General Microbiology (BIOM 360) Autumn Semester, 2017

Meeting time: 1:00 - 1:50 MWF Meeting place: HS 207 Instructor: Dr. Michael F. Minnick Office hours: Open-door policy: drop in whenever you like Office location: HS 509 Phone: 406-243-5972 E-mail: [email protected]

Text: Brock Biology of Microorganisms, 15th ed. Madigan et al., 2017.

Performance- 502 points are possible from three 100-point exams, a 130-point final (100 points comprehensive + 30 points from last 3 lectures), 56 points from 28 daily quizzes covering previous lecture’s material (one point for participation + one point for each correct answer) plus 16 bonus points from optional current event questions on each exam. The final exam covers material included in previous tests. Make-up exams will only be available for excused and documented absences. Quizzes cannot be made up. Performance will be evaluated by a classical grading system of: A (90-100%); B (80-89%); C (70-79%); D (60-69%); F (<60%) based on a curving comparing you against your peers.

Preparation- Reading assigned materials in advance and attending class is essential, as lecture notes, lecture slides, current events and class discussions are the sources of quiz and test questions. Chemistry (CHMY 123N or 143N) is a prerequisite for this course. Cell and Molecular Biology (BIOB 260) is a prerequisites or co-requisite. If you have not taken these courses you must obtain instructor approval.

Resources- TopHat- will be used by students to follow the lecture in real time from any portable device, take their daily quizzes, keep track of quiz grades and to access lecture materials. To enroll, see: https://tophat.com/. Moodle- will also be available to download all course materials.

Accommodations to ensure accessibility of students with disabilities will be gladly made, but to qualify you must be registered with Disability Services for Students (DSS). Arrangements for accommodations on exams must be made in advance by the student.

Academic misconduct will be reported and handled as described in UM’s Student Conduct Code. All students must practice academic honesty. Academic misconduct is subject to an academic penalty by the course instructor and/or a disciplinary sanction by the University. All students need to be familiar with the UM Student Conduct Code. The Code is available online at: http://www.umt.edu/vpesa/Dean%20of%20Students/default.php

Dropping course or changing the grading status will strictly follow UM policies and procedures, which are described in the catalog. Students cannot change to an audit after the 15th day of instruction. In addition, dropping the course or changing the grading status (to CR/NCR) are not automatically approved after the 30th day of the semester. These may be requested by petition, but the petition must be accompanied by documentation of extenuating circumstances. Requests to drop or change grading status to benefit a student's GPA will not be approved. COURSE SCHEDULE- (tentative, flexible and highly optimistic): Date Chapt. Quiz Topic(s) F Sep 01 Introduction and Expectations M Sep 04 HOLIDAY W Sep 06 1 - Microorganisms and Microbiology F Sep 08 1 - Microorganisms and Microbiology M Sep 11 2 - Microbial Cell Structure and Function W Sep 13 2 1 Microbial Cell Structure and Function F Sep 15 2 2 Microbial Cell Structure and Function M Sep 18 3 3 Microbial Metabolism W Sep 20 3 4 Microbial Metabolism F Sep 22 3 5 Microbial Metabolism M Sep 25 5 6 Microbial Growth and its Control W Sep 27 5, 7 7 Microbial Growth and its Control F Sep 29 5, 7 8 Microbial Growth and its Control M Oct 02 EXAM 1 W Oct 04 4 - Molecular Information Flow F Oct 06 4 9 Molecular Information Flow M Oct 09 4 10 Molecular Information Flow W Oct 11 6 11 Microbial Regulatory Systems F Oct 13 6 12 Microbial Regulatory Systems M Oct 16 6 13 Microbial Regulatory Systems W Oct 18 11 14 Genetics of Bacteria and Archaea F Oct 20 11 15 Genetics of Bacteria and Archaea M Oct 23 9 16 Microbial Systems Biology / Genomics W Oct 25 9 17 Microbial Systems Biology / Genomics F Oct 27 13 18 Microbial Evolution and Systematics M Oct 30 EXAM 2 W Nov 01 13 - Microbial Evolution and Systematics F Nov 03 15, 16 19 Diversity of Bacteria M Nov 06 15, 16 20 Diversity of Bacteria W Nov 08 14, 16 21 Diversity of Bacteria F Nov 10 HOLIDAY M Nov 13 17 - Diversity of Archaea W Nov 15 17 22 Diversity of Archaea F Nov 17 18 23 Diversity of Eukaryotic Microbes M Nov 20 18 24 Diversity of Eukaryotic Microbes W Nov 22 HOLIDAY F Nov 24 HOLIDAY M Nov 27 8, 10 - Virology W Nov 29 8, 10 25 Virology F Dec 01 20, 21 26 Microbial Ecosystems & Nutrient Cycling M Dec 04 EXAM 3 W Dec 06 24 - Microbial Symbioses with Humans F Dec 08 26, 27 27 Immunology M Dec 11 26, 27 28 Immunology R Dec 14 FINAL EXAM, 1:10-3:10 pm Learning outcomes-

