combined strength of its hydrogen bonds.

9. Properties of Water High heat capacity Absorbs and releases heat with little temperature change Prevents sudden changes in temperature High heat of vaporization Evaporation requires large amounts of heat Useful cooling mechanism

10. Properties of Water Polar solvent properties Dissolves and dissociates ionic substances Body’s major transport medium

11. Figure 2.12 Water molecule Ions in solution Salt crystal –– ++ ++

12. Properties of Water Reactivity A necessary part of hydrolysis and dehydration synthesis reactions Cushioning Protects certain organs from physical trauma, e.g., cerebrospinal fluid

13. Important Inorganic Compounds Salts

14. Ionic compounds that dissociate in water Contain cations other than H + and anions other than OH – Ions (electrolytes) conduct electrical currents in solution Ions play specialized roles in body functions (e.g., sodium, potassium, calcium, and iron)

15. Important Inorganic Compounds 3. Acids Can release detectable hydrogen ions (H + )(proton) 4. Bases Proton acceptors (OH - ) Neutralization reaction: Acids and bases react to form water and a salt

16. Acids and Bases Both are electrolytes Acids are proton (hydrogen ion) donors (release H + in solution) HCl  H + + Cl –

17. Acids and Bases Bases are proton acceptors (take up H + from solution) NaOH  Na + + OH – OH – accepts an available proton (H+) OH – + H +  H 2 O Bicarbonate ion (HCO 3 – ) and ammonia (NH 3 ) are important bases in the body

18. Acid-Base Concentration Acid solutions contain [H + ] As [H + ] increases, acidity increases Alkaline solutions contain bases (e.g., OH – ) As [H + ] decreases (or as [OH – ] increases), alkalinity increases

19. pH: Acid-Base Concentration pH = the negative logarithm of [H + ] in moles per liter Neutral solutions: Pure water is pH neutral (contains equal numbers of H + and OH – ) pH of pure water = pH 7: [H + ] = 10 –7 M All neutral solutions are pH 7

20. pH: Acid-Base Concentration Acidic solutions  [H + ],  pH Acidic pH: 0–6.99 pH scale is logarithmic: a pH 5 solution has 10 times more H + than a pH 6 solution Alkaline solutions  [H + ],  pH Alkaline (basic) pH: 7.01–14

21. Figure 2.13 Concentration (moles/liter) [OH – ] 10 0 10 –14 10 –1 10 –13 10 –2 10 –12 10 –3 10 –11 10 –4 10 –10 10 –5 10 –9 10 –6 10 –8 10 –7 10 –8 10 –6 10 –9 10 –5 10 –10 10 –4 10 –11 10 –3 10 –12 10 –2 10 –13 10 –1 [H + ]pH Examples 1M Sodium hydroxide (pH=14) Oven cleaner, lye (pH=13.5) Household ammonia (pH=10.5–11.5) Neutral Household bleach (pH=9.5) Egg white (pH=8) Blood (pH=7.4) Milk (pH=6.3–6.6) Black coffee (pH=5) Wine (pH=2.5–3.5) Lemon juice; gastric juice (pH=2) 1M Hydrochloric acid (pH=0) 10 –14 10 0 14 13 12 11 10 9 8 7 6 5 4 3 2 1 0

22. pH Measures relative concentration of hydrogen ions pH 7 = neutral pH below 7 = acidic pH above 7 = basic Buffers Chemicals that can regulate pH change

23. Acid-Base Homeostasis pH change interferes with cell function and may damage living tissue Slight change in pH can be fatal pH is regulated by kidneys, lungs, and buffers

24. Buffers Mixture of compounds that resist pH changes Convert strong (completely dissociated) acids or bases into weak (slightly dissociated) ones Carbonic acid-bicarbonate system

25. Buffer Lab Once completed follow the instructions for making your graph under the conclusion/analysis section. You will have 8 lines on your graph, 2 for each solution. Answer all the questions as well. Formal lab report due Friday 2/8.

26. Important Organic Compounds Contain carbon (except CO 2 and CO, which are inorganic) Unique to living systems Include carbohydrates, lipids, proteins, and nucleic acids

27. Organic Compounds Many are polymers—chains of similar units (monomers or building blocks) Synthesized by dehydration synthesis Broken down by hydrolysis reactions

28. Figure 2.14 + Glucose Fructose Water is released Monomers linked by covalent bond Water is consumed Sucrose (a) Dehydration synthesis Monomers are joined by removal of OH from one monomer and removal of H from the other at the site of bond formation. + (b) Hydrolysis Monomers are released by the addition of a water molecule, adding OH to one monomer and H to the other. (c) Example reactions Dehydration synthesis of sucrose and its breakdown by hydrolysis Monomer 1Monomer 2 Monomer 1Monomer 2 +

