BSCI 410 
Molecular Genetics 
Fall 2008  

Questions preparing for the final

The following are questions from students in preparation for the final (2008).
Each question is offset with a horizontal line

Where will the final be?

In the regular room (1250 BPS)

Can you explain why for the tetrad analysis questions on exam 1, after you make the cross you have TRP YFG mft over trp yfg MFT rather than, TRP YFG MFT / trp yfg mft?

"First, you cross your haploid mft2 strain to a haploid strain of the opposite mating type carrying trp1 and yfg4, both recessive markers on chromosome IV" is what tells you that you have mft2 / trp1 yfg4, or TRP YFG mft over trp yfg MFT.

How is the cre/lox system used ?

First, you make a knock-in (gene replacement) that has loxP sites flanking essential sequences within the gene.  That way, the gene is functional, but if cre is expressed, site-specific recombination will result in a loss-of-function allele.   The expression of cre can be tissue-specific (e.g. a transgene driven by a tissue-specific promoter) or inducible (as in a heat-shock or drug-reseponsive promoter).   The use of tissue-specific cre is probably more common, in part because it's possible to obtain the cre -expression transgenes from other research groups.

See slide 23 in the mouse lecture (lecture 22) for details, but lecture 19 covers methods for mosaic analysis more generally. The flp recombinase / FRT system is similar to the cre recombinase / loxP site system, and there are even more site-specific recombinases. For historical reasons, flp/FRT is used more often with Drosophila and cre/lox is used more often with mice.

I had a few questions about the tetrad analysis we did near the beginning of the semester.
We had three equations.

RF = (NPD + .5TT)/total

Distance = (3NPD + .5TT)/ total

RF = .5(1-e^-2w) aka w = -0.5ln(1-2*RF)

1. I also had RF = .5(1-e^m) where m = mean # of crossovers floating around in my notes.  How is that related to the third equation and what exactly is the "mean number of crossovers"?

m is the number of crossovers in meiosis.  It is twice the recombination rate (because each crossover affects two of the four chromatids).

2. Am I right about these ideas? :
- Recombination frequency is different from map distance because of double/triple/quadruple cross-overs. .

Right.

The concept of map distance only makes sense when the genes are on the same chromosome, but RF makes sense both for genes on the same chromosome and on different chromosomes (when it should always be 50%).

Right, you can still talk meaningfully about recombination when genes are unlinked, but Mendel's law of independent segregation means that the recombination frequency should be 50%.

2. I'm confused about when you use each equation.  As far as I can tell:

- Equation #1 is good in ALL cases to calculate the RF (genes can be on the same or different chromosomes, close or far apart).  It is good to estimate distance between genes ONLY when the two genes are on the same chromosome and very close to one another. .

Right.  Equation 1
RF = (NPD + 0.5TT)/total
just counts recombinants using the numbers of types of tetrad. .

- Equation #2 is good to calculate distance for ALL genes on the SAME chromosome.  It does NOT calculate recombination frequency in any case.  In cases where the genes are very close together, equation 1 and equation 2 are about the same because there will be very few NPD. .

Right.

- Equation #3 - I'm confused about this equation.  I think the function of this equation is to relate the two concepts of recombination frequency and distance.  Therefore, if you were told how far apart two genes are, this is the equation you use to figure out the RF and how many NPDs/PDs/TTs you would expect.  In what other scenarios would you use this equation .

These equations
RF = .5(1-e^-2w) and w = -0.5ln(1-2*RF)

relate recombination frequency to map distance for all cases of meiotic analyis (not only those involving tetrads). .

I was going through exam #1 about tetrad analysis as well.  Question 5 asks, "In this case (MFT2 is unlinked) could you determine whether it is near the centromere of the chromosome that it is on? Is so, how would you do that?"  I know that you can tell if a gene is unlinked to the centromere, as being further away from the centromere increases recombination which increases the number of tetratypes.  However, if mft2 is on a separate chromosome from the other markers in the problem, wouldn't you have to find another marker on the mft2 chromosome to compare mft2 against, so you can tell if crossing over has occurred or not? .

No.  If two genes are both centromere-linked, you can tell that from the lack of tetratypes. Think of the centromere themselves. Homologs segregate at the first meiotic division and then identical sister chromatids separate at the second.

Also, are the NPD considered "recombinant progeny" or has recombination occurred if the genes lie on different chromosomes (npd due to independent assortment and not due to crossing over).

NPDs are tetrads with four recombinant spores.

page by Steve Mount