1. 1 Chapter 4 Carbon and the Molecular Diversity of Life

2. What is the difference between organic and inorganic compounds? 2 Organic compounds contain____________. Inorganic compounds contain two or more chemical elements other than Carbon Organic compounds were traditionally thought to be _________and inorganic are _______in nature. carbon biological mineral

3. 3 Carbon Chemistry Carbon is the Backbone of Biological Molecules ___________________ All living organisms Are made up of chemicals based mostly on the element carbon Figure 4.1 (macromolecules)

4. 4 Carbon Chemistry __________chemistry is the study of carbon compounds Carbon atoms can form diverse molecules by bonding to ______ other atoms ________compounds range from simple molecules to complex ones Carbon has four valence electrons and may form _________________________ bonds Organic four Carbon single, double, triple, or quadruple

5. 5 The ________________of carbon gives it covalent compatibility with many different elements H O NC Hydrogen (valence = 1) Oxygen (valence = 2) Nitrogen (valence = 3) Carbon (valence = 4) Figure 4.4 electron configuration

6. 6 Carbon may bond __ _____ forming carbon chains Carbon chains form the __________of most organic molecules Carbon chains vary in __________________ H H H H H H H H H H H HHH H H H H H H H H H H H H H H H H HH HH HH HHH H HH HH H H H H H H H C C CCC CCCCCCC CCCCCCCC C C C C C C C C C C C C H H H H H H H (a) Length (b) Branching (c) Double bonds (d) Rings Ethane Propane Butane isobutane 1-Butene2-Butene Cyclohexane Benzene HH HHH Figure 4.5 A-D to itself skeletons length and shape

7. 7 Hydrocarbons Hydrocarbons are molecules consisting of only_______________________ Hydrocarbons Are found in many of a cell’s organic molecules (a) A fat molecule (b) Mammalian adipose cells 100 µm Fat droplets (stained red) Figure 4.6 A, B carbon and hydrogen

8. 8 The Molecules of Life Overview: –Another level in the hierarchy of biological organization is reached when small organic molecules are joined together –Atom ---> _________---  compound molecule

9. 9 Macromolecules –Are large molecules composed of smaller molecules –Are complex in their structures Figure 5.1

10. 10 Macromolecules Most macromolecules are_________, built from__________ Four classes of life’s organic molecules are polymers polymers monomers Carbohydrates Proteins Nucleic acids Lipids

11. 11 Is a long molecule consisting of many similar building blocks called monomers amino acids Specific monomers make up each macromolecule E.g. _________are the monomers for proteins A polymer

12. 12 The Synthesis and Breakdown of Polymers Monomers form larger molecules by condensation reactions called dehydration synthesis (a) Dehydration reaction in the synthesis of a polymer HOH 1 2 3 H 1 23 4 H H2OH2O Short polymer Unlinked monomer Longer polymer Dehydration removes a water molecule, forming a new bond Figure 5.2A

13. 13 The Synthesis and Breakdown of Polymers Polymers can disassemble by –______________ (addition of water molecules) (b) Hydrolysis of a polymer HO 1 2 3 H H 1 2 3 4 H2OH2O H Hydrolysis adds a water molecule, breaking a bond Figure 5.2B Hydrolysis

14. 14 Although organisms share the same ______________of monomer types, each organism is ________based on the arrangement of monomers into polymers An _________variety of polymers can be built from a small set of monomers limited number unique immense Macromolecules

15. 15 Carbohydrates Serve as fuel and building material Include both sugars and their polymers (starch, cellulose, etc.)

16. 16 Sugars Monosaccharides –Are the simplest sugars –Can be used for fuel –Can be converted into other organic molecules –Can be combined into polymers

17. 17 Examples of monosaccharides Triose sugars (C 3 H 6 O 3 ) Pentose sugars (C 5 H 10 O 5 ) Hexose sugars (C 6 H 12 O 6 ) H C OH HO C H H C OH HO C H H C OH C O H C OH HO C H H C OH C O H H H HHH H H HHH H H H C CCC O O O O Aldoses Glyceraldehyde Ribose Glucose Galactose Dihydroxyacetone Ribulose Ketoses Fructose Figure 5.3 The structure and classification of some monosaccharides. Sugars may be aldoses (aldehyde sugars) or ketoses(ketone sugars), depending on the location of the carbonyl group in pink. Sugars are also classified according to the length of their carbon skeletons. A third point of variation is the spatial arrangement around the asymmetric carbons. ( grey portion of glucose and galactose)

