Why does adenine bond with thymine

Move your mouse over the structure of adenine to see its potential hydrogen bond donors and acceptors. Then click on the hydrogen bond donors and acceptors on the structure of cytosine. Shown at lower right are a paper structure and a ball and stick model of uracil U , another nucleotide which sometimes fits into the DNA double helix. Move your mouse over the structures to see their patterns of hydrogen bond donors and acceptors.

Which of the four nucleotides of DNA do you think uracil will pair with? What is the identity of the nucleotide triphosphate displayed in the computer model? Adenosine triphosphate ATP. Deoxyadenosine triphosphate dATP. Guanosine triphosphate GTP. Deoxyguanosine triphosphate dGTP. Thymidine triphosphate TTP. Click the button below to examine the structure of deoxyadenine monosphosphate dAMP. Notice the angle of the sugar and phosphate groups in relation to the planar nitrogenous base. In double-stranded DNA, two long molecules twist around one another in a double helix.

These molecules are d eoxy n ucleic a cids DNA : polymers made up of nucleotides In a DNA double helix, the phosphate and sugar groups make up the outer 'backbones,' and the flat nitrogenous bases are pointed toward the middle of the helix.

Click the buttons below to examine a segment of a DNA double helix from many angles. The first button has colored the backbone sugar and phosphate groups purple to simplify the image. One key point to notice in the DNA double helix structure is that the planar nitrogenous bases from the two strands are pointing toward each other, in the middle of the helix.

Pairs of nitrogenous bases are set in the same plane, and interact with each other via hydrogen bonding. These pairs are often referred to as base pairs , abbreviated 'bp. Recall that electronegativity values generally increase toward the top and right of the periodic table, as illustrated in the image below. However, when polynucleotide strands are separate, water molecules are lined up on the bases. 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. Narahari Sastry. Cooperativity in Noncovalent Interactions.

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