Twin Cities campus

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Twin Cities Campus

Biochemistry, Molecular Biology and Biophysics Ph.D.

Biochemistry, Molecular Biology, & Biophysics TCBS
Graduate School
Link to a list of faculty for this program.
Contact Information
Department of Biochemistry, Molecular Biology and Biophysics 6-155 Jackson Hall 321 Church St. SE Minneapolis, MN 55455 612-625-6100
  • Program Type: Doctorate
  • Requirements for this program are current for Spring 2017
  • Length of program in credits: 48
  • This program requires summer semesters for timely completion.
  • Degree: Doctor of Philosophy
Along with the program-specific requirements listed below, please read the General Information section of this website for requirements that apply to all major fields.
The Biochemistry, Molecular Biology and Biophysics (BMBB) graduate program is an interdisciplinary program that is supported by the College of Biological Sciences (CBS) and the Medical School of the University of Minnesota. The program provides a broad research-based education involving faculty from BMBB as well as many faculty members from several other departments in CBS, the Medical School, the College of Science and Engineering (CSE), the College of Food, Agricultural and Natural Resources Sciences (CFANS), and the College of Veterinary Medicine. BMBB focuses on determining the molecular mechanisms that underlie basic biological functions using an integrated approach that encompasses biochemistry, chemistry, biophysics, genomics, molecular biology, proteomics, and structural biology. Special emphasis is placed on revealing how biological processes go awry in diseases including cancer, diabetes, heart disease, and AIDS. The program has four areas of emphasis: synthetic biology and biotechnology, molecular biology, metabolic and systems biology, and chemical and structural biology. All students are expected to demonstrate a minimum level of competence in these areas but will emphasize the area most related to their thesis project. While graduate training in a BMBB laboratory involves first-year coursework and associated preliminary examinations, the focal point for graduate education is thesis research. Laboratory-based exploration coupled with journal clubs, seminars, scientific meetings and retreats, career counseling and scientific ethics constitutes the major components of the program. Support for graduate education comes from a variety of sources but is augmented by several NIH and NSF-based training grants. PhD graduates from the University of Minnesota obtain full-time employment immediately after graduation or pursue advanced training in academic or corporate postdoctoral positions. Students pursuing the PhD are admitted to BMBB under the auspices of Molecular, Cellular and Structural Biology (MCSB), a first year program administered by BMBB and the Molecular, Cellular, Developmental Biology and Genetics (MCDB&G) graduate programs. After the first year, students select either BMBB or MCDB&G to complete their degree. Related Ph.D. and M.S. Programs in BMBB: As a part of the BMBB program, graduate studies leading to a PhD degree may be pursued on the Duluth Campus. A PhD in BMBB may also be obtained through the Combined MD-PhD Program. Please visit the program website for more information (http://www.med.umn.edu/mdphd/index.htm). Note: One cannot apply for admission to the master's degree in BMBB. Students are only admitted to the BMBB PhD program. Alternative, related master's degree programs that admit students are the Master of Biological Sciences (MBS) (http://cce.umn.edu/master-of-biological-sciences) and the Master in Microbial Engineering (http://bti.umn.edu/MicE/).
Program Delivery
  • via classroom (the majority of instruction is face-to-face)
Prerequisites for Admission
The program can accommodate for a variety of educational backgrounds. However, applications from students with an undergraduate degree in the biological, chemical, or physical sciences are encouraged.
The program can accommodate for a variety of educational backgrounds. However, applications from students with an advanced degree in the biological, chemical, or physical sciences are encouraged.
Other requirements to be completed before admission:
Recommended academic preparation includes one year each of calculus, organic chemistry, and basic biology, including biochemistry and genetics. For students of demonstrated ability, background deficiencies can be made up during the first year of graduate study. Successful applicants must have previous research experience in an academic or industrial setting in addition to any course-related laboratory experiences. It is important to demonstrate an aptitude for basic science research prior to embarking on a graduate career in this program.
