- Email: [email protected]
Computer simulation of experiments with enzymes
15 reinforced class work and enabled students to see the industrial applications of their subject. These visits also provided the vehicle by which students could improve personal transferable skills. This was achieved by groups of students each researching a specific topic and presenting it verbally to their colleagues, thereby practising individual research, group work, communication and presentation skills. The involvement of external organisations can also provide very useful specialist lectures and courses which would otherwise be unavailable to our students. The help of ICI, Arthur Andersen and the Medico-Legal centre is gratefully acknowledged.
to 63 local schools: a debate about pollution for a participating audience of 120 'A' level students and briefing materials for roleplay debates in schools; and a half hour lesson with a short video for ACCESS students and ' A ' level general studies groups on the importance of active site management in conservation. Key points are that (1) successful group projects do not require large blocks of teaching time; (2) there is a genuine and useful end product: the students impose their the highest standards because they know the end product will reach many people; (3) the project takes students into the outside world where they must deal with all kinds of situations and all kinds of people.
Empirical Illustration of Statistical Procedures John Garratt and Steve Smith. Department of Chemistry,
University of York, York YO1 5DD, UK Most undergraduate chemists are expected to use statistical procedures such as linear regression analysis and the calculation of confidence limits for experimentally determined constants. In the absence of a thorough understanding of statistical theory, (which most students do not have) the validity (or otherwise) of these procedures has to be taken on trust. We have written a suite of computer programs which illustrates principles of statistics by drawing at random from a normal population of numbers. The procedure makes it possible for students to collect in a few minutes many sets of numbers which simulate experimental data. The first program draws data from a normal population with user-specified mean and standard deviation. It thus allows the user to observe the relationship between sample size and calculated standard deviation or standard error of the mean, and also to observe that there really is a 5% risk that the true value of a population mean falls outside the calculated 95% confidence limits of the sample mean. The second program deals with linear relationships and allows the user to observe how confidence in slope and intercept is affected by the number of observations made, the range of x values, the amount of extrapolation needed to calculate the intercept and the standard deviation of the error in y. In this way the benefit of making multiple measurements can be compared with the benefit of reducing experimental error. The third program demonstrates the problems of applying least mean squares linear regression analysis to data obtained by transforming y values in order to obtain a linear relationship.
Group Projects Leading to End Products for the Real World Duncan Reavey. Department of Biology, University of York,
York YO1 5DD, UK A group project is a different way of covering considerable ground in a chosen topic while giving students the opportunity to work as part of a team. The group rather than the tutor decides on the subject to be addressed, the way to do it, and an appropriate end product. The tutor makes simple ground rules clear at the start, is guide and source of information when requested, watches progress and makes tea (leaving the room makes things happen). Students experience group work, management of time and priorities, decision making and communication in the broadest sense while working towards a goal that really matters to them. The approach has been used in tutorial teaching in which just eight one-hour tutorials are given over a term. There are four students in a group. The work is not assessed. The approach has succeeded beyond all of the students' (and my) expectations. End products have included a 24 page booklet putting principles of ecology into a local context with full commercial sponsorship and 2000 copies distributed at no charge
BIOCHEMICAL
EDUCATION
22(1) 1994
The Thayer Method: A Novel Approach to Teaching Biochemistry Jeffery, L Stiefel and Merrill Blackman. Dept of Chemistry, US
Military Academy, West Point, NY 10996, USA Teaching Biochemistry while keeping students interested in the subject has never been an easy task. For years Instructors forced their students to memorize everything in sight; from structures to individual reaction mechanisms to pathways. In the final analysis, what did the students really learn? The true answer is that within one semester many of these students forgot the salient points and how to apply them in the upper level courses. How can a student learn to retain important concepts and possibly even enjoy the time spent in Biochemistry? To try to accomplish this challenging task we refined the tenets of Colonel Sylvanus Thayer, the Superintendent of the United States Military Academy from 1817-1833. The tenents, known as the 'Thayer Method', place the impetus of learning on the student. Students are expected to thoroughly prepare for each lesson and come ready to ask questions concerning the assignment. The Instructor guides the class through the assignment objectives by constant questioning. This not only keeps the students on their toes but allows them to think their way through the concepts by verbalizing them. Emphasis is placed on current research to impart the practicality of understanding biochemistry in everyday situations. This style of questioning also mandates that the Instructor keeps current in the field. Frequent unannounced quizzes also serve to keep the students focussed. Memorization is kept to a minimum. When required to memorize a pathway, such as glycolysis, the emphasis is placed on where substrates/ products enter or leave, and the regulation involved, not how to draw structures in the pathway. Students are also given an opportunity to write a research paper on any subject involving biochemistry. This allows a student to pick a subject that they find interesting and gain insight into a realm of biochemistry. It has the added benefit of introducing the student to library search techniques. By using the 'Thayer Method' we found that students started to enjoy biochemistry a bit more and increased their retention of important concepts.
