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MBIO 3401 - 001 Principles of Microbiology Fall 2019 Faculty information Name: Amanda Brown Office: Biology 312 Tel: 806-834-0984 (office) Office hour: Tues 3:40-5:30 pm E-mail: [email protected] (preferred communication) Course information/Materials Pre-requisites: BIOL 1401 and BIOL 1402 or BIOL 1403 and 1404; successful completion or concurrent enrollment in Organic Chemistry I (CHEM 3305). Lecture location/time: Biology 101; Monday, Wednesday, Friday: 9:00-9:50 am Lab location/time: Biology 3rd Floor. Room & Time by section number (see MBIO 3401 Lab Schedule). Required Materials: 1. Textbook (Microbiology: An Evolving Science, Fourth Edition, by Joan Slonczewski and John Foster. ISBN: 978-0393614039. 2017) 2. TurningPoint app or Clicker https://www.turningtechnologies.com/clickers/ 3. Lab manual, Lab coat, Lab goggles (Please purchase on 3rd floor from Mon. Aug. 26th through Thu. Aug 29th, 9 am – 4 pm and 5:30 pm – 6:30 pm; and Tue. Sep. 3, 9 am – 4 pm and 5:30 pm - 6:30 pm; and Wed. Sep. 4, 9 am – 2 pm) Course description Microbiology is an exceptionally broad and vibrant discipline. This course will provide a balanced introduction to all major groups of microorganisms including viruses, bacteria, archaea, fungi, and protozoa. We will discuss the structure, metabolism, genetics, pathogenesis, and ecology of microbes. This course is intended for all biology major students, especially those preparing careers in life sciences (teaching/research), medicine, dentistry, nursing, and food/pharmaceutical industry. It also serves as a foundation for upper level courses including Pathogenic Microbiology, Bacterial Genetics, Microbiomes, Molecular Pathogenesis of Protozoans, Virology, Immunology, Microbialand Bacterial Physiology. Expected learning outcomes This course covers multiple aspects of microbiology. Upon completion of this class, students are expected to have a clear understanding of the impact microorganisms have in virtually all aspects of our daily lives (environment, medicine, agriculture, and industry). Specifically, students should: 1) gain sufficient knowledge on the morphology and physiology of microbes, their roles in diseases, and their interactions with other organisms in the environment; 2) learn to identify certain groups of microorganisms and 3) critically reflect on topics pertinent to microbes. Methods of learning outcome assessment besides exams o Evaluation of the course at the local, departmental, and university levels; collect study focus group reports on curriculum and facilities that pertain to microbiology; collect results for senior questionnaires and exit exams.

o Evaluation of students’ lab performance. For example, students need to identify unknown bacteria and prepare a lab report, which requires the use of techniques and knowledge from the class and lab practice. We will also evaluate lab notebooks which should reflect students’ understanding of procedures and concepts, and document their activities and progress. o Documentation of students’ development towards careers related to microbiology (graduate school, medical/dental school, pharmacy, nursing, biotech industry, etc). Classroom Policies § Civility in the classroom: Students are expected to assist in maintaining a classroom environment that is conducive to learning. Do not arrive late, talk while others are speaking, text, play video games or engage in any other behavior that can distract or disrupt either the professor, your TA or your fellow classmates. Violators may be asked to leave the classroom but will remain responsible for all material missed. § Lectures may not be recorded and slides should not be photographed during lecture. Copies of lecture slides will be available online for course use only. § Students are expected to attend class consistently and on time. Absence or tardiness may substantially lower your exam grades due to missing crucial information, lecture notes, or discussions. A score of 0 on at least 2 exams or 80%, they may use that grade for this course if they provide documentation of their final lab grade. For this documentation, they may have their TA or previous instructor send the grades. If this is not given as a percentage, students will receive a 90 for an “A” or an 80 for a “B”. The necessary supporting information must be provided to the instructor prior to the start of labs. There are two tracks of grading: Track 1: Default track

