Undergrad & Grad Course Descriptions

Undergraduate

Honors Option - H-Options are an enrichment opportunity for Honors College members and other academically talented students to undertake Honors-caliber study and receive Honors credit for non-Honors courses authorized by the department and the Honors College.

CHM/COM students

Graduate

Undergraduate Courses

For the most up to date list of course offerings by semester, please visit the MSU schedule of courses page: www.schedule.msu.edu  


Course: BMB 101 "Frontiers in Biochemistry"  UP
Description: Topics in Biochemistry research
Semester(s) offered: Fall of every year
Credits: 1
Restrictions: Open only to freshman and sophomores.
Prerequisites: None
Most Recent Syllabus:  Fall 2017 (PDF)
Previous: Fall 2016  (PDF)

Course: BMB 200  "Introduction to Biochemistry" UP
Description: Introductions to the major classes of biomolecules and the metabolism of these molecules. This course is designed to provide an introduction to the relationship between the components of food and the components of living organisms. Special attention is paid to biochemistry in the context of human nutrition. This course is especially applicable for students wishing to pursue careers related to human and animal nutrition. 
Semester(s) offered: Summer and Fall of every year
Credits: 4
Restrictions: Not for Biochemistry majors.
Prerequisites: CEM 143 or CEM 251 or CEM 351.
Recommended Background: CEM 252 or CEM 352.
Most Recent Syllabus:  Fall 2017 (PDF)
Previous: Fall 2016 (PDF)

Course: BMB 400 "Introduction to Bioinformatics"  UP
Interdepartmental with Plant Biology, and Microbiology and Molecular Genetics. Administered by Plant Biology
Description: Bioinformatic theory and practice. How to manage and analyze sequences, structures, gene expression, and other types of biological data.
Semester(s) offered: Spring of odd years (Fall of even years beginning Fall 2016)
Credits: 3
Prerequisites: (STT 200 or STT 201 or STT 231 or STT 421) and (PLB 203 or MMG 201 or BMB 200)
Recommended Background: An introductory biology course covering basic genetics, macromolecules, evolution, energy metabolism, genetic materials, and signal transduction is recommended for non-biology majors. A statistic course covering random variable, distributions, and basic probability theory is recommended for biology majors.
Course: BMB 401 "Comprehensive Biochemistry"
Description: Structure and function of major biomolecules, organization and regulation of metabolic pathways. Special emphasis on eukaryotic systems and the biochemical basis of human disease.
This four-credit course is especially appropriate for those students preparing for careers in human and veterinary medicine and the allied health professions and fulfills the biochemistry requirements of many majors at Michigan State University. It does not meet the requirements for BMB and BMB/Biotechnology majors.
Semester(s) offered: Fall, Spring, and Summer of every year
Credits: 4
Restrictions: Not open to students in the Biochemistry or Biochemistry/Biotechnology major. Not open to students with credit in BMB 461.
Prerequisites: CEM 252 or CEM 352.
Recommended Background: BS 161 or BS 181H or LB 145
Most Recent Syllabus: Traditional Section (#001): Spring 2017 (PDF)
Previous:  Traditional Section:Spring 2016 Course Info and Syllabus (PDF)

BMB 401 ONLINE SECTIONS:  To access information (and syllabi) for the Online Sections of BMB 401, click here:  https://bmb.natsci.msu.edu/undergraduate/undergrad-grad-course-descriptions/bmb-401-online-course/
Course: BMB 461 "Advanced Biochemistry I"
Description: This course is the first part of a two-semester series designed to provide biochemistry majors with a detailed understanding of the structure, function, and biophysical properties of biomolecules in a wide variety of organisms.. This half of the series focuses on proteins and carbohydrates including enzyme catalysis and kinetics, the central metabolic pathways, and photosynthesis.
This three-credit course fulfills a portion of the biochemistry requirements for BMB and BMB/Biotechnology majors and is designed to meet the needs of students wishing to pursue research-oriented careers in the life sciences.
Semester(s) offered: Fall of every year (and Spring of every year beginning 2015)
Credits: 3
Restrictions: Not open to students with credit in BMB 401.
Prerequisites: (CEM 251 or CEM 351) and (CEM 252 or CEM 352) and (MTH 124 or MTH 132 or MTH 152H or LB 118) and (BS 161 or BS 181H or LB 145) and (BS 162 or concurrently) or (BS 182H or concurrently) or (LB 144 or concurrently)
Most Recent Syllabus: Fall 2017 (PDF)
Previous: Spring 2017 (PDF)
Course: BMB 462 "Advanced Biochemistry II"
Description: Continuation of BMB 461. Structure, function, and biophysical properties of lipids and nucleic acids including membranes, lipid metabolism, signaling and metabolic regulation, DNA replication and repair, transcription, translation, and regulation of gene expression.
Semester(s) offered: Spring of every year (and Fall of every year beginning 2015)
Credits: 3
Restrictions: None
Prerequisites: BMB 461 or BMB 401
Most Recent Syllabus:  Fall 2017 (PDF)
Previous: Spring 2017 (PDF)
 
