Category Archives: Biology GRE

Writings on the Biology GRE Subject Test

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!

Linktastic (Or: I’m feeling crappy so I can’t really write….)

Ok, so today was a cruddy day. Ever heard of endometriosis? Well, I have it all bad like, and I therefore spent most of today unconscious. Fun for me! Today’s post, therefore, is admittedly a bit phoned-in (I’m pretty sure the spelling is going to be bad, too). Here are some interesting links about things you should know about. Enjoy! I’ll be back when I’m feeling better.

How to take multiple choice tests
The GRE is multiple choice, after all, so knowing how to effectively manage a multiple choice test is critical.

What is endometriosis?
The stupidest, worstest, most horrible thing afflicting my lower abdomen at the moment. That’s what it is.

XKCD
Oh, man, is this a funny comic. Start at the beginning (his first ones are a bit strange–I think he was just doodling at first). They get really, really funny after awhile. Awesome!

The Rh factor and hemolytic disease of the newborn

This is how I’m going to structure things (at least until I figure out a better way or someone asks a question): I have gotten my hands on a variety of old GRE subject tests, and I have gone through them and read the questions. During my study groups, I have the students take practice tests and we go over the answers. I’m going to post one (or two or three) question(s) that are about a particular subject, then explain the concepts that are involved. How’s that? Good! Let’s get started.

Question: A homozygous, Rh-positive man (RR) marries an Rh-negative (rr) woman. Their first child is normal, but their second child has hemolytic disease (Rh disease). The first child did not have hemolytic disease because….

Alright–this questions is mostly about the Rh factor and its effect on the unborn child. First: the vocab of this question.

Homozygous–the condition of having two identical alleles for a particular gene
Rh-factor–a specific antigen present on the surface of the red blood cell
Hemolytic disease–a condition in which the red blood cells of an Rh-positive fetus or newborn are destroyed by anti-Rh antibodies previously produced in the bloodstream of an Rh-negative mother.

The first thing you need to do when reading a question about biology is to dissect the question itself. This questions has a lot of vocab and parenthesis that may cause confusion. Read the question at least twice to get at the real meat. The question introduces you to a couple with, now, two children. We learn the genotype (genetic makeup) of the parents: both are homozygous for the Rh-factor; dad is homozygous dominant for the Rh-factor, while mom is homozygous recessive.

The question is really testing your knowledge of red blood cells and the antigens present on the cells. An antigen is anything that causes an immune response. Every person has a blood type depending up on the glycoproteins (carbohydrates attached to proteins) attached to the red blood cell membrane. The lucky person who discovered these glycoproteins decided to give each type a letter: A or B. A person who has glycoprotein “A” on his blood cells has type A blood. A person who has glycoprotein “B” has type B blood. A person who has both glycoproteins on his blood cells has type AB blood, and a person with neither of these glycoproteins has type O blood.

What these blood types are missing is that “+” or “-” that you all see on your birth certificate. The positive or negative is called the Rh-factor, and either you have it or you don’t. “Rh” stands for rhesus, and was named for the rhesus monkey, which is where the protein was first noticed. This protein reacts just like the other glycoproteins on your blood cells–if your body recognizes the antigen (glycoprotein) then it will not attack it. If your body doesn’t recognize the antigen, then it will initiate the non specific and specific defenses to attack the perceived threat. If this was the first time your body saw the antigen, the non specific defenses would take care of the problem, while the specific defenses created antibodies to protect the body from future invasions. (Well, actually it’s a bit more complicated than that, but I’ll go into the intricacies of immuno-defense in a later post).

Your blood type becomes important when you need blood from a donor, or you are donating blood to someone who needs it. In the case of an emergency, hospitals use type 0- blood, since these red blood cells have no antigens on them at all, any person will accept this blood into his veins without triggering the immune system. This same idea applies to the transfer of blood from mother to child.

During most of pregnancy, the fetal circulatory system is closed off from the mother’s circulatory system. The fetus produces its own red blood cells, which accept oxygen and nutrients from the mother’s blood stream via capillaries in the placenta. The mother’s red blood cells do not cross over to the fetus, and the fetus’s red blood cells do not cross into the mother’s blood stream. During the trauma of birth, however, blood exchange happens. This usually isn’t that big of a deal, however. Even if the baby’s blood type is different from the mom’s, mom’s immune system will take care of any foreign blood cells quickly (and produce antibodies against future invasion from these blood cells). A problem arises only during the second pregnancy and in relation to the Rh-factor.

If mom is Rh-positive, it doesn’t matter what her child is (Rh-negative or Rh-positive) her body will not react to the child’s blood during birth. Her immune system will recognize the Rh protein, and therefore not attack a cell that is Rh positive. If it encounters a cell without the Rh-factor, it won’t recognize the cell as foreign because it is the protein present on the cell’s membrane that identifies it as foreign. If there’s no protein, there’s no problem. However, if mom is Rh-negative, her body will recognize any Rh-positive blood cell as foreign, and activate her immune system accordingly. The Rh-factor is passed on via normal Mendelian genetics, with Rh-positive being dominant and Rh-negative being recessive. Therefore, it is possible to determine the possible genotypes of the child in regards to the Rh-factor using a simple Punnett square.

