Amino Acids and DNA

Let's do an easy one, shall we? Ok! Here's the question:

The cDNA fragment that includes the ricin gene is 5.7 kilobases. If the entire fragment codes for the ricen polypeptide,the approximate number of amino acids in the poly peptide would be: (enter some weird numbers with lots of zeros here).

Well, once again the GRE just loves trying to confuse people with scary names and things. In this case, it throws in that whole ricin thing to throw you off. You can really just take that out of this question, so it reads something like "The cDNA fragment is 5.7 kilobases. How many amino acids does this code for?"

Alright, this is another one of those you-have-to-know-it questions. How much DNA does it take to code for a single amino acid? First, some very basic background. Amino acids are the building blocks of protein, and really what DNA codes for. Remember when we talked about DNA? DNA strands are studded with genes. Genes are simply lengths of DNA that code for certain proteins. Since the lengths of DNA make proteins, parts of the genes must code for the building blocks of proteins, or amino acids.

The next logical question is what percentage of each length of DNA codes for each amino acid? Ok, I'll just tell you: 3 base pairs. Yep, that's it. 3. Once you know how many base pairs are in a gene, then you just divide by three and that gives you the number of amino acids the gene codes for. How many base pairs are in the gene the question is asking about? 5.7 kilobases. Once again, don't be afraid of words here. "Kilo" simply means 1000, while "bases" means, well, bases. So 5.7 kilobases is 5700 bases or base pairs. Divide that by three, and you get the nice round number of 1900. There you go!

How DNA moves through a electrophoretic gel

Well, I'm sitting at a conference at the moment, and have decided that it has been too long since I have indulged in the joy of biological teaching. Seriously! Stop laughing. Here's the question I randomly chose for today:

The rate at which a DNA fragment moves in an electrophoretic gel is primarily a function of the fragment's....

Isn't it lucky that I totally by accident chose a question that can be answered pretty quickly? I know! Lucky! Anyhow, let me tell you a little about electrophoresis. This process is a step used in laboratories to study DNA, and is often taught in every single lab class in college simply because it's rather simple and rather impressive. (Seriously--try this the next time you're having dinner with your family "So I was studying deoxyribonucleic acid the other day, and needed to separate the fragments after I broke the bonds at known gene sites, so I simply ran an electrophoretic gel." This is good for at least an extra helping of dessert and hours of proud bragging by your mom at the next knitting circle).

Well, how exactly does this work? DNA, as you might imagine, is huge. Think about the amazinhg amount of information stored in the genetic code--all that information just sitting there waiting to be expressed. When we study DNA, we usually want to study a particular section, or a particular gene. We do this by cutting the big string of DNA into fragments using enzymes. We then copy the DNA (lots and lots and lots through PCR which I'll explain in a later post) and then somehow have to pick out the genes we want to focus upon.

This is where electrophoresis comes in. An electrophoretic gel is basically really stiff Jell-O. The gel is melted and poured into a rectangular mold, and 8 (or so) wells are formed in one end of the solidified gel. These wells give us a place to put the DNA. Now, DNA has a charge. Due to it's chemical make up and all that jazz, it has a an overall negative charge. At this point, we want to separate the DNA into its different fragments, so some smarty somewhere decided to use that overall negative charge to do just this. The gel (with its wells filled to the brim with DNA in a liquid medium) is subjected to an electrical current. The DNA fragments are pulled through the pores of the gel as it is attracted to the positively charged energy at the far end of the gel.

Now, the DNA separates depending upon its size. The bigger the DNA fragment, the harder it is to force it through those tiny, tiny pores in the solid gel. Therefore, the bigger (or longer) the DNA fragment, the more slowly it moves through the gel. After a predetermined amount of time, the electrical current is removed, and the gel is stained with some horrible substance that causes DNA to glow under a black light. You then take a picture of the gel and look at the bands (see the picture above) and the ones that are furthest away from the wells are the shortest, while the ones closest to the wells are the longest.

So, back to the question:

The rate at which a DNA fragment moves in an electrophoretic gel is primarily a function of the fragment's:
A) Length
B) double helical structure
C) Radioactivity
D) Degree of methylation
E) Adenine content

Can you pick out the correct answer now? Movement through an electrophoretic gel is strictly due to size, therefore the answer is "A."

DNA Replication (i.e. Base Pair Porn!)

Could I come up with a more boring title? I don't think so! But how in the world do you write something interesting about how DNA copies itself? Maybe "base pair porn!" That would totally work! I'm putting that now...hee for me! Anyhow, on to today's question!

When DNA replicates semi conservatively, which of the following is true of each daughter DNA molecule?

A) Both strands are newly synthesized
B) One strand is newly synthesized, whereas the other is a strand from the parent DNA molecule
C) Both strands are the original strands of the parent molecule
D) One strand has more AT-rich regions than the other strand has
E) The newly synthesized strands are more susceptible to melting and renaturation than the parental DNA strands are

Ok, the big question in this question is "What is semi conservative replication?"

Remember that blog I did about complimentary base pairing? Yeah, me too! That was a good one. Sigh. Well, this is sort of a continuation of that last post. When DNA needs to copy itself, it undergoes replication. There are three methods the books talk about when discussing DNA replication: conservative, dispersive, and semi conservative.

Conservative DNA replication is when an entirely new double helix of DNA is replicated for the new (or daughter) cell. This works just like a copy machine--it's based on the mother cell's dna, and an exact copy is made. The two new strands are what are sent on to the daughter cell, while the strands they were copied from are left in the mother cell. This method of DNA replication has not been found to be biologically significant, so most people don't really care about it. And neither do we!

Dispersive replication is when bits and pieces of the mother strands are mixed up with new sections and all put together into a new double helix. The two daughter cells end up with a strange mix-and-match version of the DNA made up of both mother and daughter sections. Just like the last one, no one thinks this is a biologically significant method of replication.

Finally, the big one: semiconservative replication. This is the main way DNA is totally replicated during cell division. During this type of replication, the entire DNA double helix unzips. A new strand is made to match up with each original strand using complimentary base pairing. The result is two double helices where only one was before. Each double helix is made up of an old strand of DNA (the mother strand) and a new strand of DNA (the daughter strand). Each new daughter cell gets a double helix of DNA--one strand from the mother cell and one brand-spankin'-new strand. This is the only replication method of the three that is considered biologically significant (meaning, this is what we care about!)

Ok, back to the question:

When DNA replicates semi conservatively, which of the following is true of each daughter DNA molecule?

A) Both strands are newly synthesized
B) One strand is newly synthesized, whereas the other is a strand from the parent DNA molecule
C) Both strands are the original strands of the parent molecule
D) One strand has more AT-rich regions than the other strand has
E) The newly synthesized strands are more susceptible to melting and renaturation than the parental DNA strands are

Let's go through the answers. "A" is obviously incorrect, since we just learned that when both strands of a double helix are newly synthesized, that is called conservative replication. "C" is also wrong, because if both strands were of the parent molecule, no replication would have happened at all....the DNA would have just moved from one cell to another. "D" just doesn't make much sense. We know from complimentary base pairing, that each strand has exactly the same number of bases, so it's impossible for a semi conservatively replicated strand to have more AT regions than the other. "E" tries to throw you off by mentioning melting and renaturation, but we don't care about that.That leaves "B." This answer is the definition of semiconservative replication--one strand is newly synthesized, whereas the other is a strand from the parent DNA molecule.

There you go! Yay us!

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!