Reversible ligand binding reactions: Why do biochemistry students have trouble connecting the dots?

Biochem Mol Biol Educ

From the Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California 93106-9610.

Published: March 2007

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.

Download full-text PDF

Source
http://dx.doi.org/10.1002/bmb.29DOI Listing

Publication Analysis

Top Keywords

reversible equilibrium
20
biological systems
12
biochemistry courses
8
equilibrium reactions
8
chemistry courses
8
entering students
8
equilibrium chemistry
8
reversible
6
students
6
chemical
6

Similar Publications

Thermoelectrochemical Method for Quantification of the Micellization Entropy of Redox-Active Polymers.

ACS Macro Lett

January 2025

Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

Redox-active micelles undergo reversible association and dissociation in response to their redox potential and are promising materials for various applications, such as drug delivery and bioimaging. Evaluation of the micellization entropy is critical in controlling the thermodynamics of micelle formation. However, conventional methods such as isothermal titration calorimetry and surface tensiometry require a long measurement time to observe changes in the heat flow or the surface tension caused by the micellization.

View Article and Find Full Text PDF

Hydrophobicity is associated with drug transport across membranes and is expressed as the partition coefficient log P for neutral drugs and the distribution coefficient log D for acidic and basic drugs. The log P and log D predictions are deductively (or with artificial intelligence) estimated as the sum of the partial contributions of the scaffold and substituents of a single molecule and are used widely and affirmatively. However, their predictions have not always been comprehensively accurate beyond scaffold differences.

View Article and Find Full Text PDF

αβT cells protect vertebrates against many diseases, optimizing surveillance using mechanical force to distinguish between pathophysiologic cellular alterations and normal self-constituents. The multi-subunit αβT-cell receptor (TCR) operates outside of thermal equilibrium, harvesting energy via physical forces generated by T-cell motility and actin-myosin machinery. When a peptide-bound major histocompatibility complex molecule (pMHC) on an antigen presenting cell is ligated, the αβTCR on the T cell leverages force to form a catch bond, prolonging bond lifetime, and enhancing antigen discrimination.

View Article and Find Full Text PDF

Reversible protein phosphorylation directs essential cellular processes including cell division, cell growth, cell death, inflammation, and differentiation. Because protein phosphorylation drives diverse diseases, kinases and phosphatases have been targets for drug discovery, with some achieving remarkable clinical success. Most protein kinases are activated by phosphorylation of their activation loops, which shifts the conformational equilibrium of the kinase toward the active state.

View Article and Find Full Text PDF

Most of the recent work in psychedelic neuroscience has been done using noninvasive neuroimaging, with data recorded from the brains of adult volunteers under the influence of a variety of drugs. While these data provide holistic insights into the effects of psychedelics on whole-brain dynamics, the effects of psychedelics on the mesoscale dynamics of neuronal circuits remain much less explored. Here, we report the effects of the serotonergic psychedelic N,N-diproptyltryptamine (DPT) on information-processing dynamics in a sample of in vitro organotypic cultures of cortical tissue from postnatal rats.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!