Computer Simulation of Experiments with Enzymes John Garratt, Doug Clow and Peter Groves. Department of
Chemistry, University of York, York YO1 5DD, UK Laboratory work is an essential feature of all courses, but too often students work by following a recipe and do not learn the skill of planning experiments. To help students to develop these skills, we use a computer to simulate results of an enzyme kinetics experiment. The program stores a set of parameters which allow it to define about 50 000 different enzymes, and one of these is chosen at random for the user. This ensures that no two students have exactly the same problem. Given a limited volume of a solution of their enzyme and its specific activity, their task is to characterize the enzyme as fully as possible. They
16 select a volume of enzyme, concentration of substrate, and pH; the computer then simulates a value for the rate of reaction by calculating an exact value from the Michaelis equation and adding a random error with a standard deviation of 3% of the value. In three hours more than 50 'results' can be obtained; if carefully planned this allows the user to determine the enzyme's optimum pH, its K m and Vmaxat that pH, the effect of pH of K m and Vmaxand the mode of action of a reversible inhibitor.
A New Approach to the Teaching of Experimental Design John Garratt and Mary Aitken. Department of Chemistry,
University of York, York YO1 5DD, UK We have developed a series of classroom activities designed to allow students to develop the skills of planning and interpreting laboratory investigations. Each activity is based on a published paper which has been divided into short sections. A number of tasks are associated with each section, and students work on these in small groups. There is opportunity for interaction between students within their groups, between groups and with tutors. Examples of the questions discussed are: (a) Why is the problem interesting? (b) What data are necessary and how should they be collected? (c) How might the data be presented and interpreted? At each stage, participants compare their proposals with those used in the paper, and discuss whether they could be improved on. This requires students to draw widely on their knowledge, and to apply it to a problem of greater complexity than could be tackled in a laboratory course. The study of this type of problem, to which there is frequently more than one correct answer, helps students to gain an insight into how scientists work.
Using 'Miniposters' to Reinforce the Teaching of Structure and Function of Biological Molecules CHRISTOPHER A SMITH,* MAUREEN M DAWSON, MICHAEL B HEAD and MARTIN J JONES Department of Biological Sciences the Manchester Metropolitan University Manchester M1 5GD, UK
Introduction Biochemistry forms a substantial c o m p o n e n t of the BSc (Hons) in Applied Biological Sciences at the Manchester Metropolitan University, although the specific Biochemistry Units studied by students depends upon their point of entry into the course. Most students enter at the so-called 'stage two' and attend a three-year degree course, although a significant n u m b e r enter at 'stage one' (the foundation year) and study for four years. This dual entry system allows recruitment of mature students and those with less conventional entry qualifications. This degree course is currently being reviewed and is likely to change in structure and entry requirements in the near future. Biochemistry is taught both as a single honours subject or as a subsidiary subject on virtually all Life Sciences courses, although its learning and teaching often presents problems to students and staff respectively. The subject matter is sometimes abstract, and Biological Science *To whom all correspondence should be addressed
BIOCHEMICAL EDUCATION 22(1) 1994
students often complain of difficulties in "visualizing' biomolecules and metabolic processes. Students on general Life Sciences courses are usually strongest in the Biological rather than the Chemical or Physical Sciences, and this presents particular problems to the teacher. However, the structural data on biomolecules now available from X-ray crystallography and nuclear magnetic resonance m e a s u r e m e n t s and the use of advanced computer graphics means that models of molecules and simulations of their activities may be viewed and examined. These facilities undoubtedly aid student learning.
Preparation of posters The wide availability of molecular models was used with a stage one group of diverse ages and educational backgrounds (Table 1) attending a unit called Organic Chemistry, Biochemistry and Cell Ultrastructure. As part of their unit assessment, students were required to prepare a 'miniposter' on the structure and activity of a specified protein, chosen for the students from a restricted list (Table 2). Proteins were used in this exercise because they are the most diverse of biological molecules in terms of structures and functions, 1"2 and thus numerous different examples are available for use with students. The poster preparation and presentation was used to reinforce the teaching by lecture and 'wet' practical classes of the hierarchical structures and the general functions of proteins. Hendrickson and Wiithrich 3'4 are excellent sources of up-to-date references on the structures and activities of proteins and peptides. The m a j o r restrictions imposed on the students were
Table 1 Educational background ('A' level studied) and age structure of the Stage 1 group which prepared the 'miniposters' GCE A level subject
Number of A level passes
Art Biology Business Studies Chemistry Design Economics English General Studies Geography Government & Politics History Mathematics Medical History Music Philosophy Physics Psychology Social Biology Social & Environmental Biology Sociology
3 32 1 19 1 6 6 17 4 1 1 7 1 l 1 7 3 1 1 2
Mean age (years) Age range (years)
20 18-36
to 63 local schools: a debate about pollution for a participating audience of 120 'A' level students and briefing materials for roleplay debates in schools; and a half hour lesson with a short video for ACCESS students and ' A ' level general studies groups on the importance of active site management in conservation. Key points are that (1) successful group projects do not require large blocks of teaching time; (2) there is a genuine and useful end product: the students impose their the highest standards because they know the end product will reach many people; (3) the project takes students into the outside world where they must deal with all kinds of situations and all kinds of people.