18. 18 Monosaccharides –May be linear –Can form rings H H C OH HO C H H C OH H C O C H 1 2 3 4 5 6 H OH 4C4C 6 CH 2 OH 5C5C H OH C H OH H 2 C 1C1C H O H OH 4C4C 5C5C 3 C H H OH OH H 2C2C 1 C OH H CH 2 OH H H OH HO H OH H 5 3 2 4 (a) Linear and ring forms. Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. To form the glucose ring, carbon 1 bonds to the oxygen attached to carbon 5. OH 3 O H O O 6 1 Figure 5.4

19. 19 Disaccharides –Consist of two monosaccharides –Are joined by a glycosidic linkage

20. 20 Dehydration reaction in the synthesis of maltose. The bonding of two glucose units forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide. Dehydration reaction in the synthesis of sucrose. Sucrose is a disaccharide formed from glucose and fructose. Notice that fructose, though a hexose like glucose, forms a five-sided ring. (a) (b) H HO H H OH H OH O H CH 2 OH H HOHO H HOHHOH H OHOH O H OHOH H O H H OH H OH O H CH 2 OH H H2OH2O H2OH2O H H O H HO H OH O H CH 2 OH HO OH H CH 2 OH HOHHOH H H HO OH H CH 2 OH HOHHOH H O O H OH H CH 2 OH HOHHOH H O H OH CH 2 OH H HO O CH 2 OH H H OH O O 1 2 1 4 1– 4 glycosidic linkage 1–2 glycosidic linkage Glucose Fructose Maltose Sucrose OH H H Figure 5.5

21. 21 Polysaccharides –Are polymers of sugars –Serve many roles in organisms

22. 22 Storage Polysaccharides Starch –Is a polymer consisting entirely of ________ monomers –Is the major storage form of glucose in___________ Chloroplast Starch Amylose Amylopectin 1  m (a) Starch: a plant polysaccharide Figure 5.6 plants glucose

23. 23 Glycogen –Consists of glucose____________ –Is the major storage form of glucose in ___________ Mitochondria Giycogen granules 0.5  m (b) Glycogen: an animal polysaccharide Glycogen Figure 5.6 monomers animals

24. 24 Structural Polysaccharides Cellulose –Is a ____________of glucose polymer

25. 25 –Has different ___________linkages than starch (c) Cellulose: 1– 4 linkage of  glucose monomers H O O CH 2 O H H OHOH H H OHOH OHOH H H HOHO 4 C C C C C C H H H HOHO OHOH H OHOH OHOH OHOH H O H H H OHOH OHOH H H HOHO 4 OHOH O OHOH OHOH HOHO 4 1 O O OHOH OHOH O O OHOH OHOH O OHOH OHOH O O O OHOH OHOH HOHO 4 O 1 OHOH O OHOH OHOH O O OHOH O OHOH O OHOH OHOH (a)  and  glucose ring structures (b) Starch: 1– 4 linkage of  glucose monomers 1  glucose  glucose CH 2 O H 1 4 4 1 1 Figure 5.7 A–C glycosidic

26. 26 Plant cells 0.5  m Cell walls Cellulose microfibrils in a plant cell wall  Microfibril CH 2 OH OH OHOH O O O CH 2 OH O O OH O CH 2 OH OH O O CH 2 OH O O OHOH O O OHOH O O OH CH 2 OHOH O O CH 2 OH OH O CH 2 OH O O OHCH 2 OH OH  Glucose monomer O O O O O O Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6. About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall. A cellulose molecule is an unbranched  glucose polymer. OH O O Cellulose molecules Figure 5.8 –Is a major component of the tough walls that enclose plant cells

27. 27 Cellulose is difficult to digest –Cows have microbes in their _________to facilitate this process Figure 5.9 stomachs

28. Identify the Structure 28 Glucose Ribose Amino Acid Fatty Acid

29. 29 Chitin is another important structural polysaccharide –Is found in the ______________of arthropods –Can be used as surgical_________ (a) The structure of the chitin monomer. O CH 2 O H OH H H H NH C CH 3 O H H (b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emerging in adult form. (c) Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals. OH Figure 5.10 A–C thread exoskeleton

30. 30 Lipids Lipids are a diverse group of ____________ molecules Lipids hydrophobic Are the one class of large biological molecules that do not consist of polymers Share the common trait of being hydrophobic

31. Lipid Functions 31

32. 32 Fats (subgroup of lipids) Vary in the length and number and locations of double bonds they contain Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids

