Model building to facilitate understanding of holliday junction and heteroduplex formation, and holliday junction resolution

Selvarajah, Geeta; Selvarajah, Susila

doi:10.1002/bmb.20964

Cited by 4 publications

(5 citation statements)

References 53 publications

(65 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…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 .…”

Section: Introductionmentioning

confidence: 99%

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

Cooper

Oliver-Hoyo

2017

Biochem Molecular Bio Educ

View full text Add to dashboard Cite

The high degree of complexity of macromolecular structure is extremely difficult for students to process. Students struggle to translate the simplified two-dimensional representations commonly used in biochemistry instruction to three-dimensional aspects crucial in understanding structure-property relationships. We designed four different physical models to address student understanding of electrostatics and noncovalent interactions and their relationship to macromolecular structure. In this study, we have tested these models in classroom settings to determine if these models are effective in engaging students at an appropriate level of difficulty and focusing student attention on the principles of electrostatic attractions. This article describes how to create these unique models for four targeted areas related to macromolecular structure: protein secondary structure, protein tertiary structure, membrane protein solubility, and DNA structure. We also provide evidence that merits their use in classroom settings based on the analysis of assembled models and a behavioral assessment of students enrolled in an introductory biochemistry course. By providing students with three-dimensional models that can be physically manipulated, barriers to understanding representations of these complex structures can be lowered and the focus shifted to addressing the foundational concepts behind these properties. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(6):491-500, 2017.

show abstract

Section: Introductionmentioning

confidence: 99%

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

Cooper

Oliver-Hoyo

2017

Biochem Molecular Bio Educ

View full text Add to dashboard Cite

show abstract

“…Even though educators in both fields have used concrete models for explicit instruction, there are pronounced differences on the nature of the models. Biochemistry education has started to move toward the use of detailed concrete models based on the Protein Data Bank (PDB) files of molecules. ,, However, recent studies use models that lack realistic physiological shape to represent molecular components , such as chromatids represented by pipe cleaners. Concrete models in chemistry education distinctly reflect structural accuracy.…”

Section: Discussionmentioning

confidence: 99%

“…Simple, inexpensive, and readily available objects have also been used as visual literacy tools. As original examples we can mention the use of pipe cleaners to represent chromosomes to enact the Holiday junction, and the use of clothespins to represent tRNAs in conjunction with small binder clips representing amino acids to study protein translation . It has been shown that students perform better with the combination of physical models and molecular graphics tools and that students prefer to manipulate physical models .…”

Section: Biochemistry Educationmentioning

confidence: 99%

Promotion of Spatial Skills in Chemistry and Biochemistry Education at the College Level

Oliver-Hoyo

Babilonia-Rosa

2017

J. Chem. Educ.

View full text Add to dashboard Cite

Decades of research have demonstrated the correlation of spatial abilities to chemistry achievement and career selection. Nonetheless, reviews have highlighted the need and scarcity of explicit spatial instruction to promote spatial skills. Therefore, the goal of this literature review is to summarize what has been done during the past decade in chemistry and biochemistry education to promote spatial skills at the college level. In this review, we compare and contrast how these fields of study have used external representations and visualization tools in their instructional practices as well as the kinds of interventions and assessment efforts directed to promote and evaluate spatial skills. Our findings show that explicit instruction to promote spatial skills has been on the rise but not at the level of other cognitive skills. Therefore, implications for teaching and potential areas for investigation are suggested.

show abstract

“…The medical career is characterized by the constant reading as a method of study, where most students find the subjects of biochemistry and molecular biology are difficult to understand due to the amount of information on the topics that involve metabolic pathways and molecular mechanisms, especially during the first years [1]. Theoretical reading provides valuable information and basic knowledge for students; however, this study habit limits the interaction between students and teacher-student [2].…”

Section: Introductionmentioning

confidence: 99%

“…Students who study the subject of molecular biology often find it difficult to differentiate biological mechanisms such as DNA replication, transcription and translation through mental categorization [3], or understanding a dynamic sequence of events through the physical organization of the molecules in an image, model or mental scheme. Comprehend the molecular mechanisms and interactions in their baseline state, will help the student to compare, establish and elucidate the biological consequences of possible alterations [1,3,4]. An important issue in the content of the molecular biology course is "gene silencing by DNA methylation" considered as an epigenetic mechanism that can control gene expression without altering its sequence and categorized as a risk biomarker for cancer development [5][6][7].…”

Section: Introductionmentioning

confidence: 99%

Use of MethHC and SurvExpress database in the course of molecular biology for medical students: Understanding of epigenetic modifications in gene expression with problem-based learning

Villarreal

Valero

Urbano

et al. 2019

Preprint

View full text Add to dashboard Cite

Background: Currently, there are teaching methods that allow students to understand clinical conditions, pathologies and hereditary diseases, mainly supported by problem-based learning (PBL), simulation-based learning (SBL), image analysis, case studies, and use of platforms electronic and mobile applications. However, the use of databases and PBL in the compression of molecular biology applied to research has not been well investigated. The scientific literature has reported combinations of pedagogical strategies with positive results compared to the traditional method based on reading, therefore, this study aimed to design a pedagogic method making use of databases applied in scientific research to understand the relation of methylation on gene expression and its relationship in the appearance of diseases such as cancer. Methods: Three databases were used, Genetics Home Reference (GHR) for the theoretical understanding of the study gene, MethHC for the analysis of the effect of methylation on gene expression and SurvExpress for biomarker validation for cancer gene expression. All databases support your information from The Cancer Genome Atlas (TCGA) program of the National Cancer Institute (NCI). The guidelines of each platform for the analysis of the information were followed. The present study exemplified with the analysis of the POT1 gene that is involved with the maintenance of telomere length and has been associated with breast cancer. Results: The function of the POT1 gene, chromosomal and molecular position, number of exons and their transcriptional variants in invasive breast carcinoma were described. It was found that the expression of POT1 depends on the positioning of the levels of methylation within the structures that comprise the gene in healthy and tumor tissue, besides it was reported through a survival analysis that the gene is best expressed in the low group's risk compared to the high-risk group. Conclusion: The use of databases allows the student to make use of his theoretical knowledge and take them to clinical practice and research, the results obtained from the use of GHR, MethHC, and SurvExpress allow to apply molecular biology in clinical research and promote problem-based learning developing analysis and interpretation skills in students. This pedagogical method allows the understanding of epigenetic effects on the expression of cancer-related genes.

show abstract

Model building to facilitate understanding of holliday junction and heteroduplex formation, and holliday junction resolution

Cited by 4 publications

References 53 publications

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

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

Promotion of Spatial Skills in Chemistry and Biochemistry Education at the College Level

Use of MethHC and SurvExpress database in the course of molecular biology for medical students: Understanding of epigenetic modifications in gene expression with problem-based learning

Contact Info

Product

Resources

About