Special Application Requirements:
Additionally, applicants must submit three letters of recommendation from persons familiar with their academic and research capabilities. A statement of interests and goals, a complete set of transcripts, and official scores from the General Test of the GRE are required. The GRE Subject Test in biochemistry, cell and molecular biology, biology, or chemistry is strongly recommended, but not required. The deadline to submit a completed application is December 1. Completed files are reviewed between January and February. Graduate studies begin fall semester only. Related Ph.D. and M.S. Programs in BMBB: As a part of the BMBB program, graduate studies leading to a PhD degree may be pursued on the Duluth Campus. A PhD in BMBB may also be obtained through the Combined MD-PhD Program. Please visit the program website for more information (http://www.med.umn.edu/mdphd/index.htm). Note: One cannot apply for admission to the master's degree in BMBB. Students are only admitted to the BMBB PhD program. Alternative, related master's degree programs that admit students are the Master of Biological Sciences (MBS) (http://cce.umn.edu/master-of-biological-sciences) and the Master in Microbial Engineering (http://bti.umn.edu/MicE/).
Applicants must submit their test score(s) from the following:
  • GRE
Key to test abbreviations (GRE).
For an online application or for more information about graduate education admissions, see the General Information section of this website.
Program Requirements
24 credits are required in the major.
0 credits are required outside the major.
24 thesis credits are required.
This program may not be completed with a minor.
Use of 4xxx courses towards program requirements is not permitted.
A minimum GPA of 3.00 is required for students to remain in good standing.
Requirements for the doctoral degree include core coursework, thesis credits, and laboratory experiences taken by all students, as well as coursework in one of the four BMBB empahses listed below. To obtain a PhD degree, students must register for a minimum of 24 thesis credits (BIOC 8888). Upon completion of the 24 thesis-credit requirement, students are required to register every fall and spring, up through the term they are awarded the PhD, for 1 credit of advanced doctoral credits (BIOC 8444) in order to maintain full-time, active student status. Additional requirements for the PhD degree include seminar presentations, examinations, and teaching assignments. BIOC 8084 is a weekly student seminar on current literature and research, and students must register for 1 credit of BIOC 8084 each term until they have reached advanced doctoral status. Students must attend at least 50% of weekly meetings for BIOC 8084 and BIOC 8184, which is a departmental seminar involving prominent national and international scientists. Three examinations for the PhD degree include a written preliminary proposal (4th semester), preliminary oral exam (4th semester), and a final oral exam with thesis defense (typically year 5). Examinations will be conducted by the student's preliminary and graduate committees. Students are also required to complete two semesters of teaching, typically between years 2 to 4.
Biochemistry Core
To obtain a PhD in BMBB, all students must complete the biochemistry core coursework.
BIOC 8001 - Biochemistry: Structure, Catalysis, and Metabolism (3.0 cr)
BIOC 8002 - Molecular Biology and Regulation of Biological Processes (3.0 cr)
BIOC 8401 - Ethics, Public Policy, and Careers in Molecular and Cellular Biology (1.0 cr)
BIOC 8888 - Thesis Credit: Doctoral (1.0-24.0 cr)
Laboratory and Field Course
In August of the first year, all PhD BMBB students must register for this hands-on, intensive lab course which takes place at the Itasca Biological Station and Laboratories. This course will provide first-year students with exposure to a range of modern methods and model systems.
MCDG 8920 - Special Topics (1.0-4.0 cr)
Electives for Emphases
All students must complete 15 credits of coursework in one of the four BMBB empahses: synthetic biology and biotechnology, molecular biology, metabolic and systems biology, or chemical and structural biology. Courses from disciplines other than BMBB may be used to build an emphasis in consultation with the student's advisor.