Course: BMB 469 "Special Topics in Biochemistry - Computers in Biochemistry and Molecular Biology"
Description: This is a practical, hands-on course in the use of personal computers to access and interpret on line mega data for Biochemistry and Molecular Biology. Topics include genes, proteins, cancers, epigenetics, evolution, genomics and bioinformatics. On line databases include essential information for biochemists, so familiarity with these resources is of increasing importance. The instructors aim to train students in techniques every biochemist must know. No programming is required in BMB 469.
Semester(s) offered: Spring of every year
Credits: 3
Restrictions: None
Prerequisites: BMB 461 and 462 (or concurrent) recommended
Most Recent Syllabus:  Spring 2016 (PDF)
Previous:  Spring 2015 (PDF)
Course: BMB 471 "Biochemistry Laboratory
Description: Biochemical methods and principles used in the study of enzymes (proteins), carbohydrates, lipids and cell organelles.
Semester(s) offered: Spring of every year
Credits: 3
Restrictions: Open to students in the BMB/Biotechnology major or in the BMB major or in the Lyman Briggs BMB Coordinate Major or in the Lyman Briggs-Biochemistry/Biotechnology Coordinate Major or approval of department.
Prerequisites: BMB 461 and CEM 262
Most Recent Syllabus: Spring 2017 (PDF)
Previous: Spring 2016 (PDF)
Course: BMB 472 "Biochemistry Laboratory"
Description: Methods of molecular biology and the underlying principles on which these methods are based.
Semester(s) offered: Fall of every year
Credits: 3
Restrictions: Open to students in the BMB/Biotechnology major or in the BMB major or in the Lyman Briggs BMB Coordinate Major or in the Lyman Briggs-Biochemistry/Biotechnology Coordinate Major or approval of department.
Prerequisites: BMB 461 and CEM 262.
Recommended Background: BMB 462.
Most Recent Syllabus: Fall 2017  (PDF)
Previous: Fall 2016 (PDF)
Course: BMB 490 "Biochemistry Research"
Description: Participation in a laboratory or library research project by arrangement with a BMB faculty member.
Semester(s) offered: Fall, Spring, and Summer of every year
Credits: 1-4
Restrictions: Approval of department. A student may earn a maximum of 8 credits in all enrollments for this course. Total credits in BMB 490 and BMB 499 may not exceed 8.
Prerequisites: None
Course: BMB 495 "Undergraduate Seminar (W)"
Description: Extension and synthesis of concepts of biochemistry. Relationships to societal issues.
Semester(s) offered: Spring of every year
Credits: 2
Restrictions: Open only to students in BMB or Biochemistry/Biotechnology majors.
Prerequisites: BMB 462 or concurrently and Completion of Tier I Writing Requirement
Most Recent Syllabus: Spring 2017 (PDF)
Previous: Spring 2016 (PDF)
Course: BMB 499 "Senior Thesis (W)"
Description: Laboratory research culminating in a thesis.
A senior thesis is a capstone experience typically conducted over 2 semesters of 2-3 credits per semester. Students will conduct significant laboratory research and write a thesis based on their research. The thesis should be 15-20 pages long and shall include a significant survey of the field (2 page min) with references to original literature in biochemistry, molecular biology, and related fields. The thesis will be assessed by 2 professors (at least 1 from BMB). The research will be presented at the UURAF or a lab meeting/similar event if the UURAF conflicts with the student`s schedule.
Semester(s) offered: Fall, Spring, and Summer of every year
Credits: 1-8
Restrictions: Open to juniors or seniors. Approval of department. A student may earn a maximum of 8 credits BMB 490 and BMB 499. A student may earn a maximum of 8 credits in all enrollments for this course.
Prerequisites:  Completion of Tier I Writing Requirement

