Answers to DNA Structure Questions

DNA Structure: http://dna.molviz.org

Set A (for ages 14 and older)

1. What is a "strand" of DNA? A long chain of "chain links", called "bases" or "nucleotides", held together by strong chemical bonds.
2. How many strands make up a DNA double helix? Two.
3. Each strand is made up of two zones or regions. One zone of each strand is made up of identical repeating units, while another zone is made up of differing units. What are these zones of each strand called? "Backbone" and "bases", respectively.
4. What holds one strand against the other in the double helix? The bases (chain links) form matched pairs. This pairing holds the strands together.

   The pairing is relatively weak, so one strand can be "peeled" away from the other without breaking either strand. (In chemical terminology, the pairing bonds are noncovalent hydrogen bonds, while the stronger bonds are covalent ones.)

5. How do cells make accurate copies of DNA? Cells make use of the pairing between bases to copy DNA. The two strands are separated. New bases are paired with the bases in each old strand, lining up along the old strand. The new bases are hooked together to form a new strand. This process is shown schematically when you press the Replicate button in section B. The Code.

   Thus, one DNA double helix becomes two. Each copy has one strand from the original, and one new strand. It may help to draw this!

6. When do cells duplicate their DNA? Every time a cell divides, its DNA must be duplicated because each cell must have a complete copy of all the genes.

   (Cells must divide as an organism grows, for example, as a fertilized egg cell grows into a baby, and when babies grow up. But some cells also continue to divide in adults to keep renewing tissues. Tissues like skin, blood cells (made in bone marrow), and the lining of your digestive tract are used up the fastest, so their cells divide the most often.)

7. What information is coded into DNA? The DNA in each organism (for example tree, insect, person, dog, or bacterium) contains plans for making all of its proteins.

   There are many thousands of kinds of proteins in each organism. Proteins are chains of building blocks called amino acids. The DNA specifies the order or sequence in which the amino acids must be hooked together for each protein. The complete DNA sequence for each protein is called a "gene".

8. What is a "codon"? A codon is three consecutive bases in a gene. Each codon codes for one amino acid in a protein.
9. What is "transcription" of DNA? The process of making a messenger RNA (mRNA) copy of a stand of DNA.
10. What is "translation" of DNA? The process of hooking amino acids together to make a protein, according to the sequence of codons in the messenger RNA.

    Translation requires transfer RNA's charged with their corresponding amino acids to translate the codons of the mRNA into amino acids.

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Set B (for ages 18 and older)

11. What are the four pairs of DNA bases that form in the double helix? AT, CG, GC, and TA.
12. How can A distinguish T from C? On the basis of the number and direction of hydrogen bonds T or C can form with A.

    Each base can form either two or three hydrogen bonds in a matched pair. The AT pair forms two, and the GC pair, three. However, when C is lined up against A, no hydrogen bonds can be formed (because donors do not line up with acceptors).

13. Which DNA double helix do you think would be harder to separate into two strands: DNA composed predominantly of AT base pairs, or of GC base pairs? Why? GC, because it has one more hydrogen bond per base pair.
14. What is a mutation? When a base is replaced by a different base.
15. The DNA double helix looks like a twisted ladder. What makes up each rung of the ladder? What holds the rungs together at the sides? Each rung is made of a base pair. and their attached sugar (deoxyribose) rings. The rungs are held together by the phosphates and sugars that make up the DNA "backbone".
16. Is there mostly empty space between the atoms in a DNA double helix? No.

    The "thin" and "thick" renderings show covalent bonds. These renderings hide the atoms so you can see the bonds clearly, and get a sense of the skeletal layout of DNA. In contrast, the "spacefill" rendering shows the way the atoms of DNA occupy space.

18. 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.

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Set C (for ages 20 and older)

19. 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.

20. 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.
21. 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.

22. How many kinds of 5-membered rings are in DNA? Three: the pentose ring, and the two 5-membered rings in the purines.
23. How many kinds of 6-membered rings are in DNA? Four: the 6 membered rings in each of the four bases.
24. 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.
25. 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.