CHEM 30B  Dr. R. Rinehart

DNA & RNA Exercises on the Web

You need to be familiar with the Chime instructions used before in the Chime and Insulin tutorials.

I.  If you weren’t paying attention during Monday’s class, and/or if you haven’t looked at Chapter 24, and/or if you haven’t yet learned the names and structures of the “bases” and the backbone of nucleic acids, including terms like 5’ à 3’, start by taking the tutorial at

            http://www.worthpublishers.com/lehninger3d/index.html  [USE NETSCAPE 4.7x]

and  select Nucleotides: Building Blocks of Nucleic Acids. Follow the tutorial in sequence.

What are the components of a nucleotide? _____________  ______________  ______________

What are the characteristics of the nitrogenous base? _______________ __________________

To what is the base attached? How? _____________________________________________________

What links the sugars together? ________________________________________________

Draw and number the 5 bases. Which are purines _______________ _________________

● and which are pyrimidines? _________________ _________________ __________________

● Which bases are found in DNA? ___ ___ ___ ___  RNA? ___ ___ ___ ___  [use 1-letter codes]

 

cytosine

 

 

 

 

 

 

thymine

uracil

adenine

 

 

 

 

 

 

 

guanine

 

● What is the attachment point for purines to the sugar molecule? __________

● What is the attachment point for pyrimidines to the sugar molecule? __________

● Which position of the 5-carbon sugar carries the base? ________

● Is the base a or b with respect to the sugar? _________

● What are the linkages attaching the sugars to form a chain called? ____________________

● What is “directionality” of the chain? _____________________________________________

__________________ ___________________________ _________________________________

● What are the two different ends of the chain called? ______________ _________________

● What are the two main characteristics of the backbone? _______________ ________________

● What color code is used for the bases in the next diagram?

 A=___________  T=___________  G=___________  C=___________ U= ____________

● What two sets of forces favor the formation of the double-stranded structure? _______________________________ ____________________ ___________________ _________________________________________ ____________________ ___________________ _________________________________________ ____________________ ___________________ _______________________

 

II.  Now, using Netscape 4.7x go to http://c4.cabrillo.edu/ and  access the Molecular Library 2.0 .  Select MacroViewer and 800x600. A new window will pop up. In the Select Model box at the upper left corner, select DNA. Manipulate the slide controls on the left to narrow the bond width, decrease the sphere size somewhat, and narrow the ribbon width. Then increase the hydrogen bond width slowly to the max setting and back. Describe what you see. ____________________

______________________ ______________________ __________________ _________________

● How can you tell the difference between a GC pair and an AT pair? ______________________ _______________________________________________________________________________

Next, select DNA and benzo{a}pyrene [an aromatic hydrocarbon] from the upper left-hand Select Model box. ● Where in the DNA is the benzopyrene located?   ____________________________. ● What effect does it have on the neighboring groups? [look closely and increase H-bond width] ______________________________________________________________________________________________________________________________________________________________

● What might be the result of this? _______________________________________________

Next, select zinc finger peptide. Do not change the display type [at least it’s not rotating!]  How many zinc fingers are shown? __________  ● With what part of the DNA molecule are they associated? ________________________. ● What do the Zn2+ ions look like? _______________ __________________________  ● How many amino acid side chains coordinate with each zinc ion? _________  From the box marked “Scripts” , select color CPK [red = O, blue = N, yellow = S] ● Identify the amino acids whose side chains coordinate with Zn: ______ _____ ______ ______.

 

III. Go to  http://www.umass.edu/molvis/freichsman/NucAcids/title.html  [USE NETSCAPE]

First, click on Nucleotide at the bottom of the screen. In the new screen that appears you will see a base pair in Chime with components labelled.  

● Which elements are represented by the following colors: 

Gray _________ White _________ Red __________ Blue _________ Orange _________

Go through the  ⊠’s in sequence.

● What are the components of a nucleotide? _____________  ______________  ______________

● Which two bases are shown? _________________ ___________________. 

● How many H-bonds join these bases? __________ .

Next, click on Double Helix at the bottom of the screen. When you get there, the first thing you’ll want to do is to stop the rotation by right-clicking on the molecule and UNchecking “Rotation” on the pop-up menu. Once again, go through the  ⊠’s in sequence. Restore the original picture when appropriate. When you click ⊠ Backbone Only, look carefully at the ends of the two strands to see which has the 5’ end showing and which has the 3’end showing [in this picture, neither end has a phosphate group on it]. ● Are the chains parallel or antiparallel? ______________________ 

 In the ⊠ Bases Only view, ● what generalization can you make about the orientation of the bases relative to the long axis of the molecule? _______________________________

__________________________________.  In the ⊠ H Bonds (zoom) picture, ● which base pair is joined by 2 H-bonds? _________  ● Which by 3 H-bonds? ____________. When you click the

⊠ One Strand , can you see how this strand can serve as the template for synthesis of the complementary strand? ____________________________________________

 

IV.  Go to  http://www.biosciences.bham.ac.uk/labs/minchin/tutorials/default.html and follow the links to the the tRNA tutorial and once again stop the rotation by right-clicking on the molecule and UNchecking “Rotationon the pop-up menu.. Proceed through the tutorial by clicking the ‘s in sequence. Put the molecule in an orientation where you will be able to observe the features being discussed.  Select wireframe and view the molecule from a number of angles. 

● Where is the backbone? ____________________________________ 

● Where are the bases? ____________________________________________________

Do you see any resemblance to DNA structure? What? _______________________________ 

What forces are responsible for the formation of this structure ?[see last answer in part I]

____________________ ____________________ ____________________ _________________

● Sketch the ribbon cartoon of the backbone in the space on the left below and label the anticodon loop and the acceptor stem, the D-loop and the TYC loop.

● Regions between loops are called ___________, and are stabilized by _____________________.

● In the space at the right below, sketch and label the “cloverleaf” structure shown in the tutorial.

 ribbon cartoon

 

cloverleaf structure

       
 

 

 

 

 

 

 

 

 

   Proceed to the DNA double helix tutorial and once again stop the rotation. Play with it a while. Make sure you can identify the major and minor grooves. Take a tour through the ‘s in sequence. You can also view the DNA animation if you like [the small version is actually better].

 

V. Using Netscape you can now go to
<http://www.chem.umass.edu/~cmartin/Courses/BioStruct/DNA/ABZCHIME/CHIME.htm>  
 [or you can try <http://www.tulane.edu/~biochem/nolan/lectures/rna/bzcomp2.htm> in a pinch] and follow the instructions to compare the structures of the A-, B-, and Z- forms of DNA. Alternatively, there is a site in Spanish at <http://www2.uah.es/biomodel/model1/dna/2frmcont.htm>  where you can make the same comparison.

Which of these three is the “normal” form of DNA? ______________

Briefly describe how the other two forms differ: ____________________ _______________________________________ _____________________ ____________________ ______________________________________ _____________________ ____________________ __________________

© Ronald W. Rinehart, 2002-2007