Take 15 or more credit(s) from the following:
· BIOC 5352 - Biotechnology and Bioengineering for Biochemists (3.0 cr)
· BIOC 5361 - Microbial Genomics and Bioinformatics (3.0 cr)
· MICA 8002 - Structure, Function, and Genetics of Bacteria and Viruses (4.0 cr)
· GCD 8151 - Cellular Biochemistry and Cell Biology (2.0-4.0 cr)
· MICA 8003 - Immunity and Immunopathology (4.0 cr)
· MICA 8004 - Cellular and Cancer Biology (4.0 cr)
· GCD 8131 - Advanced Molecular Genetics and Genomics (3.0 cr)
· GCD 8008 - Mammalian Gene Transfer and Genome Engineering (2.0 cr)
· PUBH 6450 - Biostatistics I (4.0 cr)
· SCB 8181 - Stem Cell Biology (3.0 cr)
· STAT 5021 - Statistical Analysis (4.0 cr)
· MICA 8010 - Microbial Pathogenesis (3.0 cr)
· BIOC 5216 - Current Topics in Signal Transduction (2.0 cr)
· BIOC 5527 {Inactive} (4.0 cr)
· BIOC 5528 - Spectroscopy and Kinetics (4.0 cr)
· CHEN 8754 - Systems Analysis of Biological Processes (3.0 cr)
· BIOC 5213 {Inactive} (3.0 cr)
· BIOC 5444 - Muscle (3.0 cr)
· BIOC 5531 {Inactive} (1.0 cr)
· BIOC 5532 {Inactive} (1.0 cr)
· CHEM 8011 - Mechanisms of Chemical Reactions (4.0 cr)
· CHEM 8021 - Computational Chemistry (4.0 cr)
· CHEM 8411 - Introduction to Chemical Biology (4.0 cr)
· CHEM 8412 - Chemical Biology of Enzymes (4.0 cr)
· CHEM 8735 - Bioinorganic Chemistry (4.0 cr)
· PHCL 5111 - Pharmacogenomics (3.0 cr)
· PUBH 7445 - Statistics for Human Genetics and Molecular Biology (3.0 cr)
· MICA 8013 - Translational Cancer Research (2.0 cr)
· GRAD 8101 - Teaching in Higher Education (3.0 cr)
· GRAD 8200 - Teaching and Learning Topics in Higher Education (1.0 cr)
· BIOC 5309 - Biocatalysis and Biodegradation (3.0 cr)
· BIOC 5351 - Protein Engineering (3.0 cr)
· CSCI 5461 - Functional Genomics, Systems Biology, and Bioinformatics (3.0 cr)
· GRAD 5102 - Preparation for University Teaching for Nonnative English Speakers (2.0 cr)
 
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BIOC 8001 - Biochemistry: Structure, Catalysis, and Metabolism
Credits: 3.0 [max 3.0]
Typically offered: Every Fall
Protein structure, methods to determine structure, protein folding, forces stabilizing macromolecular structure, protein engineering, design. Dynamic properties of proteins/enzymes, enzyme substrate complexes, mechanism of enzyme catalysis. Enzymology of metabolic regulation and cell signaling. prereq: BMBB or MCDBconcurrent registration is required (or allowed) in G grad student or instr consent
BIOC 8002 - Molecular Biology and Regulation of Biological Processes
Credits: 3.0 [max 3.0]
Grading Basis: A-F only
Typically offered: Every Fall
Classical to current topics in molecular biology. Aspects of DNA, RNA, and protein biology. DNA replication, repair, and recombination. RNA transcription, editing, and regulation. Protein translation/modification. Technologies such as deep-sequencing micro-RNA and prions. prereq: [BMBB or MCDBG] grad student or instr consent
BIOC 8401 - Ethics, Public Policy, and Careers in Molecular and Cellular Biology
Credits: 1.0 [max 2.0]
Course Equivalencies: Bioc 8401/GCD 8401
Grading Basis: S-N or Aud
Typically offered: Every Spring
Ethics of scientific investigation from viewpoint of western scientific enterprise. Relationship between science, culture, and public policies. Careers in molecular/cellular biology. Nontraditional career tracks. Invited speakers, case studies, small-group discussions, lectures. prereq: Grad student in [BMBB or MCDBconcurrent registration is required (or allowed) in G]
BIOC 8888 - Thesis Credit: Doctoral
Credits: 1.0 -24.0 [max 100.0]
Grading Basis: No Grade
Typically offered: Every Fall, Spring & Summer
(No description) prereq: Max 18 cr per semester or summer; 24 cr required
MCDG 8920 - Special Topics
Credits: 1.0 -4.0 [max 8.0]
Grading Basis: S-N only
Typically offered: Every Fall
Special Topics Course in the Molecular, Cellular, Developmental Biology and Genetics Program, including Itasca Research. prereq: Grad MCDG or BMBB major or dept consent
BIOC 5352 - Biotechnology and Bioengineering for Biochemists
Credits: 3.0 [max 3.0]
Course Equivalencies: BioC 5352/MicB 5352
Grading Basis: A-F or Aud
Typically offered: Periodic Spring
