BEST 240 Biomolecular Engineering Spring, 2016

Professor: Prof. Victor Muñoz Office Hours: F 10:00 am -12:00 am in Room 383 SE2 Phone: (209) 228-2430 e-mail: [email protected]

Lecture: T R 9:30 am - 11:20 am, SSM 100

Required Text: This course requires two textbooks (one for each of its two parts) 1) Fundamentals of Biochemistry by Donald Voet, Judith G. Voet & Charlotte W. Pratt. Wiley ISBN: 978-0470570951 2) Protein Engineering and Design by Sheldon J. Park & Jennifer R. Cochran. CRC Press ISBN: 978-1420076585

Additional readings: Additional readings can be found at the UC Merced Kolligian Library, or through the ILL system.

Course Overview: This course focuses on the structural and quantitative analysis as well as the design of custom biomolecules, including proteins, nucleic acids, and macromolecular complexes. The students will learn the fundamental concepts of biomolecular structure and function and the experimental and computational tools/approaches for engineering biomolecules and how to apply these new technologies to solving some of the most pressing problems in biotechnology, medicine and bioengineering. The covered approaches range from rational and computational design to combinatorial and evolutionary optimization and biophysical characterization, whereas the target products span customized enzymes, molecular switches and actuators, recombinant biosensors, therapeutic antibodies, and protein and DNA assemblies.

Course Learning Goals and Outcomes: By the end of this course, students will be able to: 1. Select, explain, and use appropriate tools and techniques for research on structural and functional analysis of biomolecules 2. Critically select and use various experimental and computational strategies for engineering and designing biomolecules 3. Understand the fundamental concepts of biomolecular structure and function and demonstrate ability to apply them in strategies for engineering and designing new biomolecules 4. Show mastery of fundamental topics in biomolecular engineering and design, including sequence/structure/function relationships; physical factors determining biomolecular structure, folding and stability; methods and techniques for structural and functional analysis of biomolecules; enzymatic catalysis; protein chemistry; directed molecular evolution; combinatorial biochemistry; computational approaches to biomolecular design. At the end of the course, students will be able to communicate with scientists and contribute to the literature in these topics 5. Communicate effectively research issues and results in biomolecular engineering and design.

Relationship to Program Learning Outcomes: BEST 240 maps directly onto 4 of the Program Learning Outcomes for the BEST Ph.D. and M.S. degrees.

PLO 1: Possess a broad foundation in the fundamentals and current topics in either biological or materials science and engineering, as well as, an in-depth understanding of their chosen research topic area. PLO 3: Be able to identify new, important, and interesting research opportunities, and be able to develop effective strategies, including the experimental plan, for pursuing these opportunities. PLO 4: Communicate both fundamental concepts and details of their own research effectively, both in written and oral form, including in a classroom setting to expert and non-expert audiences. PLO 5: Be able to critically evaluate the experimental design, data analysis and data interpretation of our peers.

Prerequisites by Topic: Graduate status

Course Policies: Attendance is mandatory. No cell phone or recording devices are allowed in class.

Grading for BEST 240 50% Research Project Proposal 15% Graduate Discussion Group Participation 35% Lecture Presentation

Academic Dishonesty Statement: a. Each student in this course is expected to abide by the University of California, Merced's Academic Honesty Policy. Any work submitted by a student in this course for academic credit will be the student's own work. b. You are encouraged to study together and to discuss information and concepts covered in lecture and the sections with other students. You can give "consulting" help to or receive "consulting" help from such students. However, this permissible cooperation should never involve one student having possession of a copy of all or part of work done by someone else, in the form of an e mail, an e mail attachment file, a diskette, or a hard copy. Should copying occur, both the student who copied work from another student and the student who gave material to be copied will both automatically receive a zero for the assignment. Penalty for violation of this Policy can also be extended to include failure of the course and University disciplinary action. c. During examinations, you must do your own work. Talking or discussion is not permitted during the examinations, nor may you compare papers, copy from others, or collaborate in any way. Any collaborative behavior during the examinations will result in failure of the exam, and may lead to failure of the course and University disciplinary action.

Disability Statement: Accommodations for Students with Disabilities: The University of California Merced is committed to ensuring equal academic opportunities and inclusion for students with disabilities based on the principles of independent living, accessible universal design and diversity. I am available to discuss appropriate academic accommodations that may be required for student with disabilities. Requests for academic accommodations are to be made during the first three weeks of the semester, except for unusual circumstances. Students are encouraged to register with Disability Services Center to verify their eligibility for appropriate accommodations.

Lecture Schedule: Spring 2016

Week 1 Jan 19 Course Introduction Jan 21 Water and the Chemistry of Biomolecules Week 2 Jan 26 Aminoacids and Protein Primary Structure Jan 28 Working with Proteins I (Isolation and Purification) Week 3 Feb 2 Protein 3D Structure Feb 4 Working with Proteins II (Spectroscopy) Week 4 Feb 9 Protein Stability (Thermodynamics) Feb 11 Protein Folding (Kinetics) Week 5 Feb 16 Protein Function 1 Feb 18 Protein Function 2 Week 6 Feb 23 Computer Practicum Protein Structure, Folding, Stability Feb 25 Computer Practicum Protein Function Week 7 Mar 1 Enzymes Mar 3 Enzymatic Catalysis and Regulation Week 8 Mar 8 Review of Covered Materials and Exercises Mar 10 MIDTERM Exam Week 9 Mar 15 DNA Structure, Function and Properties Mar 17 RNA Structure and Function Week 10 Mar 22 Spring Break Mar 24 Spring Break Week 11 Mar 29 Working with Nucleic Acids Mar 31 Introduction to Protein Engineering Week 12 Apr 5 Protein Expression and Mutagenesis Apr 7 Protein Engineering Week 13 Apr 12 Protein Engineering: Combinatorial Approaches 1 Apr 14 Protein Engineering: Combinatorial Approaches 2 Week 14 Apr 19 Computational Protein Design 1 Apr 21 Computational Protein Design 2 Week 15 Apr 26 Computational Protein Design 3 Apr 28 DNA Nanotechnology Week 16 May 3 Student Oral Presentations May 5 Review of Covered Materials and Exercises