TOPICS LEARNING OUTCOMES Introduction -professor and student introductions (1 lecture) -familiarize students with course expectations, assessment tools, grading and learning resources -utilize pop quiz as a springboard for discussion Microorganisms and Microbiology -Review cell structure / function (2 lectures) -Learn key differences between prokarya and eukarya -Introduction to basic phylogeny and the dominance of unicellular life-forms -Become familiar with the main contributors to microbiology over the course of history Microbial Cell Structure and Function -Learn essentials of microbial cell structure (3 lectures) / function:  Morphologies  Why are prokaryotes small?  The unit membrane and transport  The cell wall and its chemistry  Microbial structures- spores, inclusions, etc.  Locomotion Microbial Metabolism -become familiar with nutrients and their (3 lectures) roles -learn basic types of growth media -learn about bioenergetics, catalysis, redox -learn catabolism with a focus on glycolysis, TCA cycle and electron transport system -become familiar with metabolic diversity Microbial Growth and its Control -Learn how bacteria grow- (3 lectures)  binary fission  growth cycle  physical parameters affecting growth  osmolarity, oxygen need and pH Molecular Information Flow -Learn how genes are arranged (3 lectures) -Flow of information -Learn Chromosomal architecture -Understand translation Microbial Regulatory Systems -Learn basic feedback mechanisms (3 lectures) -Repression versus induction -learn how bacteria and archaea regulate expression of genes:  arg operon  lac operon  Catabolite repression  Nitrogen assimilation in archaea Learn global response mechanisms:  Stringent response  Attenuators  2-component regulators  Quorum sensing Genetics of Bacteria and Archaea -Learn basic terminology (2 lectures) -learn about mutations -understand recombination -Learn lateral gene transfer mechanisms: transformation, transduction, conjugation -mobile elements and plasmids -Learn about restriction modification and CRISPR-Cas Microbial Systems Biology / Genomics -Survey the diversity of prokaryotic (2 lectures) genomes -understand why there is a range in size -understand gene content as a function of organism’s lifestyle -learn about genomes of organelles Microbial Evolution and Systematics -Appreciate the evolutionary timescale (2 lectures) -Understand early-earth physiology -Learn about the appearance of O2 -Learn microbial phylogeny -Understand concepts of species / speciation Diversity- Bacteria, Archaea and --Survey / learn diversity of bacteria- Eukaryotic Microbes natural history and physiological (7 lectures) adaptations --Survey / learn diversity of archaea- natural history and physiological adaptations --Survey / learn diversity of eukaryotic microbes- natural history and physiological adaptations Virology -Learn basic virological terms (2 lectures) -Understand the virus “life”cycle -Learn different strategies of replication based upon genome content -Learn the different outcomes of a virus infection Microbial Ecosystems & Nutrient -Learn about ecosystems Cycling -Appreciate carbon and nitrogen cycling (1 lecture) -Appreciate the role of microbes in these processes -Discuss community structure and how microbes interact with other members The Human Ecosystem and -Learn about symbiosis Immunology -Survey human microbial communities in (3 lectures) various body systems -Learn about innate immune response of the human host -Discover what makes a bacterium pathogenic -Learn about the adaptive immune response