Protein biotechnology. Microorganisms used as hosts for protein expression, protein expression, and engineering methods. Production of enzymes of industrial interest. Applications of protein biotechnology in bioelectronics. Formulation of therapeutic biopharmaceuticals. Recommended prerequisites: Biochemistry (BiOC 3021 or 3022 or 4331) and Microbiology MICB 3301
BIOC 5361 - Microbial Genomics and Bioinformatics
Credits: 3.0 [max 3.0]
Typically offered: Every Fall & Spring
Introduction to genomics. Emphasizes microbial genomics. Sequencing methods, sequence analysis, genomics databases, genome mapping, prokaryotic horizontal gene transfer, genomics in biotechnology, intellectual property issues. Hands-on introduction to UNIX shell scripting, genomic data analysis using R and Excel in a computer lab setting. prereq: College-level courses in [organic chemistry, biochemistry, microbiology]
MICA 8002 - Structure, Function, and Genetics of Bacteria and Viruses
Credits: 4.0 [max 4.0]
Grading Basis: A-F or Aud
Typically offered: Every Fall
Structure, function, and metabolism of microorganisms. Microbial genetics. Molecular virology. prereq: [One undergrad or grad course each in [microbiology, genetics, biochemistry]] or instr consent
GCD 8151 - Cellular Biochemistry and Cell Biology
Credits: 2.0 -4.0 [max 4.0]
Grading Basis: A-F only
Typically offered: Every Fall
This course introduces graduate students to fundamental concepts of Biochemical Unity (Part 1) and Cell Theory (Part 2). For Part 1, we will discuss matter of life, equilibrium, entropy & law of mass action, two state systems, random walks & diffusion, rate equations of chemical reactions, and explore how they relate to regulation of biological networks (gene regulation and signal transduction). For Part 2 we will focus on properties of biological membranes, membrane trafficking, protein import & degradation, nuclear structures and their function, as well as molecular motors, cytoskeletal dynamics, and mitosis. The course assumes students have had previous undergraduate courses in cell biology, biochemistry and genetics. prereq: [[[4034 or 8121 or BioC 8002], Biol 4004] or BMBB or MCDBG grad student] or instr consent
MICA 8003 - Immunity and Immunopathology
Credits: 4.0 [max 4.0]
Typically offered: Every Fall
Lymphocyte activation, signal transduction in lymphocytes, antigen receptor genetics, antigen presentation, lymphoid anatomy, adaptive immune responses to microbes, immunodeficiency, immunopathology, cytokines, transplantation, autoimmunity. prereq: Upper level undergrad immunology course or instr consent
MICA 8004 - Cellular and Cancer Biology
Credits: 4.0 [max 4.0]
Grading Basis: A-F or Aud
Typically offered: Every Spring
Fundamental concepts in cellular, molecular, and genetic basis of disease. Molecular basis of inflammation and cancer metastasis. Genetic basis for inherited disorders and gene therapy. Molecular mechanisms of pathogenesis. prereq: [One undergrad or grad course each in [biochemistry, cell biology]] or instr consent
GCD 8131 - Advanced Molecular Genetics and Genomics
Credits: 3.0 [max 3.0]
Typically offered: Every Fall & Spring
Literature-based course in modern molecular genetic and genomic analysis. Students will gain a deep understanding of the fundamental molecular mechanisms controlling inheritance in biological systems. Students will gain a facility in thinking critically and creatively about how genes work at cellular, organismal, and transgenerational levels. Course instruction emphasizes active-learning approaches, student presentations, and group projects. prereq: [3022 or BIOL 4003], [BIOC 3021 or BIOC 4331] or instr consent
GCD 8008 - Mammalian Gene Transfer and Genome Engineering
Credits: 2.0 [max 2.0]
Grading Basis: A-F or Aud
Typically offered: Every Spring
Current gene transfer and genome engineering technology. Applications of genetic modifications in animals, particularly transgenic animals and human gene therapy. prereq: instr consent
PUBH 6450 - Biostatistics I
Credits: 4.0 [max 4.0]
Grading Basis: A-F only
Typically offered: Every Fall & Spring
