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The Origin and Chemistry of Life Chapter 2 Water and Life Water makes up a large portion of living organisms. It has several unusual properties that make it essential for life. Hydrogen bonds lie behind these important properties. Water and Life High specific heat capacity – 1 calorie is required to elevate temperature of 1 gram of water 1°C. Moderates environmental changes. High heat of vaporization – more than 500 calories are required to convert 1 g of liquid water to water vapor. Cooling produced by evaporation of water is important for expelling excess heat. Water and Life Unique density behavior – while most liquids become denser with decreasing temperature, water’s maximum density is at 4°C. Ice floats! Lakes don’t freeze solid – some liquid water is usually left at the bottom. Water and Life Water has high surface tension. Because of the hydrogen bonds between water molecules at the water-air interface, the water molecules cling together. Water has low viscosity. Water and Life Water acts as a solvent – salts dissolve more in water than in any other solvent. Result of the dipolar nature of water. Water and Life Hydrolysis occurs when compounds are split into smaller pieces by the addition of a water molecule. R-R + H2O R-OH + H-R Condensation occurs when larger compounds are synthesized from smaller compounds. R-OH + H-R R-R + H2O Acids, Bases, and Buffers Acid: Substance that liberates hydrogen ions (H+) in solution. Base: Substance that liberates hydroxyl ions (OH-) in solution. The regulation of the concentrations of H+ and OH- is critical in cellular processes. Acids, Bases, and Buffers pH – A measure of the concentration of H+ in a solution. The pH scale runs from 0 - 14. Represents the negative log of the H+ concentration of a solution. Acids, Bases, and Buffers Neutral solution with a pH of 7: [H+] = [OH-] Basic solution with a pH above 7: [H+] < [OH-] Acidic solution with a pH below 7: [H+] > [OH-] Acids, Bases, and Buffers Buffer: Molecules that prevent dramatic changes in the pH of fluids. Remove H+ and OH- in solution and transfers them to other molecules. Example: Bicarbonate Ion (HCO3-). Chemistry of Life Recall the four major categories of biological macromolecules: Carbohydrates Lipids Proteins Nucleic acids Carbohydrates Carbohydrates are compounds of carbon (C), hydrogen (H) and oxygen (O). Usually found 1C:2H:1O. Usually grouped as H-C-OH. Function as structural elements and as a source of chemical energy (ex. glucose). Carbohydrates Plants use water (H2O) and carbon dioxide (CO2) along with solar energy to manufacture carbohydrates in the process of photosynthesis. 6CO2 +6H2O C6H12O6 + 6O2 light Life depends on this reaction – it is the starting point for the formation of food. Carbohydrates Three classes of carbohydrates: Monosaccharides – simple sugars Disaccharides – double sugars Polysaccharides – complex sugars Monosaccharides Monosaccharides – Single carbon chain 4-6 carbons. Glucose C6H12O6 Can be straight chain or a ring. Monosaccharides Some common monosaccharides: Disaccharides Disaccharides – Two simple sugars bonded together. Water released Sucrose = glucose + fructose Lactose = glucose + galactose Polysaccharides Polysaccharides – Many simple sugars bonded together in long chains. Starch is the common polymer in which sugar is usually stored in plants. Glycogen is an important polymer for storing sugar in animals. Found in liver and muscle cells – can be converted to glucose when needed. Cellulose is the main structural carbohydrate in plants. Lipids Lipids are fatty substances. Nonpolar – insoluble in water Neutral fats Phospholipids Steroids Neutral Fats Neutral fats are the major fuel of animals. Triglycerides – glycerol and 3 fatty acids Neutral Fats Saturated fatty acids occur when every carbon holds two hydrogen atoms. Unsaturated fatty acids have two or more carbon atoms joined by double bonds. Phospholipids Phospholipids are important components of cell membranes. They resemble triglycerides, except one fatty acid is replaced by phosphoric acid and an organic base. The phosphate group is charged (polar). Phospholipids Amphiphilic compounds are polar and water– soluble on one end and nonpolar on the other end. They have a tendency to assemble themselves into semi-permeable membranes. Steroids Steroids are complex alcohols with fatlike properties. Cholesterol Vitamin D Adrenocortical hormones Sex hormones Proteins Proteins are large complex molecules composed of amino acids. Amino acids linked by peptide bonds. Two amino acids joined – dipeptide Many amino acids – polypeptide chain Proteins There are 20 different types of amino acids. Protein Structure Proteins are complex