Protein gel electrophoresis in the undergraduate physics laboratory

Miles, Danny G.; Bushman, David W.; Chen, Zhongying

doi:10.1119/1.1943431

Cited by 5 publications

(4 citation statements)

References 16 publications

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“…15.9 nm), leading to a lower deposition rate. 29 We observed that light could be well-scattered for both of the deposited MTN and P90 films, and that the films could be easily damaged by scratching because of their poor intrinsic mechanical strength. However, adhesion of the films to the plastic substrates was so strong that the films could not be peeled off even after bending the electrodes.…”

Section: Fabrication Of Mtn and P90 Films By Epd Processesmentioning

confidence: 78%

Fabrication and characterization of plastic-based flexible dye-sensitized solar cells consisting of crystalline mesoporous titania nanoparticles as photoanodes

et al. 2011

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Section: Fabrication Of Mtn and P90 Films By Epd Processesmentioning

confidence: 78%

Fabrication and characterization of plastic-based flexible dye-sensitized solar cells consisting of crystalline mesoporous titania nanoparticles as photoanodes

et al. 2011

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“…(1) vanishes; in this case, one can solve for the velocity as vf = qElk. Equation (2) can be rewritten as = V, l-e (3) Equation (3) is experimentally relevant since one no longer has to quantify the drag coefficient k a priori. Instead, one can experimentally measure the terminal velocity of the molecule and rescale a theoretical curve to match up with empirically derived data.…”

Section: The Equations Of Motionmentioning

confidence: 99%

Modeling the Dynamics of Gel Electrophorresis in the High School Classroom

Saucedo¹

2012

The Physics Teacher

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G el electrophoresis, used by geneticists and forensic experts alike, is an immensely popular technique that utilizes an electric field to separate molecules and proteins by size and charge. At the microscopic level, a dye or complex protein like DNA is passed through agarose, a gelatinous three-dimensional matrix of pores and nano-sized tunnels. When forced through a maze of holes, the molecule unravels, forming a long chain, slithering through the field of pores in a process colloquially coined "reputation." ' As a result, the smaller molecules travel farther through the gel when compared to molecules of larger molecular weight. This highly effective "molecular sieve" provides consistent data and allows scientists to compare similar sequences of DNA base pairs in a routine fashion.^ When performed at the high school level, gel electrophoresis provides students the opportunity to learn about a contemporary lab technique of great scientific relevance. Doing real science certainly excites students and motivates them to learn more.In many cases, students learn how to use a micropipette, create an agarose gel, and (if all goes to plan) have the opportunity to actually see dyes move across the gel. Instructors typically provide a qualitative explanation (the electric field/ current moves the molecules; the smaller the molecule, the faster and farther it moves across the gel, for example) or an explanation that is beyond the scope ofthe class.A common misconception held by students (and instructors alike) is that the electric field provides a force that continuously accelerates a charged molecule across the gel; this explanation is correct to some extent, but fails to explain the role ofthe molecules drag force and subsequent terminal velocity.^ In gel electrophoresis, the drag force plays a dominant role in the early stages ofthe dynamics, and, as a consequence, the molecule has no net acceleration through the duration of the experiment. Such details are trivial when introducing this lab to students at a conceptual level. Excited as the students are, many are left with little to no opportunity to explore on their own, and ultimately follow a rigid sequence of procedures that does little more than verify that the process actually works.This paper proposes an inquiry-based method to investigate the robust dynamics of gel electrophoresis at the high school level. The goal is to motivate students to develop a working kinematic model and to test the model experimentally. Such an exercise works best in an AP Physics classroom, at a point in the course when concepts in electrostatics, specifically dealing with charges and electric forces and fields, are fresh in students' minds. Student misconceptionsPrior to performing the experiment, it is important to address three common misconceptions (dealing with electric fields and forces) held by students and how this exercise may address these problems. As outlined by Randall Knight:'* The three-dimensionality of electric fieldsStudents are introduced to the concept ofthe electric...

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“…The detection of enzyme activity on electrophoretic gels, or zymography, has become an important tool to evaluate and analyze many enzymes [18][19][20][21][22][23][24], and has received attention on educational journals as well [25][26][27][28][29][30]. The use of zymography to instruct students in the biochemistry laboratory for the study of catalysis mechanisms or to follow activity in purification steps as well as biochemical characterization has also been reported [31][32][33].…”

mentioning

confidence: 99%

“…The use of zymography to instruct students in the biochemistry laboratory for the study of catalysis mechanisms or to follow activity in purification steps as well as biochemical characterization has also been reported [31][32][33].…”

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confidence: 99%

Guaiacol peroxidase zymography for the undergraduate laboratory

Wilkesman

Castro

Contreras

et al. 2014

Biochem Molecular Bio Educ

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This laboratory exercise presents a novel way to introduce undergraduate students to the specific detection of enzymatic activity by electrophoresis. First, students prepare a crude peroxidase extract and then analyze the homogenate via electrophoresis. Zymography, that is, a SDS-PAGE method to detect enzyme activity, is used to specifically detect peroxidase activity and furthermore, to analyze the total protein profile. After the assay, students may estimate the apparent molecular mass of the enzyme and discuss its structure. After the 4-h experiment, students gain knowledge concerning biological sample preparation, gel preparation, electrophoresis, and the importance of specific staining procedures for the detection of enzymatic activity. V C 2014 by The International Union of Biochemistry and Molecular Biology, 42(5): 420-426, 2014.

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Protein gel electrophoresis in the undergraduate physics laboratory

Cited by 5 publications

References 16 publications

Fabrication and characterization of plastic-based flexible dye-sensitized solar cells consisting of crystalline mesoporous titania nanoparticles as photoanodes

Fabrication and characterization of plastic-based flexible dye-sensitized solar cells consisting of crystalline mesoporous titania nanoparticles as photoanodes

Modeling the Dynamics of Gel Electrophorresis in the High School Classroom

Guaiacol peroxidase zymography for the undergraduate laboratory

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