Separating DNA with Gel Electrophoresis Lab Worksheet

Lab 9 Gel Electrophoresis Virtual Lab Worksheet and Homework Questions SEPARATING DNA WITH GEL ELECTROPHORESIS VIRTUAL LAB WORKSHEET Answer the following questions in the spaces provided. 1. What structural component of DNA causes it to move towards the positive electrode when a gel is being run? The phosphate group in the DNA is negatively charged that allows the DNA to move towards the positive end of the gel electrophoresis. 2. How many base pairs are found in a piece of DNA that is composed of 36 nucleotides? 18 3. What is the purpose of a DNA ladder? DNA ladder is DNA molecules of known sizes that is used to estimate the size of DNA band. 4. Why is it harder to conduct plasmids through a gel than linear DNA? List the three conformations that plasmids may occur in. Plasmids can occur in nicked, multimer, and supercoiled conformations. 5. What is the purpose of loading dye? Loading dye is used for sinking the sample to the bottom of the well. 6. How are individual DNA bands visualized after the gel has been run? They can be visualized by using fluorescent dye, which will be placed under a UV light to be compared with the DNA ladder. BIOL1500 Lab 9 Gel Electrophoresis Virtual Lab Worksheet and Homework Questions GEL ELECTROPHORESIS VIRTUAL LAB WORKSHEET Complete the simulation, beginning at Level 1, and answer the Reflection questions. Record your answers to the Reflection questions in the spaces provided below. 1. Study your gel electrophoresis results. Which sample contained a single dye, and what evidence from your experiment supports this choice? The 1st sample contained the single dye because there is no other dye color present in the result with another band. 2. What charge did the dyes in this experiment have? Negative 3. The dyes you separated in this simulation are orange G (yellow), bromophenol blue (purple) and xylene cyanol (blue). If these dyes were fragments of DNA, which color dye would represent the smallest piece of DNA? Yellow because the dye traveled the furthest. 4. If you compared two molecules that were found in the blue band in the gel, what could you infer about them? It indicates that the two molecules have almost the same size or the charge. 5. If you ran a gel like the one pictured below with wells in the middle, and loaded positively charged dye molecules into the gel, where would you expect to see a band in the gel? The dyes will go to the negative end instead of the positive side. BIOL1500 Lab 9 Gel Electrophoresis Virtual Lab Worksheet and Homework Questions HOMEWORK ASSIGNMENT QUESTIONS Answer the following questions in paragraph form. Note: Some questions may require additional research (e.g. a Google search) to complete. 1. Explain how positive and negative charges are important when performing gel electrophoresis. a. The negatively charged samples will go to the positive end so the charges dictates the direction of the samples. 2. What is an allele ladder? What is its function in DNA profiling? a. Allele ladder acts as a marker that serves as a reference to the samples’ sizes or charges. 3. What is required to visualize DNA following electrophoresis? a. UV light 4. What is the purpose of the running buffer? a. Buffer contains ions that enables the electricity to flow and maintain a good pH value of the gel. 5. You are running a gel with DNA fragments that are 150bp, 500bp, and 1200bp in size. Which fragment will travel the furthest? Which will travel the least? Why? a. 150bp will travel the furthest and 1200bp will travel the least. The heavy molecule is more difficult to travel to the further side while the smallest will be lighter to travel to the further positive end. 6. Name two macromolecules other than DNA that can be separated for analysis by gel electrophoresis. a. RNA b. Proteins The gel pictured below contains a DNA ladder in the first lane, followed by four DNA samples. Use this image to complete questions 7-9. BIOL1500 Lab 9 Gel Electrophoresis Virtual Lab Worksheet and Homework Questions 7. Which DNA fragment is the largest? Justify your answer. a. E: the largest is the heaviest fragment that will travel the least. 8. Which two fragments are the same size? How do you know this? a. B and F: they are on the same line 9. Which lane has a DNA fragment that is approximately 700 bp? a. C BIOL1500 Lab 9 Gel Electrophoresis Virtual Lab Worksheet and Homework Questions 10. DNA profiling is routinely used for investigations of crime scenes, missing persons, mass disasters, human rights violations, and paternity. Crime scenes often contain biological evidence (such as blood, semen, hairs, saliva, bones, pieces of skin) from which DNA can be extracted. If the DNA profile obtained from evidence discovered at the scene of a crime matches the DNA profile of a suspect, this person is included as a potentially guilty person; if the two DNA profiles do not match, the individual is probably innocent. See the figure below for representative results of a DNA profiling experiment ending with PCR products of DNA from a crime scene run on a gel, sizes of the ladder bands, and labeling of the alleles in the ladder. Assign each band in each PCR reaction with an allele assignment according to the band of corresponding size in the allele ladder. The bands in the allele ladder are numbered from top to bottom starting with the largest allele, #15, at the top. For example, the genotype for the crime scene is 5-2, since there is one #5 allele and one #2 allele in that lane. Write down the genotype for each of your samples in the following table. Lane 1 2 3 4 5 6 Sample BXP007 Allele Ladder Crime Scene DNA Suspect A DNA Suspect B DNA Suspect C DNA Suspect D DNA Number of bands 8 2 2 2 2 2 What BXP007 Alleles are present? 15, 10, 7, 5, 4, 3, 2, 1 5, 2 7, 4 5, 2 7, 2 10, 3 11. What do your results tell you about which suspects should be included in the investigation? Does the crime scene DNA sample have a genotype that matches any of the suspects? If so, which one matches? Explain your answer. a. Suspect B: it matches the sample from the crime scene, so this person is most likely to be arrested. BIOL1500 Lab 9 Gel Electrophoresis Virtual Lab Worksheet and Homework Questions 12. A distant relative set out a food lure and a hidden camera in the Everglades to catch the elusive “Swamp Yeti” on film. Unfortunately, his hidden camera wasn’t quite so well-disguised, and it got stolen (what did he expect, it’s Florida). However, a clump of hair and skin was left at the site, and being the expert biologist you are, you get commissioned to identify what the sample is from. You decide to assess the sample against a number of wildlife DNA profiles you have and figure out whether this sample is from a known species before jumping to conclusions. Interpret the gel below and explain how you reached your conclusion, using specific bp values. The unknown is most likely to be the bear because it shows the closest band pattern to that of a bear in this result. There are 2 bands close to the 500bp and another 2 bands close to the 300bp band.