29. 1. Carbohydrates Contain carbon, hydrogen, and oxygen in a 1:2:1 ration (CH 2 O) n Include sugars and starches Classified according to size Monosaccharides – simple sugars Pentoses – 5 carbon sugars Ribose, deoxyribose Hexoses – 6 carbon sugars Glucose, fructose, galactose Disaccharides – two simple sugars joined by dehydration synthesis Sucrose, lactose, maltose

30. Carbohydrates Figure 2.12a, b

31. Figure 2.15b PLAY Animation: Disaccharides Example Sucrose, maltose, and lactose (these disaccharides are isomers) GlucoseFructoseGlucose SucroseMaltoseLactose Galactose (b) Disaccharides Consist of two linked monosaccharides

32. Carbohydrates Figure 2.13b Disaccharides or double sugars

33. Polysaccharides – long branching chains of linked simple sugars. Polymers of simple sugars. Starch, cellulose, glycogen

34. Figure 2.15c PLAY Animation: Polysaccharides Example This polysaccharide is a simplified representation of glycogen, a polysaccharide formed from glucose units. (c) Polysaccharides Long branching chains (polymers) of linked monosaccharides Glycogen

35. 2. Lipids Contain carbon, hydrogen, and oxygen not in a 1:2:1 ration C and H outnumber O Insoluble in water Glycerol and fatty acids Are the building blocks

36. Common lipids in the human body a. Neutral fats (triglycerides) - Found in fat deposits - Composed of 3 fatty acids & 1 glycerol - Source of stored energy - found in subcutaneous tissue and around organs

37. Saturated vs Unsaturated Fats

38. Saturation of Fatty Acids Saturated fatty acids Single bonds between C atoms; maximum number of H Solid animal fats, e.g., butter

39. Unsaturated Fatty Acids Unsaturated fatty acids One or more double bonds between C atoms Reduced number of H atoms Plant oils, e.g., olive oil

40. What are trans fats??

41. Trans fats Unsaturated fats LDL (bad) cholesterol & lower HDL (good) cholesterol Used to extend shelf life of processed foods – cookies, cakes, fries, donuts “hydrogenated oil” or “partially hydrogenated oil” likely contains trans fats Hydrogenation = chemical process that changes liquid oils into solid fats Since Jan. 2006: food manufacturers must list trans fats on their labels for consumers.

42. b. Phospholipids - chief component of cell membranes

43. Phospholipids Modified triglycerides: Glycerol + two fatty acids and a phosphorus (P)- containing group “Head” and “tail” regions have different properties Head is hydrophilic and tail hydrophobic Important in cell membrane structure

44. Figure 2.16b Phosphorus- containing group (polar “head”) Example Phosphatidylcholine Glycerol backbone 2 fatty acid chains (nonpolar “tail”) Polar “head” Nonpolar “tail” (schematic phospholipid) (b) “Typical” structure of a phospholipid molecule Two fatty acid chains and a phosphorus-containing group are attached to the glycerol backbone.

45. c. Steroids - cholesterol, bile salts, vitamin D, sex hormones, and adrenal cortical hormones

46. Other Lipids Found in the Body Fat-soluble vitamins – vitamins A, D, E, and K Lipoproteins – transport fatty acids and cholesterol in the bloodstream

47. 3. Proteins Contain C, O, H, N, and sometimes sulfur Over ½ of body’s organic matter Made of amino acids

48. Figure 2.17 (a) Generalized structure of all amino acids. (b) Glycine is the simplest amino acid. (c) Aspartic acid (an acidic amino acid) has an acid group (—COOH) in the R group. (d) Lysine (a basic amino acid) has an amine group (–NH 2 ) in the R group. (e) Cysteine (a basic amino acid) has a sulfhydryl (–SH) group in the R group, which suggests that this amino acid is likely to participate in intramolecular bonding. Amine group Acid group

49. Figure 2.18 Amino acid Dipeptide Dehydration synthesis: The acid group of one amino acid is bonded to the amine group of the next, with loss of a water molecule. Hydrolysis: Peptide bonds linking amino acids together are broken when water is added to the bond. + Peptide bond

50. Structural Levels of Proteins PLAY Animation: Introduction to Protein Structure

51. Figure 2.19a (a) Primary structure: The sequence of amino acids forms the polypeptide chain. Amino acid PLAY Animation: Primary Structure

52. Figure 2.19b  -Helix: The primary chain is coiled to form a spiral structure, which is stabilized by hydrogen bonds.  -Sheet: The primary chain “zig-zags” back and forth forming a “pleated” sheet. Adjacent strands are held together by hydrogen bonds. (b) Secondary structure: The primary chain forms spirals (  -helices) and sheets (  -sheets). PLAY Animation: Secondary Structure

53. Figure 2.19c Tertiary structure of prealbumin (transthyretin), a protein that transports the thyroid hormone thyroxine in serum and cerebro- spinal fluid. (c) Tertiary structure: Superimposed on secondary structure.  -Helices and/or  -sheets are folded up to form a compact globular molecule held together by intramolecular bonds. PLAY Animation: Tertiary Structure

