Nucleic Acids and Protein Synthesis: Question 7
Syllabus 6.1
A biochemist is investigating how a single strand of DNA is built up from individual nucleotides, and then works out the sequence of the complementary strand.
(a) Describe how a phosphodiester bond is formed between two DNA nucleotides as a polynucleotide strand is built up, including the type of reaction involved and the small molecule produced. [3]
(b) A new nucleotide can only be added to one particular end of a growing DNA strand. State this end (in terms of 5' and 3'), and explain, in terms of the free hydroxyl group involved, why growth can only happen at this end. [2]
(c) One strand of a short DNA molecule has the sequence 5'-G C T A A C-3'. State the base sequence, written in the 5' to 3' direction, of the complementary strand of this DNA molecule. [2]
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Worked solution
Part (a): Forming a phosphodiester bond
Two DNA nucleotides are joined together by a condensation reaction: the phosphate group of one nucleotide reacts with the deoxyribose (pentose sugar) of the next nucleotide, forming a covalent phosphodiester bond between them. As with other condensation reactions in biology, this bond formation releases a small molecule, one molecule of water, as a by-product. Repeating this reaction, nucleotide after nucleotide, builds up the sugar-phosphate backbone of a polynucleotide strand, with the nitrogenous bases projecting out to the side.
Part (b): Direction of strand growth
Each deoxyribose sugar has a free hydroxyl group on its 3’ carbon (once the phosphate at the 5’ carbon of that same nucleotide is already linked into the chain). A new nucleotide can only be added at the 3’ end of the growing strand, because it is this free 3’-OH group that reacts with the phosphate group of the incoming nucleotide to form the next phosphodiester bond. There is no free reactive group of the right kind at the 5’ end of the growing strand for a new nucleotide to attach to, so the strand can only be extended at its 3’ end. Meaning a polynucleotide strand is always synthesised in the 5’ to 3’ direction.
Part (c): Finding the complementary strand
The complementary strand pairs with the given strand by complementary base pairing (adenine with thymine, guanine with cytosine) and runs antiparallel to it. Aligning each base of the given strand (read 5’ to 3’) with its complementary partner, directly opposite:
| Given strand (5’→3’) | G | C | T | A | A | C |
|---|---|---|---|---|---|---|
| Complementary strand (3’→5’) | C | G | A | T | T | G |
Because the two strands are antiparallel, the complementary strand’s 3’ end lines up with the given strand’s 5’ end, and its 5’ end lines up with the given strand’s 3’ end. Reading the complementary strand in its own 5’ to 3’ direction therefore means reversing the row above:
5’-G T T A G C-3’
Final answers
- (a) A condensation reaction joins the phosphate of one nucleotide to the sugar of the next, forming a phosphodiester bond and releasing a water molecule.
- (b) Growth occurs at the 3’ end, because the free 3’-OH group there reacts with the phosphate of the next nucleotide.
- (c) Complementary strand (5’ to 3’): G T T A G C.