The Effects of Plasmid on Genotype and Phenotype, Study notes of Genetics

Download The Effects of Plasmid on Genotype and Phenotype and more Study notes Genetics in PDF only on Docsity! GEL ELECTROPHORESIS PURDUE UNIVERSITY INSTRUMENT VAN PROJECT The Effects of Plasmid on Genotype and Phenotype (Revised 1/31/96) Introduction Plasmids are small circular DNA molecules that often found in bacteria in addition to the large circular DNA molecule of the bacterial chromosome. Plasmid DNAs replicate independently of the bacterial chromosome, and many plasmids can also be transferred naturally among their bacterial hosts. Generally, plasmid genes code for proteins that are not essential for the survival of their host in its normal environment. However, some plasmid DNAs encode genes that confer on their host the ability to live in conditions that would ordinarily kill the host. For example, plasmids can encode proteins that can break down antibiotics that would otherwise prevent the bacterial cell from growing. One such protein is an enzyme called beta-lactamase which can break down penicillin and certain modified penicillins such as ampicillin. If a bacterial cell contains a plasmid carrying this gene, then the bacteria can grow in the presence of ampicillin and are said to have the phenotype "ampicillin-resistant". The plasmid you will be using in your experiments is a plasmid constructed by scientists for use in recombinant DNA experiments. The beta-lactamase gene was included in this plasmid in order to be able to easily test for its presence in bacteria by determining whether they can grow on media containing ampicillin. A gene used this way is commonly referred to as a "selectable marker". Since having this gene allows bacteria to grow in the presence of the antibiotic, you can readily appreciate how this type of gene can cause serious medical problems when it occurs in pathogenic bacteria. For this reason, the plasmids such as pUC 18 which are used in recombinant DNA experiments were designed so that they cannot be exchanged with other bacteria except by special techniques used in the laboratory. In this laboratory, you will be incorporating plasmids into bacteria ( E. coli) and this process is called transformation. It involves treating the bacteria in such a way that their cell wall becomes permeable to DNA for a period of time. The transformed bacterialcells will be cultured on agar broth containing Luria broth, ampicillin, and a chemical X-gal (5-bromo-4-chloro-3-indolyl-betaD-galactoside). Luria broth provides essential nutrients for growth and ampicillin will act as a selection agent. When X-gal is broken down by an enzyme called beta-galactosidase, it forms a blue color. Therefore bacterial cells containing a gene coding for the enzyme will form blue colonies on this agar. pUC18 is a plasmid that includes in its DNA a gene for a portion of beta- galactosidase. The bacterial hosts used with pUC 18 contain in their chromosome genetic information coding for the remainder of the complete enzyme. 1 GEL ELECTROPHORESIS PURDUE UNIVERSITY INSTRUMENT VAN PROJECT Any bacterial cells which have taken up pUC 18 and contain a functional beta- galactosidase will form blue colonies on this medium. If the gene in pUC 18 has been inactivated, the colonies will be white. Scientists using pUC 18 as a gene cloning vector take advantage of this by inserting foreign DNA into a site within the beta-gal gene and inactivate it in order to distinguish those plasmid DNAs containing the new DNA from the parental unmodified pUC 18 plasmids. During this laboratory exercise you will be examining the effects of plasmids on the phenotype of E. coli. In addition, you will use gel electrophoresis to examine some aspects of the genotype of the plasmids you are using in these experiments. In the third part of the laboratory you will screen the colonies of transformed E. coli from the first part of the laboratory for the presence of plasmid. You will do this by extracting and recovering plasmid DNA from the cultures. I. The Effects of Plasmids On Phenotype II. Plasmid Genotype III. Screening for Plasmids Please note: As you can probably tell, there are many new terms that you will learn by doing these labs. The complexity of the lab procedure, the expense of the lab supplies, and the need to use time wisely REQUIRES that you read and study the lab procedures and introductions prior to coming to class. This lab requires that you get the maximum use of time out of the limited time available. 2 GEL ELECTROPHORESIS PURDUE UNIVERSITY INSTRUMENT VAN PROJECT Preparation of Competent Cells Calcium chloride is used to make the cells competent (ready for the uptake of plasmid). It is unclear exactly what the calcium chloride does to the cells to get them ready. But, it does have some kind of effect on the cell wall of the E. coli. The calcium chloride probably breaks open pores in the cell membrane and also helps to carry the plasmid DNA near the openings (see figure 2). After adding the calcium chloride, the mixture is put on ice to cool everything down. Then, the mixture is “heat shocked” by immediately placing it in a 42°C water bath, it is placed back on ice, and is then incubated so that new cells containing the plasmid are generated. In most cells, plasmids replicate at the same time as the host cell; so, when the cells divide, the new cell will have the plasmid. That form of plasmid replication is called “stringent control.” In plasmids under “relaxed control,” replication of plasmid DNA is not coupled to replication of the host. Procedure: 1. Use a sterile pipet to add 250 µL of ice-cold 0.1 M calcium chloride solution to each of the four 1.5 mL tubes. Label the four tubes: A, B, C , and X (X is the control.) Place all tubes on ice. 2. Flame an inoculating loop, then cool it by sticking it into an agar plate in an area where no bacteria are growing. Use the loop to transfer a large cell mass into tube A. • Be careful not to transfer agar from the plate along with the cell mass. • Vigorously tap the loop against the wal of the tube to dislodge the cell mass. • Suspend the cells immediately by repeated pipeting using a sterile blue micropipet tip. Examine the tube by holding it up to the light and continue until no visible clumps remain. 