1. Copyright © 2010 Pearson Education, Inc. Chemistry Comes Alive 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) PART B

2. Copyright © 2010 Pearson Education, Inc. Classes of Compounds Inorganic compounds Do not contain a carbon backbone Water, salts, and many acids and bases Organic compounds Contain a carbon-based structure or “carbon backbone” Usually large and complex Atoms are covalently bonded Carbohydrates, fats, proteins, and nucleic acids

3. Copyright © 2010 Pearson Education, Inc. Properties of Water High heat capacity – absorbs and releases large amounts of heat before changing temperature High heat of vaporization – requires large amounts of heat to change from a liquid to a gas Polar solvent properties – dissolves ionic substances, forms hydration layers around large charged molecules (e.g., proteins), and serves as the body’s major transport medium

4. Copyright © 2010 Pearson Education, Inc. Figure 2.12 Water molecule Ions in solution Salt crystal –– ++ ++ Water Dissolves and Dissociates Ionic Substances

5. Copyright © 2010 Pearson Education, Inc. Properties of Water  Reactivity A necessary part of hydrolysis and dehydration synthesis reactions  Cushioning Protects certain organs from physical trauma, e.g., cerebrospinal fluid

6. Copyright © 2010 Pearson Education, Inc. Salts 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 Nervous and muscular physiology (e.g., sodium, potassium, calcium, and iron)

7. Copyright © 2010 Pearson Education, Inc. Acids and Bases Like other ionic molecules, acids and bases dissociate in water (cations and anions separate in solution) Acids release H + and are therefore proton donors HCl  H + + Cl – Bases release OH – and are proton acceptors NaOH  Na + + OH – Bicarbonate ion (HCO 3 – ) and ammonia (NH 3 ) are important bases in the body

8. Copyright © 2010 Pearson Education, Inc. 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

9. Copyright © 2010 Pearson Education, Inc. pH: Acid-Base Concentration  Acidic solutions have higher H + concentration (H + > OH - ); pH value below 7  Alkaline (basic) solutions have lower H + concentration (H + < OH - ); pH value above 7

10. Copyright © 2010 Pearson Education, Inc. 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

11. Copyright © 2010 Pearson Education, Inc. 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

12. Copyright © 2010 Pearson Education, Inc. Buffers Mixture of compounds that resist pH changes Convert strong (completely dissociated) acids or bases into weak (slightly dissociated) ones Carbonic acid-bicarbonate system

13. Copyright © 2010 Pearson Education, Inc. Organic Compounds Molecules unique to living systems contain carbon (except CO 2 and CO, which are inorganic) They include: Carbohydrates Lipids Proteins Nucleic acids

14. Copyright © 2010 Pearson Education, Inc. Organic Compounds Many are polymers—chains of similar units (monomers or building blocks) Synthesized by dehydration synthesis Broken down by hydrolysis reactions

15. Copyright © 2010 Pearson Education, Inc. 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 +

16. Copyright © 2010 Pearson Education, Inc. Carbohydrates Contain C, H, and O [(CH 2 0) n ] Three classes: Monosaccharides Disaccharides Polysaccharides Functions Major source of cellular fuel (e.g., glucose) Structural molecules (e.g., ribose sugar in RNA)

17. Copyright © 2010 Pearson Education, Inc. Figure 2.15a Example Hexose sugars (the hexoses shown here are isomers) Example Pentose sugars GlucoseFructose GalactoseDeoxyriboseRibose (a) Monosaccharides Monomers of carbohydrates Monosaccharides Simple sugars containing three to seven C atoms

18. Copyright © 2010 Pearson Education, Inc. Figure 2.15b Example Sucrose, maltose, and lactose (these disaccharides are isomers) GlucoseFructoseGlucose SucroseMaltoseLactose Galactose (b) Disaccharides Consist of two linked monosaccharides Disaccharides Double sugars Too large to pass through cell membranes

19. Copyright © 2010 Pearson Education, Inc. Figure 2.15c 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 Polysaccharides Polymers of simple sugars, e.g., starch and glycogen Not very soluble

20. Copyright © 2010 Pearson Education, Inc. Lipids Contain C, H, and O (the proportion of oxygen in lipids is less than in carbohydrates), and sometimes P Insoluble in water Main types: Neutral fats or triglycerides Phospholipids Steroids Eicosanoids

21. Copyright © 2010 Pearson Education, Inc. Triglycerides Neutral fats—solid fats and liquid oils Composed of three fatty acids bonded to a glycerol molecule Main functions Energy storage Insulation Protection

22. Copyright © 2010 Pearson Education, Inc. Figure 2.16a Glycerol + 3 fatty acid chainsTriglyceride, or neutral fat 3 water molecules (a) Triglyceride formation Three fatty acid chains are bound to glycerol by dehydration synthesis

23. Copyright © 2010 Pearson Education, Inc. Saturation of Fatty Acids  Saturated fatty acids Single bonds between C atoms; maximum number of H Solid animal fats, e.g., butter  Unsaturated fatty acids One or more double bonds between C atoms Reduced number of H atoms Plant oils, e.g., olive oil

24. Copyright © 2010 Pearson Education, Inc. Phospholipids  Modified triglycerides: Glycerol + two fatty acids and a phosphorus (P)-containing group  “Head” and “tail” regions have different properties  Important in cell membrane structure

25. Copyright © 2010 Pearson Education, Inc. 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.

26. Copyright © 2010 Pearson Education, Inc. Steroids Steroids—interlocking four-ring structure Cholesterol, vitamin D, steroid hormones (sex hormones), and bile salts

27. Copyright © 2010 Pearson Education, Inc. Figure 2.16c Example Cholesterol (cholesterol is the basis for all steroids formed in the body) (c) Simplified structure of a steroid Four interlocking hydrocarbon rings form a steroid.

