Biochemistry education: from theory to practice

Biochemistry Education: From Theory to Practice......Page 2
 Biochemistry Education: From Theory to Practice......Page 4
  Library of Congress Cataloging-in-Publication Data......Page 5
Foreword......Page 6
Best Practices in Summative Assessment......Page 8
Subject Index......Page 9
Preface......Page 10
 References......Page 11
Visual Literacy......Page 12
Quantifying the Types of Representations Used in Common Biochemistry Textbooks......Page 14
 Types of External Representations in Biochemistry......Page 15
 Modes of External Representations......Page 16
 Potential Outcomes of Using External Representations......Page 17
 Potential Benefits of Using External Representations......Page 18
 Potential Negative Results of Using External Representations......Page 19
 Sample Collection and Analysis......Page 21
 What Types of Representations Are Most Prevalently Used in Biochemistry Textbooks?......Page 22
  Figure 2. Percentage of representations in each type of representation by textbook.......Page 23
  Figure 3. Percentage of representations based on the number of types of representations included.......Page 24
 Is There a Difference in the Types of Representations Used Depending on the Content Discussed?......Page 25
  Figure 6. Percentage of types of representations by content covered. Solid colored categories indicate single representations and patterned categories indicate use of multiple representations.......Page 26
 Discussion......Page 27
 Implications, Limitations and Future Areas of Research......Page 28
 References......Page 29
Virtual Exploration of Biomolecular Structure and Function......Page 32
 Introduction......Page 33
 Visual Communication of Molecular Structures: A Brief History......Page 34
 Structural Data: Source, Assumptions, Errors......Page 37
  Figure 2. Engineered proteins used for molecular structure determination. A. Cytoplasmic domain of the insulin receptor tyrosine kinase in ribbon representation, PDB ID 1irk 43; B. Yellow fluorescent protein-glutaredoxin fusion protein shown in ribbon representation, PDB ID 2jad 44; C. Ribbon representation of human insulin receptor ectodomain in complex with four Fab fragments (in grey and circled), PDB ID 4zxb 45; D. HIV-1 reverse transcriptase, with an active site residue mutation (D498N), PDB ID 3v6d 46, the nuclease and polymerase domains in the structure are marked with circles; E. Cytoplasmic domain of the insulin receptor tyrosine kinase in ribbon representation, complexed with a substrate peptide (magenta and circled) and ATP (ball and stick representation and circled), PDB ID 3bu5 47. All structural images in this figure were created with UCSF Chimera.......Page 39
  Figure 3. Method- and experiment-specific manipulations of PDB coordinate data prior to virtual exploration. A. Structure of the oxyhemoglobin asymmetric unit (top) and biological assembly (bottom), PDB ID 1hho 48; B. Structure ensemble of human translation initiation factor eIF1A (top) and representative model (bottom), PDB ID 1d7q 49; C. Structure of the Dengue virus icosahedral unit (top) and complete virus (bottom), PDB ID 1k4r 50. All structural images in this figure were created with UCSF Chimera.......Page 40
 Visualization Tools: Affordances and Constraints......Page 41
 Scientific Practices for Visual Comprehension......Page 42
 Assessment of Virtual Biomolecular Visual Literacy......Page 43
 Educational Resources......Page 44
 Conclusions......Page 46
 References......Page 47
 Introduction......Page 54
  Figure 1. Physical models of molecular structures. A. An amino acid – constructed by students using a small molecule kit. Models B-E are “assemblies of atoms,” constructed by 3D printing. B. ATP with magnet-docked phosphate groups. C. A zinc finger (PDB ID: 1ZAA) D. A four-subunit potassium channel (PDB ID: 1J95). E. The 70S E. coli ribosome (PDB ID: 4V5D) with magnet-docked large and small subunits, three tRNAs and a short stretch of mRNA.......Page 56
 Modeling Projects......Page 57
 Case Study II: Carbohydrate Models......Page 58
 Case Study III: Serine Protease Active Site Models......Page 60
  Figure 3. Serine protease physical model. A. Backbone, surface place, substrate epimers, and inhibitor for chymotrypsin. B. Surface plate snapped on top of backbone with the substrate epimers and inhibitor on the left side. C. Substrate bound in the active site. Photos courtesy of Cassidy Terrell.......Page 62
 Case Study IV: Flow of Genetic Information Models......Page 63
  Figure 5. Model based activities showed dramatic learning gains for all students, including low performers (bottom quartile) and deaf/hard of hearing (D/HH). In this analysis, each multiple-select question was scored as right or wrong (no partial credit). Students were ranked in quartiles by their scores on the entire CDCI at the beginning of the semester, although their performance is shown only for questions related to model-taught concepts. Dotted lines show that on average, D/HH students fell between the 2nd and 3rd quartile, both pre and post instruction. Error bars are SEM, n=426 with 34 D/HH.......Page 64
 Reduction of Cognitive Load......Page 65
