MICROBIOLOGY METX 119-02 - Summer Session
Microbiology (METX 119-02)Course InformationMICROBIOLOGY METX 119-022019 Summer Session 2Class Number: 71121Location & TimesJack Baskin Engineering Room 165 (J Baskin Engr 165)Mondays and Wednesdays1:00 pm to 4:30 pmInstructorDr. Jiunn Nick FongE-mail: jiunn@ucsc.eduOffice HourDay: WednesdaysTime: 11:00 am to 12:00 noonOffice: Biomed 234Teaching AssistantMichael KempnichE-mail: mkempnic@ucsc.eduOffice HourDay: FridaysTime: 12:00 noon to 1:00 pmOffice: Thimann 365Discussion SectionDay: TuesdaysTime: 2:00 pm to 3:00 pmLocation: Jack Baskin Engineering Room 3721
Microbiology (METX 119-02)Course InformationCourse OverviewIn this course, students will be introduce to the microbial world and learn about the biologyof bacteria (and a little on archaea and viruses). These prokaryotes are (almost)everywhere: in the ocean, in the soil, on your skin and even inside your mouth, stomachand intestines. They make up the vast majority of the biomass on earth and are capableof growing under very diverse conditions. While most prokaryotes are beneficial to us andour environment, some bacteria cause diseases and epidemics.Learning ObjectivesAfter completing this course, students will understand the fundamental concepts inmicrobiology and be able to explain the biology of bacteria. Specifically, students will: Know the structure and function of the microbial cells. Understand fundamental concepts of microbial diversity, metabolism, physiology, andgenetics molecular biology. Be familiar with medical, industrial and environmental aspects of microbiology. Develop an understanding of the methods and the research tools used bymicrobiologist. Develop skills at designing experimental plans to test new hypotheses and interpretingnew data.Students will learn these concepts via lectures, readings, and participations in DiscussionSections. Students will also learn to design and critically evaluate experiments thatanswer questions about microbial biology.Course MaterialsRecommended textbooks: Prescott’s Microbiology (11th edition). Earlier editions of the book can also be used.Lecture materials for this course will mainly be based from this book. Readingassignments are meant to supplement the information presented in class.This book has some interesting online resources (via Connect), including adaptivereading using SmartBook. You can log onto Connect by typing in the online accesscode that comes with your book. SmartBook is designed to help students maximizetheir study time by blending LearnSmart (an intelligent adaptive study resource) withan interactive eBook.Several copies of Prescott’s Microbiology will be on reserve at the Science &Engineering Library. Todar’s Online Textbook of Bacteriology (http://textbookofbacteriology.net/). Thisis a free online book that describe an overview of some of the topics covered in thiscourse. Other microbiology text books, such as Brock Biology of Microorganisms,Microbial Life and Microbe also cover some topics taught in this course.2
Microbiology (METX 119-02)Course InformationCourse Structure Course Website (Canvas)The course website can be accessed through Canvas. It is important that you be ableto access the site to gain access to the lecture notes. It is a good idea to downloadthe lecture notes and additional materials onto a separate storage space (e.g. yourcomputer or online cloud), in case the site is down and inaccessible during criticaltimes (e.g. midterm and final). Lecture Notes and Print-outsPDF documents of the lecture slides will be posted on the course web site. You canuse them as a format for your own notes. Please note that in lecture slides wherethere are questions and answers, the answers may not be in the posted PDFdocuments. Please also be aware that new materials may be added during classes.The lecture notes are only a learning tool meant to supplement the lectures.Downloading and reading the lecture notes alone is NOT a good substitute for comingto classes. WebcastsWebcast is available at https://webcast.ucsc.edu/.Username: metx-119-1Password: microbesDiscussion SectionsAttendance is strongly encouraged. Generally, sections will focus on the week’s studyquestions and parts of lecture that students want to cover.Exams, Assignments and GradingThe final grade will be from:(1) Three assignments – 30% total (10% per assignment).