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Chapter One Chemistry Is the Logic of Biological Phenomena 1.1 Distinctive Properties of Living Systems 1.2 Biomolecules: The Molecules of Life 1.3 A Biomolecular Hierarchy: Simple Molecules Are the Units for Building Complex Structures 1.4 Properties of Biomolecules Reflect Their Fitness to the Living Condition 1.5 Organization and Structure of Cells 1.6 Viruses Are Supramolecular Assemblies Acting as Cell Parasites 1.1 Distinctive Properties of Living Systems Complicated and highly organized The Orion Nebula, a tremendous cloud of gas in which many hot, young stars are evolving rapidly toward cataclysmic cosmic explosions called supernovea. Energy released by nuclear explosions in such supernovea brought about the fusion of simple atomic nuclei, forming the more complex elements of which the earth, its atmosphere, and all living things are composed. • (a) Mandrill (b) Tropical orchid (Mandrillus sphinx), a (Bulbophyllum blumei), baboon native to West New Guinea. Africa. Some characteristic of living matter. Kaleidoscopes of life Biological structures serve functional purposes. Microscopic complexity and organization are apparent in this colorized thin section Living systems are actively engaged in energy transformations Food pyramid Carnivores, Herbivores, Photosynthesis A prairie falcon acquires nutrients by consuming a smaller bird. ATP and NADPH, two biochemically important energy-rich compounds. Living systems have a remarkable capacity for self- Living systems have a remarkable capacity for self-replication. replication. Biological reproduction occurs with near- perfect fidelity (zebra). The DNA double helix. Two complementary polynucleotide chains running in opposite directions can pair through hydrogen bonding between their nitrogenous bases. Their complementary nucleotide sequences give rise to structural complementarity. 1.2 Biomolecules: The Molecules of Life The chemical composition of living material, such as this jellyfish(水母), differs from that of its physical environment, which for this organism is salt water. The elemental composition of living matter differs markedly from the relative abundance of elements in the earth’s. Hydrogen, oxygen, carbon, and nitrogen constitute more than 99% of the atoms in the human body, with most of the H and O occurring as H2O. Elements essential to animal life and health 水母 Biomolecules Are Carbon Compounds Aliphatic(脂肪族的, 脂肪质的) Metabolites and Macromolecules The major precursors for the formation of biomolecules are water, carbon dioxide, and three inorganic nitrogen compounds—ammonium (NH4+), nitrate (NO3-), and dinitrogen (N2). Metabolic processes assimilate and transform these inorganic precursors through ever more complex levels of biomolecular order. Some functional groups of biomolecules 1.3 · A Biomolecular Hierarchy: Simple Molecules Are the Units for Building Complex Structures Macromolecules are composed of building blocks Proteins----amino acids Nucleic acids----nucleotides Polysaccharides----sugars Lipids----fatty acids, glycerol and choline etc. Prebiotic Evolution The finding that all biological macromolecules in all organism are made from the same three dozen subunits has provided strong evidence that modern organism are descended from a single primordial cell line whose fundamental chemistry would be recognizable even today. Biomolecules first arose by chemical evolution Aleksandr I Oparin’s theory: Electrical energy from lightning discharges or heat energy from volcanoes cause ammonia, methane , water vapor, and other compounds of the primitive atmosphere to react, forming simple organic compounds. These compounds then dissolved in the ancient seas, which over many millenia became enriched with a large variety of simple organic substances. In the warm solution(the “primordial soup”), some organic molecules had a greater tendency than others to associate into larger complexes. Over millions of years, these in turn assembled spontaneously to form membranes and catalysts (enzyme), which came together to become precursors of earliest cells. Chemical evolution can be simulated in the laboratory. A spark-discharge apparatus RNA or related precursors may have been the first genes and catalysts In modern organism, nucleic acids encode the genetic information that specifies the structure of enzymes, and enzymes have the ability to catalyze the replication and repair of nucleic acids, the mutual dependence of two classes of biomolecules bring up the perplexing question: which came first, DAN or proteins? which came first, DAN or proteins? The answer may be: neither. The discover that RNA molecules can act as catalysts in their own formation suggests that RNA or similar molecules may have been the first gene and the first catalyst. One possible “RNA world” scenario, showing the transition from the prebiotic RNA world(shades of yellow) to the biotic DNA world (orange). The “RNA world” hypothesis is plausible but by no means universally accepted. The hypothesis does make testable prediction, and to the extent that experimental tests are possible within finite time, the hypothesis will be tested and refined. Biological evolution began more than three and half billion years ago. Ancient reefs in Australia contain fossil evidence of microbial life in the sea of 3.5 billion years ago. Bits of sand and limestone became trapped in the sticky extracellular coats of cyanobacteria, gradually building up these stromatolites(岩层)found in Hamelin Bay, Western Australia. Microscopic examination of sections of such ancient rock reveals microfossils of filamentous becteria(b), interpreted as shown in the drawing(b). 