1. 3 Announcements On-line quiz – Chapter 2 deadline: ……..midnight tonight! Review guidelines for on-line quizzes, they are on the BIO 121/122 website. Note: Once you begin taking the quiz, be sure to complete it. Otherwise a grade of zero will be submitted to the database.

2. 3 Life and Chemistry: Large Molecules

3. 3 Theories of the Origin of Life Macromolecules: Giant Polymers Condensation and Hydrolysis Reactions Proteins: Polymers of Amino Acids Carbohydrates: Sugars and Sugar Polymers Lipids: Water-Insoluble Molecules Nucleic Acids: Informational Macromolecules That Can Be Catalytic All Life from Life

4. 3 Life on Earth Source: http://pubs.usgs.gov/fs/2001/fs084-01/images/reef2.jpg

5. 3 The Building Blocks of Organisms MONOMER  MACROMOLECULE  LIFE Amino AcidProtein NucleotideNucleic Acid WERE DID THE MONOMERS COME FROM???

6. 3 Theories of the Origin of Life There are two theories for the origin of life:  Life from extraterrestrial sources  Chemical evolution

7. 3 Meterorite ALH 84001 Mars to Antarctica 11,000 years ago Polycyclic aromatic hydrocarbons: formed by decaying organisms Magnetite: iron oxide mineral made by living things Water: water is required by life, as we know it Other meteorites contained water, purines, pyrimidines, and amino acids.

8. Figure 3.1 Synthesis of Prebiotic Molecules in an Experimental Atmosphere

9. 3 The Building Blocks of Organisms MONOMER  MACROMOLECULE  LIFE Amino AcidProtein NucleotideNucleic Acid

10. 3 Macromolecules: Giant Polymers There are four major types of biological macromolecules:  Proteins  Carbohydrates  Lipids  Nucleic acids

11. Table 3.1 The Building Blocks of Organisms

12. 3 Macromolecules: Giant Polymers The functions of macromolecules are related to their shape and the chemical properties of their monomers. Some of the roles of macromolecules include:  Energy storage  Structural support  Transport  Protection and defense  Regulation of metabolic activities  Means for movement, growth, and development  Heredity

13. 3 Condensation and Hydrolysis Reactions Macromolecules are made from smaller monomers by means of a condensation or dehydration reaction in which an OH from one monomer is linked to an H from another monomer. Energy must be added to make or break a polymer. The reverse reaction, in which polymers are broken back into monomers, is a called a hydrolysis reaction.

14. Figure 3.3 Condensation and Hydrolysis of Polymers (Part 1)

15. Figure 3.3 Condensation and Hydrolysis of Polymers (Part 2)

16. 3 Proteins: Polymers of Amino Acids Proteins are polymers of amino acids. They are molecules with diverse structures and functions. Each different type of protein has a characteristic amino acid composition and order. Proteins range in size from a few amino acids to thousands of them. Folding is crucial to the function of a protein and is influenced largely by the sequence of amino acids.

17. 3 Proteins: Polymers of Amino Acids An amino acid has four groups attached to a central carbon atom:  A hydrogen atom  An amino group (NH3 + )  The acid is a carboxyl group (COO–).  Differences in amino acids come from the side chains, or the R groups.

18. 3 Source: http://www.hcc.mnscu.edu/programs/dept/chem/V.27/amino_acid_structure_2.jpg

19. 3 Proteins: Polymers of Amino Acids Amino acids can be classified based on the characteristics of their R groups.  Five have charged hydrophilic side chains.  Five have polar but uncharged side chains.  Seven have nonpolar hydrophobic side chains.  Cysteine has a terminal disulfide (—S—S—).  Glycine has a hydrogen atom as the R group.  Proline has a modified amino group that forms a covalent bond with the R group, forming a ring.

20. Table 3.2 The Twenty Amino Acids Found in Proteins (Part 1)

21. Table 3.2 The Twenty Amino Acids Found in Proteins (Part 2)

22. Table 3.2 The Twenty Amino Acids Found in Proteins (Part 3)

23. 3 Proteins: Polymers of Amino Acids Proteins are synthesized by condensation reactions between the amino group of one amino acid and the carboxyl group of another. This forms a peptide linkage. Proteins are also called polypeptides. A dipeptide is two amino acids long; a tripeptide, three. A polypeptide is multiple amino acids long.

24. Figure 3.5 Formation of Peptide Linkages

25. 3 Proteins: Polymers of Amino Acids There are four levels of protein structure: primary, secondary, tertiary, and quaternary. The precise sequence of amino acids is called its primary structure. The peptide backbone consists of repeating units of atoms: N—C—C—N—C—C. Enormous numbers of different proteins are possible.

26. 3 Proteins: Polymers of Amino Acids A protein’s secondary structure consists of regular, repeated patterns in different regions in the polypeptide chain. This shape is influenced primarily by hydrogen bonds arising from the amino acid sequence (the primary structure). The two common secondary structures are the  helix and the  pleated sheet.

