What Are The Core Concepts in Biochemistry? Part II. Abstract

Transcription

1 What Are The Core Concepts in Biochemistry? Part II Abstract Biochemistry recently introduced subject in science as our understanding improves with better technology in the field. The aim of this study is to define the key concepts of biochemistry and give clear idea to student what is the core concepts in biochemistry which can leads to develop as future scientist. Through the electronic survey, 320 responses were collected. All the data has not been analysed yet, however, even experienced lectures and researchers are also very confused what is the core concepts of biochemistry. In conclusion, before making more convincing conclusion, further data analysis requires. Introduction Biochemistry is fairly new subject compare to some of field of science. As our technology gets better, our understanding of biochemistry expands rapidly. This may helped to form the impression to many students that biochemistry is subject of difficult and contentheavy. Furthermore, to teaching academics also faces the problems of how to teach all in just a few courses during the semester. There are couple of strategies that academics uses when design a course curriculum. One of them is textbook structured approach. This is teaching from a textbook and focus on isolated important content. This approach is sequential and inflexible, because it follows the contents of textbook [1]. Moreover, it also prevents from lateral thinking or transfer of concepts from one course to another. Another approach is to cover the whole filed and teach everything, in an attempt to build a big picture by default. This supplies a lot of information to a class, but large-scale information transfer often occurs at the expense of a deeper conceptual understanding [2]. The aim of this study is to help student develop a set of key understandings in biochemistry that would enrich their understanding of other courses in their programs of study and be useful to them in the long-term, regardless of their career ambitions. Methods The first step in this process was to determine what working biochemists considered the key concepts in biochemistry.

2 We invited potential respondents by to access a Survey Monkey link. This survey at this link delivered a question set entitled The Fundamentals of Biochemistry International. The part of questions is shown in Table 1. Respondents could choose to include a contact address in their responses, but this was not accesses during processing of the results. No other identifying information was collected. The amount of data we collected was overwhelming, in total 320 people responded; for some question, there are over 800 data to need to be analysed. Hence, to have big picture of data, we decided to have look at which words were most frequently appeared for question 4 and 5 from Table 1 via The data was needed to process as the wordle program to understand, we followed previous outline to maintain continuality. The common words such as at, the etc were removed. Then, unrelated words to science such as I think that, or I frequently use were removed. Sentence was rearranged to remove negatives phrase link not bulk properties. Also, any word appeared less than 16 times were removed. Lastly, checked spelling and unified plural/singular of all the words. Next step was to analysing question 4 and 5 into content and concepts. In previous study, we noticed that many respondents were not sure of contents vs. concepts. Hence, for this study, we had to define what are the concepts and contents related to biochemistry. We define content as; (i) words or phrase that define a topic or fact that could be taught as a stand-alone, decontextualised item and (ii) words or phrase which do not link, explicitly give meaning to, or contextualise discrete facts and skills. We applied both of these criteria to responses to gauge if they were content. For example, the term sugar chemistry exemplified content because it is not a contextualized statement that gives a sense of how or why things happen in biology; sugar chemistry could be taught as a set of chemistry reactions without an understanding of how these reactions fit into the biochemistry of a cell or organism. Similarly, we consider submissions of single words like proteins, metabolism, and central dogma to be content because they are decontextualised, devoid of abstraction, and limited in their wider meaning. We define concepts as; (i) words, phrases, or sentences that give a sense of how or why things happen in biology and (ii) words, phrases, or sentences that give meaning and connection to discrete facts and skills and (iii) words, phrases, or sentences that require understanding of more than one content area in an abstract manner.

