A Genetics Question

Meninger

I am currently enrolled in molecular genetics taught by John Meninger (Harvard graduate) who has worked with scientists such as Messelson, Holliday, and such. This is one of his questions which I thought was a bit confusing at first. He seems to think that the question makes perfect sense. It may be a bit difficult for some of you nevertheless it is a practical problem having to do with practical logic skills which does not require one to be proficient in genetics.

After you answer the question, please comment on a scale of 1-5 on how difficult you thought the question was and if there was any ambiguity in how the question was phrased. It is a bit of a tricky question. Again, anyone can solve this problem; no knowledge of genetics is required.

E coli has a base content of A=.247, G=.260, T=.236, C=.257. Recombination hot spots (X sites) are reported to exist every 5000 base pairs. Is the distribution of X sites random? Briefly explain your answer. The chi site sequence is 5' GCTGGTGG 3'.{for those of you who don't remember, dna is made up of four different kinds of nucleotides, each different nucleotide made up of either A, G, T, or C}

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iansmith

Staff Emeritus
Gold Member
This question is quite easy i you said that its a 2 out a 5.

First the 5000 base pair is there to confuse you but you have to it prove that the X site does not happen by accident and at random. There is about 4 639 Kb in the E. coli K12 genome (http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=genome&gi=115 [Broken]). Therefore X sites happen should happen about 928 times.

Second the probably to have the X sequence (GCTGGTGG)is about
0.260*0.257*0.236*0.260*0.260*0.236*0.260*0.260=1.7*10^-5 or 17 every 1 000 000 base pair.

Therefore by chance X site would happen 4.639*17= 79 times.

We can conclude that X site are not random because it occurs about 928 times in the genome whereas by random event it would only occurs 79 times.

That how i would do it and maybe Monique and Another God can add moer information or an alternative how to solve it

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Meninger

Yeah, I think you basically have the right idea. Nevertheless, I don't think that he intended to confuse us with the "every 5000" base pair information. Also, he did not gives us any information on how many total base pairs e.coli had so it made it slightly more difficult on understanding his concept of randomness, and using the word "distributed" did not help either.

iansmith

Staff Emeritus
Gold Member
From my point of view the every 5000 base pair was there to confuse some people. Because it says every 5000 bp people would think that it happens regularly and at every 5000 bp.

You did not have to know that the genome of E. coli was 4.6 Gb, you could of assume a random number such as 1.5 Gb.

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