28. Copyright © 2010 Pearson Education, Inc. Other Lipids in the Body  Fat-soluble vitamins Vitamins A, E, and K  Lipoproteins Transport fatty acids and cholesterol in the bloodstream  Eicosanoids 20-carbon fatty acids found in cell membranes Prostaglandins

29. Copyright © 2010 Pearson Education, Inc. Proteins  Polymers of amino acids (20 types) Joined by peptide bonds  Contain C, H, O, N, and sometimes S and P Amino Acids  Building blocks of protein, containing an amino group (NH 2 ) and a carboxyl group (COOH)

30. Copyright © 2010 Pearson Education, Inc. 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 Amino Acids

31. Copyright © 2010 Pearson Education, Inc. 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 Proteins: Polymer of Amino Acids Joined by Peptide Bonds

32. Copyright © 2010 Pearson Education, Inc. Structural Levels of Proteins Primary structure – consists of amino acid sequence Secondary structure – consists of alpha helices or beta pleated sheets Tertiary structure – consists of superimposed folding of secondary structures forming more complex, 3 dimensional globular structure Quaternary structure – consist of more than one polypeptide chains linked together in a specific manner

33. Copyright © 2010 Pearson Education, Inc. Figure 2.19a (a) Primary structure: The sequence of amino acids forms the polypeptide chain. Amino acid

34. Copyright © 2010 Pearson Education, Inc. 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).

35. Copyright © 2010 Pearson Education, Inc. 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.

36. Copyright © 2010 Pearson Education, Inc. 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.

37. Copyright © 2010 Pearson Education, Inc. Fibrous and Globular Proteins  Fibrous (structural) proteins Strand-like, water insoluble, and stable Examples: keratin, elastin, collagen, and certain contractile fibers  Globular (functional) proteins Compact, spherical, water-soluble and sensitive to environmental changes Specific functional regions (active sites) Examples: antibodies, hormones, molecular chaperones, and enzymes

38. Copyright © 2010 Pearson Education, Inc. Protein Denaturation Shape change and disruption of active sites due to environmental changes (e.g., decreased pH or increased temperature) Reversible in most cases, if normal conditions are restored Irreversible if extreme changes damage the structure beyond repair (e.g., cooking an egg)

39. Copyright © 2010 Pearson Education, Inc. Functional enzymeDenatured enzyme

40. Copyright © 2010 Pearson Education, Inc. Molecular Chaperones (Chaperonins) Help other proteins to achieve their functional three-dimensional shape Maintain folding integrity Assist in translocation of proteins across membranes Promote the breakdown of damaged or denatured proteins

41. Copyright © 2010 Pearson Education, Inc. Figure 2.20 Activation energy required Less activation energy required WITHOUT ENZYMEWITH ENZYME Reactants Product Reactants Enzymes  Biological catalysts Lower the activation energy, increase the speed of a reaction (millions of reactions per minute!)

42. Copyright © 2010 Pearson Education, Inc. Characteristics of Enzymes  Often named for the reaction they catalyze; usually end in -ase (e.g., hydrolases, oxidases)  Some functional enzymes (holoenzymes) consist of: Apoenzyme (protein) Cofactor (metal ion) or coenzyme (a vitamin)

43. Copyright © 2010 Pearson Education, Inc. Characteristics of Enzymes Enzymes are chemically specific Like all other proteins, each enzyme has a specific 3-dimensional shape The active site (region on the enzyme where the substrate binds) has a specific shape for each particular enzyme This means each enzyme binds to specific substrate

44. Copyright © 2010 Pearson Education, Inc. Mechanism of Enzyme Action Enzyme binds with substrate Product is formed at a lower activation energy Product is released Freed enzyme binds with another substrate to continue process Process ends when enzyme breaks down, no more enzymes are produced, and/or an inhibitor prevents the functioning of the enzyme

45. Copyright © 2010 Pearson Education, Inc. Figure 2.21 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

46. Copyright © 2010 Pearson Education, Inc. Nucleic Acids  Two major classes - DNA and RNA Largest molecules in the body  Contain C, O, H, N, and P  Building block = nucleotide, composed of N- containing base, a pentose sugar, and a phosphate group

47. Copyright © 2010 Pearson Education, Inc. Deoxyribonucleic Acid (DNA)  Four nitrogen bases contribute to structure: adenine (A), guanine (G), cytosine (C), and thymine (T)  Double-stranded helical molecule found in the cell nucleus  Provides instructions for protein synthesis  Replicates itself before cell division, ensuring genetic continuity

48. Copyright © 2010 Pearson Education, Inc. 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 Structure of DNA

49. Copyright © 2010 Pearson Education, Inc. Ribonucleic Acid (RNA) Uses the nitrogenous base uracil (U) instead of thymine (T) Single-stranded molecule found in both the nucleus and the cytoplasm of a cell Three varieties of RNA carry out the DNA orders for protein synthesis messenger RNA, transfer RNA, and ribosomal RNA

50. Copyright © 2010 Pearson Education, Inc. Adenosine Triphosphate (ATP) Source of immediately usable energy for the cell Adenine-containing RNA nucleotide with two additional phosphate groups

51. Copyright © 2010 Pearson Education, Inc. 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.

52. Copyright © 2010 Pearson Education, Inc. Function of ATP  Phosphorylation: Terminal phosphates are enzymatically transferred to and energize other molecules Such “primed” molecules perform cellular work (life processes) using the phosphate bond energy

53. Copyright © 2010 Pearson Education, Inc. 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)

54. Copyright © 2010 Pearson Education, Inc. Biological Molecules