Teaching the Biochemistry/Molecular Biology Lab¹
Introduction
The Biochemistry/Molecular Biology (BMB) teaching laboratory course has become
a prominent and essential component in the training of undergraduate students for
careers related to the molecular life sciences (biochemistry, molecular biology,
chemistry, genetics, cell biology, immunology, microbiology, neurochemistry, forensic
science, biotechnology, etc.). These students must acquire extensive experience
working with biomolecules and biological processes in the laboratory and a formal lab
course is usually the best, first step to that experience. This step provides students the
skills needed for future research participation at the undergraduate and graduate level,
and for jobs in the biotechnological and pharmaceutical industries. In addition, a lab
experience is an asset for those science majors preparing for careers in law and
business which may be related, but outside the realm of the basic sciences (patent law,
pharmaceutical sales, etc.). With the acknowledged importance of a lab experience for
all students, it is necessary for instructors to think clearly about the elements that make
up an effective BMB laboratory experience, and attempt to answer several questions
before designing laboratory activities for their students. For example, what technical
skills and procedures must be practiced and mastered by students? What teaching
modes work best to most effectively train students in the lab? What instrumentation
should undergraduate students become familiar with? What is the importance of the
“other lab skills” such as communication (written and oral), teamwork, ethics, fairness,
and responsibility? How are these best taught?
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¹Adapted from Biochemistry and Molecular Biology Education, 31, 102-105 (2003).
(Updated April, 2009)
A. A Brief History
The standard approach to teaching the BMB lab has been, for many years, to:
1) select appropriate experiments from a textbook/manual adopted for the class
(References [1-5] for current lab books); or
2) utilize a set of self-designed experiments; or
3) choose experiments and projects published in biochemical education journals,
notably, Biochemistry and Molecular Biology Education (BAMBED), The Journal
of Chemical Education (JCE), and others.
These three options have provided instructors the opportunity to select lab activities that
emphasize certain desirable biochemical principles, techniques, and skills, and those
methods that are compatible with the instructor’s background/expertise and with the
institution’s instrumentation and facilities.
However, major changes are now occurring in biochemistry and molecular biology
and these changes require that we begin to adopt new instructional methods in the
classroom and teaching lab [6-9]. For example, the recent advent of bioinformatics,
the merging of computer science with biology, is transforming the way we investigate
protein and nucleic acid structure and function as we can now obtain important
information from computer databases and thus avoid days of “wet” work in the lab [10].
The continuous development of new instrumentation and methods also will
require changes in the way labs are presented. Now that protein characterization
may be approached by NMR [11] and MS [12], should students struggle through
an Edman degradation experiment in the lab just to see how it used to be done?
It is also important that labs have a multidisciplinary nature so students begin to
experience the current merging of biology, chemistry, physics, math, and computer
science.
B. A Variety of Teaching Methods
Many instructors around the world have responded to the rapid changes in BMB by
incorporating new teaching methods into their lab activities and have developed courses
with more realistic expectations about student involvement in experimental design, data
analysis, and data interpretation. Domin has written a detailed review of laboratory
instruction styles prevalent in chemistry [13]. He characterizes four distinct styles that
are differentiated by three descriptors—outcome, approach, and procedure (Table 1).
Table 1. Descriptors of the laboratory instruction styles [13]
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Style
Descriptor
______________________________________________________________________
Outcome
Approach
Procedure
Expository
Predetermined
Deductive
Given
Inquiry
Undetermined
Inductive
Student generated
Discovery
Predetermined
Inductive
Given
Problem-based
Predetermined
Deductive
Student generated
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The outcome or result from a laboratory activity is predetermined when the style is
expository, discovery, or problem-based. In expository labs, both the students and the
instructor know the expected results. The outcome is usually known only by the
instructor in discovery and problem-based activities. The outcome from an inquiry-type
lab is not known by the students or instructor. The approach for the expository and
problem-based styles are deductive; that is, students use a fundamental principle
to understand their results. Inquiry and discovery styles are inductive; that is, students
are to derive the fundamental principle.
