1. Carbon is the backbone of biological molecules in living organisms and can form single, double, triple, or quadruple bonds. 2. Hydrocarbons like methane, ethane and ethene are molecules made of only carbon and hydrogen. Lipids, which do not form polymers, include fats and phospholipids. 3. Carbohydrates, proteins, nucleic acids and lipids are the four major classes of macromolecules that make up living things and carry out essential functions.

1. 1 Carbon and the Molecular Diversity of Life

2. 2 Figure 4.1 Carbon Chemistry Carbon is the Backbone of Biological Molecules (macromolecules) All living organisms Are made up of chemicals based mostly on the element carbon

3. 3 Ball-and-Stick Model Name and Comments Space-Filling Model Molecular Formula Structural Formula H (a) Methane CH4 C H H H H H (b) Ethane C2H6 C H H C H H H H (c) Ethene (ethylene) C C C2H4 H H Figure 4.3 A-C Carbon Chemistry Organic chemistry is the study of carbon compounds Carbon has four valence electrons and may form single, double, triple, or quadruple bonds

4. 4 H H C C C C H H C H H H H H H C H H H H H H H H H H H H C C C C C C C H H H H H H H H H H H H (a) Length H Ethane Propane H H H H H H H H H H H C C C C C C C C H H H H (b) Branching Butane isobutane H H H H C H (c) Double bonds H H C C C H H C C H H C C 1-Butene 2-Butene H H C C C (d) Rings Figure 4.5 A-D Cyclohexane Benzene Carbon may bond to itself forming carbon chains Carbon chains form the skeletons of most organic molecules Carbon chains vary in length and shape

5. 5 Fat droplets (stained red) 100 µm (b) Mammalian adipose cells (a) A fat molecule Figure 4.6 A, B Hydrocarbons Hydrocarbons are molecules consisting of only carbon and hydrogen Hydrocarbons Are found in many of a cell’s organic molecules

6. 6 H H H C H H C H H H H H H H (a) Structural isomers H C C C C C H H H C C C H H H H H H H H H X X X C C C C (b) Geometric isomers X H H H CO2H CO2H C C (c) Enantiomers H H NH2 NH2 CH3 CH3 Figure 4.7 A-C Isomers Isomers are molecules with the same molecular formula but different structures and properties Three types of isomers are Structural Geometric Enantiomers

7. 7 L-Dopa (effective against Parkinson’s disease) D-Dopa (biologically inactive) Figure 4.8 Enantiomers Are important in the pharmaceutical industry

8. 8 OH CH3 Estradiol HO Female lion OH CH3 CH3 O Testosterone Male lion Figure 4.9 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

9. 9 Six functional groups are important in the chemistry of life Hydroxyl Carbonyl Carboxyl Amino Sulfhydryl Phosphate

10. 10 FUNCTIONAL GROUP HYDROXYL CARBONYL CARBOXYL O O OH C C OH (may be written HO ) 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–.) STRUCTURE The carbonyl group( CO) consists of a carbon atom joined to an oxygen atom by a double bond. 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).  Figure 4.10 Some important functional groups of organic compounds

11. 11 Ketones if the carbonyl group is within a carbon skeleton Aldehydes if the carbonyl group is at the end of the carbon skeleton NAME OF COMPOUNDS Alcohols (their specific names usually end in -ol) Carboxylic acids, or organic acids EXAMPLE H H H H O O C C H OH C C H C H C H OH H H H H C Ethanol, the alcohol present in alcoholic beverages H H Acetic acid, which gives vinegar its sour tatste Acetone, the simplest ketone H H O C C C H H H H Propanal, an aldehyde Figure 4.10 Some important functional groups of organic compounds

12. 12 AMINO SULFHYDRYL PHOSPHATE O H SH N P OH O (may be written HS ) H OH 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 (—OPO32–) is an ionized form of a phosphoric acid group (—OPO3H2; note the two hydrogens). The amino group (—NH2) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton. The sulfhydryl group consists of a sulfur atom bonded to an atom of hydrogen; resembles a hydroxyl group in shape. Figure 4.10 Some important functional groups of organic compounds

13. 13 Macromolecules Most macromolecules are polymers, built from monomers Four classes of life’s organic molecules are polymers Carbohydrates Proteins Nucleic acids Lipids

14. 14 Carbohydrates Serve as fuel and building material Include both sugars and their polymers (starch, cellulose, etc.)

