Session 4 -- Page 4
July 7, 2000


DNA

DNA, which stands for deoxyribonucleic acid, is the prime informational polymer of most organisms. DNA's are, in one way, much simpler molecules than proteins. Instead of being composed of the 20 different kinds of monomers that make up proteins, DNA is comprised of only four kinds of units. These building blocks are called nucleotides, and the structure of one (A) is pictured below.

Notice that the monomers are rather similar to one another. At first glance, they also appear a bit more complex than most of the monomers found in proteins. But this complexity is more apparent than real. Nucleotides are composed of only three parts: an acid group (different than the acid group in amino acids in that it carries a phosphorous atom, the yellow one in the middle),

a sugar (called deoxyribose),

and a ring structure called a base.

The four nucleotides are identical to one another in their sugar and acid components. They only differ in which base they carry. The four bases (called A, C, G, and T) come in two sizes: large and small. A and G are the large ones; and C and T, the small (for those of you who are sticklers for nomenclature, A stands for adenine, C for cytosine, G for guanine, and T for thymine. I'll refer to them simply by their one letter designations here, and in subsequent sessions).

In a DNA polymer, the phosphorous-containing acid group of one nucleotide forms a strong bond with the sugar of the next monomer. The base is not involved in this bond and it sticks out, somewhat as the side chain of amino acids sticks out from the peptide bond. The result of attaching one nucleotide to another is a dinucleotide.

More nucleotides can be added, and this process can be continued indefinitely to produce very long chains. As a first approximation, these chains can be thought of as half of a ladder with a series of half rungs extended out from a leg. The leg of the ladder is made up of the sugar and phosphates linked together, and the half rungs are the bases sticking out. In this analogy, the large bases stick out a lot, and the small bases a little. Another polymer of DNA can saddle up to the first, and the two half rungs can interact via hydrogen bonds to produce a complete double-legged ladder as shown. What is actually produced, of course, is a double-stranded molecule, two polymers closely associated with one another.

Actually, this ladder-like arrangement is somewhat of a simplification. The legs of the ladder are not straight; they actually assume a coiled, spring-like configuration and intertwine with one another. The result is the well known DNA double-helix pictured below.

Directionality

There are two further aspects of this picture that are important to note. First, keep in mind that each of the two legs of the ladder has a directionality (remember the beads and elephants in an earlier class?). It turns out that the two legs are always arranged so that one strand heads in one direction, and the other in the opposite.

Complementarity

A second complication has to with the pairing of the two polymers that make up each ladder. In order for the two ladder to form properly, the rungs -- the bases -- must be of appropriate size and character. For example, it is impossible for a long rung (A or G) on one leg to match up properly with a molecule also containing a long rung at the same position on the other leg. Thus an A on one strand never is matched with a G or an A on the other. Similarly, two short half rungs on opposite strands won't interact properly to form a complete rung. And even when a short rung is opposite a long one, only one possible pairing works properly: an A bonds well with a T, and a G with a C; no other matches are allowed. (The picture above shows a closeup of two nucleotides on opposite strands. The one on the right is a G and the one on the left a C.). One consequence of this pairing is that the DNA double helix has a uniform diameter throughout its length. The bonds formed across the rungs are, by the way, hydrogen bonds, and you can easily see the three hydrogen atoms that comprise these bonds.

This property, where the presence of one nucleotide on a strand dictates which one (and only one) of the three other nucleotides is positioned on the opposite strand is called complementarity or base pairing. We will keep referring back to DNA base pairing throughout the rest of the summer. It is a very important principle.

Size

Finally, it should be noted that DNA is a polymer that can reach immense lengths. Molecules that are millions, tens of millions, even hundreds of millions of nucleotides long are known. What is truly mind boggling is the fact that even molecules of the longest size possess a specific sequence of monomers. For example, a molecule of DNA that is 150 million base pairs long (one that has 150 million monomers on each of two strands) in one of our skin cells, for example, will have a specific sequence of A's, C's, G's and T's reading from one end to the other. As we'll see later in the course, there are almost fifty of these polymers in each of the several trillion cells in our bodies, each molecule with its own distinct sequence.

The Role of DNA

We'll have more to say about what DNA does and how it does it in later sessions. For now, we will only hint at DNA's function by stating that the sequence of nucleotides that we alluded to above comprises the set of instructions that tell organisms how they are to be assembled and how they are to operate.

RNA

RNA is very similar in structure to DNA. Both classes of polymers are polynucleotides (another term that you will often come across is "nucleic acids") meaning that they are polymers composed of nucleotide monomers. As in DNA, the nucleotides of RNA are linked by phosphate acid groups in one unit to sugar groups in another.

However, there are some differences between DNA and RNA. For one thing, RNA carries one base that is different from DNA. It doesn't have any T's. Instead, RNA has U's in their place (the U stands for uracil, incidentally). For another, the sugar in the two polymers is different: RNA substitutes ribose for deoxyribose. (The pictures below are of the two sugars plus a phosphate attached to one of the carbons. They illustrate the difference between the two sugars. Ribose has an additional oxygen atom. Which one is it?)

And finally, RNA can't form the beautifully regular double helical structures that DNA most often does. In fact, a typical RNA molecule is composed of only a single strand. However, many RNAs are capable of folding back upon themselves, with complementary parts base pairing with each other.

The Role of RNA

RNA plays two roles, both of which we will expand upon in later sessions: It can act like a protein and participate in the machinery of the cell. Or, more commonly, it can serve as an intermediary in the process by which the information in DNA is translated into elements that play a role in the cell.

Summary

Proteins

DNA

RNA

Some molecules of RNA carry information; others perform functions similar to those of proteins.