(2) One Midterm exam – 30%.(3) One Final exam – 40%.Questions on the exams will come from material presented in the lectures. Pleaseremember to bring your ID. Assignments will contain materials related to the lectures.Materials and instructions for the assignments will be provided. Assignment 1 is due on Mon (8/5, by 1:30pm, J Baskin Engr 165).Assignment 2 is due on Mon (8/12, by 1:30 pm, J Baskin Engr 165).Assignment 3 is due on Fri (8/16, by 12:30 pm, Thimann Lab 365).Midterm exam is on Mon (8/12, 1:00 pm to 2:30 pm, J Baskin Engr 165) and coverslectures 1 to 9.Final exam is on Wed (8/28, 1:00 pm to 4:00 pm, J Baskin Engr 165) and coversall lecture materials.3
Microbiology (METX 119-02)Course InformationGrades will be determined according to a percentage scale:At or over 98%: A 87% - 89%:93% - 97%:A83% - 86%:90% - 92%:A- 79% - 82%:B 75% - 78%:B 66% - 74%:B- 62% - 65%:C CC-55% - 61%:Below 55%:DFPolicies Policy on make-upsExams (Midterms and Final). You must take both the Midterm and the Final Examin order to receive credit for this course. If you have to miss the midterm due to alegitimate reason (e.g. illness accompanied by medical doctor’s note, or familyemergency with documents), you must notify the instructor in advance of the examand will be assess on a case-by-case basis. Make-up Midterm will be given within oneweek of the scheduled exam. There will be NO make-up for the Final Exam. Policy on re-grades.If you would like to submit a graded question for a re-grade, please provide a writtenjustification (e.g. an e-mail) explaining why you should receive additional point within1 week after you get the exam or assignment back. We will review your request andadjust the grade if necessary. Policy on e-mail and chat room.Course content questions: The TA and instructor will not answer any course contentquestions via e-mail. If you have any questions related to the course content, pleaseask these questions (1) before, during, or after the lectures, (2) during discussionsections, (3) during office hours or (4) utilize the chat room feature on the coursewebsite. For Canvas chat, it is best if questions are answered by other students, andthis is a great way to make sure you know the answers. The teaching team will monitorthe site and provide corrections or additional supporting information if needed.Administrative questions: Any administrative issues should be addressed to theinstructor via e-mail or in-person. Academic integrityBy enrolling in the university, students are automatically agreeing to abide by itspolicies, including those on academic misconduct. Plagiarism and cheating are veryserious academic offenses. Penalties include a failing grade in the course, and/orsuspension or expulsion from the university. Students are expected to followuniversity's Rules of Conduct regarding student conduct and conduct/).4
Microbiology (METX 119-02)Course InformationPrerequisites and needed knowledgeBIOL 100 or BIOC 100A.A solid understanding of biochemistry as gained through upper division Biochemistry(UCSC BIOL100, BIOC100A or CHEM103) and molecular biology as gained throughcollege-level molecular biology (UCSC BIO20A or BIO101). You will need to know thefollowing: (i) Protein and nucleic acid composition/structure; (ii) Glycolysis and the TCAcycle; (iii) Transcription and Translation.Disabilities statementUC Santa Cruz is committed to creating an academic environment that supports itsdiverse student body. If you are a student with a disability who requires accommodationsto achieve equal access in this course, please submit your Accommodation AuthorizationLetter from the Disability Resource Center (DRC) to the instructor privately before/afterlectures, during office hours, or by appointment, within the first week of the course. At thattime, we can also discuss ways to ensure your full participation in the course. I encourageall students who may benefit from learning more about DRC services to contact DRC byphone at 831-459-2089 or by email at drc@ucsc.edu.Diversity and inclusion statementThe teaching team strives to create a learning environment for