COM/CHM Courses

Course: BMB 515 "Medical Biochemistry and Molecular Biology"
Description: Basic biochemical principles and terminology. Overview of metabolism of biomolecules of importance to medical biology and human pathophysiology.
Semester(s) offered: Fall of every year
Credits: 2
Restrictions: Open to graduate-professional students in the College of Osteopathic Medicine.
Most Recent Syllabus: Fall 2017 (PDF)
Previous: Fall 2016 (PDF)
Course: BMB 527 "Medical Genetics"
Description: Basic principles of human medical genetics. Storage and expression of genetic information. Transmission of genetic information to progeny.
Semester(s) offered: Fall of every year
Credits: 1
Restrictions: Open only to graduate-professional students in the College of Osteopathic Medicine.
Most Recent Syllabus: Fall 2017 (PDF)
Previous: Fall 2016 (PDF)
Course: PSL (BMB) 539 "Principles of Cell Biology and Pathophysiology"
Description: Modern concepts of cell biology as a basis for understanding integration of structure (histology) and function (physiology) in health and disease (pathology). Introductions to adaptive growth response, cell injury, inflammation, hemodynamic disorders, and tissue repair.
Semester(s) offered: Fall of every year
Credits: 4
Restrictions: Open only to graduate-professional students in the College of Osteopathic Medicine.
Interdepartmental With: Human Anatomy, Microbiology
Administered By: Physiology
Most Recent Syllabus: Fall 2017 (PDF)



Graduate Course Offerings UP

For the most up to date list of course offerings by semester, please visit the MSU schedule of courses page: www.schedule.msu.edu