These predominant teaching methods, and others, are now available for laboratory
instruction in biochemistry and professors may want to experiment with some of the
different pedagogical styles. Following is a brief description of laboratory teaching
methods that may be appropriate for biochemistry labs. Examples of published
experiments are provided with each style.
(1) Expository Instruction: Most BMB lab courses in the past have been taught in this
very traditional, techniques-oriented style. Sometimes called the “cookbook approach”,
laboratory activities emphasize mastery of the primary tools and techniques of the trade,
and reinforce basic principles. The descriptors for this type of lab are “predetermined”,
“deductive”, and “given” (See Table 1). Expository (also called skill-building) labs are
characterized by the achievement of well-defined goals and a very high success rate on
the part of the students [13, 14]. Students completing these labs often attain high marks
for technique, but may show weakness in understanding the research process, the
steps one goes through to solve a problem, and they miss out on the excitement of
discovery. Most of the experiments published in lab manuals [1-5] and many in the
education journals are in the skill-building, expository mode [15-17, for examples].
(2) Inquiry Instruction [18A, B; 19]: This style of lab instruction (also called openinquiry instruction) displays more active learning as it goes beyond a ‘follow the recipe’
approach. It is characterized as “undetermined”, “inductive”, and “student generated”
(Table 1). Students, who usually work in teams of up to four, are assigned a specific
BMB problem to solve. The student team is responsible for designing and completing
experiments, integrating data, and finally arriving at reasonable conclusions which are
reported in a written and/or verbal format. Students share the excitement of discovery
(they experience ‘real’ research), but they also must face the possibility of failure, just as
in research. Not all students in a lab course may be prepared for this independent
approach so teams must be organized carefully so that less experienced students are
matched up with those with some laboratory experience.
(3) Discovery Instruction [20]: This instruction style is similar to inquiry instruction (#2
above), and is often called the guided-inquiry style. Students are provided a detailed
procedure and the outcomes of experiments are known by the instructor and students
(Table 1). Students learn important skills, but do not gain the experience of designing
a project to solve a research-type problem as in the inquiry method.
(4) Problem-based Instruction: In this method of instruction, the instructor poses a
problem, usually in the form of a question, for students to solve [21, 22]. Students are
prepared for the project with lectures and assigned reading and are expected to
generate the lab procedure, make observations, collect data, and deduce significant
conclusions. This method of instruction gives students the opportunity to learn and
practice skills, and devise a research-type procedure, but, usually no new discoveries
are made.
(5) Project-based Instruction: This lab format usually involves students working on a
series of connected lab activities that revolve around a central BMB theme [23-27].
Using the descriptors in Table 1, this type of instruction is “predetermined”,
“deductive”, and “given.” Students will have the opportunity to participate in all aspects
of the project and learn many skills in the process. Although these are called “researchbased” projects by some, because of the continuity (current work is based on previous
results), this term is somewhat misleading as students usually follow a preset schedule
of activities and seldom waiver from the plan. The central theme may be a biomolecule
(i.e. enzymes and proteins are popular) or a biochemical process (i.e. recombinant DNA
cloning techniques). Many of these projects originate in an instructor’s research lab and
make much sense at that instructor’s institution. However, they often require unique and
expensive resources, and because they are based on someone else’s research, are
logistically difficult to transfer to other institutions. Instructors who set these up
have extensive experience with the theme so are very familiar with the system, its
advantages, and its pitfalls. While this research-based approach may be desirable for
those students who will later attend science graduate school, some instructors may
prefer a more skill-based lab program for the average student.
Lab courses with experiments that integrate and apply several of the above teaching
formats may better approach the balance of teaching styles that instructors want for
their students. Many instructors find it valuable to begin a semester with skill-based labs
and gradually progress to inquiry-based, problem-based, or project-based experiments.
The combination of different formats allows students to learn by the reinforcement of
fundamental principles and techniques, yet still experience the excitement of the
research process. Several experiments that use integrated, project-based learning
techniques are listed in Part D-VII below.
