Structures, But Not Architectural

WARNING: Biology post ahead!

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Recently, we've been discussing the components of DNA and how they fit together to create the genetic code. I also found this nice, although admittedly outdated piece [from the University of Arizona ;) !] that aided me in these discoveries.

First off, we have to understand that DNA is a polymer, meaning that it is comprised of several smaller pieces (the monomers) that have joined together. DNA, however, is special, so we can't just call its components monomers--they have their own names. Each monomer is called a nucleotide, and when combined, you get a polynucleotide.

Make sense so far?

Now, there are four nucleotides, and they're all mostly similar. Each one has a 5-carbon sugar (deoxyribose), a phosphate group, and a nitrogenous base. The only difference between the four is in that nitrogenous base. You're probably familiar with the notation for these bases:

A=Adenine

T=Thymine

C=Cytosine

G=Guanine

Let's take some time to examine the bases themselves in more depth.  Two, A and G, are purines, while their counterparts in the DNA sequence, T and C, are pyrimidines. (After a few minutes of Googling...I'm not even going to try to define those terms. I like going in depth, but there's a limit.). Adenine and guanine both have 5 carbon atoms and 4 nitrogen atoms, these atoms are both numbered according to their positions, and both have an NH₂ molecule attached to the rings of carbon and nitrogen. The only real difference between these two is that guanine also has an oxygen atom attached to the C₆ atom and that the NH₂ is at the C₆ atom in adenine, while it is found at the C₂ atom in guanine.

Cytosine and thymine have are also quite similar to each other, but only consist of one C/N ring, instead of two as the other two bases did. They both have 4 carbon and 2 nitrogen atoms. In fact, the only difference between the two is that thymine has an extra NH₂ molecule instead of two oxygen atoms and that guanine has an additional CH₃.

We've been focusing on the bases, so let's take some time to examine the backbone, if you will, of DNA--the deoxyribose phosphate. This structure has 5 carbon atoms, two hydroxyl groups, and one lone oxygen atom. These two hydroxyl groups bond with the phosphate groups to build the backbone. This means that there is a polarity to the chain--it goes from 5' to 3'. (Interestingly, compared to ribose, deoxyribose lacks one hydroxyl group, hence the name "DEOXYribose.")

Ok. So, now, we have one side of the DNA chain built. But DNA has a double helix shape, as Watson and Crick discovered. To explain how these sides join and why they twist, we have to examine the bonds within the DNA molecule. First off, when two of the sugar-phosphate "sides" we've been discussing combine, they do so in opposite directions--the two 5' atoms are at opposite ends of the combined chain. Now, along this backbone, the phosphate and sugar are covalently bound--pairs of electrons are shared between the two molecules. The base pairs, however, use hydrogen bonds (remember them? They're caused by charge differences between hydrogen and other atoms.) to join. This is particularly useful because when it is time for them to be separated for RNA synthesis (more on that soon!) these bonds can be easily broken. It is also interesting to note that, although adenine and thymine bond with two bonds, cytosine and guanine use three bonds.

More coming soon! 

Synthesizers: They're in Your Cells

This marks two posts in a row for Biology! Don't worry...I have a few personal ones stewing away.

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Pretty much everyone knows that DNA is in your cells. That's a well known, widely accepted fact.

Not as many people know that proteins do the dirty work of the body. When you look in the mirror, you are seeing the result of the work of proteins.

But this means that, somehow, the information encoded in your DNA has to be used to make proteins. How is this done?

The answer to this question is the RNA molecule. RNA is somewhat similar to DNA, but it has a few important differences. First off, uracil is used as a base instead of thymine. (Both uracil and thymine are pyrimidines, but uracil is missing a methyl group.) Then, the sugar used in its formation is ribose instead of deoxyribose. RNA also only has one strand instead of DNA's two.

Now, there are three classes of RNA. Let's take some time to examine each.

Messenger RNA (mRNA)

Messenger RNA is what carries the information from DNA to the ribosomes to create proteins. It's almost like the photo negative--every base in RNA is the complement of the base in DNA. For example, a DNA sequence of

ATGTGCA

would be transcribed as

UACACGU

(Remember, RNA uses uracil instead of thymine.)