Track 2: Students scoring ≥90% in all three in-semester exams after factoring in curves and TurningPoint credit

Exam 1 Exam 2 Exam 3 Final Exam Lab grade Total 100%

Exam 1 25% Exam 2 25% Exam 3 25% No Final Exam Necessary Lab grade 25% Total 100%

15% 15% 15% 30% 25%

Grading scale 98-100 A+ 92-97 A 90-91 A88-89 82-87 80-81

B+ B B-

78-79 70-77 60-69 0-59

C+ C D F

Academic Integrity o Academic Misconduct: It is the aim of the faculty of Texas Tech University to foster a spirit of complete honesty and a high standard of integrity. The attempt of students to present any work as their own that they have not honestly performed is regarded by the faculty and administration as a serious offense and renders the offenders liable to serious consequences, possibly suspension. o Descriptions of Cheating and Plagiarism can be found in https://www.depts.ttu.edu/studentconduct/academicinteg.php o We have a zero-tolerance policy for cheating and plagiarism in any form. Such misconduct will result in severe punishment including (but not limited to) failing exams and/or the entire course! Disabilities Any student who, because of a disability, may require special arrangements in order to meet course requirements should contact the instructor as soon as possible to make any necessary arrangements. Students should present appropriate verification from Student Disability Services (http://www.depts.ttu.edu/students/sds/) during the instructor’s office hours. Please note instructors are not allowed to provide classroom accommodations to a student until appropriate verification from Student Disability Services has been provided. For additional information, you may contact the Student Disability Services office at 335 West Hall or 806-742-2405.

Tentative Class Schedule Date Mon Wed Fri Mon Wed Fri Mon Wed Fri Mon Wed Fri Mon Wed Fri Mon Wed Fri Mon Wed Fri Mon Wed Fri Mon Wed Fri Mon Wed Fri Mon Wed Fri Mon Wed Fri Mon Wed Fri Mon Wed Fri Mon Wed

8/26 8/28 8/30 9/2 9/4 9/6 9/9 9/11 9/13 9/16 9/18 9/20 9/23 9/25 9/27 9/30 10/2 10/4 10/7 10/9 10/11 10/14 10/16 10/18 10/21 10/23 10/25 10/28 10/30 11/1 11/4 11/6 11/8 11/11 11/13 11/15 11/18 11/20 11/22 11/25 11/27 11/29 12/2 12/4

Topic Chapter Course Introduction; Entrance Quiz Microbial life 1 Microscopy 2 No class (Labor Day) Bacterial Culture and Growth 4 Environmental Limitations on Microbes 5 Microbial Control 5 Bacterial Cell Structure/Function I 3 Bacterial Cell Structure/Function II 3 Bacterial Genomes/Replication 7 Bacterial Gene Transfer 9 Bacterial DNA Repair Pathways 9 Bacterial Translation/Secretion 8 Exam 1 1-5, 7-9 Operons 10 Gene Regulation 10 Metabolism I 13 Metabolism II 13 Metabolism III 14 Metabolism IV 14 Biosynthesis 15 Food/Industrial microbiology 16 Virus Structure and Function 6 Viral Molecular Biology I 11 Viral Molecular Biology II 11 Archaea 19 Exam 2 6, 10, 11, 13-16, 19 Bacteria I 18 Bacteria II 18 Human microbiota 23 Biofilms 4+ Fungi 20 Plant fungal/bacterial path. & soil enzymes parts of 6, 21 Microbial Pathogenesis 25 Epidemiology 28 Antimicrobials 27 TA lecture: Genetic Recombination; Yersinia (plague) TA lecture: Leishmaniasis; Bacterial Symbiosis Exam 3 18, 23, 25, 27, 28 +bonus Microbial Ecology 21 No class (Thanksgiving holiday) No class (Thanksgiving holiday) Microbiology Research I CLASS NOTES Microbiology Research II CLASS NOTES

Mon

12/9

Final Exam (7:30 am – 10:00 am)

Comprehensive...