This means their structure is a nitrogen-containing six atom ring joined with a nitrogen-containing five atom ring that share two atoms to combine the two rings. Thymine and cytosine are examples of pyrimidine bases.
These bases are made up of a single nitrogen-containing six atom ring. Chargaff's rule, also known as the complementary base pairing rule, states that DNA base pairs are always adenine with thymine A-T and cytosine with guanine C-G.
A purine always pairs with a pyrimidine and vice versa. However, A doesn't pair with C, despite that being a purine and a pyrimidine. This rule is named after the scientist Erwin Chargaff who discovered that there are essentially equal concentrations of adenine and thymine as well as guanine and cytosine within almost all DNA molecules.
These ratios can vary between organisms, but the actual concentrations of A are always essentially equal to T and same with G and C. For example, in humans, there's approximately:. It has to do both with the hydrogen bonding that joins the complementary DNA strands along with the available space between the two strands.
Two purines and two pyrimidines together would simply take up too much space to be able to fit in the space between the two strands. This is why A cannot bond with G and C cannot bond with T. When strands come together in the double helix, the water molecules are displaced from the bases.
This creates disorder and increases entropy, thereby stabilizing the double helix. Hydrogen bonds are not the only force that stabilizes the double helix. A second important contribution comes from stacking interactions between the bases. The bases are flat, relatively water-insoluble molecules, and they tend to stack above each other roughly perpendicular to the direction of the helical axis.
Electron cloud interactions it— tr between bases in the helical stacks contribute significantly to the stability of the double helix. Hydrogen bonding is also important for the specificity of base pairing. Suppose we tried to pair an adenine with a cytosine. Then we would have a hydrogen bond acceptor Nl of adenine lying opposite a hydrogen bond acceptor N3 of cytosine with no room to put a water molecule in between to satisfy the two acceptors Figure , Likewise, two hydrogen bond donors, the NH; groups at C6 of adenine and C4 of cytosine, would lie opposite each other.
Thus, an A:C base pair would be unstable because water would have to be stripped off the donor and acceptor groups without restoring the hydrogen bond formed within the base pair. As we have seen, the energetics of the double helix favor the pairing of each base on one polynucleotide strand with the complementary base on the other strand. Sometimes, however, individual bases can protrude from the double helix in a remarkable phenomenon known as base flipping shown in Figure 6-B.
As we shall see in Chapter 9, certain enzymes that methylate bases or remove damaged bases do so with the base in an extra-helical configuration in which it is flipped out from the double helix, enabling the base to sit in the catalytic cavity of the enzyme.
Furthermore, enzymes involved in homologous recombination and DNA repair are believed to scan DNA for homology or lesions by flipping out one base after another. This is not energetically expensive because only one base is Hipped out at a time. Clearly, DNA is more flexible than might be assumed at first glance. Remember: Hydrogen bond donors are only those H atoms bound to an electronegative atom such as N or O. Hydrogen bond acceptors are electronegative atoms with at least one lone pair of electrons.
Also notice that potential hydrogen bond donors and acceptors close to the sugar R group are ignored in the image above.
This is because those parts of the nitrogenous base close to the sugar-phosphate backbone will be unavailable for hydrogen bonding with the other base in the pair. Let's examine a single guanine residue to identify potential hydrogen bond donors and acceptors. Guanine will be highlighted in yellow , and the attached sugar and phosphate in the backbone will blink purple.
Keeping in mind the point of sugar attachment, we can identify guanine's hydrogen bond donors and acceptors that are available to interact with a paired nitrogenous base.
Locate these parts of the molecule yourself, then click the button below to see the relevant atoms blink yellow. Which of the following statements best describes the hydrogen bonding potential in guanine? Guanine has 3 H-bond donors. Guanine has 3 H-bond acceptors. Guanine has 2 H-bond acceptors and 1 H-bond donor. Guanine has 1 H-bond acceptor and 1 H-bond donor. Guanine has 1 H-bond acceptor and 2 H-bond donors.
Can you find one H-bond donor and 2 H-bond acceptors in cytosine? Examine the molecule yourself, then click the button below to see the relevant atoms blink green. For them to bond with each other would be chemically unfavorable. Why does adenine pair with thymine and not cytosine? Feb 11, The chemical structure of the molecules determine what they are most likely to pair with. I hope that helps!
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