33. Comparison of carbohydrate and lipid as an energy sources 33

34. 34 Saturated fatty acids –Have the maximum number of hydrogen atoms possible –Have no double bonds (a) Saturated fat and fatty acid Stearic acid Figure 5.12

35. 35 Unsaturated fatty acids –Have one or more double bonds (b) Unsaturated fat and fatty acid cis double bond causes bending Oleic acid Figure 5.12

36. 36 Phospholipids –Have only two fatty acids –Have a phosphate group instead of a third fatty acid

37. 37 Phospholipid structure –Consists of a __________“head” and ___________“tails” CH 2 O P O O O CH CH 2 OO C O C O Phosphate Glycerol (a) Structural formula (b) Space-filling model Fatty acids (c) Phospholipid symbol Hydrophobic tails Hydrophilic head Hydrophobic tails – Hydrophilic head CH 2 Choline + Figure 5.13 N(CH 3 ) 3 hydrophilic hydrophobic

38. 38 The structure of phospholipids –Results in a bilayer arrangement found in cell membranes Hydrophilic head WATER Hydrophobic tail Figure 5.14

39. 39 Steroids –Are lipids characterized by a carbon skeleton consisting of four fused rings

40. 40 One steroid, cholesterol –Is found in cell membranes –Is a precursor for some hormones HO CH 3 H3CH3C Figure 5.15

41. 41 Proteins Proteins have many structures, resulting in a wide range of functions Proteins do most of the work in cells and act as ____________ Proteins are made of monomers called__________________ enzymes amino acids

42. 42 An overview of protein functions Table 5.1

43. 43 Enzymes –Are a type of protein that acts as a catalyst, speeding up chemical reactions Substrate (sucrose) Enzyme (sucrase) Glucose OH H O H2OH2O Fructose 3 Substrate is converted to products. 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. Substrate binds to enzyme. 22 4 Products are released. Figure 5.16

44. 44 Polypeptides –Are polymers (chains) of amino acids A protein –Consists of one or more polypeptides

45. 45 Amino acids –Are organic molecules possessing both carboxyl and amino groups –Differ in their properties due to differing side chains, called R groups

46. 46 Twenty Amino Acids 20 different amino acids make up proteins O O–O– H H3N+H3N+ C C O O–O– H CH 3 H3N+H3N+ C H C O O–O– C C O O–O– H H3N+H3N+ CH CH 3 CH 2 C H H3N+H3N+ CH 3 CH 2 CH C H H3N+H3N+ C CH 3 CH 2 C H3N+H3N+ H C O O–O– C H3N+H3N+ H C O O–O– NH H C O O–O– H3N+H3N+ C CH 2 H2CH2C H2NH2N C H C Nonpolar Glycine (Gly) Alanine (Ala) Valine (Val)Leucine (Leu)Isoleucine (Ile) Methionine (Met) Phenylalanine (Phe) C O O–O– Tryptophan (Trp) Proline (Pro) H3CH3C Figure 5.17 S O O–O–

47. 47

48. 48 Amino Acid Polymers Amino acids –Are linked by peptide bonds

49. 49 Protein Conformation and Function A protein’s specific conformation (shape) determines how it functions

50. 50 Four Levels of Protein Structure Primary structure –Is the unique sequence of amino acids in a polypeptide Figure 5.20 – Amino acid subunits + H 3 N Amino end o Carboxyl end o c Gly ProThr Gly Thr Gly Glu Seu Lys Cys Pro Leu Met Val Lys Val Leu Asp Ala Val Arg Gly Ser Pro Ala Gly lle Ser Pro Phe His Glu His Ala Glu Val Phe Thr Ala Asn Asp Ser Gly Pro Arg Tyr Thr lle Ala Leu Ser Pro Tyr Ser Tyr Ser Thr Ala Val Thr Asn Pro Lys Glu Thr Lys Ser Tyr Trp Lys Ala Leu Glu Lle Asp

51. 51 O C  helix  pleated sheet Amino acid subunits N C H C O C N H C O H R C N H C O H C R N H H R C O R C H N H C O H N C O R C H N H H C R C O C O C N H H R C C O N H H C R C O N H R C H C O N H H C R C O N H R C H C O N H H C R C O N H H C R N H O O C N C R C H O C H R N H O C R C H N H O C H C R N H C C N R H O C H C R N H O C R C H H C R N H C O C N H R C H C O N H C Secondary structure –Is the folding or coiling of the polypeptide into a repeating configuration –Includes the  helix and the  pleated sheet H H Figure 5.20