Course: BMB 801 "Molecular Biology" UP
Description: Organization of genes. Regulation of gene expression, replication, and recombination.
Semester(s) offered: Fall of every year
Credits: 3
Restrictions: Not open to students with credit in BMB 897A
Recommended background: BMB 462, CEM 383
Most Recent Syllabus: Fall 2017 (PDF)
Previous:  Fall 2016 (PDF)
Course: BMB 802 "Metabolic Regulation and Signal Transduction"
Description: Molecular basis for metabolic regulation. Molecular signalling mechanisms and mechanisms for allosteric and covalent protein modifications.
Semester(s) offered: Spring of every year
Credits: 3
Recommended background: BMB 801
Most Recent Syllabus:  Spring 2017 (PDF)
Previous:  Spring 2016 (PDF)
Course: BMB 803 "Protein Structure and Function"
Description: Protein structure and relationship of function to structure. Applications of kinetic methods to elucidation of enzyme mechanisms and regulation. (NOTE: This course is to serve students in non-BMB programs who desire a course in protein structure, but who do not require training in enzyme mechanisms. NOT open to Biochemistry majors or students who already have credit in BMB 805.)
Semester(s) offered: Spring of every year (1st ten weeks of the semester)
Credits: Total Credits: 2 Lecture/Recitation/Discussion Hours: 2
Recommended Background: BMB 462 and CEM 383
Most Recent Syllabus:  Spring 2017 (PDF)
Previous: Spring 2016 (PDF)
Course: BMB 805 "Protein Structure, Design, and Mechanism"
Description: Protein architecture, dynamics, folding, stability, and evolution. Conformational changes, ligand binding, and kinetics. Elucidation of enzyme mechanisms.
Semester(s) offered: Spring of every year
Credits: 3
Recommended background: BMB 462 and CEM 383
Most Recent Syllabus:  Spring 2017 (PDF)
Previous:   Spring 2016 (PDF)
Course: BMB 810 "Theories and Practices in Bioinformatics" (interdepartmental with PLB and MMG)
Description: Theories and algorithms behind bioinformatics tools. Basic tool development by writing scripts in the Python programming language for data analysis. 
Semester(s) offered: Spring of odd years
Credits: Total Credits: 3 Lecture/Recitation/Discussion Hours: 2 Lab Hours: 2
Recommended Background: Basic genetics, macromolecules, evolution, energy metabolism, genetic materials, and signal transduction is recommended for non-biology majors. A statistic course covering random variable, distributions, and basic probability theory is recommended for biology majors.
Administered By: Plant Biology
Course: BMB 816 "Integrative Toxicology: Mechanisms, Pathology and Regulation" (Interdepartmental with PHM)
Description: Biochemical, molecular, and physiological mechanisms of toxicology. Functional and pathological responses of major organ systems to chemical insult. Mechanisms of mutagenesis, carcinogenesis, and reproductive toxicology. Concepts in risk and safety assessment.
Semester(s) offered: Fall of odd years
Credits: 3
Prerequisite: PHM 819
Course: BMB 825 "Cell Structure and Function" (Interdepartmental with MMG and PSL)
Description: Molecular basis of structure and function. Cell properties: reproduction, dynamic organization, integration, programmed and integrative information transfer. Original investigations in all five kingsdoms.
Semester(s) offered: Spring of every year
Credits: 3
Recommended background: BMB 401 or BMB 461.
Most Recent Syllabus: Spring 2017 (PDF)
Previous: Spring 2016 (PDF)
Course: BMB 829 "Methods of Macromolecular Analysis and Synthesis"
Description: Techniques of isolation and characterization of macromolecules. Computer use in structure-function analysis of macromolecules.
Semester(s) offered: Fall of every year
Credits: 2
Recommended background: BMB 462 or concurrently.
Most Recent Syllabus: Fall 2017 (PDF)
Previous:  Fall 2016  (PDF)
Course: BMB 855 "Special Problems"
Description: Laboratory or library research on special problems in biochemistry.
Semester(s) offered: Fall, Spring, and Summer of every year.
Credits: 1-4
Restrictions: Approval of department. A student may earn a maximum of 8 credits in all enrollments for this course.
Course: BMB 856 "Plant Molecular and Omic Biology" (Interdepartmental with PLB, CSS. Administered by PLB.)
Description: Recent advances in genetics and molecular biology of higher plants.
Semester(s) offered: Spring of every year
Credits: 3
Recommended background: ZOL 341
Most Recent Syllabus:  Spring 2017 (PDF)
Previous:  Spring 2016 (PDF)
Course: BMB 864 "Plant Biochemistry" (Interdepartmental with PLB)
Description: Biochemistry unique to photosynthetic organisms. Photosynthetic and respiratory electron transport, nitrogen fixation, carbon dioxide fixation, lipid metabolism, carbon partitioning, cell walls, sulfur and nitrogen metabolism and specialized metabolism including isoprenoids, phenylpropanoids and alkaloids.
Semester(s) offered: Fall 2017 and then TBD after that
Credits: 3
Recommended background: (BMB 401 or BMB 462) and prior undergraduate course in plant physiology.
Most Recent Syllabus: Fall 2017 (PDF)
Previous: Fall 2016 (PDF)
Course: BMB 888 "Laboratory Rotation"
Description: Participation in research laboratories to learn experimental techniques and approaches, broaden research experience, and assess research interests prior to selecting a thesis or dissertation advisor.
Semester(s) offered: Fall, Spring, and Summer of every year
Credits: 1-4
Restrictions: Open only to graduate students in Biochemistry. A student may earn a maximum of 12 credits in all enrollments for this course.
Course: BMB 899 "Master's Thesis Research"
Description: Master's thesis research.
Semester(s) offered: Fall, Spring, and Summer of every year
Credits: 1-12
Restrictions: Open only to master's students in Biochemistry. A student may earn a maximum of 36 credits in all enrollments for this course.

Course: BMB 960 "Selected Topics in Biochemistry I" UP
Description: Selected topics in Biochemistry with substantial student presentations
Semester(s) offered: Fall and Spring of every year
Credits: 1-3
Restrictions: Open to graduate students in the Department of Biochemistry and Molecular Biology or approval of department. A student may earn a maximum of 7 credits in all enrollments for this course.
 
Course: BMB 960 Sect 301 "Plant Biotechnology Research Forum"
Semester(s) offered: Fall 2017 (First 8 weeks of the semester)
Credits: 1
Restrictions: Restricted to Biochemistry Graduate Students or Approval of the Instructor
Description:

This is an advanced seminar focusing on reading of the literature and student presentations on topics related to plant biotechnology. Topic areas in general address modern problems in human health and environmental sustainability. Specifically in 2016 areas have included the engineering of ABA receptors for drought tolerance, engineering a plant biosynthetic pathway for sustainable production of a natural compounds, navigation of agricultural biotechnology workplaces from industrial perspective, repurposing the cutin pathway for triacylglycerol synthesis. The course is part of the training program in plant biotechnology 'Plants for Health and Sustainability' (https://plantmetabolism.natsci.msu.edu/), though students not participating in the training program are also very welcome to take the course. Confirmed speakers for 2017 are representatives from the industry, NASA, national labs and academia.

