So, when last we left our Mr. Protein O’Interest and the A. Body clones, the A. Body clones had each attached itself to the hat of a different Mr. O’Interest in a different park. As I mentioned before, the fact that the A. Body clones have attached themselves to the Messr. Interest hardly helps you to find the bathroom, boathouse, ranger station, or campground since it is well nigh impossible to see people from high up in the air.
This is the situation I am in with my sample of cells after step 1. I have put antibodies on my sample that will recognize the epitope tag on my protein and this in turn will tell me where the ER is in the cell. However, proteins are incredibly small. So small that you cannot see an individual protein even if you magnified it 1 million times (and I assure you, the microscope I’m using does not have that sort of magnification capabilities). The fact that I’m now looking at a complex containing two proteins doesn’t help me very much.
So, the next step in the procedure is to 1) give me something to amplify the signal–so that I’m not just looking at a complex of two proteins–and 2) to give me something that I can actually see. This is, again, done with antibodies. However, these antibodies are a little more indiscriminate. They will recognize anything that came from a mouse (remember, my first antibody–called the primary antibody–originally came from a mouse). And, these secondary antibodies will recognize a variety of parts of the first antibody. This means that you will have many molecules of the secondary antibody attached to one molecule of the primary antibody.
Back to the park analogy. Okay, you’re high up in a helicopter and below, an A. Body clone has found the hat-bearing Mr. O’Interest and has grabbed onto that hat. Now, you release a second set of clones into the park–the Clone Grabber clones. The CG clones are a mixed group of clones. They have been trained to recognize the A. Body clones that are in the park, but they have been trained to recognize different parts of the A. Body clones. Some of the CG clones recognize the A. Body shoes, some recognize the A. Body right pantleg, some recognize the Star Wars insignia on the A. Body t-shirt, some recognize the A. Body hair, etc., etc. Therefore, when the CG clones find the A. Body clones, each of them will grab onto the part that they recognize–the shoe-recognizing clones to the shoes, the pantleg-recognizing clones to the pantleg–such that in the end you have quite a number of CG clones attached to the A. Body clone (who is, in turn, holding onto Mr. O’Interest’s hat). So now, instead of having a group of two people to detect from your helicopter, you have a group of 10 people to see. But, if you’ve ever been in an airplane flying high over a city, you will know that is not enough. Especially if you are flying over it at night. When you are flying over it at night, in fact, mostly all you see are lights….
To be continued…..
