Mura Lab

at the University of Virginia

Teaching activities, Educational resources

Lecture– or lab–based courses (this page)
  • Chem 4411: Biochemistry Laboratory I (Fa2010, Fa2012½, Fa2013½, Fa2014½, Fa2015, Fa2016)
  • Chem 4421: Biochemistry Laboratory II (Sp2010, Sp2012, Sp2013½, Sp2014½, Sp2017)
  • Chem 5410/5430/7430: Advanced Biochemistry I (Fa2008, Fa2009, Fa2010, Fa2014½)
  • Chem 5420: Advanced Biochemistry II (Sp2016)
  • Biop 7051/8559: X-ray Diffraction Series (Fa2013, Fa2014)
  • Biop 5060: Molecular Physiology & Biophysics (guest lectures in Sp2009, Sp2010)
  • Biol 4480: Biomolecular Structure (guest lectures in Fa2010, Fa2011, Sp2014)
Educational initiatives
  • UVaCompBio (v0.1, Sp2011)
  • P4BProgramming for Bioscientists
  • SbCbMbStructural biology, Computational biology, Molecular biophysics series (2010–)
  • BioLEdBiochemistry Lab Education Resource (2011–)
Other pedagogical resources
General notes:
  • [u] = undergrad, [g] = grad (mostly)
  • 'Fa'/'Sp' = Fall/Spring semester
  • '½' = co-taught

Biop7051/8559 — X-ray Diffraction Series [g/u]

Description

This X-ray Diffraction & Macromolecular Crystallography Series grew out of our SbCbMb initiative. The 1-credit course is largely student-led: There are generally no formal presentation slides — rather, each session progresses on the chalkboard. Together, we work our way through the chapters of Sherwood & Cooper's crystallography text. When pertinent, there are occasional journal club-style presentations (e.g., the discussion of crystal symmetry includes a presentation on Wukowitz & Yeates' theory of non-uniform space-group distributions). Further information is at http://muralab.org/SbCbMb.

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, 3-credit 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 2012

Course website → See the UVa Collab site.

Spring 2010

Syllabus → Chem4421_Syllabus_Sp2010.pdf
Course website → UVa Collab site for the class

Chem5410/5430/7430 — Advanced Biochemistry I [g/u]

General Information

I am the developer and instructor of this 3-credit course, attened by graduate (mostly) and undergraduate students. 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 2014

Course website → See the UVa Collab site.

Fall 2010

Course website → See the UVa Collab site.

Fall 2009

Syllabus → Chem7430_Syllabus_24aug09.pdf
Course website → See the UVa Collab site.

Fall 2008

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

For the Sp2010 course, see BIOP_PHY_5060_Announcement_Sp2010.pdf.

Lecture Slides & Notes

  • Spring 2009 → See the UVa Collab site.
  • Spring 2010 → See the UVa Collab site.

Biol4480 — Structure and Function of Complex Macromolecules [u]

General Information

  • Prof. Bob Kretsinger is the director and 1° instructor of this upper-level biology course. I provide a guest lecture on nucleic acid flexibility and dynamics.

Course Description

Coming soon...

Lecture Slides & Notes

  • Fall 2010 → See the UVa Collab site.
  • Fall 2011 → See the UVa Collab site.