1.4 · Properties of Biomolecules Reflect Their Fitness to the Living Condition Biological Macromolecules and Their Building Blocks Have a “Sense” or Directionality The macromolecules of cells are built of units— amino acids in proteins, nucleotides in nucleic acids, and carbohydrates in polysaccharides—that have structural polarity. That is, these molecules are not symmetrical, and so they can be thought of as having a “head” and a “tail.” Polymerization of these units to form macromolecules occurs by head-to-tail linear connections. Because of this, the polymer also has a head and a tail, and hence, the macromolecule has a “sense” or direction to its structure. Biological Macromolecules Are Informational Biological Macromolecules Are Informational Biological Macromolecules Are Informational Biomolecules Have Characteristic Three- Dimensional Architecture IgG, Immunoglobulin G is a major type of G( circulating antibody. Each of the spheres represents an atom in the structure. Weak Forces Maintain Biological Structure and Determine Biomolecular Interactions Covalent bonds hold atoms together so that molecules are formed. In contrast, weak chemical forces or noncovalent bonds, (hydrogen bonds, van der Waals forces, ionic interactions, and hydrophobic interactions) are intramolecular or intermolecular attractions between atoms. Hydrogen bonds, Van der Waals forces, Ionic interactions, Hydrophobic interactions Structural Complementarity Determines Biomolecular Interactions This principle of structural complementarity is the very essence of biomolecular recognition. Structural complementarity is the significant clue to understanding the functional properties of biological systems. Biological systems from the macromolecular level to the cellular level operate via specific molecular recognition mechanisms based on structural complementarity: a protein recognizes its specific metabolite, a strand of DNA recognizes its complementary strand, sperm recognize an egg. All these interactions involve structural complementarity between molecules. Biomolecular Recognition Is Mediated by Weak Chemical Forces Weak Forces Restrict Organisms to a Narrow Range of Environmental Conditions---The central role of weak forces in biomolecular interactions restricts living systems to a narrow range of physical conditions. Enzymes The sensitivity of cellular constituents to environmental extremes places another constraint on the reactions of metabolism. Metabolic Regulation Is Achieved by Controlling the Activity of Enzymes Thousands of reactions mediated by an equal number of enzymes are occurring at any given instant within the cell. Metabolism has many branch points, cycles, and interconnections. This metabolic regulation is achieved through controls on enzyme activity so that the rates of cellular reactions are appropriate to cellular requirements. A glance at a metabolic pathway map 1.5 · Organization and Structure of Cells prokaryotic eukaryotic All living cells fall into one of two broad categories—prokaryotic and eukaryotic. The distinction is based on whether or not the cell has a nucleus. Prokaryotes are single-celled organisms that lack nuclei and other organelles; the word is derived from pro meaning “prior to” and karyot meaning “nucleus.” Eukaryotic cells have true nuclei and other organelles such as mitochondria, with the prefix eu meaning “true.” Structural Organization of Prokaryotic Cells A dividing Escherichia coli (E. coli ) cell Dividing Saccharomyces cerevisiae (baker’s yeast ) cell Structural Organization of eukaryotic Cells Nuclear pores Nuclear pores nucleus chromosome Structure of a mitochondrion Structure of a chloroplast Portion of a skeletal muscle cell(artificial color) Collenchyma （厚 角组织）cells of a plant stem Human sperm cells (artificial color) Mature human erythrocytes (artificial color) Human embryo at the two-celled stage cells 1.6 · Viruses Are Supramolecular Assemblies Acting as Cell Parasites Virus Virions, nonliving particles(outside of the host cells) Bacteriophages, simply phages, specific for the becteria. HIV SARS :Coronavirus (a) a bacterial virus, bacteriophage T4; (b) an animal virus, adenovirus (inset at greater magnification); (c) a plant virus, tobacco mosaic virus. New Words Review Orion Nebula Prebiotic Prior Cataclysmic Primitive Erythrocytes Kaleidoscopes Apparatus Virus Carnivore Virion Herbivore Perplexing Phenomena Prairie Hypothesis Reflect Fidelity Plausible Properties Material Microbial Assembly Elemental Covalent Fitness Ammonium Complicated Metabolite Parasite Tremendous Hierarchy instant Atmosphere Complementarity Scenario Complement Microbial Leukocyte Complementary Stromatolites Erythrocytes Composition Filamentous Embryo Glycerol Reveal Bacteriophage Polysaccharides Directionality Tobacco mosaic virus Nucleotide Polarity Amino acids Carbohydrates Spontaneously Symmetrical Catalyst Architecture Precursor Immunoglobulin simulated Sphere The End of Chapter 1 Topics of Discussion 1 What Are Distinctive Properties of Living System? 2 How Many Types of the Important Biomacromolecules? 3 What Are Features of Biomolecules? 4 Talk About the Organization and Structure of Cells.
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