27. 3 Proteins: Polymers of Amino Acids The  helix is a right-handed coil. The peptide backbone takes on a helical shape due to hydrogen bonds. The R groups point away from the peptide backbone. Fibrous structural proteins have  -helical secondary structures, such as the keratins found in hair, feathers, and hooves.

28. 3 Proteins: Polymers of Amino Acids  pleated sheets form from peptide regions that lie parallel to each other. Sometimes the parallel regions are in the same peptide, sometimes the parallel regions are from different peptide strands. This sheetlike structure is stabilized by hydrogen bonds between N-H groups on one chain with the C=O group on the other. Spider silk is made of  pleated sheets from separate peptides.

29. Figure 3.6 The Four Levels of Protein Structure (Part 1)

30. Figure 3.6 The Four Levels of Protein Structure (Part 2)

31. Figure 3.6 The Four Levels of Protein Structure (Part 3)

32. 3 Proteins: Polymers of Amino Acids Tertiary structure is the three-dimensional shape of the completed polypeptide. The primary determinant of the tertiary structure is the interaction between R groups. Other factors can include the location of disulfide bridges, which form between cysteine residues.

33. Figure 3.4 A Disulfide Bridge

34. 3 Proteins: Polymers of Amino Acids Other factors determining tertiary structure:  The nature and location of secondary structures  Hydrophobic side-chain aggregation and van der Waals forces, which help stabilize them  The ionic interactions between the positive and negative charges deep in the protein, away from water

35. 3 Proteins: Polymers of Amino Acids It is now possible to determine the complete description of a protein’s tertiary structure. The location of every atom in the molecule is specified in three-dimensional space.

36. Figure 3.7 Three Representations of Lysozyme

37. 3 Proteins: Polymers of Amino Acids Quaternary structure results from the ways in which multiple polypeptide subunits bind together and interact. This level of structure adds to the three- dimensional shape of the finished protein. Hemoglobin is an example of such a protein; it has four subunits.

38. Figure 3.8 Quaternary Structure of a Protein

39. 3 Proteins: Polymers of Amino Acids Shape is crucial to the functioning of some proteins:  Enzymes need certain surface shapes in order to bind substrates correctly.  Carrier proteins in the cell surface membrane allow substances to enter the cell.  Chemical signals such as hormones bind to proteins on the cell surface membrane. The combination of attractions, repulsions, and interactions determines the right fit.

40. 3 Proteins: Polymers of Amino Acids Changes in temperature, pH, salt concentrations, and oxidation or reduction conditions can change the shape of proteins. This loss of a protein’s normal three-dimensional structure is called denaturation.

41. Figure 3.11 Denaturation Is the Loss of Tertiary Protein Structure and Function

42. 3

43. 3 Announcements On-line Quiz – Chapter 3 Deadline: Monday

44. 3 Life and Chemistry: Large Molecules Theories of the Origin of Life Macromolecules: Giant Polymers Condensation and Hydrolysis Reactions Proteins: Polymers of Amino Acids Carbohydrates: Sugars and Sugar Polymers Lipids: Water-Insoluble Molecules Nucleic Acids: Informational Macromolecules That Can Be Catalytic All Life from Life

45. 3 Carbohydrates: Sugars and Sugar Polymers There are four major categories of carbohydrates:  Monosaccharides (e.g., glucose, fructose)  Disaccharides, which consist of two monosaccharides (e.g., sucrose, lactose)  Oligosaccharides, which consist of between 3 and 20 monosaccharides  Polysaccharides, which are composed of hundreds to hundreds of thousands of monosaccharides

46. 3 Carbohydrates: Sugars and Sugar Polymers The general formula for a carbohydrate monomer is multiples of CH 2 O, maintaining a ratio of 1 carbon to 2 hydrogens to 1 oxygen. During the polymerization, which is a condensation reaction, water is removed.

47. Figure 3.13 Glucose: From One Form to the Other

48. 3 Carbohydrates: Sugars and Sugar Polymers Different monosaccharides have different numbers or different arrangements of carbons. Most monosaccharides are optical isomers. Hexoses (six-carbon sugars) include the structural isomers glucose, fructose, mannose, and galactose. Pentoses are five-carbon sugars.

49. Figure 3.14 Monosaccharides Are Simple Sugars (Part 1)

50. Figure 3.14 Monosaccharides Are Simple Sugars (Part 2)

51. 3 Carbohydrates: Sugars and Sugar Polymers Monosaccharides are bonded together covalently by condensation reactions. The bonds are called glycosidic linkages. Disaccharides have just one such linkage: sucrose, lactose, maltose, cellobiose.