15. 15 The Synthesis and Breakdown of Polymers 1 HO H 3 2 HO H Unlinked monomer Short polymer Dehydration removes a watermolecule, forming a new bond H2O 1 2 3 4 HO H Longer polymer (a) Dehydration reaction in the synthesis of a polymer Figure 5.2A Monomers form larger molecules by condensation reactions called dehydration synthesis

16. 16 The Synthesis and Breakdown of Polymers 1 3 HO 4 2 H Hydrolysis adds a watermolecule, breaking a bond H2O 1 2 H HO 3 H HO (b) Hydrolysis of a polymer Figure 5.2B Polymers can disassemble by Hydrolysis (addition of water molecules)

17. 17 Triose sugars(C3H6O3) Pentose sugars(C5H10O5) Hexose sugars(C6H12O6) H H H H O O O O C C C C H C OH H C OH H C OH H C OH H C OH H C OH HO C H HO C H Aldoses H H C OH H C OH HO C H H C OH H C OH H C OH Glyceraldehyde H C OH H C OH H Ribose H H Glucose Galactose H H H H C OH H C OH H C OH C O C O C O HO C H H C OH H C OH Ketoses H C OH H C OH H Dihydroxyacetone H C OH H C OH H C OH H Ribulose H Figure 5.3 Fructose Examples of monosaccharides

18. 18 Disaccharides Consist of two monosaccharides Dehydration Synthesis occurs (glycosidic linkage)

19. 19 (a) 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. CH2OH CH2OH CH2OH CH2OH O O O O H H H H H H H H 1–4glycosidiclinkage HOH HOH HOH HOH 4 1 H H H H OH OH O H OH HO HO OH O H H H H OH OH OH OH H2O Glucose Maltose Glucose CH2OH CH2OH CH2OH CH2OH O O O O 1–2glycosidiclinkage H H H H H HOH HOH H 2 1 H OH H HO H HO H 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. (b) HO H O O HO CH2OH CH2OH OH H H OH H H OH OH H2O Glucose Sucrose Fructose Figure 5.5

20. 20 Polysaccharides Polysaccharides Are polymers of sugars Serve many roles in organisms

21. 21 Storage Polysaccharides Chloroplast Starch 1 m Amylose Amylopectin (a) Starch: a plant polysaccharide Figure 5.6 Starch Is a polymer consisting entirely of glucose monomers Is the major storage form of glucose in plants

22. 22 Giycogen granules Mitochondria 0.5 m Glycogen (b) Glycogen: an animal polysaccharide Figure 5.6 Glycogen Consists of glucose monomers Is the major storage form of glucose in animals

23. 23 Structural Polysaccharides H O CH2OH C CH2OH OH OH H C H O O H H H H HO OH OH C H 4 4 1 H H HO OH HO OH H C H OH OH H OH H C H OH  glucose C  glucose H (a)  and  glucose ring structures CH2OH CH2OH CH2OH CH2OH O O O O OH OH OH OH 1 4 4 4 1 1 1 HO O O O O OH OH OH OH (b) Starch: 1– 4 linkage of  glucose monomers OH CH2OH OH CH2OH O O OH OH O O OH OH HO OH 4 O 1 O O CH2OH CH2OH OH OH (c) Cellulose: 1– 4 linkage of  glucose monomers Figure 5.7 A–C Cellulose Is a polymer of glucose

25. 25 CH2OH O OH H H OH H H H NH O C CH3 OH (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. (a) The structure of the chitin monomer. Figure 5.10 A–C Chitin, another important structural polysaccharide Is found in the exoskeleton of arthropods Can be used as surgical thread

26. 26 Lipids Lipids are a diverse group of hydrophobic molecules Lipids Are the one class of large biological molecules that do not consist of polymers Share the common trait of being hydrophobic

27. 27 Fats Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids Vary in the length and number and locations of double bonds they contain

28. 28 Stearic acid Figure 5.12 (a) Saturated fat and fatty acid Saturated fatty acids Have the maximum number of hydrogen atoms possible Have no double bonds

29. 29 Oleic acid cis double bond causes bending Figure 5.12 (b) Unsaturated fat and fatty acid Unsaturated fatty acids Have one or more double bonds

30. 30 + CH2 Choline N(CH3)3 CH2 O Phosphate Hydrophilic head – P O O O CH2 CH CH2 Glycerol O O C O C O Fatty acids Hydrophilic head Hydrophobic tails Hydrophobic tails (c) Phospholipid symbol (b) Space-filling model Figure 5.13 (a) Structural formula Phospholipid structure Consists of a hydrophilic “head” and hydrophobic “tails”

31. 31 WATER Hydrophilic head WATER Hydrophobic tail Figure 5.14 The structure of phospholipids Results in a bilayer arrangement found in cell membranes

