Directions (working in pairs)

1. The instructor will provide you will a selection of nine or differently colored paper "chromosome" strips from which you are to make a selection in the following manner. (Colors mentioned herein will probably not be in your collection, but are used only for illustration.)
   1. One student selects Mom's pair of chromosomes. They must be of two different colors. Also pick up a duplicate pair which you will later use for Mom's gametes to make babies. (E.g.: This student will walk away with two beige and two mauve.**)

   2. The other student selects from the remaining colors a pair for Dad (also of dissimilar colors). ALSO pick up another single one that is of Dad's colors. PLUS pick up yet another chromosome that is of a color different from any the colors already picked up. This lone strip will represent a gamete from Mom's male tennis instructor. (E.g.: This student will walk away with two fuchia**, one chartreuse** and one peach)

2. Pretend these strips of paper consist of one long strand of ds-DNA ("double-stranded" DNA) in the whole chromosome, which consists of many hundreds or thousands of genes. You gaol is to isolate and then to assay a specific section of the whole chromosome. Let's pretend it deals with eye construction. You must eliminate the DNA on each side of the "eye" sequence. Fortunately you have discovered a type of restriction endonuclease that does just that! Let's call it ScR1 for Scissors Restrictase No. 1. Your ScR1 likes to "cut" DNA at a very specific place where there are two vertical lines next to each other and a "||" is fortunately located right at the beginning and another one at the end of the "eye-gene". Use your ScR1 (aka your scissors!) to cut each of your chromosomes wherever you find two adjacent vertical lines.

3. You must now remember that everything you have done is in solution, and would be a process called making an ScR1 digest. The result is that you have a mix of "eye-genes" and clipped off ends. How would you go about selecting out only the "eye sequences" and throwing away the rest? Sure, it is easy on the desktop with paper - use your fingers! But in a real experiment, there must be a trick (technology) for doing this biochemically. What would you suggest? So far in this course, what methods have you studied that separate things, and then which of those sort things by size?

4. So let us assume you have collected each person's two alleles of "eye sequence." (And you have discarded the terminal scraps into the wastebasket. "Keep the world clean!")

5. Make four groupings of all these alleles on your desktop:

   Mom	Dad	Child #1	Child #2
   beige mauve	fuchia chartreuse	beige (M) fuchia (D)	mauve (M) peach (TC)

6. The numbers written on the allele strips indicate the relative length of DNA between the single line restriction sites within that allele.

7. Attack each grouping with your second restriction enzyme (what do you know, it's called "ScR2"!). Snip each of the strips at their restriction sites (the single vertical lines), and keep all the restriction fragments in their respective personal groupings. Soon you will have four piles of short and long fragments. In actuality, this process would be called making a second ScR2 digest.

8. Next electrophorese them by arranging the fragments in each pile according to size disregarding color (i.e.: pretend you are colorblind).

   

9. On linear graph paper,* make the vertical axis longwise on the paper numbering upwards from zero to 110 - but instead of "110", label that either "origin" or "start." Next divide the horizontal axis into four parts which would be labelled "Mom," "Dad," "Kid #1," and "Kid #2."
   

10. Plot the lengths of each subject's fragments in each of their own columns. Do this by making a dot in the middle of their column at the correct height. (Sometimes you will make more than one dot because two or more fragments are of the same length in that "person's" grouping.)
    

11. Center 1-inch horizontal lines through the dots. If more than one dot is at that level, make the line correspondingly thicker.

    

12. You have now simulated an electrophoresis gel, where all the fragments migrated down from the "origin" to where you drew the various lines. (If you need an analogy for electrophoresis, click HERE.)

13. Possibly Tricky Problems:
    1. Can you tell from the "ladder rungs" in your "gel" which was the husband's child, and which was the tennis coach's child?

    2. Are restriction fragments of the same length necessarily of identical DNA base sequence?

    3. Would it be possible for a mother and father to produce a child whose restriction fragment profile did not match "according to theory?" If it is possible, then what method would you use to discern the child's paternity?

    4. How could you adapt this technique to distinguish whether or not someone was the murderer in a bloody fight?

    5. Suppose you crossed a female mouse with its identical twin brother. Compare and contrast the "restriction" fragment profiles of mother, father and pups.

    6. Try the puzzles in the following boxes for more realistic applications of what you have just learned.

Local Happenings

There is a known case in Virginia Beach VA where two identical twin sisters live nextdoor to each other, and they are married to identical twin brothers. Both families have only one child, and they do not look alike. Explain how this can be. Indeed, would it be possible for one couple to produce a genetically identical twin of a child in the other family? Would it be possible for these genetically identical twins to be of different ages?! What would result were these two to "breed" with each other? Would it be incest?

Jake and Emma's four children were grown and had families of their own. Jake was murdered, and the police suspected his oldest child (#1) as the culprit, who had unexplained scratches on his arms and face. DNA was extracted from under the victim's fingernails, and that was compared with those of the other members of the family. Be a real Sherlock Holmes: was the culprit really the oldest child?

An even more convoluted story!
Only the names and places have been changed.