Empirical Illustration of Statistical Procedures John Garratt and Steve Smith. Department of Chemistry,
University of York, York YO1 5DD, UK Most undergraduate chemists are expected to use statistical procedures such as linear regression analysis and the calculation of confidence limits for experimentally determined constants. In the absence of a thorough understanding of statistical theory, (which most students do not have) the validity (or otherwise) of these procedures has to be taken on trust. We have written a suite of computer programs which illustrates principles of statistics by drawing at random from a normal population of numbers. The procedure makes it possible for students to collect in a few minutes many sets of numbers which simulate experimental data. The first program draws data from a normal population with user-specified mean and standard deviation. It thus allows the user to observe the relationship between sample size and calculated standard deviation or standard error of the mean, and also to observe that there really is a 5% risk that the true value of a population mean falls outside the calculated 95% confidence limits of the sample mean. The second program deals with linear relationships and allows the user to observe how confidence in slope and intercept is affected by the number of observations made, the range of x values, the amount of extrapolation needed to calculate the intercept and the standard deviation of the error in y. In this way the benefit of making multiple measurements can be compared with the benefit of reducing experimental error. The third program demonstrates the problems of applying least mean squares linear regression analysis to data obtained by transforming y values in order to obtain a linear relationship.
Group Projects Leading to End Products for the Real World Duncan Reavey. Department of Biology, University of York,
York YO1 5DD, UK A group project is a different way of covering considerable ground in a chosen topic while giving students the opportunity to work as part of a team. The group rather than the tutor decides on the subject to be addressed, the way to do it, and an appropriate end product. The tutor makes simple ground rules clear at the start, is guide and source of information when requested, watches progress and makes tea (leaving the room makes things happen). Students experience group work, management of time and priorities, decision making and communication in the broadest sense while working towards a goal that really matters to them. The approach has been used in tutorial teaching in which just eight one-hour tutorials are given over a term. There are four students in a group. The work is not assessed. The approach has succeeded beyond all of the students' (and my) expectations. End products have included a 24 page booklet putting principles of ecology into a local context with full commercial sponsorship and 2000 copies distributed at no charge
BIOCHEMICAL
EDUCATION
22(1) 1994
The Thayer Method: A Novel Approach to Teaching Biochemistry Jeffery, L Stiefel and Merrill Blackman. Dept of Chemistry, US
Military Academy, West Point, NY 10996, USA Teaching Biochemistry while keeping students interested in the subject has never been an easy task. For years Instructors forced their students to memorize everything in sight; from structures to individual reaction mechanisms to pathways. In the final analysis, what did the students really learn? The true answer is that within one semester many of these students forgot the salient points and how to apply them in the upper level courses. How can a student learn to retain important concepts and possibly even enjoy the time spent in Biochemistry? To try to accomplish this challenging task we refined the tenets of Colonel Sylvanus Thayer, the Superintendent of the United States Military Academy from 1817-1833. The tenents, known as the 'Thayer Method', place the impetus of learning on the student. Students are expected to thoroughly prepare for each lesson and come ready to ask questions concerning the assignment. The Instructor guides the class through the assignment objectives by constant questioning. This not only keeps the students on their toes but allows them to think their way through the concepts by verbalizing them. Emphasis is placed on current research to impart the practicality of understanding biochemistry in everyday situations. This style of questioning also mandates that the Instructor keeps current in the field. Frequent unannounced quizzes also serve to keep the students focussed. Memorization is kept to a minimum. When required to memorize a pathway, such as glycolysis, the emphasis is placed on where substrates/ products enter or leave, and the regulation involved, not how to draw structures in the pathway. Students are also given an opportunity to write a research paper on any subject involving biochemistry. This allows a student to pick a subject that they find interesting and gain insight into a realm of biochemistry. It has the added benefit of introducing the student to library search techniques. By using the 'Thayer Method' we found that students started to enjoy biochemistry a bit more and increased their retention of important concepts.