Then, the strand of mRNA exits the nucleus and heads to the ribosome. Here, it meets up with...

Transfer RNA (tRNA)

Transfer RNA is a single strand of RNA that curls back on itself, with a location for an amino acid. It's typically portrayed in textbooks as a cross-ish shape, like

This isn't the actual shape of tRNA, but this particular representation is useful for several reasons. First off, it shows the "intramolecular base pairing" in the arms of the cross--G and C, U and A. It also is a "charged" RNA, meaning that it is carrying an amino acid. Finally, below the molecule, we can see the "codon," and at the bottom of the molecule itself, we have the "anticodon." Codons are groups of three bases that each have their own specific meaning. (Because there are four possible bases and three bases in a codon, there are 4³=64 possible codons.)

Let's track a certain sequence of three bases through transcription (where DNA is transcribed to RNA) to translation (where mRNA is used by tRNA to create an amino acid sequence). Imagine that the sequence AGT is sitting on a DNA molecule. When transcribed to mRNA, it becomes UCA (remember, RNA becomes the complements of the bases in the DNA). This mRNA exits the nucleus and goes to the ribosomes. In the ribosome, it is paired with the tRNA carrying its anticodon, AGU. (As a matter of fact, this would result in the protein serine being added to the chain.)

Then, this general process continues for all of the codons. A series of amino acids is compiled, and finally a protein is made. Now, remember, all of this is happening in the ribosome, and an important part of the ribosome is

Ribosomal RNA (rRNA)

The ribosome is comprised of two subunits, both composed of rRNA. These two components are creatively known as the who on earth named these things large subunit (LSU) and the small subunit (SSU). When mRNA enters the ribosome for translation, it slides between the two subunits. Ribosomes have three binding sites for tRNA to enter as the mRNA is translated (known as A, P, and E). The A site binds with a charged tRNA--one that is carrying an amino acid. At the P site, another charged tRNA is waiting--and the amino acids of the P tRNA and the A tRNA bond. The tRNA that was at the P site moves to the E site, leaving its amino acid behind, and the molecule occupying the A site moves to the P site. Another tRNA molecule comes in to the A site, and the cycle continues.

That's a brief overview of the various types of RNA!

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I have a confession: Over the past month, my writing on science stuff has seemed increasingly dry. I haven't liked it, and I don't know why. Has anyone else noticed this?

Limited Resources: What Now?

I've been quiet here recently, mostly because I've been traveling and haven't wanted to take time out to type up my thoughts. But they've been in my head for a while, and here they are.

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Peter asked an interesting question in this post:

"What do you see as an alternative to a teacher who doesn't have he resources to have all the students participate in a lab, but still wants the concept to be taught?"

In my response, I suggested that if a student could successfully design an experiment--even without carrying it out--that should be evidence that the aforementioned student had sufficient comprehension of the ideas he or she was testing. I've actually done this myself--see this post (I know, I know--slideshows=bad. I was just getting tired of doing complex prezis for everything).

All that I really did, though, was design an experiment to test a certain question. (I can't claim that I knew everything, though--I did have information on the reactions between BTB, water, and carbon dioxide.)

Now, let's try this, and see if this can work to show if student has real understanding. Imagine the overall goal of a class period was to extract DNA from an organism--say our student chooses wheat germ. First off, we'd consider what needed to be done to isolate the DNA. We'd have to break down the cell membrane and the nucleus somehow so that the DNA could precipitate. At this point, the student (let's call her Jill) would have to come up with something along the lines of, "Because wheat germ has a phospholipid membrane, hot water and soap can break it down."

Ok. So, now we have a bunch of DNA floating around in water. What next? 

Well, let's ask Jill. "DNA isn't soluble in alcohol. So, if we add alcohol to the raw DNA, it should pull together into a precipitate."

Of course, I recognize that there are major flaws with my presentation here. After all, Jill would have to know that wheat germ has a phospholipid membrane which can be broken down by hot water and soap, and that DNA isn't soluble with alcohol. But that's the problem with examples. In a real classroom, these topics could either be covered ahead of time or Jill could be given this information (like I was on that experiment over photosynthesis). Then, of course, Jill would need to figure out how to apply these facts to obtain her desired result.

And isn't that skill what education should be about?