If you are not a declared Biochemistry graduate student, you will need to submit the online override request form (http://bmb.natsci.msu.edu/undergraduate/override-request-form/) and then contact the instructors (Drs Hideki Takahashi, htakaha@msu.edu, Björn Hamberger, hamberge@msu.edu, and Rob Last, lastr@msu.edu) for permission to enroll. Enrollment will be limited to 15 students.

IMPORTANT: Attendance of the Symposium taking place in October will be a required portion of the course.

Syllabus: Fall 2017 (PDF)
Previous: Fall 2016 (PDF)
 
Course: BMB 960 001/GEN 800 001 "Genetic Applications for Improving Food Security"
Semester(s) offered: Fall 2017
Credits: 1
Description:  As the world population is projected to reach 9 billion people by the year 2050, issues of food security are increasingly pressing. In this course, students will be introduced to ways in which genetics and genomics tools are used to enhance crop and livestock production in a changing world. We plan to investigate how -omics and other “big data” studies in particular can provide solutions to relevant issues such as climate change, antibiotic resistance, animal welfare concerns, and human malnutrition. Throughout the semester, students will be asked to present scientific papers related to these topics, prepare questions, and moderate class discussion. In addition, a component of this seminar will be focused on improving students’ science communication skills to the general public and understanding how genetic research has manifested in science policy.
Syllabus: Fall 2017 (PDF)
 
Course: BMB 960 "Photosynthesis"
Semester(s) offered: Spring of every year  (May vary in the future. Please visit the schedule of courses page for updates:  www.schedule.msu.edu)
Credits: 3
Restrictions: Approval of the Instructor (Limited to 12 students)
Description: The course will focus on the mechanisms and measurements of photosynthetic energy capture, CO2 fixation and production of energy-rich molecules, as well as the limitations and possible improvements to these processes for food and fuel. The course is designed to meet the needs of MSU graduate students with projects related to photosynthesis and integrate knowledge across a range of disciplines, ranging from chemistry and biophysics of light capture, metabolisms, bioenergy and cell biology, through synthetic biology and gene discovery. Each set of lectures will start with background and move to higher-level discussion based on literature and applications (e.g. scientific measurements, data analyses, etc.). Course evaluation will be by research-related presentations and a final poster session that demonstrates the integration of new knowledge of photosynthesis in on-going research projects.
NOTE: To reserve a spot in this course, you will first need to contact Dr. David Kramer at kramerd8@msu.edu and you'll also need to complete the BMB Course Override link.
Syllabus: Spring 2017 (PDF)
Previous:  Spring 2015 (PDF)
 
Course: BMB 960  "Lipid Signaling in Animals and Plants" (taught in conjunction with GEN and CMB)
Semester(s) offered:
Credits: 1
Description: 
Syllabus: TBD
 
Course: BMB 960 "Lipid Disease in Animals and Plants" (taught in conjunction with GEN and CMB)
Semester(s) offered: Last offered Spring 2015
Credits: 1
Description: This course will involve a literature review of current papers on lipid diseases found in animals and plants.  As par of the class, students will not only present those papers but will also learn how to review manuscripts for major journals in the field.  At the end of the semester, the Genetics Program wil holds it's annual mini-symposisum which will this year follow the theme of lipis and deiseases.  Several suthors of the papers presented will be invited as speakers to the symposium.  Students participating in the class will have the opportunity to assist with the organization and meet the invited speakers.
Syllabus: Coming Soon
Previous:  Spring 2015 (PDF)
 
