Lecture 4 presented

Lecture 4 presented - Origins of Life, How it all...

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Unformatted text preview: Origins of Life, How it all began? Origins of Life, How it all began? Chapter 4 1 QUIZ 1 1. Which two compounds are most likely to be miscible (soluble in each other)? Give a short rational. 8 pts 2. Water is a polar molecule. This property contributes to cohesion. Draw six water molecules. In your drawing, indicate how hydrogen bonding between molecules contributes to cohesion (Be sure to include appropriate covalent bonds in each molecule.) 7 pts QUIZ 1 1. Which two compounds are most likely to be miscible (liquids soluble in each other)? Give a short rational. A. Water and Methanol is the best answer: The hydroxyl groups of methanol act as Hydrogen bond donors and interacts well with water. 8 pts The amino acid may be somewhat soluble in water and methanol, but it is a solid, so it can not act as a solvent. The charge on the amino acid will depend upon pH. At pH7 it will be neutral and the methyl group will tend to act in a hydrophobic mannor. 4 pts QUIZ 1 2. Water is a polar molecule. This property contributes to cohesion. Draw six water molecules. In your drawing, indicate how hydrogen bonding between molecules contributes to cohesion. (Be sure to include appropriate covalent bonds in each molecule.) 7 pts The partially positive hydrogens of one water molecule are attracted to the partially negative oxygens of another molecule of water. This attraction tends to cause water molecules to “stick” together, creating cohesion and surface tension. How Is All Life on Earth Related? The tree of life is predicDve. Placement of a new species on the tree of life immediately informs us about its biology. Understanding relaDonships among species allows biologists to make predicDons about species that have not yet been studied. 5 Building our Tree Archaea Eukaryotes Bacteria Photosynthesis Concepts Prokaryotes Foundations Evolution Scientific Method 6 How and Where Did the Small Molecules of Life Originate? During the European Renaissance (about 1450 to 1700), most people thought that at least some forms of life arose repeatedly from inanimate or decaying maUer by spontaneous genera,on. 7 How and Where Did the Small Molecules of Life Originate? The first experiment to disprove spontaneous generaDon was done in 1668. Experiments by Louis Pasteur (1860s) showed that microorganisms can arise only from other microorganisms. 8 9 10 10 How and Where Did the Small Molecules of Life Originate? But their experiments did not prove that spontaneous generaDon never occurred. Eons ago,condiDons on Earth and in the atmosphere were vastly different. About 4 billion years ago, chemical condiDons, including the presence of water, became just right for life. 11 11 What were the conditions on Earth prior to life? H2, HCl, CO, CO2, H2O, N2 CH4, NH4, HCN, lots of volcanic activity 12 How and Where Did the Small Molecules of Life Originate? Two of the theories on the origin of life: • Life came from outside of Earth. • Life arose on Earth through chemical evoluDon. 13 13 How and Where Did the Small Molecules of Life Originate? In 1969, fragments of a meteorite were found to contain molecules unique to life, including purines, pyrimidines, sugars, and ten amino acids. Evidence from other meteorites suggest that living organisms could possibly have reached Earth within a meteorite. 14 14 How and Where Did the Small Molecules of Life Originate? Chemical evolu2on: condiDons on primiDve Earth led to formaDon of simple molecules (prebioDc synthesis); these molecules led to formaDon of life forms. ScienDsts have experimented with reconstrucDng those primiDve condiDons. 15 15 How and Where Did the Small Molecules of Life Originate? Miller and Urey (1950s) set up an experiment with gases thought to have been present in Earth’s early atmosphere. An electric spark simulated lightning as a source of energy to drive chemical reacDons. Acer several days, amino acids, purines, and pyrimidines were formed. 