This article reports the results of a recent study to evaluate the usefulness of physical models of molecular structures as a new tool with which to teach concepts of molecular structure and function. Of seven different learning tools used by students in this introductory biochemistry class, the use of the physical models in a laboratory was rated as most useful. These results suggest that physical models can play an important role in capturing the interest of students in the subject of molecular structure and function. These physical models often stimulate more sophisticated questions in the minds of students, which can then be more appropriately explored using computer visualization tools.

Micrococcal nuclease digestion of intact chicken erythrocyte nuclei is shown to result in the formation of core nucleoprotein particles containing about 140 base pairs of DNA. These core particles, which are almost entirely devoid of histones fI and f2c, are derived from transient nucleoprotein particles containing an average of approximately 180 base pairs of DNA. Oligomers of these latter particles may be isolated after brief nuclease digestion. (2). The latter has been proposed by Kornberg (9) to be the basic DNA repeating unit associated with an eight-histone complex. We will show that the eight-histone complex is associated with 140 base pairs of DNA, and that the remaining DNA in the subunit is especially nuclease-sensitive. MATERIALS AND METHODSIsolation and Digestion of Erythrocyte Nuclei. Blood was obtained from adult White Leghorn chickens by cardiac puncture in the presence of heparin. After centrifugation at 3000 X g for 10 min, the plasma and buffy coat were removed. The erythrocytes were washed twrice with an isotonic saline solution and frozen at -600 until needed. The frozen erythrocytes were thawed at 370 in an equal volume of 0.15 M NaCl, 0.015 M Na citrate, pH 7.2 (saline/citrate) and centrifuged at 3000 X g for 10 min; the nuclear pellet was resuspended in 0.25% Nonidet P-40 in saline/citrate. In some experiments 1 mM phenylmethane sulfonyl fluoride was added to inhibit protease action (15). The nuclei were repelleted, washed with saline/citrate and resuspended in 0.3 M sucrose, 0.75 mM CaCl2, 10 mM Tris-HCl, pH 7.2 at a concentration of 2 X 108 nuclei per ml. Digestion of the nuclei by micrococcal nuclease (Worthington) was carried out at 370 with 125 units of nuclease per ml of nuclei suspension. The digestion reaction was terminated by making the solution 10 mM in EDTA, 0.15 M NaCl, and 1% sodium dodecyl sulfate (NaDodSO4). After pronase treatment (0.5 mg/ml) for 4 hr at 370 the DNA was extracted by an NaDodSO4-phenol procedure (16).When the digested chromatin was to be fractionated on an agarose A-Sm column, the reaction was terminated by the addition of EDTA to 10 mM and cooling on ice. After centrifugation at 12,000 X g for 15 min, the nuclei were resuspended in 10 ml of 10 mM Tris-HCI, pH 7.5, 0.7 mM EDTA and disrupted by homogenization for about 1 min at a medium setting on a Virtis homogenizer. The nuclear debris was pelleted at 10,000 X g for 15 min. The supernatant was made 7% in sucrose and applied to a Bio-Rad A-Sm column, 90 X 2.5 cm, equilibrated with 10 mM 0

The technology now exists to construct physical models of proteins based on atomic coordinates of solved structures. We review here our recent experiences in using physical models to teach concepts of protein structure and function at both the high school and the undergraduate levels. At the high school level, physical models are used in a professional development program targeted to biology and chemistry teachers. This program has recently been expanded to include two student enrichment programs in which high school students participate in physical protein modeling activities. At the undergraduate level, we are currently exploring the usefulness of physical models in communicating concepts of protein structure and function that have been traditionally difficult to teach. We discuss our recent experience with two such examples: the close-packed nature of an enzyme active site and the pH-induced conformational change of the influenza hemagglutinin protein during virus infection.A common goal of biochemistry educators is to provide students with a deep understanding of fundamental concepts underlying protein structure and function. This is most commonly done by exposing students to stunning two-dimensional color graphics of proteins in textbooks and frequently augmenting these static figures with interactive images that can be rotated in three-dimensional space in a computer environment. Although this approach is successful for those students who are able to infer three-dimensional information from these inherently twodimensional representations, many other students fail to make this inference. For them, the molecular world of proteins remains an abstraction for which they have little interest. We have found that physical models of proteins ( Fig. 1) are amazingly effective tools that initially capture the interest of this larger group of students and motivate them to learn more about this invisible, molecular world. These physical models are synergistic with computer visualization tools, allowing students to generalize their initial understanding of a specific protein to other structures that are explored in a computer environment. We review here our recent experience with the use of physical models to make this molecular world "real" for students at both the high school and the undergraduate levels. A THEORETICAL BASIS FOR THE VALUE OF PHYSICAL MODELS IN TEACHING ABSTRACT CONCEPTS IN SCIENCEThe value of physical models of small molecules in organic chemistry courses is well known to biochemistry educators. However, these small molecule kits are not practical for modeling the higher order molecular structures of proteins. Experienced researchers have learned to infer three-dimensional information from two-dimensional images of proteins or to manipulate interactive, computergenerated images of proteins. Unfortunately, our current educational practice treats inexpert students as though they were expert researchers. Students are introduced to proteins through two-dimensional drawings or interactive computer visualiz...

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Replicating simian virus 40 (SV40) chromosomes were found to be similar to other eukaryotic chromosomes in that the rate and extent of micrococcal nuclease (MNase) digestion were greater with replicating than with nonreplicating mature SV40 chromatin. MNase digestion of replicating SV40 chromosomes, pulse labeled in either intact cells or nuclear extracts, resulted in the rapid release of nascent DNA as essentially bare fragments of duplex DNA (3-7S) that had an average length of 120 base pairs and were degraded during the course of the reaction. In addition, nucleosomal monomers, equivalent in size to those from mature chromosomes, were released. On the other hand, MNase digestion of uniformly labeled mature SV40 chromosomes resulted in the release of only nucleosomal monomers and oligomers. The small nascent DNA fragments released from replicating chromosomes represented prenucleosomal DNA (PN-DNA) from the region of replication forks that encompasses the actual sites of DNA synthesis and includes Okazaki fragments. Predigestion of replicating SV40 chromosomes with both Escherichia coli exonuclease III (3'-5') and bacteriophage T7 gene 6 exonuclease (5'-3') resulted in complete degradation of PN-DNA. This result, together with the observation that isolated PN-DNA annealed equally well to both strands of SV40 restriction fragments, demonstrated that PN-DNA originates from both sides of replication forks. Over 90% of isolated Okazaki fragments annealed only to the retrograde DNA template. The characteristics of isolated PN-DNA were assessed by examining its sensitivity to MNase and single strand specific S1 endonuclease, sedimentation behavior before and after deproteinization, buoyant density in CsCl after formaldehyde treatment, and size on agarose gels. In addition, it was observed that MNase digestion of purified SV40 DNA also resulted in the release of a transient intermediate similar in size to PN-DNA, indicating that a DNA-protein complex is not required to account for the appearance of PN-DNA. These and other data provide a model of replicating chromosomes in which DNA synthesis occurs on a region of replication forks that is free of nucleosomes and is designated as prenucleosomal DNA.