Chapter 3Revisiting the Theory of Chemical EvolutionEarly Origin-of-Life ExperimentsThe Structure of Amino AcidsSlide 5The Nature of Side ChainsFunctional Groups Affect ReactivitySlide 8Slide 9Slide 10Slide 11Monomers and PolymersSlide 13Assembling and Breaking Apart PolymersSlide 15The Peptide BondSlide 17Polypeptide CharacteristicsSlide 19Slide 20What Do Proteins Do?What Do Proteins Look Like?Primary StructureSlide 24Secondary StructureSlide 26Slide 27Slide 28Tertiary StructureR-group Interactions That Form Tertiary StructuresSlide 31Slide 32Quaternary StructureSlide 34Summary of Protein StructureSlide 36Folding and FunctionSlide 38Prions and Protein FoldingSlide 40An Introduction to CatalysisActivation Energy and Rates of Chemical ReactionsSlide 43Slide 44Catalysts and Free EnergySlide 46EnzymesHow Do Enzymes Work?Slide 49The Steps of Enzyme CatalysisSlide 51Slide 52Slide 53Do Enzymes Act Alone?Enzyme RegulationSlide 56Slide 57Chemical Modification and Enzyme RegulationWhat Limits the Rate of Catalysis?Slide 60Physical Conditions Affect Enzyme FunctionSlide 62Slide 63Rate of Enzyme-Catalyzed ReactionsWas the First Living Entity a Protein?Key ConceptsSlide 67© 2011 Pearson Education, Inc.CHAPTER 3© 2011 Pearson Education, Inc.Revisiting the Theory of Chemical Evolution•Oparin-Haldane; 1923 & 1929•Modern life arose through a series of endergonic chemical reactions.1. Production of small organic compounds–i.e., formaldehyde (H2CO), hydrogen cyanide (HCN)2. Formation of mid-sized molecules from these small compounds–i.e., amino acids, simple sugars–These molecules combined with ocean water to form “prebiotic soup.”•Mid-sized building blocks combine to form large molecules. –i.e., proteins, complex carbohydrates4. Life became possible when one of these large molecules self-replicated.© 2011 Pearson Education, Inc.Early Origin-of-Life Experiments Could the first steps of chemical evolution have occurred on ancient Earth?•To find out, Stanley Miller (1953) combined methane (CH4), ammonia (NH3), and hydrogen (H2) in a closed system with water, and applied heat and electricity as an energy source.•The products included hydrogen cyanide (HCN) and formaldehyde (H2CO), important precursors for more-complex organic molecules and amino acids.•In more recent experiments, amino acids and other organic molecules have been found to form easily under these conditions.© 2011 Pearson Education, Inc.The Structure of Amino AcidsAll proteins are made from just 20 amino acid building blocks. •All amino acids have a central carbon atom that bonds to NH2, COOH, H, and a variable side chain (“R-group”).In water (pH 7), the amino (base) and carboxyl (acid) groups ionize to NH3+ and COO–, respectively—this helps amino acids stay in solution and makes them more reactive.© 2011 Pearson Education, Inc.© 2011 Pearson Education, Inc.The Nature of Side Chains The 20 amino acids differ only in the unique R-group attached to the central carbon. The properties of amino acids vary because their R-groups vary.© 2011 Pearson Education, Inc.Functional Groups Affect Reactivity•R-groups differ in their size, shape, reactivity, and interactions with water. 1. Nonpolar R-groups: hydrophobic; do not form hydrogen bonds; coalesce in water2. Polar R-groups: hydrophilic; form hydrogen bonds; readily dissolve in water •Amino acids with hydroxyl, amino, carboxyl, or sulfhydryl functional groups in their side chains are more chemically reactive than those with side chains composed of only carbon and hydrogen atoms.© 2011 Pearson Education, Inc.© 2011 Pearson Education, Inc.© 2011 Pearson Education, Inc.© 2011 Pearson Education, Inc.© 2011 Pearson Education, Inc.Monomers and Polymers•Many mid-size molecules, such as amino acids and nucleotides, are individual units called monomers. They link together (polymerize) to form polymers, such as proteins and nucleic acids.•Macromolecules are very large polymers made up of many monomers linked together.•Thus, proteins are macromolecules consisting of linked amino acid monomers.© 2011 Pearson Education, Inc.© 2011 Pearson Education, Inc.Assembling and Breaking Apart Polymers•Polymerization requires energy and is nonspontaneous. –Follows 2nd law of thermodynamics  polymerization decreases entropy•Monomers polymerize through condensation (dehydration) reactions, which release a water molecule. •Hydrolysis is the reverse reaction, which breaks polymers apart by adding a water molecule.•In the prebiotic soup, hydrolysis is energetically favorable and thus would predominate over condensation. However, polymers clinging to a mineral surface are protected from hydrolysis, and thus polymerization of the amino acids into proteins may have occurred spontaneously.© 2011 Pearson Education, Inc.file:///Users/ericarowe/Documents/UTK%20Biology/UTK%20Bio140%20Fall%202011/Chapter_03/A_PowerPoint_Lecture_Tools/03_Lecture_Outline/CondensationHydrolysis.html© 2011 Pearson Education, Inc.The Peptide Bond•Condensation reactions bond the carboxyl group of one amino acid to the amino group of another to form a peptide bond.•A chain of amino acids linked by peptide bonds is called a polypeptide.–Polypeptides containing fewer than 50 amino acids are called oligopeptides (peptides).–Polypeptides containing more than 50 amino acids are called proteins.© 2011 Pearson Education, Inc.file:///Users/ericarowe/Documents/UTK%20Biology/UTK%20Bio140%20Fall%202011/Chapter_03/A_PowerPoint_Lecture_Tools/03_Lecture_Outline/Building_protein.html© 2011 Pearson Education, Inc.Polypeptide Characteristics •Within the polypeptide, the peptide bonds form a “backbone” with three key characteristics:1. R-group orientation–Side chains can interact with each other or water.2. Directionality –Free amino group, on the left, is called the N-terminus.–Free carboxyl group, on the right, is called the C-terminus.3. Flexibility–Single bonds on either side of the peptide bond can rotate, making the entire structure flexible.© 2011 Pearson Education, Inc.© 2011 Pearson Education, Inc.© 2011 Pearson Education, Inc.What Do Proteins Do? Proteins are crucial to most tasks required for cells to exist:–Catalysis – enzymes speed up chemical reactions.–Defense – antibodies and complement proteins attack pathogens.–Movement – motor and contractile proteins move the cell or molecules within the cell.–Signaling – proteins convey signals