3. Return tube A back to the ice and transfer a second cell mass into tube B, and a third and fourth cell mass into tubes C and D by repeating step 2. 4. All tubes should now be on ice. 5 GEL ELECTROPHORESIS PURDUE UNIVERSITY INSTRUMENT VAN PROJECT 5. Use a micropipet to add 10 µL of unknown solution A into the tube you have labeled A. (Solutions A, B, and C are unknown--they could be pUC18, pUC18 with DNA insert, or distilled water.) • Repeat Step 5 using solutions B and C. 6. Incubate all of the tubes on ICE for 15 minutes. 7. While you are waiting, obtain one Luria Broth plate (LB) and 3 LB/Amp/X-gal plates. • Label the LB plate “LB control” • Label the 3 LB/Amp/X-gal plates “A Amp/X-gal, B Amp/X-gal, and C Amp/X-gal” 8. After the 15 minutes for Step 6 has expired, carry the tubes ON ICE to the 42°C water bath and heat shock the cells immediately by placing them into the bath for 60 seconds. (It is essential that the cells be given a sharp and distinct shock: you must remove the tubes directly from the ice into the water bath.) After the 60 seconds, immediately place the cells back ON ICE for one or more minutes. 9. Use a sterile blue micropipet tip to add 250 µL of Luria broth (LB) to each tube. Mix all the tubes by tapping the tubes with your finger. Let the tubes reach room temperature. While the tubes are cooling, flame an inoculating loop in perparation for Step 11. 10. Select the X tube. Use a micropipet to add 100 µL of cell suspension from tube X onto the center of the LB only plate. Immediately proceed to Step 11. 11. Immediately spread the cells over the surface of the plate with a flamed inoculating loop. 12. Repeat Step 11 to spread suspension A on plate A, suspension B on plate B, and suspension C on plate C. Remember to flame the inoculating loop between each suspension. 6 GEL ELECTROPHORESIS PURDUE UNIVERSITY INSTRUMENT VAN PROJECT 13. Allow the plates to sit for a minute, then wrap them together with tape, and label your name(s) and the date. Invert the plates and incubate for 8-24 hours at 37°C. Results: Number Color Plasmid of Colonies of Colonies A B C 7 GEL ELECTROPHORESIS PURDUE UNIVERSITY INSTRUMENT VAN PROJECT 3. After extrapolating, use the graph to estimate the lengths of the fragments in samples A, B, and C. Length (in base pairs) Sample A Sample B Sample C 4. Examine all of your results based on phenotype and genotype. Make a data table and record your observations of all three of the samples. Finally, identify the three unknown samples. 10 GEL ELECTROPHORESIS PURDUE UNIVERSITY INSTRUMENT VAN PROJECT III. Plasmid Screening: How to Extract a Plasmid During this final part of the lab, you will be extracting the plasmids out of the colonies that you cultured. The plasmid can be taken out of the blue and white colonies of E. coli and analyzed by gel electrophoresis. The results you obtain can be compared to your results from section II. First, you will grow a fresh, new culture of E. coli containing the plasmids. Then, you will concentrate the cells and add lysozyme solution which removes the cell’s outer lipid layer and breaks down the peptidoglycan layer of E. coli. Alkaline SDS will be added next to disrupt the lipids of the cell membranes and the NaOH in the SDS denatures the chromosomal and plasmid DNA by breaking the hydrogen bonds. Finally, acidic sodium acetate (NaOAC) will be added to allow the plasmid DNA to renature. The chromosomal DNA is too complex to renature; so, it is precipitated out along with the SDS and various proteins. Plasmid DNA is about all that is left. (See figure 3) After isolating the plasmid DNA, gel electrophoresis is used to examine the genotypes of the plasmids. This is an important step in helping to confirm that the plasmids were indeed taken in by the bacteria. Questions: 1. Explain what the following substances do to help isolate a plasmid from E. coli: a. Lysozyme b. SDS c. NaOAC 2. What is a peptidoglycan layer? 11 GEL ELECTROPHORESIS PURDUE UNIVERSITY INSTRUMENT VAN PROJECT Procedure: 1. Obtain the plates containing the colonies with the two types of plasmid (the blue and white colonies). (By now you should know which type of plasmid is in each colony.) Also obtain two sterile small test tubes and label them according to the two plasmids you have. 2. Add about 10 mL of luria broth (containing ampicillin) to each test tube. Be careful not to contaminate the broth or test tubes. 3. Innoculate the two labeled test tubes with the appropriate plasmid-containing E. coli and grow them overnight. 4. Transfer 1.5 mL of each culture into an eppendorf tube. Spin for 10 seconds in a microfuge to form a pellet of cells. Pour off the supernatant. Continue to do this until you have a good-sized pellet. If questionable, ask your instructor to confirm the pellet size is large enough (50 µL+). Do the following for each tube: 5. Add 100 µL of lysozyme solution. Vortex the mixture vigorously until the pellet is resuspended. 6. Let the mixture sit at room temperature for 10 minutes. 7. Add 200 µL of alkaline SDS and shake the mixture semi-vigorously until the mixture is clear. Invert the tube about 25 times. 8. Add 150µL of 3 M NaOAC (pH 4.7) and mix gently by inverting five times. 9. Spin 5 minutes in a microfuge. 10. Pour the supernatants (plasmids) into a new tube. 11. Discard the pellet (called “E. coli brains”). 12. Add 1 mL of cold ethanol to the supernatants. Invert the tube 5-6 times. 13. Spin for 2 minutes in a microfuge. 14. Pour off the ethanol supernatant. 12