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-
dents understand enzyme activity and catalysis of reaction
rate. Students served the role of enzymes by manipulating
Pop-It Beads as the catalytic event. This activity illuminates
the relationship between reaction rate and reaction progress
by allowing students to experience first-hand the effect of
substrate depletion on catalyzed reaction rate. Preliminary
findings based on survey results and exam performance
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
topics undergraduates confront in biochemistry [1]. Implicit
in this challenge is that Michaelis-Menten kinetics is an
application of reaction kinetics that students acquire in
general chemistry courses. It has been documented that
students exhibit a variety of misconceptions about funda-
mental chemical concepts [2, 3] as well as a rapid decay in
knowledge without continued spiral use of concepts [4]. In
fact, an analysis of third year undergraduates reasoning of
reaction kinetics revealed that while they harbored a better
understanding of the definition of reaction rate compared
to secondary education students and first year
Volume 00, Number 00, Month/Month 2016, Pages 0000
Abbreviations: DHH, deaf or hard-of-hearing
*Address for correspondence to: Department of Science and Mathe-
matics, National Technical Institute for the Deaf, 52 Lomb Memorial
Dr., Rochester, NY 14623. E-mail: augnts@rit.edu
Received 1 October 2015; Revised 29 April 2016; Accepted 27 June
2016
ws Additional Supporting Information may be found in the online
version of this article.
The corresponding author has no conflict of interest to declare related
to the work described in this manuscript.
DOI 10.1002/bmb.21000
Published online 00 Month 2016 in Wiley Online Library
(wileyonlinelibrary.com)
Biochemistry and Molecular Biology Education
targeted learning outcomes. Unique to previous kinesthetic
approaches that model Michaelis-Menten kinetics, this activ-
ity models the effects of substrate depletion on catalyzed
reaction rate. Therefore, it could prove beneficial for convey-
ing the reasoning behind the initial rate simplification used
in Michaelis-Menten kinetics. V C 2016 by The International
Union of Biochemistry and Molecular Biology, 00:000000,
2016.
undergraduates, a higher percentage of them believed that
reaction rate increases with time [5]. Thus, misconceptions
about reaction dynamics persist with students at the bio-
chemistry level and likely contribute to the challenge of
learning enzyme kinetics.
Constructivist learning theory states that new meaning
is constructed in the minds of learners in ways that make
sense to them using their conceptual framework [6]. This
theory has formed the basis for alternative teaching strate-
gies to confront students conceptions about biochemistry
including the process oriented guided inquiry learning
(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
abstract topics in chemistry [9] and students exhibit a
strong preference for learning information through multiple
modes of presentation while engaging multiple senses [10].
Many have seen the value in alternative approaches to
teaching Michaelis-Menten kinetics. Student engagement
with this concept has been enhanced through computer-
based pedagogies [1, 1113] as well as kinesthetic
approaches [1417]. Regarding the latter, each approach
had students assume the role of enzyme by catalyzing a
specific manipulative event with an object. Catalysis was
modeled to explain the nature of the turnover number (kcat)
using marble transfer between bins [14] or the unscrewing
of bolt-nut substrate complexes [15]. Other approaches
1

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
mathematical construction of the Michaelis-Menten reac-
tion curve has even led to the proposal that the integrated
form of the equation be used alternatively to teach this top-
ic [18]. As Michaelis-Menten kinetics is predicated on mea-
suring V0 behavior, it is worthwhile to explore ways that
can help students grasp the rationale for why this simplifi-
cation is used.
The kinesthetic activity described herein was adminis-
tered to a biotechnology class of students who are deaf or
hard-of-hearing (DHH) learning to quantify enzyme activity.
Similar to helping hearing students develop mental con-
structs of concepts [19], active learning exercises with a
participative learning environment strongly correlate with
DHH student success and course engagement [20]. The top-
ic learning objectives focused on how to identify enzymatic
activity, best explored through time course measurements
[21]. As such, the classroom activity was designed to model
the progression of an enzyme-catalyzed reaction over time.
Based on student surveys, preliminary exam results and
teacher observations with a comparatively small (n 5 16)
student sample, the activity appears to have potential for
increasing students perceived understanding and short-
term knowledge gains with kinetics concepts. Additionally,
the design of the activity aims to allow students to experi-
ence the effect of substrate depletion on catalysis firsthand
and could prove worthy to convey the initial rate simplifica-
tion used in Michaelis-Menten kinetics.