R R
__________________

r Rr Rr

__________________

r Rr Rr

__________________

If mom is Rh-negative, as she is in this GRE question, then her first pregnancy will proceed normally. No matter what the blood type of her baby, her blood won’t come in contact with the baby’s blood cells (and therefore any possible antigens) until birth. After birth, the baby is pretty much safe from any antibodies mom’s immune system produces. The problem arises when mom and dad want to give junior a little brother or sister. If mom is Rh-negative and bundle-of-joy #1 is Rh-positive, mom’s immune system gets exposed to the Rh antigen. Her immune system reacts accordingly, destroying the perceived threat, and producing antibodies to protect her against future invasions. If bundle-of-joy #2 is also Rh-positive, mom is already primed and ready to kill off any Rh proteins she sees. Red blood cells don’t cross over the placental barrier, but antibodies do. Can you see the problem? Mom’s antibodies attack the fetus’s red blood cells, causing the fetus to die from lack of oxygen and nutrients, or causing the baby to be born severely anemic. This condition is called “hemolytic disease of the newborn.” Look familiar? Yep! This is the disease to which the question is referring.

So, now that we know the basics, let’s get back to the question:

A homozygous Rh-positive man marries an Rh-negative woman. Their first child is normal, but their second child has hemolytic disease.

This part makes sense, doesn’t it? We know the genotype of both mom and dad, so we can use a Punnett square to predict all the possible genotypes of the children: Rr, Rr, Rr, and Rr.

It appears that all the children will be heterozygous for Rh-positive. Now, we know that there may be a problem between an Rh-negative mother and an Rh-positive fetus due to mom’s immune system. However, mom’s immune system is not exposed to the Rh antigen until the moment of the first baby’s birth, so baby #1 is protected. When mom gets pregnant again, though, the child is afflicted by hemolytic disease. “Hemo” refers to blood, while “lytic” refers to bursting; “hemolytic” is the bursting of red blood cells. Bad! This occurs because mom’s immune system is primed and ready to kill off the Rh-antigen the moment it sees it, so baby #2 is attacked as soon as he begins to make red blood cells.

Good! So there is the main concept behind the question. Let’s get to the actual question part, though:

The first child did not have hemolytic disease because….

Well, can you answer the question? Yep, the first child didn’t have hemolytic disease because mom’s immune system had not yet been exposed to the Rh-antigen and therefore did not have any antibodies capable of crossing the placental barrier and attacking the fetus’s red blood cells.

Here are the multiple choice answers given to this question:

A) the child was heterozygous (Rr)
B) the child lacked the Rh antigens
C) the mother had a previous blood transfusion that protected the child against antibodies
D) anti-Rh antibodies present in the mother were destroyed by the child’s immune system
E) anti-Rh antibodies were not induced in the mother until the delivery of the child

So, given what we know, the answer to this question is E. Yes, the child was heterozygous (Rr), but this does not answer the question, and is not the reason the child did not have hemolytic disease. Because the child was Rr, we know he had the Rh antigens (remember Rh-positive is the dominant trait), so answer B doesn’t even make sense. Answer “C” just seems ridiculous to me, and hopefully to you, too. Blood transfusions don’t change the mom’s immune system, nor what diseases she is protected against. A blood transfusion is primarily used to ensure the presence of adequate red blood cells and blood volume in the circulatory system. It has nothing to do with protecting a fetus against antibodies. The growing fetus is still building its immune system, so he must rely on mom for protection and immunity. He doesn’t yet have the capacity to fight off foreign cells, so he has no defense against mom’s antibodies. Therefore, option “E” is the correct answer!

How is it, then, that Rh-negative moms have more than one child? Why aren’t they all still born? Scientists attacked the problem of hemolytic disease some time ago. One of the first questions a doctor asks a pregnant couple is their blood types. If mom is Rh-negative and dad is Rh-positive, then during the birth (or soon thereafter) mom will be injected with a serum named RhoGAM, which contains antibodies against the Rh antigen. This serum takes care of any Rh-positive red blood cells circulating in mom’s blood, so her immune system doesn’t have the chance to get all annoyed. She doesn’t make any of her own antibodies against the Rh antigen, and her future children are protected.

Questions? Comments? I hope this helped!

Ah, the GRE!


Well, kiddies, it’s that time of year again. Now that the seniors have walked off our intrepid campus and into the sunset, the juniors begin to plan their (hopefully) final year at school. Whether you are finishing up four years of high school or 7 years of graduate school, if you want to go on for an even higher degree then you have the unsurpassed pleasure of sitting for a variety of standardized tests. Lucky you! The problem is this: many great schools use your GRE scores as a way to weed out the slackers from the future Einsteins (well, Einstein was really bad at standardized tests–so maybe not future Einsteins…maybe Bill Gates? Nope, bad at tests, too…Ok, future moderate-highly paid managers of large already established businesses). There is a plethora of study classes out there–well, a plethora if you have nearly a thousand dollars just lying around doing nothing. Huh? Do ya? Yep. Me neither. Does it seem fair to you that you are expected to sit for a test for which a good portion of the other test takers had professional help in preparation? I certainly don’t.

Let me introduce myself. I’m a lecturer in biology at San Jose State University. I’ve been teaching general biology, human biology, anatomy, physiology, cell biology, botany, zoology entomology, microbiology, and bacteriology for the better part of a decade. As I teach these classes and watch my students graduate and go on for advanced degrees, I have fielded many questions about how to study for the GRE subject tests, what subjects are covered, and how to best prepare if money is an issue. I began organizing GRE study sessions several years ago, and have drawn upon my research and experience to help out students facing the mountain of study needed to get ready for this subject test. So far, so good!

So what am I doing now? I thought that since there was so much interest in my on-campus groups that I’d start a blog where I’d post my lectures each day in an effort to archive and share them with a larger audience. I have so far focused only on the biology subject test, but I am thinking of expanding this to other subject areas and the general test as well. I’ll let you know! Until that time, I will be posting new lectures on various biological subjects found on the GRE, along with study tips, anecdotes, and success stories as they come to me. I do hope this helps. If you have any questions, just ask and I’ll do my best to answer as soon as possible!

Adrienne