Student Centered Education

Austin U. Gehret*
Pop-It Beads to Introduce Catalysis
of Reaction Rate and Substrate
Depletion Effectsws

From the Department of Science and Mathematics, National Technical

Institute for the Deaf, Rochester Institute of Technology, Rochester,
New York 14623

Abstract
A kinesthetic classroom activity was designed to help stu- targeted learning outcomes. Unique to previous kinesthetic
dents understand enzyme activity and catalysis of reaction approaches that model Michaelis-Menten kinetics, this activ-
rate. Students served the role of enzymes by manipulating ity models the effects of substrate depletion on catalyzed
Pop-It Beads as the catalytic event. This activity illuminates reaction rate. Therefore, it could prove beneficial for convey-
the relationship between reaction rate and reaction progress ing the reasoning behind the initial rate simplification used
by allowing students to experience first-hand the effect of in Michaelis-Menten kinetics. V C 2016 by The International

substrate depletion on catalyzed reaction rate. Preliminary Union of Biochemistry and Molecular Biology, 00:000000,
findings based on survey results and exam performance 2016.
suggest the activity could prove beneficial to students in the

Keywords: enzyme catalysis; substrate depletion; classroom

activity; Pop-It beads

Michaelis-Menten kinetics is one of the most challenging undergraduates, a higher percentage of them believed that
topics undergraduates confront in biochemistry [1]. Implicit reaction rate increases with time [5]. Thus, misconceptions
in this challenge is that Michaelis-Menten kinetics is an about reaction dynamics persist with students at the bio-
application of reaction kinetics that students acquire in chemistry level and likely contribute to the challenge of
general chemistry courses. It has been documented that learning enzyme kinetics.
students exhibit a variety of misconceptions about funda- Constructivist learning theory states that new meaning
mental chemical concepts [2, 3] as well as a rapid decay in is constructed in the minds of learners in ways that make
knowledge without continued spiral use of concepts [4]. In sense to them using their conceptual framework [6]. This
fact, an analysis of third year undergraduates reasoning of theory has formed the basis for alternative teaching strate-
reaction kinetics revealed that while they harbored a better gies to confront students conceptions about biochemistry
understanding of the definition of reaction rate compared including the process oriented guided inquiry learning
to secondary education students and first year (POGIL) approach [7] and case-based instruction [8]. Kines-
thetic approaches have also been leveraged in an effort to
develop deeper meaning for students with conceptually
Volume 00, Number 00, Month/Month 2016, Pages 0000 abstract topics in chemistry [9] and students exhibit a
Abbreviations: DHH, deaf or hard-of-hearing strong preference for learning information through multiple
*Address for correspondence to: Department of Science and Mathe- modes of presentation while engaging multiple senses [10].
matics, National Technical Institute for the Deaf, 52 Lomb Memorial Many have seen the value in alternative approaches to
Dr., Rochester, NY 14623. E-mail: augnts@rit.edu teaching Michaelis-Menten kinetics. Student engagement
Received 1 October 2015; Revised 29 April 2016; Accepted 27 June with this concept has been enhanced through computer-
2016 based pedagogies [1, 1113] as well as kinesthetic
ws Additional Supporting Information may be found in the online
approaches [1417]. Regarding the latter, each approach
version of this article.
The corresponding author has no conflict of interest to declare related had students assume the role of enzyme by catalyzing a
to the work described in this manuscript. specific manipulative event with an object. Catalysis was
DOI 10.1002/bmb.21000 modeled to explain the nature of the turnover number (kcat)
Published online 00 Month 2016 in Wiley Online Library using marble transfer between bins [14] or the unscrewing
(wileyonlinelibrary.com) of bolt-nut substrate complexes [15]. Other approaches

