Cell and Molecular Biology for Engineers 1

Transcription

1 Cell and Molecular Biology for Engineers 1 BIOG 140 MW 10:00-10:50 Fall 2018 Instructor: Dr. Gregory A Babbitt contact Gregory A Babbitt, Office - Gosnell , - gabsbi@rit.edu office hours Friday or by appt SUMMARY The study of the cell began not long after the advent of the modern light microscope, when in 1839, Theodor Schwann and Matthias Jakob Schleiden suggested that the cell be considered the basis of all life. The role of the cell nucleus in heredity was discovered about years later by Columbia University biologists Edmund Beecher Wilson, Thomas Hunt Morgan and their students. Their pioneering studies on the chromosome ushered in the modern era of experimental biology. Yet even today, nearly 100 years later, the study of the cell has not yielded all of its secrets. Molecular cell biology remains at the forefront of the natural sciences. Our understanding of how the molecules that makeup our cells are structured, interact with each other, and carry the essential information that defines the living organism, is undergoing a renaissance...enbracing all branches of the natural sciences as well as the computer. Even now, our understanding of many key processes of the cell (e.g. gene regulation) are still woefully incomplete, and only now are beginning to encompass a whole systems perspective. As the molecular biology continues to be flooded with data in this modern "age of information", new automated technologies are arising at a rapid pace. This class is intended as introduction to the molecular workings of the nucleus of the cell to survey what we currently know, and more importantly, what we do not yet know, about the most fundamental molecular processes of the cell. The laboratory portion of the course will focus on molecular biology of the DNA and protein of prokaryotes. TEXTBOOK / MATERIALS Molecular Biology of the Cell 6th edition. Authors: Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter. Publisher: Garland Science Taylor and Francis Group ISBN ISBN: NOTE: THIS TEXT WILL ALSO BE USED FOR THE SPRING SEMESTER COURSE The Machinery of Life (OPTIONAL) David Goodsell Springer Science ISBN You will also need a lab coat and a blank, bound laboratory notebook. We will also be reading and discussing in class a variety recent reviews on subjects related to the course, but are not covered by the textbook. TEACHING PHILOSOPHY The mission of the modern university is to produce and disseminate new knowledge to the world. As an instrument towards this goal, I am an active researcher in the areas of molecular evolution and computational structural biology. However, I enjoy my role as a teacher here at RIT just as much as my research. I strive to do both of these tasks well. I ask each of you to take responsibility for the continued development of your own education. We are always here to help you, but ultimately the path of our learning is walked alone in each of our own minds. You must be actively committed towards this personal goal for yourself if you want to get a good

2 grade in this class. Self study is very important. Simply showing up without actively engaging your mind will not let you achieve success. Please communicate with me early in the semester if you feel you are having trouble understanding any concepts or material. All of us, PhD's included, have gaps in our understanding of various subjects. There is no such thing as a "dumb" question in my class. Success in academics at every level is often simply a matter of recognizing where missing information is holding us back. As an instructor, I will always try my best to achieve clarity by communicating to the least informed member of my audience, but I may miss the mark at times. During the lecture or lab, please don't feel that you cannot interrupt to ask me questions. While I am with you, my time is always your time. Unlike some of the other natural sciences which are more mathematically-based, learning concepts in biology is often rooted in specialized vocabulary. I highly recommend that you keep a vocabulary list while reading and attending lecture. ATTENDANCE Attendance at all lectures and laboratories is required but not monitored. There will always be information presented that is not otherwise available, i.e. it will not be in the books, and could be included in the exams and lab quizzes. Each week (usually on the morning of lab, unless there is a scheduled exam) some lecture time will be spent discussing the upcoming laboratory. Missing class on these days will ensure student confusion in the lab. LECTURE EXAM SCHEDULE Each of the four exams (3 mid-term exams plus the final) will be weighted equally and only the top three scores will be counted towards the final grade. Therefore, if you do well on all three of the in-class exams, you may opt out of the final exam. There will be no make-up exams. If you miss an in-class exam due to illness or other problem it will automatically count as your lowest grade and be dropped. In this case the final exam is mandatory. Exam Day Week Exam I = week 6 Exam II = week 10 Exam III week 15 Optional Comprehensive Final Exam TBA during Finals week Note: grades are scaled as follows A A B B B C C C D F below 60 PLEASE REVIEW THE RIT POLICY ON ACADEMIC DISHONESTY AND STUDENT MISCONDUCT AT THE WEBSITE BELOW WE WILL ABIDE BY THESE POLICIES AND RECOMMENDED PENALTIES...NO EXCEPTIONS. GRADE DISTRIBUTION - 50% lecture (= 2 Midterm Exams + written report) + 50% lab (Lab Practical Exams /Reports + Lab Quizzes) *student groups will use software tools to research and analyze a protein of their own choosing. They will write a report about their proteins structure, function and evolution.