This course will cover the fundamental concepts of exploratory data analysis and statistical inference for univariate and bivariate data, including: ? study design and sampling methods, ? descriptive and graphical summaries, ? random variables and their distributions, ? interval estimation, ? hypothesis testing, ? relevant nonparametric methods, ? simple regression/correlation, and ? introduction to multiple regression. There will be a focus on analyzing data using statistical programming software and on communicating the results in short reports. Health science examples from the research literature will be used throughout the course. prereq: [College-level algebra, health sciences grad student] or instr consent
SCB 8181 - Stem Cell Biology
Credits: 3.0 [max 3.0]
Course Equivalencies: GCD 8181/SCB 8181
Typically offered: Every Fall
Stem cell research and its applications. Critical analysis, written summaries/critiques, oral presentations. prereq: [[GCD 4034], [GCD 4161]] or equiv or instr consent
STAT 5021 - Statistical Analysis
Credits: 4.0 [max 4.0]
Typically offered: Every Fall & Spring
Intensive introduction to statistical methods for graduate students needing statistics as a research technique. prereq: college algebra or instr consent; credit will not be granted if credit has been received for STAT 3011
MICA 8010 - Microbial Pathogenesis
Credits: 3.0 [max 3.0]
Grading Basis: A-F or Aud
Typically offered: Fall Even Year
Molecular mechanisms of bacterial/viral pathogenesis. Strategies of disease causation/interaction with host, regulation of virulence factors, mechanism of virulence factor transmission to other microbes. prereq: MICa grad student or instr
BIOC 5216 - Current Topics in Signal Transduction
Credits: 2.0 [max 3.0]
Grading Basis: A-F only
Typically offered: Every Spring
Mechanisms by which biological signals evoke biochemical responses.
BIOC 5528 - Spectroscopy and Kinetics
Credits: 4.0 [max 4.0]
Typically offered: Every Spring
Biochemical dynamics from perspectives of kinetics and spectroscopy. Influence of structure, molecular interactions, and chemical transformations on biochemical reactions. Focuses on computational, spectroscopic, and physical methods. Steady-state and transient kinetics. Optical and magnetic resonance spectroscopies. prereq: Intro physical chemistry or equiv; intro biochemistry recommended
CHEN 8754 - Systems Analysis of Biological Processes
Credits: 3.0 [max 3.0]
Typically offered: Every Spring
Relating biological processes at molecular level to physiological level of cells/organisms/populations. Methodology for analyzing data. Quantification of molecular interplays. prereq: Grad student in [life sciences or chemical/physical sciences or engineering]; ChEn students must take A/F
BIOC 5444 - Muscle
Credits: 3.0 [max 3.0]
Course Equivalencies: BioC 5444/ Phsl 5444
Typically offered: Every Spring
Muscle molecular structure/function and disease. Muscle regulation, ion transport, and force generation. Muscular dystrophy and heart disease. prereq: 3021 or BIOL 3021 or 4331 or BIOL 4331 or PHSL 3061 or instr consent
CHEM 8011 - Mechanisms of Chemical Reactions
Credits: 4.0 [max 4.0]
Typically offered: Every Fall
Reaction mechanisms and methods of study. Mechanistic concepts in chemistry. Gas phase reactions to mechanisms, "electron pushing" mechanisms in organic reactions, mechanism of enzymatic reactions. Kinetic schemes and other strategies to investigate mechanisms. prereq: 2302 or equiv
CHEM 8021 - Computational Chemistry
Credits: 4.0 [max 4.0]
Typically offered: Every Spring
Modern theoretical methods used in study of molecular structure, bonding, reactivity. Concepts/practical applications. Determination of spectra, relationship to experimental techniques. Molecular mechanics. Critical assessment of reliability of methods. prereq: 4502 or equiv
CHEM 8411 - Introduction to Chemical Biology
Credits: 4.0 [max 4.0]
Typically offered: Every Fall
Chemistry of amino acids, peptides, proteins, lipids, carbohydrates, and nucleic acids. Structure, nomenclature, synthesis, and reactivity. Overview of techniques used to characterize these biomolecules. prereq: 2302 or equiv
CHEM 8412 - Chemical Biology of Enzymes
Credits: 4.0 [max 4.0]
Course Equivalencies: Chem 8412/MedC 8412
Typically offered: Periodic Spring
