User:Anthony Salvagno/Notebook/Research/2009/10/01/GRD Proposal 2009

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DNA is the genetic information contained inside in the cells of every living organism. This information is important because it is the code that makes each individual organism unique. It is the expression of DNA (the conversion of DNA into proteins) that determines what a person may look like, how much muscle a lion can have, have long a giraffe's neck can be, how lethal the next flu strain can be, etc. SJK 01:34, 2 October 2009 (EDT)

01:34, 2 October 2009 (EDT)
You may even want to say the central dogma of biology here: DNA goes to RNA goes to proteins (you could probably find a good figure of this on internet). You're interested in the first step, because a lot of regulation of gene expression (better term than DNA expression) happens during the process of DNA copying into RNA, aka gene transcription. Not only do the genes determine how long the Giraffe's neck can be, it is amazing how gene expression can direct the differentiation of the many different kinds of cells in your own body: neurons, skin cells, cardiac muscle, etc.

DNA is a double stranded polymer. Each strand is made of a sugar backbone with four distinct nucleotides that allow two strands to join in a helix conformation. Those bases are cytosine, guanine, thymine, and adenine. Each base plays an important role in the structure of DNA because it is the sequence of these bases that determine one's genetic code. In humans there are 23 chromosomes, each full of tightly compacted DNA, and each chromosome has a number of genes. A gene is a section of DNA that provides information about the makeup of a specific cellular component. There are literally tens of thousands of genes in the human genome (the entirety of all the DNA of an organism). SJK 01:41, 2 October 2009 (EDT)

01:41, 2 October 2009 (EDT)
Again, a picture here would help a lot. I wouldn't say that DNA is tightly compacted, because it has varying levels of compaction depending on cell cycle and whether gene is being transcribed or not.

The process by which DNA becomes a protein is a very complex process. It begins with transcription, where an RNA Polymerase (RNA Polymerase II in humans, or RNA Pol II) enzyme reads a single strand of DNA and creates a complementary strand of messenger RNA (mRNA) from it. This single stranded RNA polymer may then undergo a few changes so that it can be read by complementary tRNA during an event known as translation. Each tRNA molecule (consisting of 3 bases) comes attached with a specific amino acid and the amino acids form long chains known as polypeptides. The sequence of mRNA (which is determined by DNA) determines the sequence of tRNA which then determines the amino acid order. These polypeptides undergo a folding process and the result is a protein which the cell can use for a variety of functions, all of which are crucial to life.SJK 01:41, 2 October 2009 (EDT)

01:41, 2 October 2009 (EDT)
There is a lot of discussion of translation and even some splicing here. Definitely both interesting, but given that you're targeting a lay audience and that you want to talk mostly about Pol II, I recommend getting rid of details of splicing and translation, and only mention it in the one sentence about central dogma above. You may even want to combine this paragraph with that above.

SJK 01:45, 2 October 2009 (EDT)

01:45, 2 October 2009 (EDT)
Some comments on the rest: (a) you spend a lot of time talking about initiation, whereas you may know more about elongation and will more likely study that. It's possible that you're getting to detailed, given that you're targeting a lay audience in your first paragraph. Perhaps casting RNA Pol II as an incredibly important molecular motor or machine would help. And then say that you can get new information via your DNA unzipping technique (showing figure). (b) This proposal seems to end in the middle. You don't have your OT figure any more, and you also don't say what you need the money for?

I am interested in a specific part of this long, complicated process and that is the behavior of RNA Pol II during transcription. In order for transcription to begin, various proteins bind to the DNA in order to build the Pol II complex (the polymerase enzyme is itself a complex of proteins that work together). Once the Pol II enzyme is constructed, it will attempt to begin reading the DNA to create complementary mRNA. In order for this to occur, it must be constructed at the correct location on a DNA chain known as the promoter. The promoter marks the beginning of a gene. Once RNA Pol II reaches the end of a gene, transcription can end so that the newly formed transcript (the new mRNA molecule) can be sent off for translation.

This entire process is very complicated, and if at any point there is an error in the process there can be disastrous results. In order for proteins vital to cell life to function properly transcription must proceed effeciently and correctly. I would like to be able to study various properties of the RNA Polymerase II molecule with the use of Optical Tweezers (OT). With OT, I can study individual RNA Pol II molecules under certain conditions. I would be able to study properties during construction of the complex, during the transcription event, during termination (end of transcription), and provide never-before-seen glimpses into the behavior of this important enzyme.