You have just identified a1000bpc DNA from a plant growing near a blue, glowing-­‐volcano that is 75% identical in nucleotide sequence to a 1000bp cDNA from a jellyfish growing near a underground    blue, glowing-­‐volcano. You think that this cDNA encodes a GFP type protein. Outline the steps that you would take to show that the two predicted proteins have similar or identical properties. You answer should be written in outline form (flow chart with arrows). Please include one sentence worth of important conclusions after each step in the flow chart.

Question 2:

Please describe a series of five unique experiments using the lecture material as a guide. (Each experiment can build on the previous one, but it is not necessary.) Maximum 1 page text,plus maximum 1 page figure for each experiment (2 pages total). (Each experiment will be graded separately).Each experiment is meant to teach you something about the protein described below.

Topic: You really like to drink black coffee (nothing added). You have the same brand of coffee machine at home and at work. You are such a creature of habit that you bought the identical cup, coffee beans, etc,for both home and work. You come to realize that when you drink coffee at home alone at 9am and sit down to do work that you are very clear minded. When you drink coffee at work alone at 9am that you are clear minded, but also able to remember incredibly small details about your surroundings that you don’t observe when you are home. One day you notice that part of the design on the bottom of the cup(from work)is actually a growing greenish-brown organism. You correctly surmise that you can grow it in the lab on coffee plates. After a few months of watering your coffee plate, a little plant emerges. A few months later that plant flowers and ultimately makes seed pods. You decide to eat one of those seeds. The effect is immediate and long lasting: you remember every little detail of your day down to how many steps you have taken in the day, how many ounces of water you drank, etc. You wonder what the effect is on a mouse. So you give one of the seed pods to the mouse. After eating the seed, the mouse sits in the corner. 1hr later it emerges and starts organizing its cage. Food pellets on one side and its bedding on the other side. To your surprise the food pellets are organized in 10 rows of 10 and the bedding islaid out asa perfect square.

Assuming that there is a single polypeptide (from one gene theseed pod), then what experiments would you do to identify it?
What experiments would you do to identify the proteins with which it interacts? What experiments would you do to identify the biological function of these proteins and mechanism of action?
Please address how each experiment gets you closer to answering the questions below (it is not necessarily possible that any one experiment can give you the entire answer)

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1. Question
• First, we need to synthetize mRNA from cDNA, and translate it to proteins of interest (plant and jellyfish proteins).
• Since we know the cDNA sequence, we can find an amino acid sequence to make an antibody for Immunoprecipitation (for extraction and purifying the protein).
• We can analyze if this two proteins have similar structure (similar structure can mean that they have similar properties and function) using x-ray crystallography or Nuclear magnetic resonance (NMR) spectroscopy.
• For analyzing protein function and protein localization in cell, we can use recombinant DNA techniques to create GFP fusion constructs to a different kind of proteins (example: secreted protein and a lysosomal protein in yeast).
We can track...

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