Enzyme classification with representative examples from current literature. Strategies used to decipher enzyme mechanisms. Chemical approaches for control of enzyme catalysis. prereq: 2302 or equiv
CHEM 8735 - Bioinorganic Chemistry
Credits: 4.0 [max 4.0]
Typically offered: Periodic Fall
Survey of role of metal ions in biology; emphasizes structure, function, and spectroscopy of metalloproteins and their synthetic analogs. prereq: 4701 or equiv, grad chem major or instr consent
PHCL 5111 - Pharmacogenomics
Credits: 3.0 [max 3.0]
Grading Basis: A-F or Aud
Typically offered: Every Spring
Human genetic variation, its implications. Functional genomics, pharmacogenomics, toxicogenomics, proteomics. Interactive, discussion-based course. prereq: Grad student or instr consent Keywords: Pharmacology, Pharmacogenomics, Toxicogenomics, Proteomics, Genetics, Drug
PUBH 7445 - Statistics for Human Genetics and Molecular Biology
Credits: 3.0 [max 3.0]
Typically offered: Every Spring
Introduction to statistical problems arising in molecular biology. Problems in physical mapping (radiation hybrid mapping, DDP), genetic mapping (pedigree analysis, lod scores, TDT), biopolymer sequence analysis (alignment, motif recognition), and micro array analysis. prereq: [6450, [6451 or equiv]] or instr consent; background in molecular biology recommended
MICA 8013 - Translational Cancer Research
Credits: 2.0 [max 2.0]
Grading Basis: A-F or Aud
Typically offered: Every Spring
Clinical issues in cancer research. Discuss translational research projects as they pertain to a variety of cancers. prereq: 8004 or instr consent
GRAD 8101 - Teaching in Higher Education
Credits: 3.0 [max 3.0]
Grading Basis: OPT No Aud
Typically offered: Every Fall, Spring & Summer
Teaching methods/techniques. Active learning, critical thinking, practice teaching, and preparing a portfolio to document/reflect upon teaching. Readings, discussion, peer teaching, e-mail dialog, reflective writing, co-facilitation of course. prereq: Non-Degree Students: contact pffcollege consentumn.edu with questions about registration. If adding a section after first class meeting, contact your instructor as soon as you enroll.
GRAD 8200 - Teaching and Learning Topics in Higher Education
Credits: 1.0 [max 4.0]
Grading Basis: A-F only
Typically offered: Every Fall & Spring
Create course materials for context/discipline. Assess student learning. Write action plan. Topics may include active learning in sciences, teaching with technology, multicultural education, teaching in clinical settings, learning-community course design.
BIOC 5309 - Biocatalysis and Biodegradation
Credits: 3.0 [max 3.0]
Course Equivalencies: Bioc 5309/MicE 5309
Typically offered: Every Spring
Fundamentals of microbial enzymes/metabolism as pertaining to biodegradation of environmental pollutants/biosynthesis for making commodity chemicals. Practical examples. Guest speakers from industry.
BIOC 5351 - Protein Engineering
Credits: 3.0 [max 3.0]
Grading Basis: A-F or Aud
Typically offered: Every Fall
Key properties of enzymes/molecular basis, computer modeling strategies, mutagenesis strategies to create protein variants, expression/screening of protein variants. Evaluate research papers, identify unsolved practical/theoretical problems, plan protein engineering experiment.
CSCI 5461 - Functional Genomics, Systems Biology, and Bioinformatics
Credits: 3.0 [max 3.0]
Typically offered: Every Spring
Computational methods for analyzing, integrating, and deriving predictions from genomic/proteomic data. Analyzing gene expression, proteomic data, and protein-protein interaction networks. Protein/gene function prediction, Integrating diverse data, visualizing genomic datasets. prereq: 3003 or 4041 or instr consent
GRAD 5102 - Preparation for University Teaching for Nonnative English Speakers
Credits: 2.0 [max 2.0]
Grading Basis: S-N or Aud
Typically offered: Every Fall & Spring
Theory/practice of teaching in higher education in the United States. Emphasizes clear oral classroom communication and development of presentation skills. Students practice in a simulated instructional setting. prereq: English Language Proficiency Rating of 4; Contact cei@umn.edu for permission number.