 Conclusions and Future Directions......Page 66
 Acknowledgments......Page 67
 References......Page 68
Pedagogies and Practices......Page 74
 Introduction: Concepts Conquer Content......Page 76
  Figure 1. Key features of the vision and change recommendations for biology education.......Page 77
  Figure 2. Summary of concepts and skills recommended by the American Society for Biochemistry and Molecular Biology.......Page 80
  Figure 3. Concept (mind) map of key features of non-covalent interactions and the roles they play in protein structure and function.......Page 81
 What Is Modern Biochemistry and Molecular Biology?......Page 87
 Current Curricula Recommendations......Page 88
 The Central Role That Undergraduate Research Plays in Undergraduate Education in the Molecular Life Sciences......Page 90
  Figure 4. Essential elements in a student generated research hypothesis and proposal.......Page 91
 A Student-Centered Curriculum......Page 95
 Peer Review......Page 96
  Figure 6. Consensus mind map of central concepts of reactions and interactions generated from class discussion.......Page 97
 Gateway Concepts......Page 98
 Quantitative Skills in the Curriculum......Page 99
 Communication: Writing and Presentation Skills......Page 100
 The Central Role That Accessing and Assessing Knowledge Plays in Undergraduate Life Science Education......Page 101
 Content versus Concept Revisited......Page 102
 How Could the Ideal Curriculum be Structured?......Page 105
 The Critical Role of Inclusive Teaching......Page 106
 Appendix: Based upon, with Expanded Detail, Wright et al. 9 “Essential Concepts and Underlying Theories from Physics, Chemistry, and Mathematics for ‘Biochemistry and Molecular Biology’ Majors”......Page 107
 References......Page 115
 Introduction to Active Learning......Page 122
 Guided Inquiry: History and Characteristics......Page 123
 Process Oriented Guided Inquiry Learning......Page 124
 Guided Inquiry Teaching Materials for Biochemistry......Page 125
 Supporting Process Skills Development in the Biochemistry Classroom......Page 128
 The Role of the Teacher in the Guided Inquiry Classroom......Page 129
 Creating and Using Facilitation Plans......Page 130
 Navigating Challenges......Page 131
 References......Page 132
 Introduction......Page 138
 Given the Variety of Evidence-Based Pedagogies, Why Should I Choose Case Studies?......Page 139
  Figure 1. Visual representations of the potassium ion channel. A: a ribbon diagram of the ion channel in the plasma membrane, made up of 3 subunits of alpha helices labeled in yellow, lavender and cyan. B: The helices are shown as cylinders, using the same color scheme as A. Potassium ions are shown as green spheres. C: A close-up of the potassium binding site. Carbonyl oxygens are shown in red. Created using PYMOL Molecular Graphics System (Schrodinger, LLC) and PDB ID 1BL8.......Page 141
 The Types of Cases We Use......Page 143
 A Typical Week in Our Course......Page 145
 Structuring and Facilitating Group Work......Page 146
 Summative Assessment......Page 147
 Closing Thoughts......Page 148
 References......Page 149
 Why Undergraduate Research and CUREs......Page 154
 What Is a CURE?......Page 157
 Developing a Hypothesis as Part of “Scientific Practices” Activity......Page 162
 Bioinformatics Tools to Develop a Hypothesis......Page 163
 Finalize Proposal......Page 164
 How Far Along Are We?......Page 165
 The Evolution of CURES......Page 166
 SEA-Phages (www.seaphages.org)......Page 167
 Malate Dehydrogenase CUREs Community (MCC; www.mdh-cures-community.squarespace.com/contact)......Page 168
 Other CURE Examples......Page 169
 Chemistry......Page 170
 Biology......Page 171
 Pedagogical Research: CURE Learning Outcomes and Assessment......Page 172
 Practical Approaches: Organizing Your CURE......Page 176
 References......Page 177
 Lab Notebooks in the Literature – History and Role of Lab Notebooks......Page 184
 Brief Introduction to Development of ELNs from Shared Computer Files or Drives to Formal Electronic Systems That Are Cloud-Based.......Page 185
 Google Drive......Page 187
 OneNote......Page 189
 Evernote......Page 190
 Commercial ELNs......Page 192
 LabArchives......Page 193
 RSpace......Page 195
 labfolder......Page 196
 Instructor Perspective......Page 197
 Student Perspective......Page 201
 Training......Page 202
 References......Page 203
 Introduction......Page 208
 The Role of Assessment in Transforming Biochemistry Teaching and Learning......Page 209
 Formative Assessment and Feedback Support Learning......Page 211
 Assessment within the Disciplinary Context of Biochemistry......Page 212
  Figure 1. Visual representation is just one of the multiple facets of biochemical knowledge. All three figure panels demonstrate different ways of representing and making sense of protein stability.......Page 214
 Promising Practice #1: Optimize Cognitive Load to Facilitate Schema Development......Page 215
  Figure 2. Example of formative assessment prompts that can target the same biochemical principle and use the same level of visual abstraction, allowing more precise insights into students’ abilities to reason across cognitive levels.......Page 217
