DNA Structure
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DNA Structure

Let's look at the structure of deoxyribonucleic acid. There are a number of similarities between the structure of DNA and the structure of RNA.

Again, there is a phosphate sugar backbone to which are attached the bases, and again the phospho diester links the third carbon of one sugar molecule with the fifth carbon of the next sugar molecule. And, again, the bases are attached to the first carbon of the sugar molecule.

There are some important differences, however. One is that the sugar is deoxyribose instead of ribose, there is no OH on the second carbon atom. In addition, the bases would include thymine instead of uracil (along with adenine, cytosine, and guanine).

Structure of DNA segment. [69027a.jpg]

Another important difference between DNA and RNA is that the DNA polynucleotide chains tend to pair up with one another and form double strands. These double strands then tend to twine together in what is usually referred to as the double-helix.

 

DNA-RNA Comparison

Keep in mind both the similarities and the differences between the structures of DNA and RNA.

Comparison of DNA and RNA. [69033.jpg]

Both of these nucleic acids have a structure that involves a phosphate group bonded to a sugar bonded to a base, which comprises a nucleotide, and this nucleotide is bonded to another nucleotide which contains phosphate, a sugar, and a base, and this structure continues on and on and on. Both DNA and RNA have this in common and the mechanism by which those are bonded is that same and the bonding points are the same.

The differences include these: in RNA, the sugar is ribose and in DNA, the sugar is deoxy ribose. Three of the bases are the same but the fourth base is uracil in RNA and thymine in DNA. The RNA forms a single strand and the DNA forms a double strand.

Practice

Before going on the deal with the double-strand or double-helix of DNA, you should review the aspects of nucleic acid structure that we've dealt with so far. (These instructions are also given in Exercise 13 in your workbook.)  Find some diagrams of the structures of both RNA and DNA in your textbook or some other source. Copy a short segment of each structure. Then indicate and label the portions of that structure that represent the nucleotide units, the phosphate units, the sugar units, the base units. Then   identify the function of each oxygen atom in the ribose or deoxyribose unit. Take some time to do that, then continue with the lesson.

Complementary Bases

Let's focus on the match-ups that exist between the two strands of DNA. The match-ups are these: adenine matches with thymine (A-T) and cytosine matches with guanine (C-G). In each case, a purine base with two rings matches with a pyrimidine base with one ring. Also, the purine base with two hydrogen bonding sides matches up with the pyrimidine base that has two corresponding hydrogen bonding sites and the purine base that has three hydrogen bonding sites matches up with the corresponding pyrimidine base that has three corresponding hydrogen bonding sites. Both of those factors are important: the number of rings and the number of hydrogen bonding sites.

Those match-ups can be represented and diagramed in a variety of ways. In the diagrams that follow, only the bases are shown, not the sugars or phosphates. In both diagrams the single-ring pyrimidine is shown on the left and would be attached to deoxyribose using the H that sticks out to the left. The double-ring purine is shown on the right and would be attached to deoxyribose using the H that sticks out to the lower right. Note that in both cases the overall left-to-right dimensions are essentially the same.

Here we have the structures of thymine and adenine. Where the two molecules approach each other, the hydrogen atoms that stick out are next to either an oxygen atom or a nitrrogen atom in the neighboring molecule. This allows for two hydrogen bonds between these molecules.

Thymine - Adenine base pair. [TApair.jpg]

thymine adenine
This diagram shows the match-up between cytosine and guanine. Note that three hydrogen bonding sites exist between these two molecules. So you can see that there's a good match.

Cytosine - Guanine base pair. [CGpair.jpg]

cytosine guanine

So there you have the structural reasons for the match-up between T and A, C and G.

The heterocyclic base structures in your workbook can also be cut out (or traced) and used to show this same relationship (but note that you would have to turn over one of the structures in each pair to make them match). If you do work with those you can see that other combinations of these bases do not provide complementary matches for hydrogen bonding.

Layers of Structure

Like the proteins that we studied earlier, DNA molecules have several layers of structure. First of all, there is the sequence of nucleotides that we've just been looking at (primary structure). They bond together in a double-strand which twists into a double-helix (secondary structure). This double-helix then wraps around some proteins (tertiary structure) and then these coils wrap and fold around each other and this wrapping and folding continues until the chromosomes are formed which are sometimes visible in a microscope. You can see diagrams of these several layers of DNA structure in your textbook.

Another source of good diagrams and much additional information about the structure of DNA is the Biochemistry in 3D web site maintained by Worth Publishers as a supplement to an excellent Biochemistry text by Lehninger. You can find the site at http://www.worthpublishers.com/lehninger3d/index.html. When you get there, check out the tutorial on Nucleotides (Building Blocks of Nucleic Acids).

 

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E-mail instructor: Sue Eggling

Clackamas Community College
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