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1. Take the log10 of the length of each molecular weight marker you can identify on your agarose gel photograph. Graph the log10 of their length on the y-axis versus the distance they migrated from the well on the x-axis, measured in mm using a ruler and the picture of your agarose gel. An example of such a graph is found in the introduction to today’s experiment. Use the equation of the line from your graph to determine the size of your M13K07 backbone (use the band in the lane in which you loaded the cut DNA). How does this measurement compare with the predicted size?

Marker Log(bp) Distance (mm)
10 4 19
8 3.903 21
6 3.78 23.5
5 3.70 25.5
4 3.60 27.5
3 3.48 31
2 3.30 35
1.5 3.17 39
1 3 49
0.5 2.70 52

The cut fragment was at 19mm. Thus, from the equation of the line on the graph above, y=3.9421 and the size of the fragment is ~8700bp, which is comparatively close to the expected size of M13K07 of 8669bp.

2. How many plaques do you expect if you plated 10 ul of a 10^-8 dilution of phage, if the titer of phage was 10^12th plaque forming units/ml? How many plaques would you expect if you tested the phage stock on strain DH5?

2. (10^12PFU/mL)(10^-8)*(10uL)/(10^3uL/1mL) = 100. Thus, you would expect to see 100 plaques. The DH5 strain has an F- genotype, which makes it less susceptible to bacteriophage infection. Thus, I don't expect to see any plaques if I tested the phage stock on strain DH5.

3. E-mailed.

4. The oligonucleotide you are adding to p3 uses traditional genetic engineering ("recombinant") techniques. These are powerful and precise ways to move single genes from one organism to another and to make useful chimeric protein products like the one you are now working on. Synthetic biology is a newer approach to programming cells. Please read one (or more!) of the following articles and then write a paragraph exploring the legitimacy of the following statement: "synthetic biology is about engineering while genetic engineering is about biology."

4. Synthetic biology is an extension of the foundations established by genetic engineering. The difference between the two is that genetic engineering involves the transfer of genes from one organism to another while synthetic biology aims to make it possible to assemble new microbial genomes from a set of standardized genetic parts (which include natural and modified genes as well as artificial genes synthesized de novo). Thus, in the same way that mechanical engineering involves using standard parts to build new systems, synthetic biology aims to do the same with biological systems. In this way, synthetic biology is indeed about engineering. On the other hand, genetic engineering involves a great deal of dependence on the understanding of the biology behind how natural genes and organisms operate. Genetic engineering is a tool that can be used in synthetic biolgy. However, I don't think that the labels should be adhered to too strictly, since a lot can be accomplished with genetic engineering based on far beyond simple biology. For instance, making an organism produce some valueable compound via inserting the appropriate set of genes is, in my opinion, on a higher level than simply knowing the science of biology and thus can be considered a type of engineering.

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