32. 32 H3C CH3 CH3 CH3 CH3 HO Figure 5.15 Steroids One steroid, cholesterol Is found in cell membranes Is a precursor for some hormones Steroids Are lipids characterized by a carbon skeleton consisting of four fused rings

33. 33 Proteins Proteins have many structures, resulting in a wide range of functions Proteins do most of the work in cells and act as enzymes Proteins are made of monomers called amino acids

34. 34 Table 5.1 An overview of protein functions

35. 35 Substrate binds to enzyme. 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. 2 2 Substrate (sucrose) Glucose Enzyme (sucrase) OH H2O Fructose H O 4 Products are released. 3 Substrate is converted to products. Figure 5.16 Enzymes Are a type of protein that acts as a catalyst, speeding up chemical reactions

36. 36 Polypeptides Polypeptides Are polymers (chains) of amino acids A protein Consists of one or more polypeptides

37. 37 Amino acids Are organic molecules possessing both carboxyl and amino groups Differ in their properties due to differing side chains, called R groups

38. 38 Twenty Amino Acids CH3 CH3 CH3 CH CH2 CH3 CH3 H CH3 H3C CH3 CH2 CH O O O O O H3N+ H3N+ H3N+ H3N+ C H3N+ C C C C C C C C C O– O– O– O– O– H H H H H Valine (Val) Leucine (Leu) Isoleucine (Ile) Glycine (Gly) Alanine (Ala) Nonpolar CH3 CH2 S H2C CH2 O NH CH2 H2N C C CH2 O– CH2 CH2 O O O H H3N+ H3N+ C C C C H3N+ C C O– O– O– H H H Phenylalanine (Phe) Proline (Pro) Methionine (Met) Tryptophan (Trp) Figure 5.17 20 different amino acids make up proteins

39. 39 OH NH2 O C NH2 O C OH SH CH2 CH3 OH Polar CH2 CH CH2 CH2 CH2 CH2 O O O O O O H3N+ H3N+ H3N+ H3N+ H3N+ H3N+ C C C C C C C C C C C C O– O– O– O– O– O– H H H H H H Glutamine (Gln) Tyrosine (Tyr) Asparagine (Asn) Cysteine (Cys) Serine (Ser) Threonine (Thr) Basic Acidic NH3+ NH2 NH+ O– O –O O CH2 C NH2+ C C NH Electrically charged CH2 CH2 CH2 CH2 CH2 O O H3N+ H3N+ CH2 CH2 C CH2 C C C O O– H3N+ O– CH2 C CH2 C H O H H3N+ O– C C CH2 H O O– H3N+ C C H O– H Lysine (Lys) Histidine (His) Arginine (Arg) Glutamic acid (Glu) Aspartic acid (Asp)

40. 40 Amino Acid Polymers Amino acids Are linked by peptide bonds

41. 41 Protein Conformation and Function A protein’s specific conformation (shape) determines how it functions

42. 42 Four Levels of Protein Structure Amino acid subunits +H3NAmino end Pro Thr Gly Gly Thr Gly Glu Seu Lys Cys Pro Leu Met Val Lys Val Leu Asp Ala Arg Val Gly Ser Pro Ala Glu Lle Asp Thr Lys Ser Tyr Trp Lys Ala Leu Gly lle Ser Pro Phe His Glu His Ala Glu Val Thr Val Phe Ala Asn lle Thr Asp Ala Tyr Arg Ser Ala Arg Pro Gly Leu Leu Ser Pro Tyr Ser Tyr Ser Thr Thr Ala o Val c Val Glu – Lys o Thr Pro Asn Carboxyl end Figure 5.20 Primary structure Is the unique sequence of amino acids in a polypeptide

43. 43 H H H H H H O O O O O O O H H H H H H R R R R R R R C C C C C C C C C C C C C N N N N N N N N N N N N N C C C C C C C C C C C C C C R R R R R R H H H H H H H O O O O O O O H H H H H H H  pleated sheet H O H H Amino acidsubunits C C N N N C C C R H O H H H H H H N N N N N N  helix C C O C H H H C C C R R R R R H H C C C C C C O O O O H C R O C C O H C O N N H C C H R H R Figure 5.20 Secondary structure Is the folding or coiling of the polypeptide into a repeating configuration Includes the  helix and the  pleated sheet

44. 44 Hydrophobic interactions and van der Waalsinteractions CH CH2 CH2 H3C CH3 OH Polypeptidebackbone CH3 H3C Hydrogenbond CH O HO C CH2 S S CH2 CH2 Disulfide bridge O -O C CH2 CH2 NH3+ Ionic bond Tertiary structure Is the overall three-dimensional shape of a polypeptide Results from interactions between amino acids and R groups