  Figure 3. Example of formative assessment prompts that assess students’ understanding of a concept using difference levels of visual abstraction (Prompt #1 vs. Prompt #2) while holding the cognitive skill level constant (“How does the described mutation affect the stability of the protein?).......Page 218
 Promising Practice #2: Use Assessments to Facilitate Retrieval of Relevant Information......Page 219
 Promising Practice #3: Use a Range of Formative Assessment Prompts to Diagnose and Respond to Students’ In-Progress Learning......Page 221
 References......Page 223
 The Purposes of Assessment......Page 230
 Course Revision......Page 231
 Curriculum Development......Page 232
 Additional Resources......Page 233
 Categorizing Learning Outcomes......Page 234
  Figure 1. Sample summative assessment question.......Page 236
 Types of Questions Used for Summative Assessments......Page 237
 Multiple Choice Questions (MCQ)......Page 238
 True/False......Page 240
 Essay (Large Project) Prompt......Page 241
 Summative Assignments......Page 242
 Considerations......Page 243
 Exams......Page 244
 Considerations......Page 245
 Presentations......Page 246
 Fair Grading Practices......Page 247
 Question/Assignment Grading......Page 248
 Training and Reviewing Graders......Page 249
 Tips for Grading Faster and More Accurately (i.e. for Large Classes)......Page 250
 Larger Projects......Page 251
 References......Page 252
Implementation......Page 256
 Introduction......Page 258
 Importance of Communities......Page 259
 Core Collaborators Workshop......Page 260
  Figure 1. Number of active learning activities implemented by workshop participants after attending at least one workshop. Participants are categorized by the number of workshops attended: one workshop (5 respondents), two or three (4 respondents), four (5 respondents), or more than five (4 respondents) CCWs attended. The number of responses in each category are indicated in the bar graphs as either, no increase (black), increase in 1 to 5 activities (gray), and increase in 6+ activities (hashed). There were a total of 7 CCW events held and 58 participants were sent surveys with 19 collaborators responding.......Page 262
 Challenges and Ways to Overcome Them......Page 264
 Communities Foster Research......Page 265
 Moving Forward......Page 266
 References......Page 267
 Introduction......Page 272
 Bridging Threshold Concepts and Foundational Concepts......Page 273
 An Iterative Process for Introducing Active Learning......Page 274
 Literature Review and Pre-assessment of Foundational Concepts......Page 275
 Identification of Potential Concept Interventions......Page 276
 Workbook......Page 277
 Problem-Based Worksheets......Page 278
 Learning Cycle Activity......Page 279
 Re-assessment and Revision......Page 280
 References......Page 282
 Introduction: Transition to Half Lecture and Half In-Class Activities......Page 286
 Active Learning Pedagogies......Page 287
 Active Learning Modifications to Biochemistry I......Page 288
 Impact on Attendance......Page 289
 Biochemistry I ACS Final Exam Scores......Page 290
 Impact on Ratings of Instruction......Page 291
 Opportunity to Introduce a CURE......Page 292
 In-Class Activity Development......Page 294
 Unfolding of the Learning Process......Page 295
 Goals......Page 296
 Feedback and Assessment......Page 297
 References......Page 298
 The Warburg Project......Page 302
 Student Feedback......Page 303
 References......Page 304
 Introduction......Page 306
  Figure 1. POGIL learning cycle with the approached used in the biochemistry labs at Auburn University.......Page 308
 Background......Page 309
 Thinking about the Data: Part 1......Page 310
 Experiment Phase 2......Page 311
 Pre-experiment Questions......Page 312
 General Protocol......Page 313
 Pre-experiment Questions......Page 314
  Figure 3. Pathway for melanin production showing the reactions catalyzed by tyrosinase. The molar absorptivity of dopachrome 2 is 3600 M-1cm-1.......Page 315
 Chemicals......Page 316
 Biomass (Corn or Other Samples)......Page 317
 Chemicals......Page 318
 Pre-experiment Questions......Page 319
 Chemicals......Page 320
 Background......Page 321
 References......Page 322
 Original Research in the Undergraduate Curriculum......Page 324
 Alternate Approaches......Page 325
 Advantages of the Topic-Focused, Student-Derived Project Model......Page 326
 Project Guidelines......Page 327
 Proposal Requirements......Page 328
 Kinetic Studies......Page 329
 Inhibition......Page 330
 Effects of Temperature on Enzyme Stability......Page 331
  Figure 2. pH dependence of heart and muscle LDH.......Page 332
 Exploration of the Relationship Between Structure and Function of Lactate Dehydrogenase from Rabbit Muscle through Heat Denaturation......Page 333
  Figure 5. Time dependent loss of LDH activity.......Page 334
  Figure 7. Effects of temperature on alpha helical secondary structure.......Page 335
 Comments and Practical Considerations......Page 336
 Conclusions......Page 337
 References......Page 338
 Rodney C. Austin......Page 340
Indexes......Page 342
Author Index......Page 344
 B......Page 346
 I......Page 349
 S......Page 350
 T......Page 351