molecules organized on many levels. Primary structure – sequence of amino acids. Secondary structure – helix or pleated sheet. Stabilized with Hbonds. Protein Structure Tertiary structure – 3dimensional structure of folded chains. Eg. Disulfide bond is a covalent bond between sulfur atoms in two cysteine amino acids that are near each other. Quaternary structure describes proteins with more than one polypeptide chain. Hemoglobin has four subunits. Proteins Proteins serve many functions. Structural framework Enzymes that serve as catalysts Nucleic Acids Nucleic acids are complex molecules with particular sequences of nitrogenous bases that encode genetic information. The only molecules that can replicate themselves – with help from enzymes. Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) Nucleic Acids The repeated units, called nucleotides, each contain a sugar, a nitrogenous base, and a phosphate group. Chemical Evolution Life evolved from inanimate matter, with increasingly complex associations between molecules. Life originated ~3.5 billion years ago. Chemical Evolution Origin of Life Oparin-Haldane Hypothesis (1920s) Alexander Oparin and J.B.S. Haldane proposed an explanation for the chemical evolution of life. Chemical Evolution Early atmosphere consisted of simple compounds: Water vapor Carbon Dioxide (CO2) Hydrogen Gas (H2) Methane (CH4) Ammonia (NH3) No free Oxygen Early atmosphere → Strongly Reducing Chemical Evolution Such conditions conducive to prebiotic synthesis of life. Present atmosphere is strongly oxidizing. Molecules necessary for life cannot be synthesized outside of the cells. Not stable in the presence of O2 Chemical Evolution Possible energy sources required for chemical reactions: Lightning UV Light Heat from volcanoes Chemical Evolution Simple inorganic molecules formed and began to accumulate in the early oceans. Over time: Simple Organic Molecules Complex Organic Molecules Cells Chemical Evolution Prebiotic Synthesis of Small Organic Molecules Stanley Miller and Harold Urey (1953) simulated the Oparin-Haldane hypothesis. Chemical Evolution Miller & Urey reconstructed the O2 free atmosphere they thought existed on the early Earth in the lab. Circulated a mixture of H2 H2O CH4 NH3 Energy source: electrical spark to simulate lightening and UV radiation. Chemical Evolution Results: In a week, 15% of the carbon in the mixture was converted to organic compounds such as: Amino Acids Urea Simple Fatty Acids Chemical Evolution Conclusion: life may have evolved in “primordial soup” of biological molecules formed in early Earth’s oceans. Chemical Evolution Today it is believed that the early atmosphere was only mildly reducing. Still……if NH3 and CH4 are omitted from the mixture: Organic compounds continue to be produced (smaller amount over a longer time period). Chemical Evolution More recent experiments: Subjecting a reducing mixture of gases to a violent energy source produces: Formaldehyde Hydrogen Cyanide Cyanoacetylene All highly reactive intermediate molecules Significance? Chemical Evolution All react with water and NH3 or N2 to produce a variety of organic compounds: Amino Acids, Fatty Acids, Urea, Sugars, Aldehydes, Purine and Pyrimidine Bases Subunits For Complex Organic Compounds. Chemical Evolution Formation of Polymers The next stage of chemical evolution required the joining of amino acids, nitrogenous bases and sugars to form complex organic molecules. Does not occur easily in dilute solutions. Water tends to drive reactions toward decomposition by hydrolysis. Chemical Evolution Condensation reactions occur in aqueous environments and require enzymes. Chemical Evolution The strongest current hypothesis for prebiotic assembly of biologically important polymers suggests that they occurred within the boundaries of semipermeable membranes. Membranes were formed by amphiphilic molecules. Meteorites are common sources of organic amphiphiles. Origin of Living Systems Life on Earth: 4 billion years ago First cells would have been autonomous, membrane-bound units capable of selfreplication requiring: Nucleic Acids This causes a biological paradox. How could nucleic acids appear without the enzymes to synthesize them? How could enzymes exist without nucleic acids to direct their synthesis? Origin of Living Systems RNA in some instances has catalytic activity (ribozymes). First enzymes could have been RNA. Earliest self-replicating molecules could have been RNA. Proteins are better catalysts and DNA is more stable and would eventually be selectively favored. Origin of Living Systems Protocells containing protein enzymes and DNA should have been selectively favored over those with only RNA. Before this stage, only environmental conditions