C. Essential BMB Concepts and Skills for Student Learning
No matter how sophisticated the instrumentation, how new the techniques,
or how brilliant the instructor’s pedagogy, a lab course without thoughtful content
is meaningless. How can beginning instructors learn about developing new courses?
We often turn to our scientific societies to gain advice on what principles and concepts
they think students should learn.
The American Chemical Society (ACS) divides recommendations for biochemistry
lab activities into two categories [28].
Important general techniques:
error and statistical analysis of experimental data
spectroscopic methods
electrophoretic techniques
chromatographic separations
isolation and characterization of biological materials
Selected additional techniques:
use of radioisotopes
enzyme kinetics
immunoassay methods
DNA cloning and sequencing
plasmid isolation and mapping
peptide isolation and sequencing
computer graphics and structure calculations
The American Society for Biochemistry and Molecular Biology (ASBMB)
has just recently prepared a recommended curriculum for the undergraduate
biochemistry/molecular biology degree [29]. Lab skills suggested include isolation and
characterization of proteins and other biomolecules, enzyme kinetics and inhibition,
genetic engineering techniques, quantitative techniques, data acquisition/statistics, use
of computer databases, spectroscopy (UV/VIS, fluorescence, NMR, MS),
chromatography (HPLC, gel filtration, ion exchange, affinity), electrophoretic techniques
(PAGE, agarose gel, IEF, CE), DNA isolation and sequencing, cloning, PCR,
microscopy, aseptic techniques, and microarrays.
The Biochemical Society (U. K.) has recently published a list of topic objectives to
define the main content of the core curriculum for the Biochemistry First Degree [30].
Specific laboratory experiences mentioned in the report include:
analytical methods in chemistry (NMR, MS, HPLC, etc.)
basic techniques for analyzing, cloning, and sequencing DNA
experimental techniques for the study and analysis of enzyme kinetics
techniques for studying macromolecular structure including purification
and characterization, and use of the computer for structural information
5
the main techniques used in cell biology
The Biosciences Industry Skill Standards Project (BISSP) sponsored by
the United States Department of Education has recently generated an extensive
list of skills, both technical and non-technical, expected of a bioscience technician [31].
Suggestions for designing lab curricula
The goal of all BMB lab instructors is to offer practical, hands-on experiences
that introduce their students to the most contemporary instrumentation, techniques,
and principles the institution can afford. It is also important that students learn and
practice all the steps necessary to design an appropriate experimental plan to solve a
problem. Instructors may wish also to experiment with different teaching styles.
In Domin’s words [13], “Research is needed that addresses which style of instruction
best promotes the following specific learning outcomes:
1
conceptual understanding
2
retention of content knowledge
3
scientific reasoning skills
4
laboratory manipulative skills
5
better attitude towards science
6
a better understanding of the nature of science.”
Table 2 lists general lab skills, procedures, and methods. This listing defines
Table 2. General lab skills/procedures/principles
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Lab safety
Writing and reporting results (maintaining lab notebook, lab reports, posters, oral
presentations)
Experimental design, collection and statistical analysis of data, controls
Reading the research literature with understanding
Computer (data analysis, graphing, spreadsheet, literature search, databases)
Preparation of solutions
Pipetting liquids
Buffers and pH
Measurement of protein and nucleic acid solutions
Isolation and/or characterization of biomolecules (amino acids, peptides,
proteins, enzymes, carbohydrates, lipids, nucleic acids)
Centrifugation
Microfiltration/membranes and dialysis
Centrifugal vacuum concentration and lyophilization
Using commercial kits
Microarrays (nucleic acid and protein)
Radioisotopes
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broadly those concepts that are used routinely and regularly in a lab setting for work on
all types of biomolecules and for all types of measurements. This list is not all-inclusive
as instructors will be able to add a few of their own. The manner in which these general
skills are presented by the instructor and practiced by the students will be dependent on
many factors including the time and facilities available for the lab, the size of the class,
the past experiences of the students, and the specific interests of the instructor.
