A project‐based biochemistry laboratory promoting the understanding and uses of fluorescence spectroscopy in the study of biomolecular structures and interactions

Abstract

A laboratory project for a first semester biochemistry course is described, which integrates the traditional classroom study of the structure and function of biomolecules with the laboratory study of these molecules using fluorescence spectroscopy. Students are assigned a specific question addressing the stability/function of lipids, proteins, or nucleic acids, and asked to design an experiment to answer the question using fluorescence methodologies. Students study phase equilibria and determine the critical micelle concentration of single chain amphiphiles, the melting point of multilamellar vesicles, and the melting points and thermodynamic constants (K eq , DG 0 , DH 0 and DS 0 ) for denaturation of ds-DNA and proteins. In addition, they examine binding properties of proteins. These laboratory experiments are designed to support student learning of the major themes of structure and function in the course.Keywords: Laboratory exercises, protein structure function and folding, nucleic acid structure function and processing, membrane assembly and vesicle trafficking.Fluorescence spectroscopy is an increasingly essential tool for the study of biomolecular properties. Steadystate fluorescence properties (emission intensity, excitation and emission wavelength maxima) are very sensitive to the environment of the fluorophore and are readily used to study complex biological processes such as molecular interactions, stability, structure, and function. Given its widespread application in the study of biomolecules, it is important to extend the study of fluorescence theory and its applications past physical or biophysical chemistry courses [1] to traditional biochemistry courses as well. Undergraduate students in biology and biochemistry often have qualitative exposure to fluorescence microscopy, but are offered little that would increase their understanding of the principles involved and of a myriad of additional applications.If understanding is enhanced by providing a ''need-toknow'' environment, then continual integration of fluorescence theory into course and application into laboratory would provide maximal opportunity for students to learn the science and utility of fluorescence. Previous methods to achieve integration of content or methodology in course and laboratory have ranged from project-based laboratories based on specific techniques/instrumentation [2-5], specific molecules/molecular systems [6][7][8][9], or the development of entirely new project-based biochemistry laboratory courses [10,11]. Many articles have been published concerning the use of fluorescence spectroscopy in undergraduate laboratories to study specific biomolecules [12][13][14][15][16][17][18], but none have addressed the concept of applying the technique more broadly to complement the course and its themes in general. Over the last six years, we have conducted a variety of experiments for a biochemistry laboratory project integrating experimental uses of fluorescence spectroscopy with the fundamental themes of structure and function pres...

A survey on faculty perspectives on the transition to a biochemistry course‐based undergraduate research experience laboratory

“…Several well‐known biochemistry laboratory manuals have been published but I do not recall meeting any biochemists who teach their entire undergraduate biochemistry laboratory course from one of these texts. One or two experiments may be adopted, but we frequently develop our courses around projects that may connect to our research interests . The members of the team had all developed unique biochemistry teaching laboratory courses on their campuses and had all experimented to some extent with inquiry‐based learning.…”

“…A recent search of the literature revealed 19 different articles about noncookbook teaching laboratories containing elements of research dating back to a 1975 article by Paul Melius entitled, “A creative, research approach to the undergraduate biochemistry laboratory” . Many of the article titles included the words “integrated” “project‐based” or “project‐oriented” . In addition, many of these courses were designed around a single enzyme or protein The incorporation of research in the teaching setting has been widely advocated .…”

The Interaction Mode of Groove Binding Between Quercetin and Calf Thymus DNA Based on Spectrometry and Simulation

“…Fluorescence spectroscopy, which is used to measure the change in fluorescence intensity, can be used to study the interaction between compounds and DNA . However, CT‐DNA has very weak fluorescence in solution.…”

The effect of student-centered teaching and problem-based learning on academic achievement in science

“…Hedley (2013) revealed that the use of geospatial technologies (GST) within a student/teacher/scientist partnership improved the geospatial skills and atmospheric science concept knowledge. Briese and Jakubowsk (2007) found that a laboratory project biochemistry course which integrates the traditional classroom study of the structure and function of biomolecules with the laboratory study improved understanding of the students on fluorescence spectroscopy. Differentiated teaching (Alexander, 2013), and experiential learning (Mohan, 2015) had statistically significant greater mean scores in academic performance and in critical thinking questions on the living environment, earth science and chemistry.…”