Classroom Activity
Students were grouped into pairs and given a bin (2 3 4 3
7.75 in3) of 40 Pop-It Bead pairs (Carolina Biological Sup-
ply) that served as the substrates for the reaction (Fig. 1).
One student served as the enzyme by separating Pop-It
Bead pairs into two products (the catalytic event); the sec-
ond student was timekeeper for the duration of the activity
(3 minutes). To simulate simple diffusion between enzyme
and substrate, students were instructed to avert their eyes
from the bin while catalyzing the reaction. (Blindfolds could
2 Enzyme Catalysis with Pop-It Beads
Biochemistry and
Molecular Biology Education
Pop-It Bead pair substrates. Each student group
FIG 1 (two students per group) was given a bin con-
taining forty Pop-It Bead pairs (substrates) to cat-
alyze over a span of 3 minutes. One bin of
substrates was not assigned to any group to rep-
resent the un-catalyzed reaction. [Color figure
can be viewed in the online issue, which is avail-
able at wileyonlinelibrary.com.]
also suffice but were not used owing to the need for stu-
dents to maintain visual communication.) After each timed
interval, students tallied total products made. To alleviate
confusion, products were removed from bins for accurate
counting and then returned and mixed with substrate Pop-
It Bead pairs prior to resuming. This process was repeated
four times at 20-second intervals followed by two 40-
second intervals (Supporting Information File 1). At the
conclusion of the activity, the instructor presented a bin of
Pop-It Beads that had not been catalyzed by any student
group (Fig. 1) to represent un-catalyzed reaction progress.
Analysis
Following the activity, students were guided by worksheets
(Supporting Information File 1) to plot the reaction pro-
gress of both the un-catalyzed reaction and their catalyzed
reactions. These plots were intended to provide students
the opportunity to observe how their influence over the
reaction (enzyme activity) influenced the reaction progress
graphically (Fig. 2). Reaction rate determination is inherent
in this type of graphical analysis; thus, students were also
guided by the worksheets (Supporting Information File 1) to
determine the reaction rates over time for both conditions.
The instructor facilitated the connection between these val-
ues and their mathematical determination from the kinetic
data. Survey results assessing students confidence with
enzyme activity and reaction rate suggested students per-
ceived gains in knowledge for both kinetics concepts (Table
I). These self-perceptions in knowledge gains were general-
ly supported by exam performance (Table II). Students had

Plot of student-catalyzed product formation as a
FIG 2 function of time. Catalyzed reaction progress is
shown as the average 6 standard deviation for all
student groups (n 5 8). The averaged initial rate
of product formation (0.98 6 0.06 (6 SEM) prod-
ucts/s) was determined by linear regression over
the initial forty seconds of the activity
(R2 5 0.8269). The un-catalyzed reaction progress
was plotted for comparison and independently
determined by each student group.
many opportunities to practice calculation of reaction rate
during the activity and exam results suggested engagement
with this practice might be beneficial. All but one student
in the class received at least partial credit for their
approach to the calculation (if not given a specific time
frame, students were expected to calculate V0) (Table II).
The average catalyzed V0 for the class was 0.49 Pop-It
Bead pairs/s [0.98 6 0.06 (6 SE) products/s as determined
by linear regression]. Individual student groups showed
variation in V0, yet seven out of eight groups had sustained
V0 values over the first two time intervals (040 s). The
Student survey responses
TABLE I
Survey question Excellent
Before you did this activity. . ..
What was your understanding of reaction rate? 0 (0)a
What was your understanding of enzyme activity? 0 (0)
After you did this activity. . ..
What is your understanding of reaction rate? 5 (31.2)
What is your understanding of enzyme activity? 5 (31.2)
a
The percentage of the class response (n 5 16).
Gehret
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
recognition that their catalytic abilities were not being
accurately reflected by the catalyzed reaction rate. Initially,
the catalysis step (the velocity of Pop-It Bead separation)
limited the overall reaction rate, but after sufficient sub-
strate depletion, the collision step (the velocity that students
locate Pop-It Beads) became rate-limiting. Based on obser-
vation, students appeared to be perceiving these effects
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
taught the same material without the benefit of the activity
as described were also assessed for their ability to calculate
reaction rate and explain substrate depletion effects; exam
score averages were modestly higher for students who
received the activity compared to these students (Table II).
