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01 intro macromolecules

01 intro macromolecules - CIVIL& ENVIRONMENTAL...

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Unformatted text preview: CIVIL & ENVIRONMENTAL ENGINEERING 266 ENVIRONMENTAL BIOTECHNOLOGY 4 units, Fall Quarter, 2011 Lectures: Mon. & Wed. 12-1:50 PM 5419 Boelter Hall Professor Shaily Mahendra 5732C Boelter Hall (310) 794-9850 E-mail: [email protected] Office Hours: M 2-3 PM, F 1-2 PM CEE 266 “Approximate” Schedule   Weeks 1-2: Microbiology Fundamentals   Weeks 3-4: Microbial Genetics   Weeks 5-6: Ecology & Biogeochemistry   Weeks 7-9: Engineering Applications   Week 10: Catch-up & Review Course Philosophy •  Challenging coursework and projects in the area of environmental biotechnology. •  ABET criteria including teamwork, effective communication, knowledge of contemporary issues, and recognition of the need for life-long learning. •  Open atmosphere where students are able to ask questions, share original ideas or relevant experiences, and critically evaluate their work and the work of others. Reference Textbooks   Environmental Biotechnology: Principles and Applications, Bruce E. Rittmann & Perry L. McCarty. 2001. McGraw Hill 1st Edition (TD192.5 .R58 2001).   Environmental Microbiology: From Genomes to Biogeochemistry, Eugene L. Madsen. 2008. Wiley-Blackwell (QR100 .M33 2008).   Brock Biology of Microorganisms, M. T. Madigan, J. M. Martinko, and J. Parker. 2009. Prentice Hall, N.J., 12th Edition (QR41.2 .M336 2009).   Molecular Biotechnology, B. R. Glick and J. J. Pasternak. 2010. ASM Press 4th Edition (TP248.2 .G58 2010).   Biological Wastewater Treatment, C. P. L. Grady, G. T. Daigger and H. C. Lim. 2011. Marcel Dekker, Inc., N.Y. 3rd Edition (TD755 .G72 2011).   Wastewater Engineering: Treatment, Disposal, Reuse, Metcalf and Eddy, 2003. McGraw-Hill Book Company, New York. Third Edition (TD645.W293 2003). More Reference Books   Principles of Biochemistry, A. L. Lehninger, D. L. Nelson, and M. M. Cox. 2008. Worth Publishers, New York, Fifth Edition (QD415 .L44 2008).   Fundamentals of Biochemistry, D. Voet, J. G. Voet, C. W. Pratt. (2008) Wiley, 3rd Edition (QD415 .V63 2008).   Modern Biotechnology: Connecting Innovations in Microbiology and Biochemistry to Engineering Fundamentals, N. Mosier and M. Ladisch. 2009. John Wiley (TP248.2 .M675 2009).   Microbial Ecology, Fundamentals and Applications, R. M. Atlas and R. Bartha, Benjamin/ Cummins Publishing Company, 4th Edition (QW 4 A881m 1998).   Prescott's Microbiology. Joanne Willey, Linda Sherwood, Chris Woolverton. 2011. McGraw Hill, 8th Edition. (QR41.2 .P74 2011). + journal articles on relevant topics provided as handouts or posted on course web. Grading Homeworks (4) 20% Midterm 25% Paper/Presentation 25% Final 30% Definitions Microbiology - study of microscopic organisms; medical, agricultural, industrial, environmental fields Environmental Engineering - physical, chemical, hydraulic, and biological principles applied to water supply, waste treatment, and environmental remediation Environmental Microbiology - interfaces between environmental sciences and microbial ecology; understanding of microbes and microbial processes in natural and engineered environmental systems Definitions (cont.)   Biotechnology - integrated use of biochemistry, molecular biology, genetics, and process engineering to obtain industrial goods and services   Environmental Biotechnology - application of microbes and microbial processes in natural and engineered environmental systems   Omics – umbrella term that encompasses bioinformatics-based systematic analysis of genes (genomics), mRNA (transcriptomics), proteins (proteomics) and metabolites (metabolomics) Microorganisms as Cells Cells as Machines and as Coding Devices (1) Cells can be considered machines that carry out chemical transformation   Enzymes: protein catalysts of this chemical machine; accelerate the rate of chemical reactions (2) Cells can also be considered coding devices that store and process information that is eventually passed on to offspring during reproduction through DNA (deoxyribonucleic acid) and evolution The Machine and Coding Functions of the Cell Figure 1.4 Microorganisms and Their Natural Environments   Diversity and abundances of microbes are controlled by resources (nutrients) and environmental conditions (e.g., temp, pH, O2)   The activities of microbial communities can affect the chemical and physical properties of their habitats Death Rates and the Leading Causes of Death in the U.S. Figure 1.8 The Impact of Microorganisms on Humans Figure 1.7 Macromolecules  Proteins: polymers of amino acids   Most abundant macromolecules in cells   Found throughout cell   Have important structural and enzymatic roles  Nucleic acids: polymers of nucleotides   Two forms (RNA and DNA)   [RNA]>>>[DNA] Macromolecules in the Cell Figure 3.3a Macromolecules in the Cell Figure 3.3b Macromolecules  Lipids   Polar compounds   Have both hydrophobic and hydrophilic properties   Play crucial roles as membrane backbones and as storage molecules  Polysaccharides   Polymers of sugar units bonded together by glycosidic bonds   Play important roles in cell walls and as storage molecules Macromolecules in the Cell Figure 3.3c Macromolecules in the Cell Figure 3.3d Polysaccharides  Carbohydrates (sugars)   Organic compounds that contain carbon, hydrogen, and oxygen at a ratio of 1:2:1   Most biologically relevant contain 4–7 carbon atoms   Pentoses (C5 sugars): structural backbones of nucleic acids   Hexoses (C6 sugars): monomeric constituents of cell wall polymers and energy reserves Polysaccharides  Polysaccharides can combine with other classes of macromolecules to form complex polysaccharides   Glycoproteins: polysaccharides + proteins   Glycolipids: polysaccharides + lipids   Cellular functions   Cell-surface receptor molecules; typically reside on external surfaces of the membrane   Glycolipids important in cell walls of gram-negative bacteria Lipids  Triglycerides and Complex Lipids   Simple lipids (fats, triglycerides): three fatty acids bonded to the C3 alcohol glycerol   Complex lipids: simple lipids that contain additional elements such as phosphorus, nitrogen, sulfur, or small hydrophilic organic compounds (e.g., sugars)   Phospholipids: complex lipids containing phosphate groups; play a major structural role in cytoplasmic membranes Simple Lipids Figure 3.7b Complex Lipids Figure 3.7c Complex Lipids Figure 3.7d Nucleotides Figure 3.8 Structure of the Nitrogen Bases of DNA and RNA Figure 3.9 Nucleic Acids   Nucleoside: nitrogen base bonded to its C5 sugar   Nucleotide: nitrogen base attached to C5 sugar by glycosidic linkage and bonded to a phosphate   Major components of nucleic acids   Key forms of chemical energy (e.g., ATP)   Carriers of sugars in biosynthesis of polysaccharides   Regulatory molecules for certain enzymes or metabolic events Components of the Important Nucleotide, ATP Figure 3.10 Nucleic Acids: DNA Figure 3.11ab Nucleic Acids: RNA Figure 3.11c Amino Acids and the Peptide Bond  Amino Acids   Most consist of carbon, hydrogen, oxygen, and nitrogen; 2 of 22 contain sulfur, 1 contains selenium   All contain two important functional groups   Carboxylic acid group (-COOH)   Amino group (-NH2)   Amino acid monomers held together by covalent bonds (peptide bonds) Peptide Bond Formation Figure 3.13 Proteins: Primary and Secondary Structure  Enzymes   Catalytic proteins; catalysts for chemical reactions  Structural Proteins   Integral parts of cellular structures   Primary Structure   Amino acid sequence Secondary Structure of Polypeptides Figure 3.15a Secondary Structure of Polypeptides Figure 3.15b Tertiary Structure of Polypeptides Figure 3.16 Quaternary Structure of Human Hemoglobin Figure 3.17 Denaturation of the Protein Ribonuclease Figure 3.18 The Cytoplasmic Membrane in Bacteria and Archaea   Cytoplasmic membrane: thin structure that surrounds the cell   6–8 nm thick   Vital barrier that separates cytoplasm from environment   Highly selective permeable barrier; enables concentration of specific metabolites and excretion of waste products Structure of a Phospholipid Bilayer Figure 4.4 Structure of the Cytoplasmic Membrane Figure 4.5 The Major Functions of the Cytoplasmic Membrane Figure 4.9 Transporters versus Diffusion Figure 4.10 The Three Classes of Membrane Transport Systems Figure 4.11 Structure of Membrane-Spanning Transporters Figure 4.12 Cell Walls of Gram-Positive Bacteria Figure 4.16a, c, and e Cell Walls of Gram-Negative Bacteria Figure 4.16b, d, and f Teichoic Acids and Structure of the Gram-Positive Cell Wall Figure 4.20 The Gram-Negative Cell Wall Figure 4.23a ...
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