Biochemistry, Biophysics & Structural Biology

 

BBSB Degree Requirements

Schedule of Classes

 

 


Molecular Biology 254A: Concepts in Molecular Biosciences – Core Course

Limited to human genetics and molecular biology graduate students. Five-week course covering four basic experimental approaches of biochemistry and molecular biology in context of various specific topics, including (1) structural biology, with protein and nucleic acid structure and molecular recognition, (2) use of cell-free and purified in vitro systems to dissect reaction mechanisms, (3) biochemical approaches to dissecting complex reactions/pathways in cells, and (4) enzymology and protein chemistry. Letter grading.

Units: 3

Instructors:


Molecular Biology 254B: Concepts in Molecular Biosciences – Core Course

Five-week course. Molecular mechanisms underlying complex problems in cell biology. Experimental approaches used to define mechanisms involved in protein targeting, cell structure and subcellular organization, cell communication, and intracellular signaling. Analysis of pathways that connect these cellular processes. Letter grading.

Units: 3

Instructors:


Molecular Biology 255: Scientific Writing –Core Course

Limited to first-year Molecular Biology Ph.D. students. Improvement of academic literacy through development of specific skills in scientific writing. Review of principles of effective writing using practical examples and exercises. Topics include principles of good writing, tricks for writing faster and with less anxiety, format of scientific manuscripts, art of editing, and issues in publication and peer review.

Units: 3

Instructors: Luisa Iruela-Arispe


Molecular Biology 254C: Concepts in Molecular Biosciences – Core Course

Important biological problems that have been genetically analyzed in different organisms or small number of related problems. Major genetic approaches used in relevant organisms, including both forward and reverse genetic approaches, genetic interactions between genes (genetic enhancers and suppressors), transgenic technology, and systematic genomic strategies

CHEM M230B & D may be taken instead of MOL BIO 254 C & D.

Units: 3

Instructors: Human Genetics: Paivi Pajukanta & Roel Ophoff, Unraveling Developmental Pathways: Deborah Krakow, Using Genetics: Jeff Long.


Molecular Biology 254D: Concepts in Molecular Biosciences – Core Course

Application of biochemical, molecular biological, genetic, and cell biological approaches to understand specialized topics in life and biomedical sciences, including developmental disease, stem cell biology, synaptic transmission in nervous system, cancer, and heart disease.

CHEM M230B & D may be taken instead of MOL BIO 254 C & D.

Units: 3

Instructors: Biology and Promise: April Pyle & Kathrin Plath, Mechanical Forces: Alison Frand & Srinivasa Reddy, Mechanisms: Peter Bradley, Kent Hill & Jeff Miller.


CHEM M230B: Structural Molecular Biology – Core Course

Selected topics from principles of biological structure, structures of globular proteins and RNAs; structures of fibrous proteins, nucleic acids, and polysaccharides; harmonic analysis and Fourier transforms; principles of electron, neutron, and X-ray diffraction; optical and computer filtering; three-dimensional reconstruction.

CHEM M230B & D may be taken instead of MOL BIO 254 C & D.

Units: 4

Instructors:Todd Yeates, Robert Clubb, David Eisenberg & Juli Feigon


CHEM M230D: Structural Molecular Biology Laboratory – Core Course

Methods in structural molecular biology, including experiments utilizing single crystal X-ray diffraction, low angle X-ray diffraction, electron diffraction, optical diffraction, optical filtering, three-dimensional reconstruction from electron micrographs, and model building..

CHEM M230B & D may be taken instead of MOL BIO 254 C & D.

Units: 2

Instructors:Todd Yeates, Robert Clubb, David Eisenberg & Juli Feigon


MIMG C234: Ethics and Accountability in Biomedical Research – Ethics Seminar

Designed for graduate students and undergraduates who have credit for life sciences or biomedical individual studies 199 course. Responsibilities and ethical conduct of investigators in research, data management, mentorship, grant applications, and publications. Responsibilities to peers, sponsoring institutions, and society. Conflicts of interest, disclosure, animal subject welfare, human subject protection, and areas in which investigational goals and certain societal values may conflict. Concurrently scheduled with course C134. S/U grading.