16 16 Miller & Urey Synthesized PrebioDc Molecules in an Experimental Atmosphere (Part 1) 17 17 Figure 4.9 Miller & Urey Synthesized PrebioDc Molecules in an Experimental Atmosphere 18 18 How Did the Large Molecules of Life Originate? CondiDons in which polymers might have been first synthesized: • Solid mineral surfaces—silicates within clay may have been catalysts • Hydrothermal vents—metals as catalysts • Hot pools at ocean edges—concentrated monomers favored polymerizaDon (the “primordial soup”) 19 19 How Did the Large Molecules of Life Originate? In exisDng life forms, nucleic acids and proteins require one another in order to perpetuate life. Which came first? 20 20 How Did the Large Molecules of Life Originate? Metabolism first: Life began in Dny droplets; random chemical changes increased survival rates and primiDve reproducDon. Catalysis and reproducDon could have occurred without proteins on pyrite (iron disulfide), which could serve as an energy source. 21 21 Figure 4.10 Two Pathways to Life (Part 1) 22 22 OR 23 23 How Did the Large Molecules of Life Originate? Replicator first: NucleoDdes formed polymers; some had the right shape to be catalyDc and reproduce themselves. 24 24 Figure 4.10 Two Pathways to Life (Part 2) 25 25 How could replicaDon come first? 26 26 Figure 4.11 The “RNA World” Hypothesis CatalyDc proteins increase the efficiency of RNA replicaDon and protein synthesis. They also aid the formaDon of double ­ stranded RNA, which then evolves into double ­stranded DNA DNA becomes the primary molecule for informaDon storage. DNA uses RNA to make proteins which in turn help with DNA replicaDon and transcripDon. 27 Ribose,bases, and phosphate come Figure 4.11 The “RNA World” RHypothesis together to form NA Some R Ribose bNA molecules gain the ability to replicate RNA molecules begin to make catalyDc proteins 28 How Did the Large Molecules of Life Originate? Ribozymes are folded RNA molecules that can act as catalysts. They can catalyze reacDons on their own nucleoDdes as well as other molecules. RNA may have evolved first, and catalyzed its own replicaDon as well as protein synthesis. 29 29 Figure 4.12 An Early Catalyst for Life? 30 30 How Did the Large Molecules of Life Originate? Evidence that supports the “RNA World” hypothesis: • Certain short RNA sequences catalyze formaDon of RNA polymers. • Ribozyme can catalyze assembly of short RNAs into a longer molecule. • PepDde linkages are catalyzed by ribozymes in living organisms. 31 31 How Did the Large Molecules of Life Originate? • Retroviruses have an enzyme called reverse transcriptase that catalyzes the synthesis of DNA from RNA. 32 32 How Did the First Cells Originate? The chemical reacDons of metabolism and replicaDon could not occur in a dilute aqueous environment. The compounds involved must have been concentrated in a compartment. Today, living cells are separated from their environment by a membrane. 33 33 How Did the First Cells Originate? In water, faUy acids will form a lipid bilayer around a compartment. These protocells allow small molecules such as sugars and nucleoDdes to pass through. If short nucleic acid strands capable of self ­ replicaDon are placed inside the protocells, nucleoDdes can enter and become incorporated into new polynucleoDde chains. 34 34 Figure 4.13 Protocells 35 35 How Did the First Cells Originate? In the 1990s, evidence of cells in rocks 3.5 billion years old was found in Australia. The cells were probably cyanobacteria (blue ­ green bacteria) that could perform photosynthesis. Photosynthesis uses CO2, and leaves a specific raDo of carbon isotopes (13C:12C) which were found in the fossils. 36 36 How Did the First Cells Originate? It is plausible that it took about 500 million to a billion years from the formaDon of the Earth unDl the appearance of the first cells. 