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

Abstract

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...

Creating 3D physical models to probe student understanding of macromolecular structure

“…The high complexity of molecular structure in biological macromolecules exacerbates the difficulties students face using two‐dimensional (2D) molecular representations . These molecular structures and their properties, including solubility and biological function, are governed by noncovalent interactions.…”

“…By using three‐dimensional representations, barriers to problems arising from translating between 2D and 3D can be removed . For example, studies that have developed physical models of biological macromolecules have used materials such as pipe cleaners to mimic chromosomes, clothespins to represent RNA, binder clips to represent amino acids or transparency cutouts for proteins and DNA . However, while the simplified structures in these physical models are easy to generate, they contain limited structural information .…”

Insulin as a model to teach three-dimensional structure of proteins

“…This result is in accordance with the finding of Herman et al [17] that the physical models are very useful in introducing the basic concepts of protein structure to students. In addition, Jittivadhana et al [41] observed that the use of physical models was better to understand 3D features of proteins than the textbooks illustrations or computer graphic representations.…”

From Pipe Cleaners and Pony Beads to Apps and 3D Glasses: Teaching Protein Structure

“…Students often appreciate hands-on activities, especially those that model three-dimensional processes or structures. Protein-folding models can be extremely simple and inexpensive, such as paper or overhead transparency plastic ( 4 , 7 ), or slightly more complicated, such as those made out of wire ( 13 ) or pipe cleaners, with pony beads or other small items to symbolize amino acids ( Fig. 1 ) ( 1 , 5 , 6 ).…”