Answers to Dna Structure Questions

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One base pair is not in position to form normal Watson-Crick hydrogen bonds. Can you find it? (Note: Clicking on any base in D. Ends, Antiparallelism reports its letter and sequence number at the bottom of the browser window in the status line, following the word "Group". Use this feature to obtain the letters and sequence numbers of the abnormal base pair, once you find it.) G11 and C28.

This is an error in the crystallographic data file. The authors had no reason to believe this base pair to be mis-aligned, but the software they used to model the atomic positions made this mistake, and they did not notice it. Scientists make mistakes now and then just like everyone else, and not everything published in scientific journals is correct!

How do proteins recognize specific sequences of DNA? Proteins typically recognize specific sequences of bases from the patterns of hydrogen bond donors and acceptors on the sides of the bases, which are exposed in the major groove of the DNA.

Some proteins can also recognize bases in the minor groove, which often involves bending the DNA to widen the minor groove at the contact point. Here is an animated example showing recognition in both major and minor grooves..

Set C (for ages 20 and older)

Which bases are purines? Pyrimidines? A and G are purines; T and C are pyrimidines.

"UC (you see) the pyramids" helps you remember this, if you remember that in RNA, U's replace the T's in DNA.

If a purine were substituted for a pyrimidine at a single position in one strand of a DNA double helix, what would happen? Such a mutation would cause a mismatched base pair. In addition, because purines are larger than pyrimidines, it would cause a bulge in the double helix because the new purine would not fit opposite the purine on the other strand.

In a DNA double helix, why doesn't an A or T form two hydrogen bonds (out of the three possible) with C or G? The middle hydrogen bonds run in opposite directions. In the middle bond, T donates a hydrogen to an acceptor on A. C does not have a hydrogen to donate in the middle position; rather, it accepts a hydrogen from G's middle position.

The same is true of the "third hydrogen bond" (the one that is absent in an A-T pair). T has no hydrogen to donate to the acceptor on G in the third position.

How many kinds of 5-membered rings are in DNA? Three: the pentose ring, and the two 5-membered rings in the purines.

How many kinds of 6-membered rings are in DNA? Four: the 6 membered rings in each of the four bases.

Does the "free arm" of deoxyribose (the carbon that is not a member of the pentose ring) point in the direction in which the coding strand is read, or against it? The "free arm" is the 5' carbon of deoxyribose. It defines the 5' or first end to be read (and synthesized). Hence it points against the reading direction.

Based on the codons shown (in the Codons animation in section B. The Code), is the DNA strand shown the template strand or the coding strand? The template strand. For more information, see the explanation of this animation at Codons and Anti-Codons.