Course: BMB 960 "Genetics of neural tube development and disease" (taught in conjunction with GEN and CMB)
Semester(s) offered: Last offered Spring 2015
Credits: 1
Description: As the vertebrate embryo moves from a ball of cells to an elongated worm-like structure, something magical happens along its back.  The edges of the dorsal stripe of cells are elevated above the plane and then fold so their apexes meet over the midline.  Multiple layers of cells form at the midline. The superficial layer fuses to re-establish the ectoderm, the inner cells fuse to form a tube that runs from top to bottom of the embryo, and yet other cells delaminate from this apex and migrate ventrally to populate and become the face.  Since the tube will become the central nervous system, including brain and spinal cord, we call this the neural tube. In this seminar course you will study the genes and pathways that are required for formation of the neural tube.  However, despite your best efforts, I predict that you will not be able to dispel the possibility that magic is also required.  From this baseline of knowledge and understanding, we will also discuss what is known (and what is not known) about genetic and environmental factors that cause or increase risk for spina bifida and exencephaly. These are common neural tube defects that affect about 1/1000 babies born world-wide.
Student responsibilities:  For each session, two students will choose a paper (except week 3 will be assigned), confirm the paper with the course directors and lead discussion on the paper. Since this is a 16 week course, nearly all students will have two dates to lead discussion.  Also, ALL students will be expected to be prepared to discuss both assigned readings each week, and students will fill out a short answer work sheet about one of the assigned papers each week
Syllabus: Coming Soon
Previous: Spring 2015 (PDF)
 
Course: BMB 960 "Intersection of Mitochondrial Science and Medicine "
Semester(s) offered: Spring 2018
Credits: 1
Description:  BMB and the MSU Center for Mitochondrial Science and Medicine will offer a graduate level seminar course (BMB 960) in Spring Semester 2018 on the topic of “Intersection of Mitochondrial Science and Medicine,” with the objective of exploring mitochondrial biochemistry in the context of the current field of mitochondrial medicine, including clinical correlations. The course will feature a combination of faculty and student presentations and consider topics such as: impact of nuclear and mitochondrial DNA mutagenesis and variability on organismal function, regulation of respiration and mitochondrial transcription by cell signaling, role of mitochondria in memory and neurodegenerative disease and the general field of mitochondrial health, oxidative stress and stress response, toxicity and disease.
Syllabus: Spring 2018 (PDF)
 