37 37 Figure 4.14 The Earliest Cells? This fossil is 3.5 billion years old. Its form is similar to that of t modern filamentous Cyanobacteria 38 Figure 4.15 The Origin of Life Proks 39 39 Lecture 4: Cellular Energy Chapter 8 and 9 40 What Physical Principles Underlie Biological Energy TransformaDons? The transformaDon of energy is a hallmark of life. Energy is the capacity to do work, or the capacity for change. Energy transformaDons are linked to chemical transformaDons in cells. 41 What Physical Principles Underlie Biological Energy TransformaDons? All forms of energy can be placed in two categories: • Poten9al energy is stored energy—as chemical bonds, concentraDon gradient, charge imbalance, etc. • Kine9c energy is the energy of movement 42 What Physical Principles Underlie Biological Energy TransformaDons? Metabolism: Sum total of all chemical reacDons in an organism. Anabolic reac2ons: Complex molecules are made from simple molecules; energy input is required. Catabolic reac2ons: Complex molecules are broken down to simpler ones and energy is released. 43 What Physical Principles Underlie Biological Energy TransformaDons? The laws of thermodynamics (thermo, “energy”; dynamics, “change”) apply to all maUer and all energy transformaDons in the universe. They help us to understand how cells harvest and transform energy to sustain life. 44 What Physical Principles Underlie Biological Energy TransformaDons? First law of thermodynamics: Energy is neither created nor destroyed. When energy is converted from one form to another, the total energy before and acer the conversion is the same. 45 What Physical Principles Underlie Biological Energy TransformaDons? Second law of thermodynamics: When energy is converted from one form to another, some of that energy becomes unavailable to do work. No energy transformaDon is 100 percent efficient. 46 What Physical Principles Underlie Biological Energy TransformaDons? Entropy is a measure of the disorder in a system. It takes energy to impose order on a system. Unless energy is applied to a system, it will be randomly arranged or disordered. 47 What Physical Principles Underlie Biological Energy TransformaDons? Exergonic reacDons release free energy (–ΔG): Catabolism; complexity decreases (generates disorder). Endergonic reacDons consume free energy (+ΔG): anabolism; complexity (order) increases. 48 Figure 8.3 Exergonic and Endergonic ReacDons (Part 1) 49 Figure 8.3 Exergonic and Endergonic ReacDons (Part 2) 50 What Physical Principles Underlie Biological Energy TransformaDons? In principle, chemical reacDons can run in both direcDons. At chemical equilibrium, ΔG = 0 Forward and reverse reacDons are balanced. A! B The concentraDons of A and B determine which direcDon will be favored. 51 What Physical Principles Underlie Biological Energy TransformaDons? Every reacDon has a specific equilibrium point. 52 Figure 8.4 Chemical ReacDons Run to Equilibrium 53 What are Enzymes 54 What Are Enzymes? Catalysts speed up the rate of a reacDon. The catalyst is not altered by the reacDons. Most biological catalysts are enzymes (proteins) that act as a framework in which reacDons can take place. 55 What Are Enzymes? Some reacDons are slow because of an energy barrier̶the amount of energy required to start the reacDon, called ac2va2on energy (Ea). 56 Figure 8.8 AcDvaDon Energy IniDates ReacDons (Part 1) 57 Figure 8.8 AcDvaDon Energy IniDates ReacDons (Part 2) 58 What Are Enzymes? AcDvaDon energy changes the reactants into unstable forms with higher free energy—transi2on state intermediates. AcDvaDon energy can come from heaDng the system—the reactants have more kineDc energy. Enzymes and ribozymes lower the energy barrier by bringing the reactants together. 59 What Are Enzymes? Biological catalysts (enzymes and ribozymes) are highly specific. Reactants are called substrates. Substrate molecules bind to the acDve site of the enzyme. The three ­dimensional shape of the enzyme determines the specificity. 