52. Figure 3.15 Disaccharides Are Formed by Glycosidic Linkages

53. 3 Carbohydrates: Sugars and Sugar Polymers Polysaccharides are giant polymers of monosaccharides connected by glycosidic linkages. Cellulose is a giant polymer of glucose joined by  -1,4 linkages. Starch is a polysaccharide of glucose with  -1,4 linkages.

54. Figure 3.16 Representative Polysaccharides (Part 1)

55. Figure 3.16 Representative Polysaccharides (Part 2)

56. 3 Lipids: Water-Insoluble Molecules Lipids are insoluble in water. This insolubility results from the many nonpolar covalent bonds of hydrogen and carbon in lipids. Lipids aggregate away from water, which is polar, and are attracted to each other via weak, but additive, van der Waals forces.

57. 3 Lipids: Water-Insoluble Molecules Roles for lipids in organisms include:  Energy storage (fats and oils)  Cell membranes (phospholipids)  Capture of light energy (carotinoids)  Hormones and vitamins (steroids and modified fatty acids)  Thermal insulation  Electrical insulation of nerves  Water repellency (waxes and oils)

58. 3 Lipids: Water-Insoluble Molecules Fats and oils store energy. Fats and oils are triglycerides, composed of three fatty acid molecules and one glycerol molecule. Glycerol is a three-carbon molecule with three hydroxyl (—OH) groups, one for each carbon. Fatty acids are long chains of hydrocarbons with a carboxyl group (—COOH) at one end.

59. Figure 3.18 Synthesis of a Triglyceride

60. 3 Lipids: Water-Insoluble Molecules Saturated fatty acids have only single carbon-to- carbon bonds and are said to be saturated with hydrogens. Saturated fatty acids are rigid and straight, and solid at room temperature. Animal fats are saturated.

61. 3 Lipids: Water-Insoluble Molecules Unsaturated fatty acids have at least one double-bonded carbon in one of the chains —the chain is not completely saturated with hydrogen atoms. The double bonds cause kinks that prevent easy packing. Unsaturated fatty acids are liquid at room temperature. Plants commonly have unsaturated fatty acids.

62. Figure 3.19 Saturated and Unsaturated Fatty Acids

63. 3 Lipids: Water-Insoluble Molecules Phospholipids have two hydrophobic fatty acid tails and one hydrophilic phosphate group attached to the glycerol. As a result, phospholipids orient themselves so that the phosphate group faces water and the tail faces away. In aqueous environments, these lipids form bilayers, with heads facing outward, tails facing inward. Cell membranes are structured this way.

64. Figure 3.20 Phospholipid Structure

65. Figure 3.21 Phospholipids Form a Bilayer

66. 3 Nucleic Acids: Informational Macromolecules That Can Be Catalytic Nucleic acids are polymers that are specialized for storage and transmission of information. Two types of nucleic acid are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). DNA encodes hereditary information and transfers information to RNA molecules. The information in RNA is decoded to specify the sequence of amino acids in proteins.

67. 3 Nucleic Acids: Informational Macromolecules That Can Be Catalytic Nucleic acids are polymers of nucleotides. A nucleotide consists of a pentose sugar, a phosphate group, and a nitrogen-containing base. In DNA, the pentose sugar is deoxyribose; in RNA it is ribose.

68. Figure 3.24 Nucleotides Have Three Components

69. 3 Nucleic Acids: Informational Macromolecules That Can Be Catalytic DNA typically is double-stranded. The two separate polymer chains are held together by hydrogen bonding between their nitrogenous bases. The base pairing is complementary: At each position where a purine is found on one strand, a pyrimidine is found on the other. Purines have a double-ring structure. Pyrimidines have one ring.

70. Figure 3.25 Distinguishing Characteristics of DNA and RNA

71. 3 Nucleic Acids: Informational Macromolecules That Can Be Catalytic The linkages that hold the nucleotides in RNA and DNA are called phosphodiester linkages. These linkages are formed between carbon 3 of the sugar and a phosphate group that is associated with carbon 5 of the sugar. The backbone consists of alternating sugars and phosphates. In DNA, the two strands are antiparallel. The DNA strands form a double helix, a molecule with a right-hand twist.

72. 3 Nucleic Acids: Informational Macromolecules That Can Be Catalytic Most RNA molecules consist of only a single polynucleotide chain. Instead of the base thymine, RNA uses the base uracil. Hydrogen bonding between ribonucleotides in RNA can result in complex three-dimensional shapes.

73. Figure 3.26 Hydrogen Bonding in RNA

74. 3 Nucleic Acids: Informational Macromolecules That Can Be Catalytic Nucleotides have other important roles:  The ribonucleotide ATP acts as an energy transducer in many biochemical reactions.  The ribonucleotide GTP powers protein synthesis.  cAMP (cyclic AMP) is a special ribonucleotide that is essential for hormone action and the transfer of information by the nervous system.