students that supports adiversity of thoughts, perspectives and experiences, and honors your identities (includingrace, gender, class, sexuality, religion, ability, etc.). To help accomplish this, please letthe teaching team know if you have a name and/or set of pronouns that you prefer and/ordiffer from those that appear in your official records. Feedback is always welcome toimprove the quality of the course, particularly if something was said or done in class (byanyone) that made you feel uncomfortable. Feedback can be anonymous. As aparticipant in course discussions, you should also strive to honor the diversity of yourclassmates.5
Microbiology (METX 119-02)WeekDayMonDate Lecture7/291Wed 7/31Mon8/52WedMon8/78/123Wed 8/14FriMon8/168/194Wed 8/21Mon58/26Wed 8/28SyllabusSubject1Introduction to Microbiology and Phylogeny2Prokaryotic Cell Biology I: Structures and Functions I3Prokaryotic Cell Biology II: Structures and Functions II4Microbial Physiology I: Nutrients & Growth I5Microbial Physiology II: Nutrients & Growth II6Microbial Physiology III: Metabolism I-Assignment 1 due (by 1:30 pm, J Baskin Engr 165)7Microbial Physiology IV: Metabolism II8Microbial Physiology V: Biofilms9Microbial Physiology VI: Microbial Ecology10Molecular Biology I: DNA Replication11Molecular Biology II: Transcription12Molecular Biology III: Translation and Protein Secretion-Midterm – 1:00 pm to 2:30 pm (Covers Lectures 1 to 9)-Assignment 2 due (by 1:30 pm, J Baskin Engr 165)13Molecular Genetics I: Horizontal Gene Transfer14Molecular Genetics II: DNA Mutations15Molecular Biology IV: Operons and Regulons16Molecular Biology V: Regulation of Gene Expression17Molecular Biology VI: Antibiotics and Antibiotic Resistance-Assignment 3 due (by 12:30 pm, Thimann Lab 365)18Molecular Biology VII: Viruses19Human Microbe Interactions I : Pathogenesis20Human Microbe Interactions II : Vibrio cholerae21Human Microbe Interactions III : Pseudomonasaeruginosa22Human Microbe Interactions IV : Legionella pneumophila23Human Microbe Interactions V : Salmonella24Human Microbe Interactions: Human Microbiota-Final Exam (Covers ALL Lecture Materials)Time: 1:00 pm to 4:00 pm6
Microbiology (METX 119-02)LectureSubjectAdditional ReadingPrescott’s Microbiology9th edition10th edition11th edition1Introduction toMicrobiology andPhylogenyCh. 1 – The evolution of microorganisms and microbiology.Ch. 19 – Microbial taxonomy and the evolution of diversity.2Prokaryotic Cell Biology I:Structure and Function ICh. 3 – Bacterial cell structure, up to 3.5 (Capsules, slime layers and S-layers).3Prokaryotic Cell Biology II:Structure and Function IICh. 3 – 3.6 (Bacterial Cytoskeleton), 3.7 & 3.8 (Flagella and flagellar movement).4Microbial Physiology I & II:Nutrients & Growth ICh. 7.5 – Culture media.Microbial Physiology I & II:Nutrients & Growth IICh. 7 – Binary Fission, Cell Cycles, Growth Curves & Measurements.Ch. 14.5 – Chemotaxis in E. coli.Ch. 14.6 – Chemotaxis in E. coli.Ch. 3.3 – Nutrient uptake, Types of nutrient transport systems.56Microbial Physiology III &IV: Metabolism ICh. 7.6 – Culture media.Ch. 7.7 – Culture media.Ch. 11.1 – Nutrient types.Ch. 10 – 10.1 (Metabolism), 10.2 (ATP), 10.3 (Redox reactions), 10.4 (Electron transport chain).Ch. 11 – 11.3 (Aerobic respiration), 11.4 (Glycolytic pathways), 11.5 (TCA cycle), 11.6 (Electrontransport chain).Ch. 11.11 – Phototrophy & photophosphorylationCh. 11.12 – Phototrophy &photophosphorylation7Microbial Physiology III &IV: Metabolism IICh. 11 – 11.2 (Chemoorganotrophy), 11.7 (Anaerobic respiration), 11.8 (Fermentation), 11.9(Catabolism of organic molecules).8Microbial Physiology V:BiofilmsCh. 7 – 7.3 (Environmentalfactors on microbial growth), 7.4(Biofilm).Ch. 7 – 7.4 (Environmentalfactors on microbial growth), 7.5(Biofilm).Microbial Physiology VI:Microbial EcologyCh. 18.8 – Metagenomics.Ch. 18.3 – Metagenomics.910Molecular Biology I: DNAReplicationCh.13 – 13.2 (Nucleic acid structure), 13.3 (DNA replication).11Molecular Biology II:TranscriptionCh. 13 – 13.4 (Bacterial genes), 13.5 (Transcription).Ch. 29 – 29.1 & 29.2 (Methods used in microbial ecology).Ch. 31.3 – Microbe-plant interaction, Nitrogen-fixing bacteria.Ch. 7 – 7.5 (Environmentalfactors on microbial growth), 7.6(Biofilm).
