User:Ketan Mathavan/Sandbox 1: Difference between revisions

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~~Test~~ <Structure load='~~1UM8~~' size='~~500~~' frame='true' align='right' caption='~~Insert caption here~~' scene='Insert optional scene name here' />

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

'''Transcription and the human mitochondrial RNA polymerase '''

~~<Structure load='1UM8' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />~~

The central dogma of biology in which genetic information is transferred from DNA to RNA, and subsequently into protein, is fundamental to life. A key player in this process is the DNA-dependent RNA polymerase. RNA polymerase produces RNA in the presence of a DNA template under tight control by the cell. In the Martin lab, our goal is to elucidate the energetics and thermodynamics of this complicated process. As a model, we use T7 bacteriophage RNA polymerase. This single-subunit polymerase can transcribe DNA without assistance from other proteins, making it an ideal model to understand transcription. Likewise, it is representative of all other known RNA polymerases in that it initiates at unique positions along the DNA, undergoes abortive cycling, transitions to a stable elongation complex, and terminates transcription at specific sequences.

~~[['''Bold text'''Image:intactModelLargeText.jpg|frame|Bacterial chemotaxis receptor]]~~

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

~~Many bacteria can "smell" their surroundings~~ and ~~"choose" where to go~~. ~~They detect molecules such as amino acids or sugars using receptors that bind these molecules~~ and ~~transmit a signal into the cell~~. ~~This signal controls several proteins which ultimately control~~ the ~~direction~~ of rotation of the motors that rotate the flagella. One direction causes the cell to continue swimming; the other direction causes the cell to tumble. When an attractant molecule binds, the receptor signals: "Things look good, keep swimming!" The opposite signal occurs when bacteria sense a repellant or less attractant molecules: "Time to ~~tumble and try a new swimming direction~~."

Initially transcribing complexes are relatively unstable through about the first 8-10 bases of transcription. During this time, short RNA transcripts are made and released in a process known as abortive cycling. Abortive cycling in particular, and promoter-proximal pausing more generally, plays key roles in gene regulation. Thus understanding the mechanism of initial transcription is key to understanding cellular regulation.

@@ Line 1: / Line 1: @@
-Test <Structure load='1UM8' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />
+<Structure load='3SPA' size='250' frame='true' align='right' caption='Human mitochondrial RNA polymerase' scene='Insert optional scene name here' />
+One of the [[CBI Molecules]] being studied in the  [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].
+'''Transcription and the human mitochondrial RNA polymerase '''
-<Structure load='1UM8' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />
+The central dogma of biology in which genetic information is transferred from DNA to RNA, and subsequently into protein, is fundamental to life. A key player in this process is the DNA-dependent RNA polymerase. RNA polymerase produces RNA in the presence of a DNA template under tight control by the cell. In the Martin lab, our goal is to elucidate the energetics and thermodynamics of this complicated process. As a model, we use T7 bacteriophage RNA polymerase. This single-subunit polymerase can transcribe DNA without assistance from other proteins, making it an ideal model to understand transcription. Likewise, it is representative of all other known RNA polymerases in that it initiates at unique positions along the DNA, undergoes abortive cycling, transitions to a stable elongation complex, and terminates transcription at specific sequences.
-[['''Bold text'''Image:intactModelLargeText.jpg|frame|Bacterial chemotaxis receptor]]
-One of the [[CBI Molecules]] being studied in the  [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].
-Many bacteria can "smell" their surroundings and "choose" where to go. They detect molecules such as amino acids or sugars using receptors that bind these molecules and transmit a signal into the cell. This signal controls several proteins which ultimately control the direction of rotation of the motors that rotate the flagella. One direction causes the cell to continue swimming; the other direction causes the cell to tumble. When an attractant molecule binds, the receptor signals: "Things look good, keep swimming!" The opposite signal occurs when bacteria sense a repellant or less attractant molecules: "Time to tumble and try a new swimming direction."
+Initially transcribing complexes are relatively unstable through about the first 8-10 bases of transcription. During this time, short RNA transcripts are made and released in a process known as abortive cycling. Abortive cycling in particular, and promoter-proximal pausing more generally, plays key roles in gene regulation. Thus understanding the mechanism of initial transcription is key to understanding cellular regulation.