Bacteria Primer Comparison 2: Gel Electrophoresis

Overview & Concepts

This lesson will occur after a lesson in which the students will isolate bacterial DNA by using primers and PCR. In this lesson, each student will be able to accept or reject his or her hypothesis by completing gel electrophoresis of the PCR product and analyzing the results compared to the other bacterial primer products and a ladder.  

Concepts Covered: 

Primers, bacterial characteristics, gel electrophoresis

Prior Knowledge Required: 

Prior to this lesson, students should have a solid understanding of cell structure and function.   They should also understand how DNA is extracted from a cell (based on a previous cheek cell extraction lab), the function of primers and the process of PCR (after completing an online simulation of the lab tool.)  Students should also understand the process of gel electrophoresis (after completing an online simulation of the lab tool). 

Activity Notes

Days to Teach: 

2-3 43 minute class periods


  • PCR product for the three bacterial samples which were run with two primers to compare hypothesized results.
  • Gel electrophoresis apparatus

Teaching Tips / Activity Overview: 

This protocol is designed for a 43 minute class period, but could take up to 2-3 43 minute class periods depending upon the development of the gels.  Students may need additional time to research the bacteria and primer information before this lab if students are not very familiar with using the research tools or did not have enough time during the previous class period.

  • Gel electrophoresis  group review of purpose, technique and result (5 minutes)
  • Prepare the gels and run the gels for the 3 bacterial samples after the PCR is completed (30 minutes)
  • While the gels are running, discuss/summarize the results from research regarding basic characteristics about the 3-4 bacterial samples being used and the 2 primers (20 minutes)
  • Analyze the gel results and draw conclusions for the protocol. (5 minutes)


After the lab is completed, students should write a summary describing the lab protocol and results as well as how this procedure could be applied in research beyond this lab. This form of assessment could be summative after formatively assessing the students throughout the lab as they followed the protocol and researched the bacteria and primer information.

The following learning objectives are based on the Biology Keystone objectives:

  • Students will be able to explain how genetic engineering has impacted the fields of medicine, forensics, and agriculture (e.g., selective breeding, gene splicing, cloning, genetically modified organisms, gene therapy, gel electrophoresis, PCR).


AP level students and possibly honors level biology students could possibly repeat a similar protocol for this lesson and the previous lesson during the ecology unit by gathering soil samples from areas that surround the high school, isolate the bacteria in the soil and designing primers for the PCR and gels.




These teacher notes and resources were produced after discussing research being conducted in Dr. Jamie Blair’s lab at Franklin and Marshall College by Jessica Mountz.  Gel procedure taken from the Agarose Gel Electrophoresis of PCR Products for mtDNA Sequencing with a percent agarose adjustment.

Academic Standards
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