Biochemistry and Molecular Biology Education 1

 Biochemistry and
Molecular Biology Education

had students remove substrates from paper bags with an

emphasis on competitive inhibition [16] or the temperature
dependence of enzyme activity [17]. In all instances, the
substrate concentration was varied to observe the change
to the initial reaction rate (V0), measured using either a
fixed time period to record catalytic events [1416] or a
fixed number of catalytic events to determine the time
elapsed [17]. The change to V0 over time was not explored.
The Michaelis-Menten plot is in essence a snapshot of a
dynamic enzyme-substrate system at play. Students at all
grade levels exhibit a lack of conceptualization for the
dynamic nature of reaction systems [3]. This is exemplified
by the perpetuated misconception among third year under-
graduates, the intended audience for this topic, that reac-
tion rate increases over time [5]. Recognition of students
knowledge gap between experimental kinetic data and the
Pop-It Bead pair substrates. Each student group
mathematical construction of the Michaelis-Menten reac- FIG 1 (two students per group) was given a bin con-
tion curve has even led to the proposal that the integrated taining forty Pop-It Bead pairs (substrates) to cat-
form of the equation be used alternatively to teach this top- alyze over a span of 3 minutes. One bin of
ic [18]. As Michaelis-Menten kinetics is predicated on mea- substrates was not assigned to any group to rep-
suring V0 behavior, it is worthwhile to explore ways that resent the un-catalyzed reaction. [Color figure
can be viewed in the online issue, which is avail-
can help students grasp the rationale for why this simplifi-
able at wileyonlinelibrary.com.]
cation is used.
The kinesthetic activity described herein was adminis-
tered to a biotechnology class of students who are deaf or also suffice but were not used owing to the need for stu-
hard-of-hearing (DHH) learning to quantify enzyme activity. dents to maintain visual communication.) After each timed
Similar to helping hearing students develop mental con- interval, students tallied total products made. To alleviate
structs of concepts [19], active learning exercises with a confusion, products were removed from bins for accurate
participative learning environment strongly correlate with counting and then returned and mixed with substrate Pop-
DHH student success and course engagement [20]. The top- It Bead pairs prior to resuming. This process was repeated
ic learning objectives focused on how to identify enzymatic four times at 20-second intervals followed by two 40-
activity, best explored through time course measurements second intervals (Supporting Information File 1). At the
[21]. As such, the classroom activity was designed to model conclusion of the activity, the instructor presented a bin of
the progression of an enzyme-catalyzed reaction over time. Pop-It Beads that had not been catalyzed by any student
Based on student surveys, preliminary exam results and group (Fig. 1) to represent un-catalyzed reaction progress.
teacher observations with a comparatively small (n 5 16)
student sample, the activity appears to have potential for
increasing students perceived understanding and short-
Analysis
term knowledge gains with kinetics concepts. Additionally, Following the activity, students were guided by worksheets
the design of the activity aims to allow students to experi- (Supporting Information File 1) to plot the reaction pro-
ence the effect of substrate depletion on catalysis firsthand gress of both the un-catalyzed reaction and their catalyzed
and could prove worthy to convey the initial rate simplifica- reactions. These plots were intended to provide students
tion used in Michaelis-Menten kinetics. the opportunity to observe how their influence over the
reaction (enzyme activity) influenced the reaction progress
graphically (Fig. 2). Reaction rate determination is inherent
Classroom Activity in this type of graphical analysis; thus, students were also
Students were grouped into pairs and given a bin (2 3 4 3 guided by the worksheets (Supporting Information File 1) to
7.75 in3) of 40 Pop-It Bead pairs (Carolina Biological Sup- determine the reaction rates over time for both conditions.
ply) that served as the substrates for the reaction (Fig. 1). The instructor facilitated the connection between these val-
One student served as the enzyme by separating Pop-It ues and their mathematical determination from the kinetic
Bead pairs into two products (the catalytic event); the sec- data. Survey results assessing students confidence with
ond student was timekeeper for the duration of the activity enzyme activity and reaction rate suggested students per-
(3 minutes). To simulate simple diffusion between enzyme ceived gains in knowledge for both kinetics concepts (Table
and substrate, students were instructed to avert their eyes I). These self-perceptions in knowledge gains were general-
from the bin while catalyzing the reaction. (Blindfolds could ly supported by exam performance (Table II). Students had

2 Enzyme Catalysis with Pop-It Beads

 group that did not observe this trend had the fastest V0
(0.55 Pop-It Bead pairs/s) that was predictably not sustain-
able subsequent time intervals. Within the time allotted,
four groups catalyzed the reaction to completion and three
groups approached reaction rates that were 13% or less of
their V0. The slowest group (V0 5 0.2 Pop-It Bead pairs/s)
was still able to observe a moderate decrease in reaction
rate by the end of the time course. Based on these observa-
tions, it would appear that the activity can effectively dem-
onstrate reaction rate depreciation over time to students
with a variety of manipulative abilities.
It was the intent in the design of the activity that the
depletion of substrate would be its most tangible feature.
During the later time intervals, students were observed to
become increasingly animated and this was interpreted as
Plot of student-catalyzed product formation as a
FIG 2 function of time. Catalyzed reaction progress is recognition that their catalytic abilities were not being
shown as the average 6 standard deviation for all accurately reflected by the catalyzed reaction rate. Initially,
student groups (n 5 8). The averaged initial rate the catalysis step (the velocity of Pop-It Bead separation)
of product formation (0.98 6 0.06 (6 SEM) prod- limited the overall reaction rate, but after sufficient sub-
ucts/s) was determined by linear regression over
strate depletion, the collision step (the velocity that students
the initial forty seconds of the activity
(R2 5 0.8269). The un-catalyzed reaction progress locate Pop-It Beads) became rate-limiting. Based on obser-
was plotted for comparison and independently vation, students appeared to be perceiving these effects
determined by each student group. during the activity and, in general, could provide substrate
depletion as the reason for why reaction rate decreased
over time (Table II). A control group of DHH students
many opportunities to practice calculation of reaction rate
taught the same material without the benefit of the activity
during the activity and exam results suggested engagement
as described were also assessed for their ability to calculate
with this practice might be beneficial. All but one student
reaction rate and explain substrate depletion effects; exam
in the class received at least partial credit for their
score averages were modestly higher for students who
approach to the calculation (if not given a specific time
received the activity compared to these students (Table II).
frame, students were expected to calculate V0) (Table II).
The average catalyzed V0 for the class was 0.49 Pop-It The Activity As a Bridge to Michaelis-Menten
Bead pairs/s [0.98 6 0.06 (6 SE) products/s as determined Kinetics
by linear regression]. Individual student groups showed Survey responses, exam results and classroom observation
variation in V0, yet seven out of eight groups had sustained suggested the activity, administered in a foundational, asso-
V0 values over the first two time intervals (040 s). The ciates level biotechnology course, has the potential to

