Lecture– or lab–based courses (this page)
Educational initiatives
- UVaCompBio (v0.1, Sp2011)
- SbCbMb – Structural biology, Computational biology, Molecular biophysics series (2010–)
- BioLEd – Biochemistry Lab Education Resource (2011–)
Other pedagogical resources
UVaCompBio — Computational Biology @ UVa [u]
Description
This new, Mead-funded educational series is being developed by Cameron Mura
over Spring 2011, in order to introduce UVa undergraduates to scientific
research areas that span the biological and computational sciences. The primary
motivation stems from the fact that, in the 21st century, the bio-* sciences
(biochemistry, molecular biology, etc.) will continue to become increasingly
quantitative and computational in nature. The webspace for this new initiative
is at
http://muralab.org/UVaCompBio.
Chem4411 — Biochemistry Lab I [u]
Course Description
Coming soon, to a laboratory near you...
Fall 2010
Syllabus → Coming soon...
Course website → Coming soon...
Chem4421 — Biochemistry Lab II [u]
Course Description
This is a relatively new, one-semester undergraduate lab course. First offered in its current form in
Spring ‘09, the lab has been revamped and with a completely new approach
based on independent biochemistry research projects. Thus, the curriculum
has been designed as a research-based laboratory, wherein students will apply
the ideas learned in previous Biochemistry labs and lectures to characterize
the enzymatic activity of proteins for which 3D structures have been
determined by the federally-funded Joint Center for Structural Genomics
(JCSG). In particular, proteins from the hyperthermophilic bacterium
Thermatoga maritima ('Tma'; Table 1) were chosen if they (a) are
anticipated to have an enzymatic activity and (b) this activity can be
readily characterized via UV-VIS spectrophotometric assays. The proteins have
been previously expressed in Escherichia coli, using expression vectors
(‘plasmids’) that will be provided to the student. Most important is the fact
that the functions of these proteins remain uncharacterized. Putative
functions of your POI have been predicted (and ‘annotated’) via
bioinformatics tools, based on any structural and sequence-level
similarity between it and other proteins (of already-known enzymatic
function). Your mission is to (1) over-express & purify your POI (via
Ni2+-chelating affinity chromatography), according to the protocols which
were already used (by the JCSG) for crystallization, and (2) assay
putative enzymatic activities to try and determine the biochemical
properties and possible function of the POI.
Spring 2010
Syllabus → Chem4421_Syllabus_Sp2010.pdf
Course website → UVa Collab site for the class
Chem5430/7430 — Advanced Biochemistry I [g/u]
General Information
I am the developer and instructor of this course. Feel free to contact me for
further information about it.
Course Description
This one-semester, graduate-level course focuses on the fundamental
biochemical and biophysical properties of the two main classes of
biological macromolecules — nucleic acids (DNA, RNA), and proteins. Because
biochemistry is a vast subject that encompasses many traditional areas of
chemistry (biophysical, bioorganic, bioinorganic, etc.), as well as newer
areas (bioinformatics, genomics, proteomics, etc.), this course does not
attempt a comprehensive treatment. Instead, the focus is on a ubiquitous
cellular process (namely, information flow from DNA ➙ RNA ➙ protein),
with the three-fold aim of (i) introducing the biological context for
chemical processes such as DNA replication and RNA transcription; (ii)
elucidating the physical principles that underlie the structure and
function of proteins, nucleic acids, and other biopolymers involved in
this process; and (iii) introducing some of the key methodologies used to
acquire such knowledge (e.g., crystallography, calorimetry). By the end
of the course, one will be able to critically read a review article
(intended for a “general audience”) in some biochemical area of interest,
identify a key question or unsolved problem in that area, devise a
research project that would be suitable for addressing such questions,
and synthesize the background & investigative plan into an articulate and
well thought-out research proposal.
Fall 2008
Course website → See the UVa Collab site.
Fall 2009
Syllabus → Chem7430_Syllabus_24aug09.pdf
Course website → See the UVa Collab site.
Fall 2010
Course website → See the UVa Collab site.
Biop5060 — Molecular Physiology: From Molecular Machines to Biological Information Processing [g]
General Information
- Prof. Lukas Tamm is the director and 1° instructor of this
biophysics course, which is taught by several 2° instructors of which
I have been one. My past lectures have focused on fundamentals of
molecular dynamics (MD) simulation methods.
Course Description
Lecture Slides & Notes
- Spring 2009 → See the UVa Collab site.
- Spring 2010 → See the UVa Collab site.