3 Then, adapted from Vision and Change [3], we came up with six different categories of biochemistrical concepts; Thermodynamics and Energy Information Transfer and Storage Structure and Function of Biomolecules Regulation and Organization in Living Systems Experimental Approaches (or Disciplinary Practice) Evolution Results The demographic data obtained from the survey results are shown in Table 1. In total, 320 people completed the survey. More than 96% of the respondent answered that their primary work environment are academia. In addition, 33% of the respondents answered as they studied five or more years of biochemistry at university compare to only 11% respondents they never studied biochemistry. Furthermore, 55% of respondent did not major biochemistry while 44% of responds as biochemistry was part of their major degree. To get an idea of the most important words in the responses (rather than the commonly used ideas), we collated all the words from the answers to Question 8 and 9 and processed the data following (Figure 1). Some of the words stands out such as structure, function and molecular. However, there words are more to contents rather than concepts. The 257 respondents provided a total of 897 responses to the questions Please list three to five concepts or big ideas that you think are fundamental to an understanding of biochemistry, the results are shown Table 2. We considered all of these responses as part of our data set. For previous study, there were 12% responded that molecular recognition and interaction are important followed by metabolism (9%), and central dogma (9%). However, part II data indicated that 14% answered as structure and its relationship to function are important concepts, followed by an enzyme catalysis (12.5%) and central dogma (12.1%). Moreover, there are three more categories that were not there in previous studies, practical experiment, macromolecules and mutation and tis relation to diseases. The 257 respondents provided concepts and ideas that they defined as Please write the ONE concepts or big idea that you think is the most important in biochemistry. A summary of these are shown in Table 3. Again, many of them could be considered as content rather than concepts. In previous study, protein structure and function and metabolism are most important concepts, however in part II study, 32 people answered as

4 structure of biomoleclues are the most important concepts. Again, there are new concepts in part II, they are metabolism and evolution. Discussion Not like olden days, when lecturer stood in front of students and lectured contents, it is well understood these days that how important to understand the big idea of concepts to students. Just like other science, biochemistry covers variety subjects as our understanding grow rapidly in the fields of science such as genetic, cell biology, chemistry to name a few. This also gives teachers a dilemma of within a given time frame, they just cannot teach everything. Therefore, it is important, not only to student but also teacher, to understand what are the core concepts of biochemistry to design course to emphasis teaching conceptual-based teaching rather than content-bases. The aim of this study is to define the key concepts of biochemistry and give clear idea to student to understand core concepts in biochemistry. At the present moment, not all the data from part II has been analysed yet, it is because the amount of data was just overwhelming to process. Though, processing data has been slow, it is already shows that many respondent who are teaching biochemistry at university, are also confused of concepts vs. contents which is expected as the number of teachers who participated in part I study were also confused. This could adds extra stress to students who already puzzled with amount of information they have to learn during the course. Therefore, for this study, we tried to define the key concepts in biochemistry using Vision and Change project as guided line. They are; Thermodynamics and Energy Information Trnasfer and Storage Structure and Function of Biomolecules Regulation and Organization in Living Systems Experimental Approaches (or Disciplinary Practice) Evolution Conclusion In conclusion, further analysis of data defiantly needs to make conclusive results.

5 Reference [1] R. G. Baraniuk, C. S. Burrus, B. M. Hendricks, G. L. Henry, G.L.; A. O. Hero, III, D. H. Johnson, D. L. Jones, J. Kusuma, R. D. Nowak, J. E. Odegard, L. C. Potter, K. Ramchandran, R. J. Reedstrom, P. Schniter, I. W. Selesnick, D. B. Williams, W. L. Wilson (2002) Connexions: DSP education for a networked world. Proceedings of ICASSP '02. IEEE International Conference on Acoustics, Speech, and Signal Processing. [2] B. Vidic, H. Weitlauf (2002) Horizontal and vertical integration of academic disciplines in the medical school curriculum Clinical Anat. 15, [3] AAAS Vision and Change in Undergraduate Biology Education Initiative (2009) Vision and Change in Undergraduate Biology Education A Call to Action. Online:

6 Table 1: Questions and demographic responses from The Fundamentals of Biochemistry International survey. Question Text Answer Options Answers Given 1) What is your primary work environment? 2) Did you study biochemistry at University? 3) Was biochemistry your major at University? A) Industry B) Academia C) Others A) Not at all; B) 1 year C) 2 years D) 3 years E) 4 years F) 5 or more years A) Yes-single major B) Yes-joint major C) No 7 (2.2%) 308 (96.3%) 7 (2.2%) 38 (11.9%) 61 (19.1%) 52 (16.3%) 27 (8.4%) 35 (10.9%) 107 (33.4) 74 (23.1%) 69 (21.6%) 177 (55.3%) 4) Please list three to five concepts or 'big ideas' that you think are fundamental to an understanding of biochemistry 5) Please write the ONE concept or 'big idea' that you think is the most important in biochemistry Open answer See Table 2. Open answer See Table 3.

