Analogies

Polymerase Chain Reaction (PCR)

"Suppose you have a 10 foot banner of which you want to make an exact copy. You would take it to a copy machine, right? But will the entire banner fit on the copy machine? No, only a small portion will (either an 8 X 11 or 8 X 14 inch piece). You can make as many copies as you want, but the copy machine will only copy the selected region of the banner. Polymerase Chain Reaction or PCR works in the same manner. The banner represents a chromosome; it can be copied as many times as you want (called cycles), but only for a small region of the chromosome. Typically PCR does 30 cycles, which will copy the small region of the chromosome 210 times making over a billion copies. Now you have many copies of that chromosome region for procedures such as cloning into vectors, determining tissue types (for organ transplants), and criminal investigations."

-Lynn Gordon And Jane Obbink
1993 Woodrow Wilson Biology Institute
http://www.accessexcellence.org/AE/AEPC/WWC/1993/teaching.html

Electrophoresis

"Imagine a huge swimming pool full of water and many entangled nets (this is the agarose gel). A dump truck comes along and dumps its load into one end of the pool. That load contains an extensive collection of long, skinny things of varying lengths and sizes (analogous to DNA of varying sizes), e.g. from boa constrictors to smaller snakes to worms to microscopic bacteria. There is a vacuum at the other end of the pool (analogous to the electric current), which can be turned on and off. When on, the vacuum pulls all of the creatures across the pool. But because of the netting, movement of the skinny things is impeded."

1. Which creatures will reach the other end of the pool first--the smaller creaters or the longer creatures? Why?
2. When the vacuum stops, which creatures will have moved further? Why?

This is the idea behind electrophoresis.

-Karen Kyker
Woodrow Wilson Biology Institute, 1993
http://www.accessexcellence.org/AE/AEPC/WWC/1993/electrophoresis.html

Genotype vs. Phenotype

Have you noticed how the same recipe will turn out differently when two different people make it? If 30 people each made a plate of chocolate chip cookies using the same recipe, how do you think you would answer these questions?

1. Do all the resulting cookies come from the same recipe? 2. How do they look similar? 3. How do they look different? 4. What might be some reasons for your responses to Questions 2 and 3?

Just as in genetics, each of the cookies one person made look slightly different (phenotype) from each other, even thought the same person (environment) used the same recipe (genotype). Also, the cookies made by different people will look slightly different (phenotype) from each other, even though the bakers (environment) used the same recipe (genotype).

-Lynn Gordon And Jane Obbink
1993 Woodrow Wilson Biology Institute
http://www.accessexcellence.org/AE/AEPC/WWC/1993/teaching.html

Genotype vs. Phenotype

"Another analogy that works well to help... understand the relationship of geneotye (genetic coding) to phenotype (expression of coding) is to compare a computer to a computer program or a Nintendo machine to a Nintendo game cartridge. For years my son had two Nintendo games that Uncle Fred had sent him for his birthday. There was only one "small" problem. He had a couple of cartridges, each with coded information for one game (DNA molecules coding for one gene) but was only able to play (express) them when they were in the environment of a machine (cell) that could express the information. If the game cartridge were placed in an incompatible machine (a Nintendo cartridge in a Sega machine) the game could not be expressed. Phenotype can be equated to the expression of the game that shows up on the screen. (If more than one game is found on one cartridge, each game represents a gene on a chromosome.) The game program represents the genotype. Other cartridges (chromosomes) contain other games (genes) which express themselves when placed in the machine and accessed (turned on by cell)."

-Lynn Gordon
1993 Woodrow Wilson Biology Institute
http://www.accessexcellence.org/AE/AEPC/WWC/1993/the_spanish.html

Distinguishing between bacterial chromosomes and plasmids

"Imagine an oval plate with plain spaghetti, Spaghetti O's, and tomato sauce on it. The spaghetti is only one strand, but very long and coiled up on top of itself. The spaghetti strand is attached at one point to the edge of the plate. The Spaghetti O's are smaller circular spaghetti pieces made up of the same material as the longer strand. There are only a couple of Spaghetti O's in the plate and are not attached, but free floating in the tomato sauce. With this image in mind, you are imaging a bacterial cell. The oval plate represents the rigid capsule of the bacteria. Inside the bacteria cell, the long strand of spaghetti attached to the edge is the bacteria's main chromosome all coile up. The Spaghetti O's represent the circular plasmids. As spaghetti and Spaghetti O's are made of the same material, likewise the bacterial chromosome and plasmids are both made up of DNA. The spaghetti and Spaghetti O's float in a tomato sauce, just as the DNA floats in the bacteria cell's cytoplasm."

-Lynn Gordon And Jane Obbink
1993 Woodrow Wilson Biology Institute
http://www.accessexcellence.org/AE/AEPC/WWC/1993/teaching.html

How do restriction enzymes work?

"Imagine that you work in a manufacturing plant that produces wooden ladders. The company makes their ladders really, really long and has the rungs of the ladder painted with one of four colors: Red, Blue, Green, and Yellow. The color pattern of the rungs is random. It is your job to cut the really, really long ladder into smaller ladders. You are given the color sequence of where to cut the ladder, usually in a six color pattern. For example, every time you find the rung pattern:
Red, Red, Yellow, Yellow, Blue, Green
you are to cut the ladder. As in other types of millwork, there are two styles of cutting:

1. Cut straight across the sides of the ladder to completely sever the ladder. This is called a "Blunt end" cut. (Called a end in lumber terms) 2. Cut through one side of the ladder and down the middle of the rungs and back out another side of the ladder. This is called a "Sticky end" cut (called a Lap end in lumber terms).

Your job is to walk along the really, really long ladder and look for the RRYYBG color pattern. When you find it, you cut the ladder (usually with the "Sticky end" pattern) to make a separate, smaller piece. You continue searching down the ladder for this color sequence and repeat the cutting step until you reach the end of the ladder. Now you have cut the one really, really long ladder into many pieces, probably of different lengths.
A Restriction Enzyme does the same task of cutting a really, really long ladder of DNA. The restriction enzyme moves down the DNA Ladder looking for a specific sequence of bases, rather than colors. When it finds that specific base sequence, the restriction enzyme cuts the DNA (using a Blunt or Sticky end pattern) and a smaller piece is made. The restriction enzyme continues moving down the DNA, cutting at the specific sequence until it has reached the end of the DNA Ladder. Now the DNA is cut into many pieces, probably of different lengths."

-Lynn Gordon And Jane Obbink
1993 Woodrow Wilson Biology Institute
http://www.accessexcellence.org/AE/AEPC/WWC/1993/teaching.html