Computer Simulation of Experiments with Enzymes John Garratt, Doug Clow and Peter Groves. Department of
Chemistry, University of York, York YO1 5DD, UK Laboratory work is an essential feature of all courses, but too often students work by following a recipe and do not learn the skill of planning experiments. To help students to develop these skills, we use a computer to simulate results of an enzyme kinetics experiment. The program stores a set of parameters which allow it to define about 50 000 different enzymes, and one of these is chosen at random for the user. This ensures that no two students have exactly the same problem. Given a limited volume of a solution of their enzyme and its specific activity, their task is to characterize the enzyme as fully as possible. They
16 select a volume of enzyme, concentration of substrate, and pH; the computer then simulates a value for the rate of reaction by calculating an exact value from the Michaelis equation and adding a random error with a standard deviation of 3% of the value. In three hours more than 50 'results' can be obtained; if carefully planned this allows the user to determine the enzyme's optimum pH, its K m and Vmaxat that pH, the effect of pH of K m and Vmaxand the mode of action of a reversible inhibitor.
A New Approach to the Teaching of Experimental Design John Garratt and Mary Aitken. Department of Chemistry,
University of York, York YO1 5DD, UK We have developed a series of classroom activities designed to allow students to develop the skills of planning and interpreting laboratory investigations. Each activity is based on a published paper which has been divided into short sections. A number of tasks are associated with each section, and students work on these in small groups. There is opportunity for interaction between students within their groups, between groups and with tutors. Examples of the questions discussed are: (a) Why is the problem interesting? (b) What data are necessary and how should they be collected? (c) How might the data be presented and interpreted? At each stage, participants compare their proposals with those used in the paper, and discuss whether they could be improved on. This requires students to draw widely on their knowledge, and to apply it to a problem of greater complexity than could be tackled in a laboratory course. The study of this type of problem, to which there is frequently more than one correct answer, helps students to gain an insight into how scientists work.
Using 'Miniposters' to Reinforce the Teaching of Structure and Function of Biological Molecules CHRISTOPHER A SMITH,* MAUREEN M DAWSON, MICHAEL B HEAD and MARTIN J JONES Department of Biological Sciences the Manchester Metropolitan University Manchester M1 5GD, UK
Introduction Biochemistry forms a substantial c o m p o n e n t of the BSc (Hons) in Applied Biological Sciences at the Manchester Metropolitan University, although the specific Biochemistry Units studied by students depends upon their point of entry into the course. Most students enter at the so-called 'stage two' and attend a three-year degree course, although a significant n u m b e r enter at 'stage one' (the foundation year) and study for four years. This dual entry system allows recruitment of mature students and those with less conventional entry qualifications. This degree course is currently being reviewed and is likely to change in structure and entry requirements in the near future. Biochemistry is taught both as a single honours subject or as a subsidiary subject on virtually all Life Sciences courses, although its learning and teaching often presents problems to students and staff respectively. The subject matter is sometimes abstract, and Biological Science *To whom all correspondence should be addressed
BIOCHEMICAL EDUCATION 22(1) 1994
students often complain of difficulties in "visualizing' biomolecules and metabolic processes. Students on general Life Sciences courses are usually strongest in the Biological rather than the Chemical or Physical Sciences, and this presents particular problems to the teacher. However, the structural data on biomolecules now available from X-ray crystallography and nuclear magnetic resonance m e a s u r e m e n t s and the use of advanced computer graphics means that models of molecules and simulations of their activities may be viewed and examined. These facilities undoubtedly aid student learning.
Preparation of posters The wide availability of molecular models was used with a stage one group of diverse ages and educational backgrounds (Table 1) attending a unit called Organic Chemistry, Biochemistry and Cell Ultrastructure. As part of their unit assessment, students were required to prepare a 'miniposter' on the structure and activity of a specified protein, chosen for the students from a restricted list (Table 2). Proteins were used in this exercise because they are the most diverse of biological molecules in terms of structures and functions, 1"2 and thus numerous different examples are available for use with students. The poster preparation and presentation was used to reinforce the teaching by lecture and 'wet' practical classes of the hierarchical structures and the general functions of proteins. Hendrickson and Wiithrich 3'4 are excellent sources of up-to-date references on the structures and activities of proteins and peptides. The m a j o r restrictions imposed on the students were
Table 1 Educational background ('A' level studied) and age structure of the Stage 1 group which prepared the 'miniposters' GCE A level subject
Number of A level passes
Art Biology Business Studies Chemistry Design Economics English General Studies Geography Government & Politics History Mathematics Medical History Music Philosophy Physics Psychology Social Biology Social & Environmental Biology Sociology
3 32 1 19 1 6 6 17 4 1 1 7 1 l 1 7 3 1 1 2
Mean age (years) Age range (years)
20 18-36