Using Physical Models of Biomolecular Structures To Teach Concepts of Biochemical Structure and Structure Depiction in the Introductory Chemistry Laboratory

We have developed a multiweek laboratory project in which students isolate myoglobin and characterize its structure, function, and redox state. The important laboratory techniques covered in this project include sizeexclusion chromatography, electrophoresis, spectrophotometric titration, and FTIR spectroscopy. Regarding protein structure, students work with computer modeling and visualization of myoglobin and its homologues, after which they spectroscopically characterize its thermal denaturation. Students also study protein function (ligand binding equilibrium) and are instructed on topics in data analysis (calibration curves, nonlinear vs. linear regression). This upper division biochemistry laboratory project is a challenging and rewarding one that not only exposes students to a wide variety of important biochemical laboratory techniques but also ties those techniques together to work with a single readily available and easily characterized protein, myoglobin.

Section: Period 3 Part Ib: Myoglobin Function: Ligand Bindingmentioning

confidence: 99%

Section: Periods 4 Andmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Myoglobin structure and function: A multiweek biochemistry laboratory project

Silverstein

Kirk

Meyer

et al. 2015

“…The sequence of successive bases is easily recognized by numbering (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12) and it can be followed from both sides because of the transparency of the sheets the base pairs are printed on. One letter nucleotide codes (A, T, C, G) are also written in color.…”

Section: Model Building and Ways To Show Biochemical Detailsmentioning

confidence: 99%

“…We have found that many students fail to grasp three-dimensional details when DNA and protein structures are introduced in these ways. Several physical models of DNA and protein made of paper, wooden, metallic or plastic materials have been developed for teaching purposes [1][2][3][4][5][6][7][8][9][10]. These have features useful for illustrating certain important structural aspects of these molecules.…”

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confidence: 99%

Making ordered DNA and protein structures from computer‐printed transparency film cut‐outs

Jittivadhna

Ruenwongsa

Panijpan

2009

Instructions are given for building physical scale models of ordered structures of B-form DNA, protein ahelix, and parallel and antiparallel protein b-pleated sheets made from colored computer printouts designed for transparency film sheets. Cut-outs from these sheets are easily assembled. Conventional color coding for atoms are used for both types of biopolymers. Arrows facilitate following chain direction for the polypeptides. For DNA, the 5 0 to 3 0 direction is guided by a 5 0 phosphate group and a free hydroxyl group. Important chiral centers, for example, a-carbon, deoxyribose C1 0 , are easily made. The main advantages of this version of DNA are the proportional major and minor grooves as in the actual molecule. More importantly, because of transparency of the film one can see successive base-pair stacking very clearly and also the sense of relative base-pair rotation. Because of the introduction of two central metal wire axes, the model of B-form DNA can be twisted to give a rather good representation of A-form and even a semblance of a left-handed helix. The models of secondary structure of protein allow a better insight into the axial alignment of side chains, the formation of hydrogen bond, the handedness of the a-helix, and the backbone connection between the b-strands. Students taught by these models understand 3D features of the biopolymers better than from textbook illustrations, computer graphic representations, and even common paper and plastic versions.Keywords: biomolecular models, DNA, protein alpha-helix, protein beta-sheet.Biophysical chemistry and chemical biology will play a crucial role in the post-genomic era. Fundamental understanding of the three-dimensional structures of the macromolecules and their folding, for example, DNA and protein, may make the students better understand biology at the molecular level and may facilitate their pursuits of advanced studies. Generally, polypeptide chains, protein a-helix and b-sheet, polynucleotide chain, and B-form DNA are common biochemical structures taught to beginning students. In routine classroom teaching, twodimensional depictions in textbooks and three-dimensional computer-generated presentations are often used to show students these molecular structures. We have found that many students fail to grasp three-dimensional details when DNA and protein structures are introduced in these ways. Several physical models of DNA and protein made of paper, wooden, metallic or plastic materials have been developed for teaching purposes [1][2][3][4][5][6][7][8][9][10]. These have features useful for illustrating certain important structural aspects of these molecules. However, each of these models has a number of limitations. For example, the ball-and-stick and the space-filling models, while illustrating the molecular structure in atomic detail, are usually expensive and not easy to construct. Some of the existing models may be easy to acquire and assemble, but they are not to the scale and are too abstract as representations. Most use opaque material...

Beyond textbook illustrations: Hand‐held models of ordered DNA and protein structures as 3D supplements to enhance student learning of helical biopolymers

Jittivadhna

Ruenwongsa

Panijpan

2010

Textbook illustrations of 3D biopolymers on printed paper, regardless of how detailed and colorful, suffer from its two-dimensionality. For beginners, computer screen display of skeletal models of biopolymers and their animation usually does not provide the at-a-glance 3D perception and details, which can be done by good hand-held models. Here, we report a study on how our students learned more from using our ordered DNA and protein models assembled from colored computer-printouts on transparency film sheets that have useful structural details. Our models (reported in BAMBED 2009), having certain distinguished features, helped our students to grasp various aspects of these biopolymers that they usually find difficult. Quantitative and qualitative learning data from this study are reported.Keywords: Helical structure, DNA, polypeptide, science education.Helical structures of biopolymers are ordered and have symmetry in three dimensions. College students have to learn about helices of the double-stranded DNA, the single-stranded protein a-helix, and possibly others in bioscience classes. Even high school students studying biology are exposed to these common helical structures and are examined for their knowledge of these structures. However, when asked to draw a sketch of the DNA double helix with as little details as that drawn by Francis Crick's wife, Odile, for the seminal Nature paper in 1953 [1], quite a few students, including some graduates, cannot do it well: no clear helical (right-handed) sense, haphazard hydrogen bondings between basepairs, no major and minor grooves, the strands are not antiparallel, and so forth. Students do not perform much better with the bare-backbone polypeptide a-helix: no clear helical (right-handed) sense, haphazard hydrogen bondings, each amino acid residue is not quite correct.Given these difficulties in student learning this aspect of chemical biology, researchers recommended enhancing the learning of DNA and protein structures through the use of three-dimensional physical models [2-4]. Herman et al.[5] and Bain [6] reported that concrete visual models that can be easily manipulated, play an important role in capturing the interest of students at both high school and undergraduate levels and encouraging more sophisticated thinking about the tangible molecular world.It should be noted that one obvious limitation to the widespread use of physical models is their high cost and limited availability. To provide our students with an easy access to a useful learning tool, we had developed physical models of ordered structures of the B-form DNA, protein a-helix, and b-pleated sheet made from computer-printed transparency film cut-outs. We used the already-assembled DNA double helix with two central axes (made from straight wires) [7] to teach students, medical as well as graduate bioscience, to learn the essential structural details of DNA and their role when interacting with drugs and proteins using the hydrogen bond donor and acceptor groups on the bases and the electrostatic char...