Question

In DNA, the bases are bonded to deoxyribose at the following positions (that is a hydrogen in the Figure below is replaced by \(\mathrm{C}-1\) of the sugar); adenine and guanine, \(\mathrm{NH}\) in the five-membered ring; cytosine and thymine, the lower NH. (a) Draw the structures to show likely hydrogen bonding between adenine and thymine; between guanine and cytosine, (b) Can you account for the fact that guanine and cytosine pairs hold the chains together more strongly than do adenine and thymine pairs?

Short answer

The hydrogen bonds between adenine (A) and thymine (T) are formed through two interactions: one between hydrogen attached to N6 of adenine and N3 of thymine, and another between the hydrogen in adenine's NH2 group and the O2 atom in thymine. Guanine (G) and cytosine (C) form three hydrogen bonds: one between the hydrogen of guanine's NH2 group and the O6 atom in cytosine, and two other bonds between the hydrogen attached to N4 of cytosine and two lone electron pairs in guanine's nitrogen atoms. The stronger bond between guanine and cytosine pairs is due to their formation of three hydrogen bonds, compared to only two hydrogen bonds between adenine and thymine pairs.

Step-by-step solution

(a) Drawing hydrogen bonding between adenine and thymine; and guanine and cytosine

First, we need to know the structures of the bases: adenine (A), thymine (T), guanine (G), and cytosine (C). The hydrogen bonds are formed between the nitrogen and oxygen atoms in these structures. Adenine and Thymine: 1. Adenine has an amino group (NH2) attached to its nitrogen (N1) and thymine has an oxygen (O) atom at a similar position (O2). 2. Adenine also has a nitrogen (N6) atom with a hydrogen atom attached to it, and thymine has a nitrogen atom (N3) with a lone electron pair. 3. There will be two hydrogen bonds formed between adenine and thymine. One bond is formed between the hydrogen attached to N6 of adenine and the nitrogen atom (N3) of thymine. Another bond is formed between the hydrogen of the amino group (NH2) in adenine and the oxygen (O2)atom in thymine. Guanine and Cytosine: 1. Guanine has an oxygen (O6) atom and an amino group (NH2) attached to its nitrogen (N1). 2. Cytosine has a nitrogen atom (N3) with a lone electron pair and a nitrogen atom (N4) with a hydrogen atom attached to it. 3. There will be three hydrogen bonds formed between guanine and cytosine. One bond is formed between the hydrogen of the amino group (NH2) in guanine and the oxygen (O6) atom in cytosine. Two other bonds are formed between the hydrogen attached to N4 of cytosine and two available lone electron pairs in the nitrogen atoms of guanine.

(b) Explaining the stronger bond between guanine and cytosine pairs

The guanine and cytosine pairs hold the chains together more strongly than the adenine and thymine pairs because there are more hydrogen bonds between them. While adenine and thymine only form two hydrogen bonds, guanine and cytosine can form three hydrogen bonds. More hydrogen bonds lead to stronger interactions between the bases, and thus stronger binding between the DNA strands.

Key concepts

Hydrogen Bonding in DNA

The structure of DNA features a double helix made up of two complementary strands. Central to the stability of this double helix structure is hydrogen bonding, a weak bond essential for DNA's function. Hydrogen atoms attached to strongly electronegative atoms like nitrogen or oxygen have a partial positive charge, making them attractive to other electronegative atoms with available lone electron pairs.

Each base pair in DNA is connected by hydrogen bonds, which, while individually weak, collectively confer considerable stability to the DNA structure due to their sheer number. These hydrogen bonds allow for the DNA strands to separate during replication and transcription in a controlled manner, enabling crucial biological processes such as protein synthesis and cell division.

Improving the reliability of understanding for these hydrogen bonds can be facilitated by visualizing the DNA strands split apart, highlighting the individual bonds between the bases, thus providing a more concrete grasp of how these interactions underpin the helical DNA structure.

Adenine and Thymine Pairing

In DNA, adenine (A) pairs with thymine (T) through two specific hydrogen bonds. The pairing process is like a dance—specifically a tango of molecules. Adenine, with its amino group and an adjacent nitrogen atom, offers a hydrogen atom and an electron pair 'hand' to thymine. In response, thymine extends an oxygen atom with a lone pair of electrons and a nitrogen atom, ready to connect.

• The first bond is between the hydrogen on the N6 atom of adenine and the N3 atom of thymine.
• The second bond links the hydrogen of the NH2 group in adenine with the O2 atom in thymine.

Understanding this precise arrangement reinforces the fidelity of DNA replication. Students may benefit from mnemonics or visual aids that depict the nitrogen and oxygen atoms like puzzle pieces, fitting neatly together only when the correct base partners are aligned.

Guanine and Cytosine Pairing

The partnership between guanine (G) and cytosine (C) is marked by not just two, but three hydrogen bonds, which make their association notably stable. Consider this trio of hydrogen bonds as a firm handshake, ensuring that the guanine and cytosine do not easily part.

• The first hydrogen bond is between the O6 atom in guanine and the NH2 group in cytosine.
• The other two bonds are formed between the hydrogen attached to N4 of cytosine and the lone electron pairs on the nitrogen atoms of guanine.

This treble of connections translates to a stronger bond, which helps explain why regions rich in G-C content exhibit higher stability and a higher melting temperature. For learners, creating models or animations showing the three bonds might provide a clear and helpful visual, enhancing comprehension of why G-C pairs are so robust compared to A-T pairs.