DNA and RNA Base Pairing

Today's subject involves the basics of DNA and RNA. Here's the question from the GRE practice test I'll be answering:

"The complementary RNA sequence for GATCAA is...." (and then there is a list of answers).

This is actually a simple question, provided you know a two key bits of information--1) What is RNA? 2) What the hell are all those letters? I'll tell you!

I'm sure by this time in your life, no matter what level of education you currently have stuffed into your pretty little brain, you have heard of DNA. DNA is the handy short-hand for deoxyribose nucleic acid, and is a double stranded helical structure found in the nucleus of eukaryotic cells. The
double helix resembles a ladder, with two parallel sides and pairs of bases that match up and form the rungs.

These "rungs" are called nucleotides, and are made up of a sugar (in the case of DNA, that sugar is dexoyribose), one phosphate group, and a nitrogenous base. That nitrogenous base is what we are interested in today. Don't let the phrase "nitrogenous base" scare you--this is just a way for biologists to sound smart when talking about something relatively simple. In this case, a nitrogenous base is simply a compound that contains nitrogen and happens to be basic. Easy, yes? Ok, so the rungs of the double helix are made of a pair of nitrogenous bases--two of these nitrogen containing bases that pair up.

There are four of these bases involved with DNA: Adenine (A), Thymine (T), Guanine (G), and Cytosine (C), and these bases follow a concept called complimentary base pairing. This fancy sounding process simply means that each base only pairs up with the one that is likes the best, or the one that compliments it: adenine pairs with thymine, and guanine pairs with cytosine. Biologists hate writing out the full name of things, so each of these bases is abbreviated down to the first letter of its name: A pairs with T, and G pairs with C--AT, GC.

When DNA replicates, the double helix unzips, and free-floating bases pair up with their partners to form new strands. If we know the sequence of bases on one strand, we can predict what the complimentary strand will look like using complimentary base pairing:

ATTTCGGA will pair up with the strand TAAAGCCT. See how that works? The bases pair up with their favorite, and form a new strand in the process. There's the basics!

Now, DNA doesn't just make copies of itself. On the contrary, it most of the time codes for proteins that build things or activate things or deactivate things, or do any number of jobs in the cell. In order to code for these proteins, the DNA needs to get its message to the rest of the cell. It does this via RNA

RNA stands for ribonucleic acid--it looks a heck of a lot like DNA, except it is made up of the sugar ribose instead of deoxyribose. RNA is the messenger unit of the cell. It's job is to take memos from DNA, and give that information to the rest of the cell. RNA gets its memos from DNA via complimentary base pairing. Who knew?! When DNA wants the cell to make a protein, it unzips that little portion of the double helix that codes for that protein, RNA zips in and makes a copy of the information using complimentary base pairing, and zips out again to take the information to the rest of the cell.

So how can we tell the difference between RNA and DNA? Well, other than the fact that RNA is made of ribose while DNA is made of deoxyribose, they also use slightly different nitrogenous bases. While DNA uses the bases adenine, thymine, guanine, and cytosine, RNA uses adenine, URACIL, guanine, and cytosine. In DNA, adenine pairs up with thymine (AT). In RNA, adenine pairs up with uracil (AU). Just think of it as if RNA can't seem to produce a T, so it has to produce something else to match up with A. So, if I were to ask you, say, what is complimentary RNA sequence for GATCAA, you would say CUAGUU. See how that works? Every time you see a "G" you match it up with "C." When you see a "T" you match it up with "A," and when you see an "A" you match it up with "U."

Back to the question:

The complementary RNA sequence for GATCAA is:

A) CTAGTT
B) CUAGUU
C) AGCTGG
D) AGCUGG
E) TCGACC

In this case, you can immediately knock out three of the answers. Since we know that RNA doesn't produce any T's, then we can get rid of A, C, and E. That leaves B and D to choose from. We are also familiar with the concept of complimentary base pairing, so we know that G always pairs with C, and A with T/U. This is one of those questions that I suggest answering before you look at the answers, then just scanning the answers for the one that matches what you came up with. In this case, the answer is "B."

Incidentally, as I was scanning through the GRE, I noticed another question along these same lines:

When DNA is extracted from cells of E. coli and analyzed for base composition, it is found that 38 percent of the bases are cytosine. What percentage of the bases are adenine?

Because we know about complimentary base pairing now, we can figure out this question pretty easily. I've noticed that the GRE likes trying to scare test-takers by saying things like "DNA is extracted from E. coli." Don't let them! DNA is DNA, and it doesn't matter what species it's extracted from, it is still made up of those same 4 bases. (Isn't that amazing, by the way? This is why I love biology!).

The question tells us that 38% of the bases were cytosine. We know cytosine pairs up with guanine, so another 38% must be guanine. (Think about this for a second--remember that both strands of the double helix were being analyzed here, so every instance of cytosine was counted. You don't find cytosine in DNA with it's best friend guanine, so if 38% were cytosine, then 38% had to be guanine). Ok, 38 + 38 = 76% of the DNA accounted for. What does that leave? 24% of the bases must be adenine and thymine. Since these guys are paired up equally, then half of that 24% must be adenine, and the other half thymine, therefore 12% of the bases are adenine and 12% thymine. Here's the question again:


When DNA is extracted from cells of E. coli and analyzed for base composition, it is found that 38 percent of the bases are cytosine. What percentage of the bases are adenine?

A) 12%
B) 24%
C) 38%
D) 62%
E) 76%

Do you see how annoying the answer writers of this test can be? They put in all the possible numbers you could come up with when figuring out this answer: 12% (the percentage of adenine in the DNA), 24% (the percentage of adenine and thymine together in the DNA), 38% (the percentage of cytosine or guanine) and 76% (the percentage of guanine and cytosine together). However, because you know the basics of complimentary base pairing you are able to figure out that the correct answer is "A." Good for you!