Perhaps it is helpful to provide some ideas on the mode of presentation and the relative
amount of time spent on the general skills. In a typical BMB lab of 3-4 hours per week,
one-half of the first period may be spent discussing the first five skills listed in Table 2
(safety through computer). The remainder of the first period could be used for students
practicing the next group of skills (solutions, pipetting, pH, buffers). Perhaps these skills
could be learned with an experiment where students measure protein and/or nucleic
acid solutions. It is much more instructive to have students practice with “real samples”
rather than just going through the motions of pipetting. Students at the BMB lab level
will have already become adept at some of these general skills by work in earlier labs in
Introductory Biology and Chemistry, Organic Chemistry, and others. Therefore it is
important for instructors who know of the students’ past experiences to make judgments
about how much time should be devoted for each technique. It is expected that most
students, after completing a typical one-semester BMB lab, would be proficient in the
application of all of the general concepts in Table 2. One exception to this may be the
topic of radioisotopes where instructors need to make their own decision on the relative
importance and practicality of this concept.
The importance of teaching skills in communication (writing and reporting results in
Table 2) is secondary only to the topic of lab safety. New scientific knowledge that is
not communicated is of no value to anyone. Learning communication skills needs to
begin with introductory labs (Chemistry and Biology) and continue through all future
courses, lab and classroom [32]. Coordination and consistency among all lab
instructors in a department are of vital importance so students do not learn different
communication techniques at each level. Specific skills that students must master in the
BMB lab include maintaining a lab notebook, writing up a lab experiment, writing a
journal-style article, critical analysis of other writing (other student’s and journal articles),
giving an oral presentation on experimental results, and the preparation and
presentation of a poster [1, 2, 14, 21, 27]. Students should practice presentations at
their local institution and then gain experience at regional and national meetings.
Chapter 1 of this text [2] describes details for the preparation of written and oral
communications.
Techniques for Specific Laboratory Procedures
Table 3 presents ‘selective’ methods that serve a more specific purpose in
the BMB lab as they may not be applicable to all types of biomolecules and
measurements. It is obviously impossible for students to be introduced, in a one-
Table 3. Selective lab methods
____________________________________________________________
Spectroscopy: UV/VIS, fluorescence, NMR (2D), MS (MALDI)
Chromatography: HPLC, affinity, gel filtration, ion exchange, column
Computational biochemistry: enzyme kinetics and inhibition, ligand binding,
genomic and proteomic databases, molecular modeling, metabolic control
analysis
Electrophoresis: PAGE (SDS and native), agarose, CE, IEF
Biotechnology: recombinant DNA, PCR, restriction enzymes, plasmid DNA,
sterile techniques, growing bacteria, cloning, protein expression, gene
libraries, sequencing DNA and proteins, blotting (Southern, Northern, Western
and other immunoassays)
______________________________________________________________________
or even two-term lab, to all of the selective lab methods. Instructors usually
pick and choose those methods based on what facilities are available and what they
believe their students should practice. The methods listed in Table 3 have been
placed in order of relative importance on the basis of the author’s prejudice and
many years of experience. The most essential methods for BMB students include
spectroscopy (UV/VIS), chromatography (HPLC, affinity, gel filtration, ionexchange, column), computational (enzyme kinetics/inhibition, ligand binding,
databases), electrophoresis (all types), and biotechnology (recombinant DNA,
plasmids, PCR, and restriction enzymes). Students should be encouraged to
learn other more advanced skills and concepts in a future research experience.
Many of the methods listed in Table 3 require expensive instrumentation.
Such equipment may not be present at smaller institutions and even students at
larger institutions may not have access to it because it is reserved for research.
Instructors at these institutions must provide alternate opportunities to expose
their students to the latest techniques and instrumentation. This may be done
by visiting facilities at nearby research institutions, government labs, or
industrial labs. Additionally, students could be encouraged to increase their
understanding of the selective techniques by participating in a summer research
project at an academic, industrial, or government laboratory. Students may also
become acquainted with modern BMB principles and instrumentation by viewing
Virtual Lab Web sites, for example, the Virtual Biochemistry Lab sponsored by the
Nobel Foundation [33]. A discussion of the value of Virtual Biochemistry Labs is in
Chapter 2, Section C [2].