and chemistry shaped biogenesis. After this stage, the system responds to natural selection and evolves. The system now meets the requirements for being the common ancestor of all living things. Origin of Living Systems Origin of metabolism in the earliest organisms: Probably primary heterotrophs. Derived nutrients from environment. Anaerobic bacterium-like. No need to synthesize own food. Chemical evolution had supplied an abundant supply of nutrients in the early oceans. Origin of Living Systems Over time, nutrient supply began to dwindle as the number of heterotrophs increased. At that point, a cell capable of converting inorganic precursors to a required nutrient (autotrophs) would have a selective advantage. The evolution of autotrophic organisms required gaining enzymes to catalyze conversion of inorganic molecules to more complex ones. Origin of Living Systems Appearance of Photosynthesis and Oxidative Metabolism: Early photosynthetic organisms probably used hydrogen sulfide or other hydrogen sources to reduce glucose. Later, autotrophs evolved that produced oxygen. Modern photosynthesis 6CO2 + 6H2O → C6H12O6 + 6O2 Ozone shield formed which restricted the amount of UV radiation reaching Earth’s surface. Land and surface waters could now be occupied. Origin of Living Systems As oxygen accumulated in the atmosphere, it reacted with water to form caustic substances like hydrogen peroxide. Many life forms could not handle the new environment and were ultimately replaced by those that could tolerate the new environment and eventually by those that could take advantage of the surplus of oxygen (eukaryotes). The Great Oxygen Event (GOE) Origin of Living Systems Atmosphere slowly changed from a reducing to a highly oxidizing one. Oxidative (aerobic) metabolism (more efficient) appeared using oxygen as the terminal acceptor and completely oxidizing glucose to carbon dioxide and water. Precambrian Life Pre-Cambrian Period covers time before Cambrian began nearly 600 million years ago. Precambrian Life Most major animal phyla appear within a few million years at the beginning of Cambrian Period: the “Cambrian explosion.” This likely represents the absence of fossilization rather than abrupt emergence. Precambrian Life Prokaryotes and the Age of Cyanobacteria Primitive characteristics of Prokaryotes: A single DNA molecule, lacking histones, not bound by nuclear membranes. No mitochondria, plastids, Golgi apparatus and endoplasmic reticulum. Cyanobacteria peaked one billion years ago Dominant for two-thirds of life’s history. Precambrian Life Appearance of the Eukaryotes Arose 1.5 billion years ago. Advanced Structures of Eukaryotes: Membrane bound nucleus. More DNA, and eukaryotic chromatin contains histones. Membrane-bound organelles in cytoplasm. Endosymbiotic Theory Lynn Margulis and others propose that eukaryotes resulted from a symbiotic relationship between two or more bacteria: Mitochondria and plastids contain their own DNA. Nuclear, plastid and mitochondrial ribosomal RNAs show distinct evolutionary lineages. Endosymbiotic Theory Plastid and mitochondrial ribosomal DNA are more closely related to bacterial DNA. Plastids are closest to cyanobacteria in structure and function. A host cell that could incorporate plastids or mitochondria with their enzymatic abilities would be at a great advantage. Endosymbiotic Theory Energy producing bacteria came to reside symbiotically inside larger cells. Eventually evolved into mitochondria. Photosynthetic bacteria came to reside symbiotically in cells. Eventually evolved into chloroplasts. Mitochondria & chloroplasts have own DNA (similar to bacterial DNA). Animation Origin of Eukaryotic Cells Many bacteria have infoldings of the outer membrane. These may have pinched off to form the nucleus and endoplasmic reticulum. Precambrian Life Heterotrophs that ate cyanobacteria provided ecological space for other types of organisms. Food chains of producers, herbivores and carnivores accompanied a burst of evolutionary activity that may have been permitted by atmospheric changes. The merging of disparate organisms to produce evolutionary novel forms is called symbiogenesis. Increasing Diversity – New Developments Photosynthesis – process where hydrogen atoms from water react with carbon dioxide to make sugars and oxygen. 6CO2 +6H2O C6H12O6 + 6O2 light Autotrophs make their own food using energy from the sun, carbon dioxide & water. Build-up of oxygen in the atmosphere allows evolution of other organsisms. Heterotrophs obtain their energy from the environment. Sexual reproduction – allows for frequent genetic recombination which generates variation. Multicellularity – fosters specialization of cells. Origins http://youtu.be/jTCoKlB0s4Y