52. 52 Tertiary structure –Is the overall three-dimensional shape of a polypeptide –Results from interactions between amino acids and R groups CH 2 CH OHOH O C HO CH 2 NH 3 + C -O-O CH 2 O SS CH CH 3 H3CH3C H3CH3C Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hyrdogen bond Ionic bond CH 2 Disulfide bridge

53. 53 Quaternary structure –Is the overall protein structure that results from the aggregation of two or more polypeptide subunits Polypeptide chain Collagen  Chains  Chains Hemoglobin Iron Heme

54. 54 Review of Protein Structure + H 3 N Amino end Amino acid subunits  helix

55. 55 Sickle-Cell Disease: A Simple Change in Primary Structure Sickle-cell disease –Results from a single amino acid substitution in the protein hemoglobin

56. 56 Fibers of abnormal hemoglobin deform cell into sickle shape. Primary structure Secondary and tertiary structures Quaternary structure Function Red blood cell shape Hemoglobin A Molecules do not associate with one another, each carries oxygen. Normal cells are full of individual hemoglobin molecules, each carrying oxygen     10  m     Primary structure Secondary and tertiary structures Quaternary structure Function Red blood cell shape Hemoglobin S Molecules interact with one another to crystallize into a fiber, capacity to carry oxygen is greatly reduced.  subunit 12 3 4 567 34 567 21 Normal hemoglobin Sickle-cell hemoglobin... Figure 5.21 Exposed hydrophobic region ValThrHisLeuProGlulGluValHisLeu Thr Pro Val Glu

57. 57 What Determines Protein Conformation? Protein conformation Depends on the physical and chemical conditions of the protein’s environment Temperature, pH, etc. affect protein structure

58. 58 Denaturation is when a protein unravels and loses its native conformation (shape) Denaturation Renaturation Denatured proteinNormal protein Figure 5.22

59. 59 The Protein-Folding Problem Most proteins –Probably go through several intermediate states on their way to a stable conformation –Denaturated proteins no longer work in their unfolded condition –Proteins may be denaturated by extreme changes in pH or temperature

60. 60 Chaperonins –Are protein molecules that assist in the proper folding of other proteins Hollow cylinder Cap Chaperonin (fully assembled) Steps of Chaperonin Action: An unfolded poly- peptide enters the cylinder from one end. The cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide. The cap comes off, and the properly folded protein is released. Correctly folded protein Polypeptide 2 1 3 Figure 5.23

61. 61 X-ray crystallography –Is used to determine a protein’s three-dimensional structure X-ray diffraction pattern Photographic film Diffracted X- rays X-ray source X-ray beam Crystal Nucleic acidProtein (a) X-ray diffraction pattern (b) 3D computer model Figure 5.24

62. 62 Nucleic Acids Nucleic acids store and transmit hereditary information Genes –Are the units of inheritance –Program the amino acid sequence of polypeptides –Are made of nucleotide sequences on DNA

63. 63 The Roles of Nucleic Acids There are two types of nucleic acids –Deoxyribonucleic acid (DNA) –Ribonucleic acid (RNA)

64. 64 Deoxyribonucleic Acid DNA –Stores information for the synthesis of specific proteins –Found in the nucleus of cells

65. 65 DNA Functions –Directs RNA synthesis (transcription) –Directs protein synthesis through RNA (translation) 1 2 3 Synthesis of mRNA in the nucleus Movement of mRNA into cytoplasm via nuclear pore Synthesis of protein NUCLEUS CYTOPLASM DNA mRNA Ribosome Amino acids Polypeptide mRNA Figure 5.25

66. 66 The Structure of Nucleic Acids Nucleic acids –Exist as polymers called polynucleotides (a) Polynucleotide, or nucleic acid 3’C 5’ end 5’C 3’C 5’C 3’ end OH Figure 5.26 O O O O

67. 67 Each polynucleotide –Consists of monomers called nucleotides –Sugar + phosphate + nitrogen base Nitrogenous base Nucleoside O O OO OO P CH 2 5’C 3’C Phosphate group Pentose sugar (b) Nucleotide Figure 5.26 O

