What are the units used for the ideal gas law? How does Charle's law relate to breathing? What is the ideal gas law constant? How do you calculate the ideal gas law constant? How do you find density in the ideal gas law? The name of a nucleotide is the corresponding nucleoside name, followed by the word 'monophosphate,' 'diphosphate,' or 'triphosphate' to indicate the number of phosphate groups attached to the sugar. Click the button below to examine the structure of a nucleotide triphosphate.
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. As a result, for every hydrogen bond that is made when a base pair forms, a hydrogen bond with water is broken that was there before the base pair formed. Thust the net energetic contribution of hydrogen bonds to the stability of the double helix would appear to be modest. 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.
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. But why can't you swap which purine bonds with which pyrimidine? The answer has to do with hydrogen bonding that connects the bases and stabilizes the DNA molecule.
The only pairs that can create hydrogen bonds in that space are adenine with thymine and cytosine with guanine. A and T form two hydrogen bonds while C and G form three. It's these hydrogen bonds that join the two strands and stabilize the molecule, which allows it to form the ladder-like double helix. Knowing this rule, you can figure out the complementary strand to a single DNA strand based only on the base pair sequence. For example, let's say you know the sequence of one DNA strand that is as follows:.
It would be:. Elliot Walsh holds a B.
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