Student survey responses

TABLE I

Above Below Extremely

Survey question Excellent Average Average Average Poor

Before you did this activity. . ..

What was your understanding of reaction rate? 0 (0)a 6 (37.5) 5 (31.2) 3 (18.8) 2 (12.5)
What was your understanding of enzyme activity? 0 (0) 8 (50) 3 (18.8) 4 (25) 1 (6.2)
After you did this activity. . ..
What is your understanding of reaction rate? 5 (31.2) 8 (50) 3 (18.8) 0 (0) 0 (0)
What is your understanding of enzyme activity? 5 (31.2) 8 (50) 3 (18.8) 0 (0) 0 (0)

a
The percentage of the class response (n 5 16).

Gehret 3
 Biochemistry and
Molecular Biology Education

Student exam performance

TABLE II

Cohort Mean exam scores

Control group (n 513)a 65.4 6 2.5b

Activity group (n 516) 73.3 6 3.0
Activity group
Learning objective 100% correct 75% correct 50% correct 0% correct
c
Calculate reaction rate 10 (62.5) 3 (18.8) 2 (12.5) 1 (6.2)
Recognize enzyme catalysis 10 (62.5) n/a n/a 6 (37.5)
Explain substrate depletion effect on reaction rate 10 (62.5) n/a 1 (6.2) 5 (31.3)

a
This group of students were enrolled in the course a year prior to the activity group. They were taught the same material and tested
with near-identical assessments without receiving the kinesthetic activity as described.
b
The exam errors are reported as SEM.
c
The percentage of class (n 5 16) that scored in that percentage on the exam.

provide students a deeper engagement with substrate deple- the start of the reaction, their rate of catalysis limits the over-
tion effects and how they influence reaction rate. Third year all reaction rate as their ability to collide with the beads
undergraduates harbor misconceptions about the change to occurs relatively quickly. This condition is not in violation of
reaction rate over time [5]. Furthermore, it has been sug- the assumption that [ES] breakdown is rate-limiting. At some
gested that the instantaneous rate is a critical learning out- point, which occurs at various times for students, a threshold
come for undergraduates to effectively understand reaction of substrate depletion occurs where the rate of collision now
systems [22]. As Michaelis-Menten kinetics is an application becomes rate-limiting and students directly observe a
of these principles, this activity might benefit a discussion on decrease in the calculated reaction rate. This condition is a
the topic to model these core concepts. violation of the assumption that [ES] breakdown is rate-
A fundamental hypothesis that underlies the Michaelis- limiting. Additionally, through the experience of acting as an
Menten equation is the breakdown of [ES] is rate-limiting [23]: enzyme, students recognize that their catalytic capabilities
(V0) are not being reflected by the reaction rate at this thresh-
V0 5k2 ES
old. An instructor could link this point to the moment
The activity can be modeled after the underlying steps that substrate is no longer considered constant and [Bead Pairs]
drive Michaelis-Menten kinetic behavior: has decreased to impact the rate of collision. While instanta-
neous rate is impossible to convey kinesthetically, the activity
collision does help illustrate the notion that reaction rate is dynamic
Hands 1 Bead Pairs ! Bead Pair in Hands
and thus could aid in an explanation of instantaneous rate.
catalysis
Bead Pair in Hands ! Hands 1 2 Beads Visually-driven pedagogies have been shown to affect real
conceptual change in students perceptions of reaction system
dynamics [24] and this activity could have similar potential.
Consequently, the rate-limiting step for the activity is
The activity could also provide meaning for other basic
described as: kinetics concepts. Students harbor misconceptions between
V0 5catalysis Bead Pair in Hands the definition of reaction rate and rate constant [25] as well
as the nature of interactions between catalysts and sub-
The two individual rates that govern the overall reaction strates [5, 26]. In regards to the former, the activity demon-
rate can be described: strates a students desire to locate Pop-It Beads (collision)
remains constant while the rate of collision depends on Pop-
Rate of collision5collision HandsBead Pairs
Rate of catalysis5catalysis Bead Pair in Hands It Bead concentration and will decrease over time. Related to
the latter, students hands act directly with substrate to elicit
It was evident that students desire to locate Pop-It Bead pairs multiple turnovers but remain unchanged at the conclusion
(collision) does not change over the course of the activity. At of the reaction.

4 Enzyme Catalysis with Pop-It Beads

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Gehret 5