60 Figure 8.9 Enzyme and Substrate 61 What Are Enzymes? The enzyme ­substrate complex (ES) is held together by hydrogen bonds, electrical aUracDon, or covalent bonds. E + S → ES → E + P The enzyme may change when bound to the substrate, but returns to its original form. 62 What Are Enzymes? Enzymes lower the energy barrier for reacDons. The final equilibrium doesn’t change, and ΔG doesn’t change. 63 Figure 8.10 Enzymes Lower the Energy Barrier 64 How Do Enzymes Work? In catalyzing a reacDon, an enzyme may use one or more mechanisms. 65 Figure 8.11 Life at the Active Site (A) Enzymes orient substrate molecules, bringing together the atoms that will bond. 66 Figure 8.11 Life at the Active Site (B) Enzymes can stretch the bonds in substrate molecules, making them unstable. 67 Figure 8.11 Life at the Active Site (C) Enzymes can temporarily add chemical groups to substrates. 68 QuesDon 1 Enzymes speed up chemical reacDons by a. decreasing ∆G. b. increasing acDvaDon energy. c. shicing the equilibrium toward products. d. forming an enzyme ­substrate complex. 69 How Do Enzymes Work? Acid ­base catalysis: Enzyme side chains transfer H+ to or from the substrate, causing a covalent bond to break. Covalent catalysis: A funcDonal group in a side chain bonds covalently with the substrate. Metal ion catalysis: Metals on side chains loose or gain electrons. 70 How Do Enzymes Work? Shape of enzyme acDve site allows a specific substrate to fit (lock and key). Binding of substrate to the acDve site depends on hydrogen bonds, aUracDon and repulsion of electrically charged groups, and hydrophobic interacDons. Many enzymes change shape when they bind to the substrate—induced fit. 71 Figure 8.12 Some Enzymes Change Shape When Substrate Binds to Them 72 How Do Enzymes Work? Some enzymes require “partners”: • Prosthe,c groups: Non ­amino acid groups bound to enzymes • Cofactors: Inorganic ions • Coenzymes: Small carbon ­containing molecules; not bound permanently to enzymes 73 74 QuesDon 2 This figure illustrates all of the following features of enzymes except that they a. are larger than their substrates. b. may require coenzymes to funcDon. c. may change shape when aUached to substrates. d. can induce strain in substrates. 75 How Do Enzymes Work? The rate of a catalyzed reacDon depends on substrate concentraDon. ConcentraDon of an enzyme is usually much lower than concentraDon of a substrate. At saturaDon, all enzyme is bound to substrate—maximum rate. 76 Figure 8.13 Catalyzed ReacDons Reach a Maximum Rate 77 Four Volunteers 78 How Do Enzymes Work? Maximum rate is used to calculate enzyme efficiency: Molecules of substrate converted to product per unit Dme (turnover). Ranges from 1 to 40 million molecules per second! 79 How Are Enzyme AcDviDes Regulated? Allostery (allo, “different”; stereos, “shape”) Some enzymes exist in more than one shape: • Ac9ve form—can bind substrate • Inac9ve form—cannot bind substrate but can bind an inhibitor 80 How Are Enzyme AcDviDes Regulated? Allosteric regula2on: An effector molecule binds to a regulatory subunit, inducing the enzyme to change its shape. Effectors can either inhibit or acDvate an enzyme. 81 How Are Enzyme AcDviDes Regulated? Every enzyme is most acDve at a parDcular pH. pH influences the ionizaDon of funcDonal groups. Example: at low pH (high H+) —COO– may react with H+ to form —COOH which is no longer charged; this affects folding and thus enzyme funcDon. 82 Figure 8.20 pH Affects Enzyme AcDvity 83 How Are Enzyme AcDviDes Regulated? Every enzyme has an opDmal temperature. At high temperatures, noncovalent bonds begin to break. Enzyme can lose its terDary structure and become denatured. 84 Figure 8.21 Temperature Affects Enzyme AcDvity 85 How Are Enzyme AcDviDes Regulated? Isozymes: Enzymes that catalyze the same reacDon but have different properDes, such as opDmal temperature. Organisms can use isozymes to adjust to temperature changes. Enzymes in humans have higher opDmal temperature than enzymes in most bacteria—a fever can denature the bacterial enzymes. 86 ...
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