ABSTRACT
Adaptive chemical behavior is essential for an organism's function and survival, and it is no surprise that biological systems are capable of responding both rapidly and selectively to chemical changes in the environment. To elucidate an organism's biochemistry, its chemical reactions need to be characterized in ways that reflect the normal physiology in vivo. This is a challenging experimental problem because biological systems are inherently complex with myriads of interlinked chemical networks orchestrating processes that are mostly irreversible in nature. One successful approach for simplifying the study of biochemical reactions is to analyze them under controlled reversible equilibrium conditions in vitro that approximate the range of physiological conditions found in vivo. Because this approach has helped elucidate some of the chemical mysteries of complex biological systems, many topics presented in modern biochemistry courses are essentially rooted in the chemistry of reversible equilibrium reactions. Since most undergraduate biochemistry courses typically require students to complete year-long general and organic chemistry courses, biochemistry instructors may assume that entering students have sufficient understanding of basic reversible equilibrium chemistry to move forward into more advanced biochemical topics. However, this assumption is at odds with our experience in that many entering students seem confused by the conventions, language, symbolic formalism, and/or mathematical tools normally use to describe reversible equilibrium reactions. Part of the problem here may stem from how certain basic chemical concepts are taught (or are not taught) in their prerequisite chemistry courses. Here, we identify some conceptual barriers that many students seem to confront and we discuss instructional strategies designed to help students "connect the dots," so to speak, and better understand how dynamic biological processes can be analyzed in terms of reversible equilibrium chemistry.
ABSTRACT
Structure/function relationships are fundamental to understanding the properties of biological molecules, and thus it is imperative that biochemistry students learn how to analyze such relationships. Here we describe Chime-based web page templates and tutorials designed to help students develop their own strategies for exploring macromolecular three-dimensional structures like those on our course website. The templates can easily be customized for any structure of interest, and some templates include a Command Entry Line and a Message Recall Box for more refined macromolecular exploration using RasMol/Chime image modification commands. The tutorials present students with an integrated overview of the image modification capabilities of the Chime plug-in and its underlying RasMol-based command structure as accessed through the Command Entry Line. The tutorial also illustrates how RasMol/Chime command syntax addresses specific formatted structural information in a standard Protein Data Bank file. Judging by the high quality of structure-based presentations given by students who have used these templates and tutorials, it appears that these resources can help students learn to analyze complex macromolecular structures while also providing them with convenient tools for creating scientifically meaningful and visually effective molecular images to share with others. (The templates, tutorials, and our course website can be viewed at the following URLs, respectively: tutor.lscf.ucsb.edu/instdev/sears/biochemistry/presentations/demos-downloads.htm, tutor.lscf.ucsb.edu/instdev/sears/biochemistry/tutorials/pdbtutorial/frontwindow.html, and tutor.lscf.ucsb.edu/instdev/sears/biochemistry/.).
ABSTRACT
The mouse Fc gamma RI is one of the most fundamentally important FcRs. It participates in different stages of immunity, being a low affinity receptor for T-independent IgG3 and yet a high affinity receptor for IgG2a, the product of a Th1 immune response. However, analysis of this receptor has been difficult due largely to the failure to generate specific Abs to this FcR. We have made use of the polymorphic differences between BALB/c and NOD/Lt mice to generate mAb specific for the Fc gamma RI of BALB/c and the majority of in-bred mouse strains. Three different mAb were obtained that detected Fc gamma RI encoded by the more common Fcgr1(a) and Fcgr1(b) alleles, and although they identified different epitopes, none inhibited the binding of IgG to Fc gamma RI. When bound to Fc gamma RI, these mAb induced calcium mobilization upon cross-linking. Several novel observations were made of the cellular distribution of Fc gamma RI. Resting and IFN-gamma-induced macrophages expressed Fc gamma RI as well as mast cell lines. Both bone marrow-derived and freshly isolated dendritic cells from spleen and lymph nodes expressed Fc gamma RI. A class of DC, uniquely found in s.c. lymph nodes, expressed the highest level of Fc gamma RI and also high levels of MHC class II, DEC205, CD40, and CD86, with a low level of CD8 alpha, corresponding to the phenotype for Langerhans-derived DC, which are highly active in Ag processing. Thus, in addition to any role in effector functions, Fc gamma RI on APC may act as a link between innate and adaptive immunities by binding and mediating the uptake of T-independent immune complexes for presentation, thereby assisting in the development of T-dependent immune responses.
