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Unformatted text preview: CIVIL & ENVIRONMENTAL ENGINEERING 266
4 units, Fall Quarter, 2011
Lectures: Mon. & Wed. 12-1:50 PM
5419 Boelter Hall
Professor Shaily Mahendra
5732C Boelter Hall
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
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
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
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
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
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
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
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
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
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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This note was uploaded on 02/02/2012 for the course CEE 266 taught by Professor Shailymahendra during the Fall '11 term at UCLA.
- Fall '11