68. 68 Nucleotide Monomers Nucleotide monomers –Are made up of nucleosides (sugar + base) and phosphate groups (c) Nucleoside components Figure 5.26 CH Uracil (in RNA) U Ribose (in RNA) Nitrogenous bases Pyrimidines C N N C O H NH 2 CH O C N H HN C O C CH 3 N HN C C H O O Cytosine C Thymine (in DNA) T N HC N C C N C CH N NH 2 O N HC N H H C C N NH C NH 2 Adenine A Guanine G Purines O HOCH 2 H H H OH H O HOCH 2 H H H OH H Pentose sugars Deoxyribose (in DNA) Ribose (in RNA) OH CH Uracil (in RNA) U 4’ 5”5” 3’ OH H 2’ 1’ 5”5” 4’ 3’ 2’ 1’

69. 69 Nucleotide Polymers Nucleotide polymers – Are made up of nucleotides linked by the–OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next

70. 70 Gene The sequence of bases along a nucleotide polymer –Is unique for each gene

71. 71 The DNA Double Helix Cellular DNA molecules –Have two polynucleotides that spiral around an imaginary axis –Form a double helix

72. 72 The DNA double helix –Consists of two antiparallel nucleotide strands 3’ end Sugar-phosphate backbone Base pair (joined by hydrogen bonding) Old strands Nucleotide about to be added to a new strand A 3’ end 5’ end New strands 3’ end 5’ end Figure 5.27

73. 73 A,T,C,G The nitrogenous bases in DNA –Form hydrogen bonds in a complementary fashion (A with T only, and C with G only)

74. 74 DNA and Proteins as Tape Measures of Evolution Molecular comparisons –Help biologists sort out the evolutionary connections among species

75. 75 The Theme of Emergent Properties in the Chemistry of Life: A Review Higher levels of organization –Result in the emergence of new properties Organization –Is the key to the chemistry of life

76. 76 Isomers Isomers are molecules with the same _____ ________________but different _______ and properties Three types of isomers are –_________ H H HH H H H H HH H H H HH H H H H H H H H H H H H H CO 2 H CH 3 NH 2 C CO 2 H H CH 3 NH 2 XX X X C CCCC C C C C C C C C C C (a) Structural isomers (b) Geometric isomers (c) Enantiomers H Figure 4.7 A-C molecular formulastructures Structural Geometric Enantiomers

77. 77 Enantiomers Are important in the pharmaceutical industry L-Dopa (effective against Parkinson’s disease) D-Dopa (biologically inactive) Figure 4.8

78. 78 Functional Groups Functional groups are the parts of molecules involved in chemical reactions They Are the chemically reactive groups of atoms within an organic molecule Give organic molecules distinctive chemical properties CH 3 OH HO O CH 3 OH Estradiol Testosterone Female lion Male lion Figure 4.9

79. 79 Six functional groups are important in the chemistry of life –Hydroxyl –Carbonyl –Carboxyl –Amino –Sulfhydryl –Phosphate

80. 80 Some important functional groups of organic compounds FUNCTIONAL GROUP STRUCTURE (may be written HO ) HYDROXYL CARBONYL CARBOXYL OH In a hydroxyl group (— OH), a hydrogen atom is bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule. (Do not confuse this functional group with the hydroxide ion, OH –.) When an oxygen atom is double-bonded to a carbon atom that is also bonded to a hydroxyl group, the entire assembly of atoms is called a carboxyl group (—COOH). C OO C OH Figure 4.10 The carbonyl group ( CO) consists of a carbon atom joined to an oxygen atom by a double bond. 

81. 81 Some important functional groups of organic compounds Acetic acid, which gives vinegar its sour tatste NAME OF COMPOUNDS Alcohols (their specific names usually end in -ol) Ketones if the carbonyl group is within a carbon skeleton Aldehydes if the carbonyl group is at the end of the carbon skeleton Carboxylic acids, or organic acids EXAMPLE Propanal, an aldehyde Acetone, the simplest ketone Ethanol, the alcohol present in alcoholic beverages H H H HH CC OH H H H H H H H C C H C C C CCC O H O H H HH H O H Figure 4.10

82. 82 Some important functional groups of organic compounds The amino group (—NH 2 ) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton. AMINO SULFHYDRYL PHOSPHATE (may be written HS ) The sulfhydryl group consists of a sulfur atom bonded to an atom of hydrogen; resembles a hydroxyl group in shape. In a phosphate group, a phosphorus atom is bonded to four oxygen atoms; one oxygen is bonded to the carbon skeleton; two oxygens carry negative charges; abbreviated P. The phosphate group (—OPO 3 2– ) is an ionized form of a phosphoric acid group (—OPO 3 H 2 ; note the two hydrogens). N H H SH O P O OH Figure 4.10

83. 83