 
Course: BMB 961 "Selected Topics in Biochemistry II"
Semester(s) offered: Fall and Spring of every year
Credits: 1-3
Restrictions: Open to graduate students in the Department of Biochemistry and Molecular Biology or approval of department.
Description: Selected topics in Biochemistry with faculty lectures, laboratory, or other instruction
Course: BMB 961 "Genomics and Proteomics and Complex Genetic Systems"
Semester(s) offered: Fall of even years
Credits: 2
Restrictions: Restricted to Biochemistry Graduate Students or Approval of the Instructor
Prerequisites: BMB 801 or instructor approved equivalent
Description: Coming Soon
NOTE:  If you are NOT a Biochemistry major, you must contact Dr. John Lapres (lapres@msu.edu) for approval. (NOTE: Please fill out this override request form and then contact the instructor: https://bmb.natsci.msu.edu/undergraduate/override-request-form/).
Syllabus: Fall 2016 (PDF)
Previous: Fall 2014 (PDF)
Course: BMB 961 "Metals in Biology"
Semester(s) offered: Varies - please check the schedule of courses page for updates: www.schedule.msu.edu
Credits: 2
Restrictions: Restricted to Biochemistry Graduate Students or Approval of the Instructor
Description:  Sec 004-Topic: "Metals in Biology" is intended for graduate students with backgrounds in biochemistry, molecular/cellular biology, microbiology, and/or chemistry. (May be cross-listed with the MMG and CMB departments.)  In this course we will discuss the roles of metals in biological systems, including metalloenzymes, metallocenter biosynthesis, metal transport, metal toxicity, and metaloregulation. Discussions will focus on the catalytic mechanisms as well as they way in which the different protein environments 'tune' their active site. Student presentations will be an important emphasis in this class. THIS CLASS WILL MEET IN ROOM 502 BIOCHEMISTRY.
Note: Undergraduate students must obtain permission to enroll from Dr. Eric Hegg(erichegg@msu.edu) and then submit the online Biochemistry course override request form. Here is a link to this form: http://bmb.natsci.msu.edu/undergraduate/override-request
Syllabus: Spring 2017 (PDF)
Previous: Fall 2014 (PDF)
Course: BMB 961 "Concepts in Protein Structure & Modeling" (formally "Protein Structure Analysis and Modeling")
Semester(s) offered: Usually offered in Spring (check www. schedule.msu.edu for updates)
Credits: 2
Prerequisites: Biochemistry 803 or detailed knowledge of protein and nucleic acid sequences and structures; some use of computers; and permission of the instructors.
Description: This is a hands-on, project-oriented course dealing with several aspects of protein structure analysis and modeling. We will go through UNIX basics and some of the most commonly used graphics software packages for visualizing and manipulating macromolecule structures. Then we will look at the databases of three-dimensional structures of proteins which are determined by X-ray Crystallography and NMR and how one can assess the quality of these structures. This will be followed by identifying and aligning homologous protein sequences and structures; analyzing superimposed crystal structures and ligand binding determinants, and designing mutations. Then we will cover the various methods for protein structure prediction such as homology modeling and fold recognition followed by methods for RNA structure prediction. We will be using well tested and documented tools which are available online and other programs which are installed on our UNIX workstations. Lectures will cover the theory and demonstrate the computer methods used; lab hours will provide hands-on experience.
NOTE:  For more information and permission to enroll, please contact Kaillathe (Pappan) Padmanabhan (padmanab@msu.edu). Please also submit an override request at https://bmb.natsci.msu.edu/undergraduate/override-request-form/
Syllabus:  Spring 2017 (PDF)
Previous: Fall 2014 (PDF)
Course: BMB 961 "Dynamics and Interactions of Proteins and Nucleic Acids"
Semester(s) offered offered: Last offered Fall 2013
Credits: 2
Restrictions: BMB graduate students only, others need permission to enroll
Prerequisites: Basic-level experience with computational modeling techniques.
Description: This hands-on class introduces advanced computational methods for modeling and simulating biological macromolecules. Topics are molecular dynamics simulations, normal mode analyses, free energy calculations, solvation models, enhanced sampling algorithms, and coarse-grained modeling. Significant time is dedicated to a lab section and a project towards the end of class.
Syllabus:  Check back for updates
Previous:  N/A
Course: BMB 961 "Plant Biotechnology for Health and Sustainability"
Semester(s) offered: Spring (May vary in the future. Please visit the schedule of courses page for updates:  www.schedule.msu.edu)
Credits: 3
Restrictions: Approval of the Instructor
Prerequisites: Basic knowledge in molecular biology, genomics, or plant biochemistry as demonstrated by having completed at least one of the following graduate level classes: BMB 801, BMB 961 (Genomics), BMB 864, or BMB 856
Description:  This course is part of an interdisciplinary effort to foster opportunities for graduate students with interest in plant biotechnology. A broad overview of the state-of-the art of plant biotechnology and related fields will be provided. In addition, students are encouraged to think about concepts and ideas that can be potentially commercialized. Special emphasis will be on plant metabolic pathways that impact human health and nutrition, as well as sustainability in the production of therapeutics, food and fuels from plants and algae. Examples and case studies will be discussed that cover hosts, strategies and pitfalls in expression of foreign pathways. Examples are chosen to explain in simple terms basic metabolic engineering principles, including synthetic biology approaches to generate, analyze, and optimize transgenic plants or algae. Some of the chosen cases will be particularly suited to discuss regulatory and commercial issues related to genetically modified organisms (GMOs) and the ‘share-your-parts’ philosophy, as promoted for example by the international genetically modified machine (iGEM) initiative. To actively participate in the course, students need to have a basic understanding of molecular biology, genomics, or plant biochemistry, and are expected to read background and original research papers as assigned. Students will be guided to develop a 3-page brochure presenting a scientific idea for a plant biotechnology based product or process with a recognized need or new opportunity. The students will need to lay out the idea, present reasonable milestones and be aware of potential technical, commercial, or societal hurdles, and articulate how the proposed technology would address the need or opportunity. Relevant concepts (novel technologies for genome editing, societal acceptance and outreach, IP aspects) will be discussed and a list of topics will be developed during the first three weeks of the course together with the students. The instructor(s) will provide guidance and feedback to the students on an individual base as they develop their project. During the final sessions of the semester, students will be asked to pitch their idea in a 10 min presentation, followed by feedback from the entire group.
NOTE: Please see schedule of courses for special enrollment instructions.  www.schedule.msu.edu
Syllabus: Spring 2017 (PDF)
Previous:  Spring 2016 (PDF)