7 Figure 1 : Frequently used words in the Core Concepts in Biochemistry responses. The larger the word size, more frequently appeared on the list.

8 Table 2: Ideas, terms, and concepts identified as central to biochemistry by survey respondents. Part I Part II central to biochemistry by survey respondents 147 (%) 838 (%) 18 (12) 35 (4.2) Molecular recognition and interactions (including receptorligand binding), signal transduction, the role of affinities in interactions. 14 (9.5) 85 (10.1) Metabolism (breakdown and synthesis pathways for complex biomolecules) 14 (9.5) 101 (12.1) Central Dogma; DNA replication/transcription/translation/protein processing. Protein production is related to regulated gene expression. epigenetic 11 (7.4) 105 (12.5) Enzyme catalysis, including the regulation, structure, and function of enzymes 11 (7.4) 96 (11.5) Cellular systems are in dynamic (not thermodynamic) equilibrium. A thermodynamically favorable reaction will not necessarily proceed spontaneously. Entropy. Reaction kinetics, energetics, and rate equations for (bio)chemical reactions. 11 (7.4) 24 (2.9) Food, stored substrates, and light are converted to energy currency. This currency is used of to drive biochemical and cellular processes and build order. 10 (6.8) 122 (14.6) Structure and its relationship to function. Proteins carry out the essential functions of the cell. Molecular machines and how they work to accomplish their function. functional-group 9 (6.1) 16 (1.9) Biochemistry provides tools for analytical and quantitative measurements, assays, and analyses. Structural biology is important. 8 (5.4) 5 (0.6) Chemical structure of biomolecules (chemical structures and 3D structure) 8 (5.4) 33 (4.0) Biochemistry is chemistry in a biological setting. The same fundamental principles apply (eg: rules of organic chemistry and chemical concepts such as redox, kinetics, thermodynamics, and equilibrium) 6 (4) 37 (4.4) Compartmentalization and partitioning of cell spaces and components including the role of water as a solute. 6 (4) 15 (1.8) Membrane biology (how the properties and asymmetry of membranes define and organize biochemical processes) ion transport 5 (3.4) 7 (0.8) The idea of regulated pathways and networks and their breakdown during disease. 4 (2.7) 27 (3.2) Information storage, transmission, and conversion into structure 4 (2.7) 22 (2.6) Shapes and interactions of molecules based on charges, hydrophilicity, hydrophobicity, etc. Biomolecular tertiary

9 structure is dominated by weak intermolecular interactions while backbones are built from strong bonds. Structures are dynamic. 2 (1.4) 20 (2.4) Regulation and modification of protein function (allosterism, phosphorylation, signal transduction, etc.) 2 (1.4) 4 (0.5) Cellular structures at the molecular level (nuclear envelope, ER, Golgi, actin fibers, prokaryote structures, amino acids) 2 (1.4) 11 (1.3) The correct ph and salt concentration is required to maintain the proper function of the cell (homeostasis) acid/base 1 (0.7) 25 (3.0) Evolution and selection pressure 1 (0.7) 15 (1.8) The idea of what happens at the molecular level vs the bulk properties of the system. - 9 (1.1) practical, experiment - 21 (2.5) macromolecules(nucelic acids, amino acid, sugars, lipids, four building-blocks) - 3 (0.4) mutation and related disease

10 Table 3: Ideas, terms, and concepts identified as most important in biochemistry by respondents. Most Important Concepts in Biochemistry by respondent Part I 39 Part II 146 Protein structure and function and metabolism 8 5 Molecular recognition, interaction, pathways 7 9 The Central Dogma 6 17 Enzyme-medicated Catalysis 4 12 Information flow 2 3 Energy flow equilibrium, thermodynamics 2 21 Basic chemical concepts 2 1 Biosynthetic pathways 2 4 Homeostasis and flux 2 3 Lab approaches in biochemistry 1 4 Structure of biomolecules (proteins, nucleic acids, lipids, sugars) 1 32 Water is essential for the chemistry of life 1 how living organisms transform energy and build biological order 1 Metabolism pathway and regulation - 11 Evolution - 12 Can t answer, don t know, can t choose one concept - 12