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:
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 “Rotation” on
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