MIMG C234, CHEM C250, or CHEM 203B is required

Units: 2

Instructors: Lynn Talton


CHEM C250: Research Integrity in Cellular Biology, Molecular Biology, and Biochemistry Research –Ethics Seminar

Data analysis and management, statistical methods, use of antibody and kit reagents, figure preparation, authorship, mentoring, human subjects protection, animal subject protection, and conflict of interest.

MIMG C234, CHEM C250, or CHEM 203B is required

Units: 2

Instructors: Clarke, S.G. & Awad, A.M.


CHEM 203B: Ethics in Chemical Research – Ethics Course

Discussion of ethics in graduate education, teaching, and chemical research, including issues such as conflicts of interest, plagiarism, intellectual property, sexual harassment, and other topics related to ethical conduct of research.

MIMG C234, CHEM C250, or CHEM 203B is required

Units: 2

Instructors: Houk, K.N.

 

Bioinformatics

 

Bioinformatics Degree Requirements

 


Bioinformatics M202: Bioinformatics Interdisciplinary Research Seminar – Required Core Course

Concrete examples of how biological questions about genomics data map to and are solved by methodologies from other disciplines, including statistics, computer science, and mathematics.

Taken: Year 1. Fall Quarter.

Last Offered: Spring, F 9-9:50 a.m.

Instructors: Wollman, R.


MIMG C234: Ethics and Accountability in Biomedical Research – Required Ethics Seminar

Designed for graduate students and undergraduates who have credit for life sciences or biomedical individual studies 199 course. Responsibilities and ethical conduct of investigators in research, data management, mentorship, grant applications, and publications. Responsibilities to peers, sponsoring institutions, and society. Conflicts of interest, disclosure, animal subject welfare, human subject protection, and areas in which investigational goals and certain societal values may conflict. Concurrently scheduled with course C134. S/U grading.

MIMG C234, CHEM C250, or CHEM 203B is required

Taken: Year 1. Spring Quarter.

Last Offered: Spring, T12 – 1:50 p.m. & F 10-11:50 a.m.

Instructors: Lynn Talton


Bioinformatics M252: Seminar: Advanced Methods in Computational Biology – Required Seminar

Designed for graduate students. Examination of computational methodology in bioinformatics and computational biology through presentation of current research literature. How to select and apply methods from computational and mathematical disciplines to problems in bioinformatics and computational biology; development of novel methodologies.

Taken: Year 1 & 2

Last Offered: Spring, M 4-5:50 p.m..

Instructors: Yi Xing & Peipei Ping


Bioinformatics 224: Computational Genetics– Required Core Course

Introduction to current quantitative understanding of human genetics and computational interdisciplinary research in genetics. Topics include introduction to genetics, human population history, linkage analysis, association analysis, association study design, isolated and admixed populations, population substructure, human structural variation, model organisms, and genotyping technologies. Computational techniques include those from statistics and computer science.

Taken: Spring Quarter.

Last Offered: Spring, MW 2 – 3:50 p.m.

Instructors: Halperin, E.


Bioinformatics M260A: Introduction to Bioinformatics – Required Core Course

Introduction to bioinformatics and methodologies, with emphasis on concepts and inventing new bioinformatic methods. Focus on sequence analysis and alignment algorithms.

Taken: Fall Quarter.

Last Offered: Fall, MW 12-12:50 p.m.

Instructors:Christopher Lee


Bioinformatics M260B: Algorithms in Bioinformatics and Systems Biology – Required Core Course

Designed for engineering students as well as students from biological sciences and medical school. Development and application of computational approaches to biological questions, with focus on formulating interdisciplinary problems as computational problems and then solving these problems using algorithmic techniques. Computational techniques include those from statistics and computer science.

Taken: Winter Quarter.

Last Offered: Winter, MW 2-3:50 p.m.

Instructors:Eleazar Eskin