54. Figure 2.19d Quaternary structure of a functional prealbumin molecule. Two identical prealbumin subunits join head to tail to form the dimer. (d) Quaternary structure: Two or more polypeptide chains, each with its own tertiary structure, combine to form a functional protein. PLAY Animation: Quaternary Structure

55. Structural Levels of Proteins Figure 2.17a-c

56. Structural Levels of Proteins Figure 2.17d, e

57. Fibrous and Globular Proteins Fibrous (Structural) proteins Extended and strandlike proteins Examples: keratin, elastin, collagen, and certain contractile fibers Globular (Functional) proteins Compact, spherical proteins with tertiary and quaternary structures Examples: antibodies, hormones, and enzymes

58. Protein Denaturation Figure 2.18a Reversible unfolding of proteins due to drops in pH and/or increased temperature

59. Protein Denaturation Figure 2.18b Irreversibly denatured proteins cannot refold and are formed by extreme pH or temperature changes

60. Enzymes (Functional Proteins) Proteins Act as biological catalysts Increase the rate of chemical reactions

61. Figure 2.20 Activation energy required Less activation energy required WITHOUT ENZYMEWITH ENZYME Reactants Product Reactants PLAY Animation: Enzymes

62. Mechanism of Enzyme Action Enzyme binds with substrate Product is formed at a lower activation energy Product is released

63. Figure 2.21, step 1 Substrates (S) e.g., amino acids Enzyme (E) Enzyme-substrate complex (E-S) Substrates bind at active site. Enzyme changes shape to hold substrates in proper position. Active site + 1

64. Figure 2.21, step 2 Substrates (S) e.g., amino acids Enzyme (E) Enzyme-substrate complex (E-S) Energy is absorbed; bond is formed. Water is released. Substrates bind at active site. Enzyme changes shape to hold substrates in proper position. Internal rearrangements leading to catalysis occur. Active site + H2OH2O 12

65. Figure 2.21, step 3 Substrates (S) e.g., amino acids Enzyme (E) Enzyme-substrate complex (E-S) Enzyme (E) Product (P) e.g., dipeptide Energy is absorbed; bond is formed. Water is released. Peptide bond Substrates bind at active site. Enzyme changes shape to hold substrates in proper position. Internal rearrangements leading to catalysis occur. Product is released. Enzyme returns to original shape and is available to catalyze another reaction. Active site + H2OH2O 12 3

66. Summary of Enzyme Action PLAY Animation: How Enzymes Work

67. Enzyme Action Lab Testing the affect of concentration, temperature and pH on the enzyme catalase activity.

68. 4. Nucleic AcidsNucleic Acids Composed of carbon, oxygen, hydrogen, nitrogen, and phosphorus Their structural unit, the nucleotide, is composed of N-containing base, a pentose sugar, and a phosphate group

69. Five nitrogen bases contribute to nucleotide structure – adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U)

70. Two major classes – DNA and RNA

71. Deoxyribonucleic acid (DNA) Organized by complimentary bases to form double helix Found in the nucleus Replicates before cell division Provides instruction for every protein in the body

72. Figure 2.22 Deoxyribose sugar Phosphate Sugar-phosphate backbone Adenine nucleotide Hydrogen bond Thymine nucleotide Phosphate Sugar: Deoxyribose Phosphate SugarThymine (T) Base: Adenine (A) Thymine (T) Cytosine (C) Guanine (G) (b) (a) (c) Computer-generated image of a DNA molecule

73. Structure of DNA Figure 2.21a

74. Structure of DNA Figure 2.21b

75. Ribonucleic Acid (RNA) Four bases: adenine (A), guanine (G), cytosine (C), and uracil (U) Single-stranded molecule mostly active outside the nucleus Three varieties of RNA carry out the DNA orders for protein synthesis messenger RNA, transfer RNA, and ribosomal RNA PLAY Animation: DNA and RNA

76. 5. Adenosine Triphosphate (ATP) Adenine-containing RNA nucleotide with two additional phosphate groups

77. Figure 2.23 Adenosine triphosphate (ATP) Adenosine diphosphate (ADP) Adenosine monophosphate (AMP) Adenosine Adenine Ribose Phosphate groups High-energy phosphate bonds can be hydrolyzed to release energy.

78. Adenosine Triphosphate (ATP) Adenosine Triphosphate (ATP) Chemical energy used by all cells Energy is released by breaking high energy phosphate bond ATP is replenished by oxidation of food fuels

79. Figure 2.24 Solute Membrane protein Relaxed smooth muscle cell Contracted smooth muscle cell + + + Transport work: ATP phosphorylates transport proteins, activating them to transport solutes (ions, for example) across cell membranes. Mechanical work: ATP phosphorylates contractile proteins in muscle cells so the cells can shorten. Chemical work: ATP phosphorylates key reactants, providing energy to drive energy-absorbing chemical reactions. (a) (b) (c)