I did a DNA fingerprinting lab and I can't understand some of the questions.
1) Different restriction enzymes are isolated from different types of bacteria. What advantage do you think bacteria gain by having restriction enzymes?
2)In your lab, you ran your DNA samples on a 0.8% agarose gel. Would you get the same results if you ran your samples on a higher percentage agarose gel? why or why not?
3)If you have a restriction enzymes that cuts a piece of linear DNA at two recognition sites, how many DNA fragments would you see on a gel?
4)Hind III recognizes a sequence of six nucleotides(AAGCTT) as a cut site. What are the odds that this sequence will occur in a random chain of DNA?
5)predict what would happen if you place your gel in the electrophoresis chamber with the wells containing the DNA nexr to the red(positive) electrode instead of the black(negative)?
2.Depends on what results you're talking about. A higher percentage gel will cause the DNA samples to migrate more slowly but it won't normally change the relative order of the bands in a given lane. Higher percentages can give better separation of small fragments, but large fragments won't separate as well.
3. 3
1) The advantage bacteria gain by having restriction enzymes is the ability to protect themselves from invading foreign DNA, such as viral DNA. These enzymes recognize specific sequences of DNA and cut them at those sites, effectively destroying the foreign DNA and preventing it from being incorporated into the bacterial genome. This mechanism acts as a defense mechanism for bacteria against foreign genetic material.
2) No, running the DNA samples on a higher percentage agarose gel would not yield the same results. The percentage of agarose in the gel affects the pore size of the gel matrix. A higher percentage agarose gel would have smaller pore sizes, which would impede the movement of larger DNA fragments. So, if the DNA fragments are relatively large, they may not migrate as far in the higher percentage gel compared to the 0.8% gel. This could result in different separation patterns and banding patterns on the gel.
3) If a restriction enzyme cuts a piece of linear DNA at two recognition sites, it would produce three DNA fragments on a gel. One fragment would be the original intact DNA molecule, while the other two fragments would be the smaller fragments resulting from the cutting at the recognition sites.
4) The sequence recognized by Hind III (AAGCTT) consists of six nucleotides. Each nucleotide has four possible options (A, T, G, C). Therefore, the total possible combinations for a six-nucleotide sequence is 4^6, which equals 4096. The odds of any specific sequence occurring in a random chain of DNA would be 1 in 4096.
5) If you place your gel in the electrophoresis chamber with the wells containing the DNA next to the red (positive) electrode instead of the black (negative) electrode, the DNA would migrate in the opposite direction. Normally, during gel electrophoresis, DNA fragments migrate from the negative electrode towards the positive electrode due to the negatively charged DNA. However, if the polarity is reversed, the DNA would migrate towards the red (positive) electrode, which would cause incorrect interpretation of the gel results. The DNA fragments would not separate properly or migrate in the expected direction, affecting the accuracy of the analysis.
1) The advantage of bacteria having restriction enzymes is that they help defend against foreign DNA, such as from viruses or other bacteria. Restriction enzymes recognize specific sequences of DNA and cut it at those sites. This allows bacteria to protect their own DNA from being cut, while cutting any foreign DNA that enters the cell. By cutting foreign DNA, bacteria can prevent it from replicating and potentially causing harm.
2) Running DNA samples on a higher percentage agarose gel would likely produce different results compared to running them on a 0.8% agarose gel. The percentage of agarose in the gel affects the size range of DNA fragments that can be resolved. Higher percentage agarose gels create a tighter matrix, which makes it more difficult for larger DNA fragments to migrate through the gel. This results in better separation and resolution of smaller DNA fragments. On the other hand, lower percentage agarose gels allow larger DNA fragments to migrate more easily. Therefore, if you ran your samples on a higher percentage agarose gel, the smaller DNA fragments would likely separate better, but larger DNA fragments might not migrate as effectively.
3) If a restriction enzyme cuts a piece of linear DNA at two recognition sites, it would create three DNA fragments on a gel. The fragments would include the one between the recognition sites (which would now be two pieces), and the two end fragments formed by the cut ends of the original DNA molecule.
4) To calculate the odds of the Hind III recognition sequence (AAGCTT) occurring in a random chain of DNA, we need to consider the probability of each nucleotide base appearing at each position. Since there are four possible nucleotide bases (A, T, G, and C), the probability of each base appearing at any position is 1/4. Therefore, the probability of the Hind III sequence occurring randomly can be calculated by multiplying the probabilities of each base appearing in the correct order: (1/4) x (1/4) x (1/4) x (1/4) x (1/4) x (1/4) = 1/4^6 = 1/4096. So, the odds that the Hind III recognition sequence will occur in a random chain of DNA are 1 in 4096.
5) If you place your gel in the electrophoresis chamber with the wells containing the DNA next to the red (positive) electrode instead of the black (negative) electrode, the DNA fragments would migrate in the opposite direction. Electrophoresis works by applying an electric field, with the positive electrode pulling the negatively charged DNA fragments towards it. By placing the wells near the red (positive) electrode, the DNA would migrate towards the positive electrode instead of the negative electrode. This would lead to the DNA fragments being separated in the reverse orientation on the gel compared to the conventional setup. Therefore, the bands on the gel would appear flipped horizontally if the wells are placed next to the positive electrode.