Scientific work is being done increasingly in groups and students need to
gain experience working in teams to gain confidence and to learn how to
play the roles of team members. In addition to being adept with their hands,
they also need to understand and practice the ethical characteristics of fairness,
honesty, cooperation, and responsibility. This includes an understanding of fair
and proper use of scientific data and the literature, and a consideration of
intellectual property, patents, and copyrights [34].
The Issue of ‘Kits’
Most instructors are aware of the availability of a large number of commercial,
prefabricated kits that contain a collection of all the chemical reagents, solutions, and
disposable supplies necessary for specific laboratory procedures. Kits are now offered
for many types of procedures including assay of protein concentration, measurement of
DNA solutions, measurement of cholesterol in blood serum, isolation of plasmid DNA,
precast electrophoresis gels, immunostaining of blots, chromatographic purification of
expressed protein, and for preparing recombinant DNA. Kits for use in molecular
biology and genetic engineering projects are especially widespread because so many
complex reagents and solutions are required. In general, the kits are more expensive
than preparing one’s own solutions; however, there are other factors that must be
considered. Some of the advantages of kits include:
because the reagents and solutions in the kits are prepared under standard and
exacting conditions, they are likely to work better in the lab than self-prepared
solutions,
if kits are used, one does not need to purchase or store the many, different
individual reagents and supplies (usually in freezer or refrigerator), or prepare
and maintain extensive inventory and safety records (MSDS) for the chemicals,
prepared kits save much time for the stockroom manager and lab prep
person and are very convenient for student use,
there is less waste of expensive supplies by students because the reagents and
solutions in pre-measured quantities are much easier to dispense.
The disadvantages of using kits are fewer than the advantages, but they are
significant. In addition to the extra expense, kits can sometimes leave students
confused about what they are doing. The chemical/biochemical principles behind kit
operation must be explained so students do not perceive the kits just as ‘black boxes’ or
‘magic solutions’. Students need to be told exactly what a kit is doing, why it is being
used rather than self-made reagents and solutions, and how to troubleshoot the
procedure to see if the kit is functioning properly. Some researchers are concerned that
kits may “act as technical crutches that dull our ability to interpret experiments and
understand where they may have gone wrong” [35].
Instructors can learn from experience what kits are beneficial in terms of costs and
student learning. Students, in their future work in graduate school and jobs in
biotechnology, will undoubtedly use kits. In fact, kit use in commercial laboratories is
widespread and even encouraged. It is essential that students become familiar with the
selection and proper use of kits as soon as is possible in their training [36].
D. Experiments in Biochemistry and Molecular Biology
Following this chapter is a list of over 250 experiments that have been published in
major education journals including Biochemistry and Molecular Biology Education and
The Journal of Chemical Education. An experiment was selected if it presented the use
of fundamental principles and techniques in BMB in a pedagogically-significant and/or
novel manner, and offered every indication that it would ‘work’ in a typical teaching-lab
setting. Experiments at all levels of complexity are included. Some are appropriate for
institutions that have only minimal instrumentation and facilities, whereas others require
extensive instrumentation. Most of the experiments were published since 1995.
Experiments dated earlier were chosen because the principles demonstrated were still
of pedagogical significance.
The present list divides the experiments into the categories: I. Techniques
and Procedures; II. Isolation and Analysis of Biomolecules; III. Isolation and
Characterization of Enzymes; IV. Metabolism/Regulation/Transport; V. Clinical/
Nutritional; VI. Molecular Biology; and VII. Integrated Projects. Some experiments
may be placed in more than one category if several skills and techniques are
practiced.
The list is posted on a Web site and will be regularly updated. BMB instructors are
encouraged to report published, peer-reviewed experiments/projects to the author
(boyer@hope.edu) so they may be included in the updated list.
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