IMAT 2018 Q30 [Double Stranded DNA]

A section of unmutated double-stranded DNA contains 100 nucleotides and 38% of these
nucleotides contain thymine.

Which one of the following correctly identifies the number of hydrogen (H) bonds and
phosphodiester bonds present in this section of DNA?

A. 138 H bonds present and 98 phosphodiester bonds present
B. 224 H bonds present and 98 phosphodiester bonds present
C. 112 H bonds present and 99 phosphodiester bonds present
D. 138 H bonds present and 99 phosphodiester bonds present
E. 112 H bonds present and 98 phosphodiester bonds present

The answer to this question is choice E

Let’s try to approach this in a step-by-step manner to be able to arrive at the answer:

Before we rationalize this question, it will be useful to be reminded of a few concepts:

  • Base pairing: Within DNA, Adenine pairs with Thymine, while Guanine pairs with Cytosine. For the sake of answering this question, we will be denoting them as A, T, G, and C, respectively. You also need to remember that in terms of proportion, it’s safe to assume that A = T, G = C since these base pairs are constant.
  • H Bonds: There are 2 hydrogen bonds that bind adenine and thymine, while there are 3 hydrogen bonds that bind guanine and cytosine.
  • Phosphodiester bonds: these are the bonds that connect 2 sugar molecules together within the DNA strand.

To solve the NUMBER OF H BONDS, you will need to find out the proportions of the nucleotides first:

  1. Total thymine= 38%
  2. T = 38% (and we know that A =T), therefore;
  3. A = 38%
  4. The total nucleotides therefore of A and T combined is = (38 x 2) = 76%
  5. So it would make sense that, (G and C combined) = Total Nucleotides MINUS (A and T combined)
  6. 100% - 76% = 24%, which means that there are 24% of nucleotides that are G and C (Note that, 100% is used as the value of ‘Total nucleotides’ since the values are expressed in terms of percentages.)
  7. Since we know that G = C, we can then divide that number by 2 = (24/2) = 12%
  8. This means that there are 38% A, 38% T, 12% G, and 12% C

How do we then solve the number of H bonds?

  1. Recall that there are 2 H bonds in between A - T, and 3 H bonds between G - C.
  2. The number of H bonds between A - T = 38 x 2 H bonds = 76 H bonds in total between all the A - T base pairs in the DNA sequence given.
  3. The number of H bonds between G - C = 12 x 3 H bonds = 36 H bonds in total between all the G - C base pairs in the DNA sequence given.
  4. If you add all of that, there will be 112 H bonds in total in the DNA sequence given, which leaves choice C and E in your considerations.
  5. You might be wondering, why did we use 38% and 12% instead of 76% and 24% in the calculations? Because if you used 76% and 24%, you are assuming that each base has its own H bonds without a corresponding base to bind it with! When in reality, nucleotides that base pair with each other SHARE THE H bonds. Thus, you will need to use 38% and 12% in your calculations.

How many phosphodiester bonds are there?

  • Recall that these bonds are the bonds that connect one sugar to another within the DNA strand.
  • Remember that this “double-stranded DNA” has 100 TOTAL nucleotides. Which means that each strand has 50 nucleotides!
  • If you can imagine, a strand with 50 nucleotides only has 49 phosphodiester bonds. (because the 2 ends of the strands do not need another phosphodiester bond.)
  • Thus, if you have 2 strands, that’s 49 phosphodiester bonds x 2 strands = 98 total phosphodiester bonds. This then leaves choice E as the only correct answer.