3 INFORMATION ON THE LAB Students are expected to read the lab BEFORE their lab section meets. Labs will be posted on "mycourses" on a separate syllabus. Before of each lab, there may be a short online quiz covering the last lab and the reading for the upcoming lab. Calculations and analysis of data are good quiz questions! If you miss a lab you will receive zero points for that weekly lab quiz AND more importantly will likely fall behind on our projects. Don t miss lab! Our projects build on what was accomplished the previous week Some lab exercises often take nearly three hours (so don t expect to be done by 4pm each week!) Students will work with a partner for the semester. Notebooks will be kept individually. a lab notebook must be kept by each student At several points in the semester, we will have open lab notebook LAB PRACTICAL EXAMS. These exams are intended to assess your ability to replicate tasks done in earlier labs using you notes and the skills you have acquired. In the real world, it is essential that the scientist can replicate his/her work done at the laboratory bench. LECTURE SCHEDULE AND READINGS Note: many of the methods covered in lab are described in Chapter 8 in the textbook. Although this is not assigned reading, this chapter is a very good resource for understanding the procedures for manipulating DNA and protein in the laboratory. Week 1 A) Introduction - What kinds of molecules can carry information in the cell? How do we define function? (supplement 1 - hereditary molecules, Babbitt et al. 2016, Doolittle et al. 2014, Graur et al. 2013) B) Background, weak bonding (Ch 1; 1-39), basic cell cycle (Ch 17; , , ), review of mitosis/meiosis Week 2 A) no classes (Labor Day) B) Biological molecules - nucleic acids, lipids, carbohydrates and proteins (Ch 2; 43-73) (Ch 3; ) (Ch 4; ) Introduction to USCF Chimera 1.11 and Protein Data Bank Week 3 A) Enzyme kinetics and the energizing of the cell (Ch 2; 73-88) (supplement 2 - Michaelis-Menton kinetics) B) Energy conversion in the cell; mitochrondria and chloroplast (Ch14; ) Week 4 A) Protein structure, function, folding and disorder (Ch 3; ) (Chouard 2011, Dunker and Kriwacki 2011) B) Our concept of the gene - some historical perspective / organizational principles of the genome and the molecular evolutionary process (Ch 4; )

4 Week 5 A) DNA and chromatin structure, function and evolution (Ch 4; , , (Babbitt 2011, Misteli 2011) B) Open review for exam Week 6 A) Exam 1 B) Career Fair? Week 7 A) no class (October break) B) DNA replication and repair (Ch 5; , , ) Week 8 A) DNA replication and repair - continued B) Mobile DNA / transposable elements (Ch 5; ) Week 9 A) Transcription, mrna processing (Ch 6; ; , Tullius 2009) B) The ribosome, translation, post-translational modification and degradation of protein (Ch 6; ) Week 10 A) Evolution of genetic code and amino acid alphabets, review of the central dogma (Brian Hayes AmSci 1998) B) Control of complex gene expression in eukaryotes - (Ch 7; ; ) Week 11 A) open review B) Exam 2 Week 12 A) Introduce Bioinformatics Project (NCBI database tutorial and scientific writing) B) Methods of high-throughput DNA sequencing and protein structure determination (x-ray crystallography, NMR and cryo-em)

5 Week 13 A) Bioinformatics software tutorials (MEGA 7.0 and Chimera 1.11) B) no classes (Thanksgiving Holiday) Week 14 A) open studio time for group bioinformatics projects B) open studio time for group bioinformatics projects Week 15 A) open studio time for group bioinformatics projects B) Project reports are due at noon - note: these reports make up the midterm Exam 3 grade Week 16 A) Open review for optional final