The Activity As a Bridge to Michaelis-Menten
Kinetics
Survey responses, exam results and classroom observation
suggested the activity, administered in a foundational, asso-
ciates level biotechnology course, has the potential to
Above Below Extremely
Average Average Average Poor
6 (37.5) 5 (31.2) 3 (18.8) 2 (12.5)
8 (50) 3 (18.8) 4 (25) 1 (6.2)
8 (50) 3 (18.8) 0 (0) 0 (0)
8 (50) 3 (18.8) 0 (0) 0 (0)
3

Student exam performance
TABLE II
Cohort
Control group (n 513)a
Activity group (n 516)
Activity group
Learning objective
Calculate reaction rate
Recognize enzyme catalysis
Explain substrate depletion effect on reaction rate
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-
tion effects and how they influence reaction rate. Third year
undergraduates harbor misconceptions about the change to
reaction rate over time [5]. Furthermore, it has been sug-
gested that the instantaneous rate is a critical learning out-
come for undergraduates to effectively understand reaction
systems [22]. As Michaelis-Menten kinetics is an application
of these principles, this activity might benefit a discussion on
the topic to model these core concepts.
A fundamental hypothesis that underlies the Michaelis-
Menten equation is the breakdown of [ES] is rate-limiting [23]:
V0 5k2 ES
The activity can be modeled after the underlying steps that
drive Michaelis-Menten kinetic behavior:
collision
Hands 1 Bead Pairs ! Bead Pair in Hands
catalysis
Bead Pair in Hands ! Hands 1 2 Beads
Consequently, the rate-limiting step for the activity is
described as:
V0 5catalysis Bead Pair in Hands
The two individual rates that govern the overall reaction
rate can be described:
Rate of collision5collision HandsBead Pairs
Rate of catalysis5catalysis Bead Pair in Hands
It was evident that students desire to locate Pop-It Bead pairs
(collision) does not change over the course of the activity. At
4 Enzyme Catalysis with Pop-It Beads
Biochemistry and
Molecular Biology Education
Mean exam scores
65.4 6 2.5b
73.3 6 3.0
100% correct 75% correct 50% correct 0% correct
c
10 (62.5) 3 (18.8) 2 (12.5) 1 (6.2)
10 (62.5) n/a n/a 6 (37.5)
10 (62.5) n/a 1 (6.2) 5 (31.3)
the start of the reaction, their rate of catalysis limits the over-
all reaction rate as their ability to collide with the beads
occurs relatively quickly. This condition is not in violation of
the assumption that [ES] breakdown is rate-limiting. At some
point, which occurs at various times for students, a threshold
of substrate depletion occurs where the rate of collision now
becomes rate-limiting and students directly observe a
decrease in the calculated reaction rate. This condition is a
violation of the assumption that [ES] breakdown is rate-
limiting. Additionally, through the experience of acting as an
enzyme, students recognize that their catalytic capabilities
(V0) are not being reflected by the reaction rate at this thresh-
old. An instructor could link this point to the moment
substrate is no longer considered constant and [Bead Pairs]
has decreased to impact the rate of collision. While instanta-
neous rate is impossible to convey kinesthetically, the activity
does help illustrate the notion that reaction rate is dynamic
and thus could aid in an explanation of instantaneous rate.
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.
The activity could also provide meaning for other basic
kinetics concepts. Students harbor misconceptions between
the definition of reaction rate and rate constant [25] as well
as the nature of interactions between catalysts and sub-
strates [5, 26]. In regards to the former, the activity demon-
strates a students desire to locate Pop-It Beads (collision)
remains constant while the rate of collision depends on Pop-
It Bead concentration and will decrease over time. Related to
the latter, students hands act directly with substrate to elicit
multiple turnovers but remain unchanged at the conclusion
of the reaction.
 Several kinesthetic activities [1417] have modeled
Michaelis-Menten kinetics by having students hands act as
enzymes against increasing substrate concentrations to
observe the approach to maximum initial rate (Vmax). For
each of those activities, V0 conditions were assumed to
allow students the opportunity to explore substrate concen-
tration effects on V0. The kinesthetic activity described in
this paper focused on reaction progression for a single
substrate concentration and appears to have potential for
positively impacting student appreciation for substrate
depletion effects on reaction rate. As such, the activity
could help illustrate the reasoning behind measuring V0 for
Michaelis-Menten kinetics, a topic previously unexplored
using this pedagogy.
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