45. 45 Polypeptidechain Collagen  Chains Iron Heme  Chains Hemoglobin Quaternary structure Is the overall protein structure that results from the aggregation of two or more polypeptide subunits

46. 46 Review of Protein Structure +H3N Amino end Amino acid subunits helix

47. 47 Sickle-Cell Disease: A Simple Change in Primary Structure Sickle-cell disease Results from a single amino acid substitution in the protein hemoglobin

48. 48 Normal hemoglobin Sickle-cell hemoglobin Primary structure Primary structure . . . . . . Exposed hydrophobic region Val Thr His Leu Pro Glul Glu Val His Leu Pro Glu Thr Val 5 6 7 3 4 5 6 7 2 1 1 2 3 4 Secondaryand tertiarystructures Secondaryand tertiarystructures  subunit  subunit     Quaternary structure Hemoglobin A Quaternary structure Hemoglobin S     Molecules interact with one another tocrystallize into a fiber, capacity to carry oxygen is greatly reduced. Function Molecules donot associatewith oneanother, eachcarries oxygen. Function 10 m 10 m Normal cells arefull of individualhemoglobinmolecules, eachcarrying oxygen Red bloodcell shape Red bloodcell shape Figure 5.21 Fibers of abnormalhemoglobin deform cell into sickle shape.

49. 49 What Determines Protein Conformation? Protein conformation Depends on the physical and chemical conditions of the protein’s environment Temperature, pH, etc. affect protein structure

51. 52 Correctlyfoldedprotein Polypeptide Cap Hollowcylinder The cap attaches, causing the cylinder to change shape insuch a way that it creates a hydrophilic environment for the folding of the polypeptide. The cap comesoff, and the properlyfolded protein is released. Steps of ChaperoninAction: An unfolded poly- peptide enters the cylinder from one end. Chaperonin(fully assembled) 2 1 3 Figure 5.23 Chaperonins Are protein molecules that assist in the proper folding of other proteins

52. 53 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

53. 54 The Roles of Nucleic Acids There are two types of nucleic acids Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA)

54. 55 Deoxyribonucleic Acid DNA Stores information for the synthesis of specific proteins Found in the nucleus of cells

55. 56 DNA 1 Synthesis of mRNA in the nucleus mRNA NUCLEUS CYTOPLASM mRNA 2 Movement of mRNA into cytoplasm via nuclear pore Ribosome 3 Synthesis of protein Aminoacids Polypeptide Figure 5.25 DNA Functions Directs RNA synthesis (transcription) Directs protein synthesis through RNA (translation)

56. 57 5’ end 5’C O 3’C O O 5’C O 3’C 3’ end OH Figure 5.26 The Structure of Nucleic Acids Nucleic acids Exist as polymers called polynucleotides (a) Polynucleotide, or nucleic acid

57. 58 Nucleoside Nitrogenous base O 5’C O O CH2 P O O Phosphate group 3’C Pentose sugar Figure 5.26 (b) Nucleotide Each polynucleotide Consists of monomers called nucleotides Sugar + phosphate + nitrogen base

58. 59 Nitrogenous bases Pyrimidines NH2 O O C C CH3 C N CH HN C CH HN CH CH CH C C C CH CH N N N O O O H H H Uracil (in RNA) U Cytosine C Thymine (in DNA) T Uracil (in RNA) U Purines O NH2 C C N N C C NH N HC HC C CH C N N NH2 N N H H Adenine A Guanine G Pentose sugars 5” 5” OH OH HOCH2 HOCH2 O O H H H H 1’ 1’ 4’ 4’ H H H H 3’ 2’ 3’ 2’ H OH OH OH Deoxyribose (in DNA) Ribose (in RNA) Ribose (in RNA) Nucleotide Monomers Nucleotide monomers Are made up of nucleosides (sugar + base) and phosphate groups Figure 5.26 (c) Nucleoside components

59. 60 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

60. 61 Gene The sequence of bases along a nucleotide polymer Is unique for each gene

61. 62 The DNA Double Helix Cellular DNA molecules Have two polynucleotides that spiral around an imaginary axis Form a double helix

62. 63 3’ end 5’ end Sugar-phosphatebackbone Base pair (joined byhydrogen bonding) Old strands Nucleotideabout to be added to a new strand 3’ end A 5’ end Newstrands 3’ end 3’ end 5’ end Figure 5.27 The DNA double helix Consists of two antiparallel nucleotide strands

63. 64 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)