How Are Proteins Made?

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1 Proteins play a crucial role in almost every biological process, from cell signaling to cell division. Each protein has to be uniquely suited to its particular job, yet they are all made of the same 20 amino acids. How can this be? This is possible What Are Proteins? because every protein has a unique sequence of amino acids. This makes each protein unique Figure obtained from and allows it to perform a very specific job inside the cell. Figure by Darryl Leja, Human Genome Research Project ( Figure taken from Life Inside The Cell animation by Biovision/Harvard University How Are Proteins Made? Last week, you transformed E.Coli cells with a piece of DNA containing the gene for Cyan Fluorescent Protein, or CFP. If your transformation was successful, your cells glowed after a few days showing that the cells made the fluorescent protein correctly. This means they assembled all 239 amino acids in the correct order to make CFP. We know this because the protein wouldn t glow if the cells had made a mistake. But how did the cells know which amino acids to use and what order to put them in? Developed by Sharlene Denos for the Center for Physics of Living Cells Outreach Program. 1

2 The First Step: Transcription! In this lesson, you will learn about the first step in making proteins from genes. This process is called transcription and occurs when an RNA copy, or transcript, is made from a sequence of DNA. How is this done? Remember that DNA bases pair with each other in a specific way using hydrogen bonds. Adenine always pairs with Thymine and Guanine always pairs with Cytosine. The same is true Figure by Pearson s The Biology Place ( for RNA bases, only Uracil replaces Thymine to pair with Adenine. If the double helix is unwound so that an individual strand of DNA is exposed, RNA nucleotides will come in and form base pairs with this strand. But in order to make RNA, these individual nucleotides must be linked together with a covalent bond. This reaction requires energy and would take a very long time to happen spontaneously, but the cells have an enzyme to catalyze this reaction, to speed it up. This enzyme is called RNA polymerase. RNA Polymerase: An Enzyme Caught in the Act! In this lesson, you will take a close look at an RNA Polymerase protein that has been caught in the act of transcribing a piece of DNA into RNA. You will see a big protein with DNA in the middle (in the active site). The DNA double helix is partially unwound and has a small piece of RNA that has just been transcribed from it. Figure obtained from Developed by Sharlene Denos for the Center for Physics of Living Cells Outreach Program. 2

3 RNA Polymerase: An Enzyme Caught in the Act! Name What Do You See? Take some time to explore the protein structure and write down some of your observations here. You can use the commands in the table below to rotate and zoom in on your protein. 1. What does the overall shape of your protein look like? 2. Can you see the active site? What do you see in the active site and why do you think it s there? VMD Keyboard Shortcuts: Key Action Performed pressed r Enter rotation mode for the selected molecule s Enter scale mode for magnifying or shrinking the molecule 1 Label atoms selected with mouse left click Developed by Sharlene Denos for the Center for Physics of Living Cells Outreach Program. 3

4 Change the VMD Representation to See the Protein Better!! 3. In the VMD Main menu, select Representations under the Graphics menu. Delete the word all in the selected atoms field and type protein. Now press enter. What just disappeared from your structure???? 4. Now use the Drawing Method drop down menu in the bottom left hand corner to change the protein from the Lines representation to New Cartoon. You should see a bunch of coils. What do they represent? 5. Now select Create Rep again and type nucleic into the drop down menu. Choose VDW as the drawing method and change the coloring method to Chain. Now what do you see? What do the spheres represent? What does each color represent? Developed by Sharlene Denos for the Center for Physics of Living Cells Outreach Program. 4

5 Hide the Protein to See the Nucleic Acid Better! 6. Go back to the Graphical Representations window and double click on the representation for protein (the word protein should turn from black to red). This will hide the protein so we can look more closely at the DNA & RNA. 7. Now click on the nucleic representation. Change the drawing method to New Cartoon. Can you see each of the DNA and RNA strands? What do they look like? What are the little sticks poking out from each strand? 8. Now change the coloring method to ResName. Now what does each color represent? How many different colors do you see on the RNA strand? What color is each of the RNA bases? One of the four bases is not present in this transcript. Which one is it? Developed by Sharlene Denos for the Center for Physics of Living Cells Outreach Program. 5

6 How many bases are in the RNA strand? What is the sequence of bases in the RNA strand? What is the DNA sequence from which this RNA was transcribed? What is the protein sequence that would be made from this transcript? Use the Genetic Code shown here to translate your RNA sequence into a protein! (One base will be left over at the end. Don t worry about this). Developed by Sharlene Denos for the Center for Physics of Living Cells Outreach Program. 6

7 Let s Take A Closer Look at the Nucleic Acid Molecule! 9. Go back to the Graphical Representations menu and change the drawing method to Lines and the Coloring Method to Chain. 10. Now click Create Rep and change the drawing method to Paper Chain. What do you see? What color is each of the DNA and RNA chains? What are the red hexagons? What are the yellow pentagons? Are the yellow pentagons the same in DNA and RNA? If not, how are they different? Now Let s Look at the Whole Structure Again! 11. Go back to the Graphical Representations menu and double click on the protein representation to show it again (the word protein should turn from black to red). Take some time to explore the overall structure like you did at the beginning of this lesson. What do you notice about this structure that you didn t notice at the beginning of this lesson? Developed by Sharlene Denos for the Center for Physics of Living Cells Outreach Program. 7