Microbiology (METX 119-02)Syllabus12Molecular Biology III:Translation and ProteinSecretionCh. 13 – 13.6 (The genetic code), 13.7 (Translation), 13.8 (Protein maturation & secretion).13Molecular Genetics I:Horizontal Gene TransferCh. 16 – 16.4 (Genetic variability), 16.5 (Transposable elements), 16.6 (Conjugation), 16.7(Transformation), 16.8 (Transduction).14Molecular Genetics II:DNA MutationsCh. 16 – 16.1 (Mutations), 16.2 (Detection and isolation of mutants), 16.3 (DNA repair).15Molecular Biology IV:Operons and RegulonsCh. 14 – 14.1 (Regulation of gene expressions), 14.2 (Transcriptional regulations of lactose &tryptophan operons), 14.3 & 14.4 (Attenuation & riboswitches), 14.5 (Catabolite repression).16Molecular Biology V:Regulation of GeneExpressionCh. 14.5 – Regulation of cellularprocesses, two-componentsystems, stringent response,quorum sensing),Ch. 14.5 – Mechanisms of global regulation (two-componentsystems, stringent response, quorum sensing).Ch. 18.4 – Functional genomics(DNA microarray).Ch. 18.5 – Functional genomics (DNA microarray & RNAseq).17Molecular Biology VI:Antibiotics and AntibioticResistanceCh. 9 Antibiotic resistance – 9.1 (Development of chemotherapy), 9.2 (General characteristics ofantimicrobial drugs), 9.3 (Dilution susceptibility and Disk diffusion tests), 9.4 (Antibacterial drugs).18Molecular Biology VII:VirusesCh. 6 Viruses – 6.1 (Viruses), 6.2 (Virion structure), 6.3 (Viral multiplication), 6.4 (Types of viralinfections), 6.5 (Cultivation and enumeration of viruses), 6.6 & 6.7 (Viroids, satellites, prions).Ch.35 – 35.1 Pathogenicity and infections), 35.2 (Virulence), 35.3(Exposure and transmission).Ch.35 – 35.1 (Pathogenicity andinfections), 35.2 (Exposure andtransmission).Ch. 37 – 37.1 (Epidemiology),37.4 (Patterns of infectiousdisease), 37.5 (Emerging andreemerging infectious diseases).Ch. 37 – 37.1 (Epidemiology),37.3 (Patterns of infectiousdisease), 37.4 (Emerging andreemerging infectious diseases).Ch. 36 – 36.1 (Epidemiology),36.3 (Patterns of infectiousdisease), 36.4 (Emerging andreemerging infectious diseases).19Human MicrobeInteractions I:Pathogenesis20Human MicrobeInteractions II: VibriocholeraeCh. 22.3 – Vibrio (p529).Ch. 39.4 – Cholera (p918 –920).Ch. 22.3 – Vibrio (p526).Ch. 39.4 – Cholera (p889 –890).Ch. 22.3 – Vibrio (p525).Ch. 39.4 – Cholera (p886 –887).21Human MicrobeInteractions III:Pseudomonas aeruginosaCh. 22.3 – Pseudomonas (p527– 528).Ch. 35.2 – P. aeruginosa biofilm(p799).Ch. 22.3 – Pseudomonas(p524).Ch. 35.2 – P. aeruginosa biofilm(p779).Ch. 22.3 – Pseudomonas(p523).Ch. 35.3 – P. aeruginosa biofilm(p779 – 780).8
Microbiology (METX 119-02)SyllabusHuman MicrobeInteractions IV: LegionellapneumophilaCh. 22.3 – Legionella (p.526).Ch. 39.1 – Legionnaires’ disease(p889-891).Ch. 22.3 – Legionella (p.522523).Ch. 39.1 – Legionnaires’ disease(p860-862).Ch. 22.3 – Legionella (p.521522).Ch. 39.1 – Legionnaires’ disease(p858-859).23Human MicrobeInteractions V: SalmonellaCh. 22.3 – Salmonella (p530 –532).Ch. 35.2 – Pathogenicity islands(p794).Ch. 39.4 – Salmonellosis (p922923).Ch. 22.3 – Salmonella (p527 –529).Ch. 35.2 – Pathogenicity islands(p774).Ch. 39.4 – Salmonellosis (p892893).Ch. 22.3 – Salmonella (p525 –527).Ch. 35.4 – Pathogenicity islands(p780 – 781).Ch. 39.4 – Salmonellosis (p889).24Human MicrobeInteractions IV: HumanMicrobiotaCh. 32.2 & 32.3 – Humanmicrobiome.Ch. 32.2 & 32.3 – Humanmicrobiome.Ch. 34 – Human microbiome.229
Prescott’s Microbiology (11th edition). Earlier editions of the book can also be used. Lecture materials for this course will mainly be based from this book. Reading assignments are meant to supplement the information presented in clas
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