Structure, Process, and Translation of RNA for AP Biology

Practice problems for these concepts can be found at: Molecular Genetics Review Questions for AP Biology

RNA Structure and Function

Ribonucleic acid is known to the world as RNA. There are some similarities between DNA and RNA. They both have a sugar-phosphate backbone. They both have four different nucleotides that make up the structure of the molecule. They both have three letters in their nickname—don't worry if you don't see that last similarity right away, … remember that I have been studying these things for years. These two molecules also have their share of differences. RNA's nitrogenous bases are adenine, guanine, cytosine, and uracil. There is no thymine in RNA uracil beat out thymine for the job (probably had a better interview during the hiring process). Another difference between DNA and RNA is that the sugar for RNA is ribose instead of deoxyribose. While DNA exists as a double strand, RNA has a bit more of an independent personality and tends to roam the cells as a single-stranded entity.

There are three main types of RNA that you should know about, all of which are formed from DNA templates in the nucleus of eukaryotic cells: (1) messenger RNA (mRNA), (2) transfer RNA (tRNA), and (3) ribosomal RNA (rRNA).

RNA Processing

In bacteria, mRNA is ready to rock immediately after it is released from the DNA. In eukaryotes, this is not the case. The mRNA produced after transcription must be modified before it can leave the nucleus and lead the formation of proteins on the ribosomes. The 5' and the 3' ends of the newly produced mRNA molecule are touched up. The 5' end is given a guanine cap, which serves to protect the RNA and also helps in attachment to the ribosome later on. The 3' end is given something called a polyadenine tail, which may help ease the movement from the nucleus to the cytoplasm. Along with these changes, the introns (noncoding regions produced during transcription) are cut out of the mRNA, and the remaining exons (coding regions) are glued back together to produce the mRNA that is translated into a protein. This is called RNA splicing. I admit that it does seem strange and inefficient that the DNA would contain so many regions that are not used in the production of the gene, but perhaps there is method to the madness. It is hypothesized that introns exist to provide flexibility to the genome. They could allow an organism to make different proteins from the same gene; the only difference is which introns get spliced out from one to the other. It is also possible that this whole splicing process plays a role in allowing the movement of mRNA from the nucleus to the cytoplasm.

Translation of RNA

Now that the mRNA has escaped from the nucleus, it is ready to help direct the construction of proteins. This process occurs in the cytoplasm, and the site of protein synthesis is the ribosome. As mentioned in Chapter 5, proteins are made of amino acids. Each protein has a distinct and particular amino acid order. Therefore, there must be some system used by the cell to convert the sequences of nucleotides that make up an mRNA molecule into the sequence of amino acids that make up a particular protein. The cell carries out this conversion from nucleotides to amino acids through the use of the genetic code. An mRNA molecule is divided into a series of codons that make up the code. Each codon is a triplet of nucleotides that codes for a particular amino acid. There are 20 different amino acids, and 64 different combinations of codons. This means that some amino acids are coded for by more than one codon. For example, the codons GCU, GCC, GCA, and GCG all call for the addition of the amino acid alanine during protein creation. Of these 64 possibilities, one is a start codon, AUG, which establishes the reading frame for protein formation. Also among these 64 codons are three stop codons: UGA, UAA, and UAG. When the protein formation machinery hits these codons, the production of a protein stops.

Before we go through the steps of protein synthesis, I would like to introduce to you the other players involved in the process. We have already spoken about mRNA, but we should meet the host of the entire shindig, the ribosomes, which are made up of a large and a small subunit. A huge percentage of a ribosome is built out of the second type of RNA mentioned earlier, rRNA. Two other important parts of a ribosome that we will discuss in more detail later are the A site and the P site, which are tRNA attachment sites. The job of tRNA is to carry amino acids to the ribosomes. The mRNA molecule that is involved in the formation of a protein consists of a series of codons. Each tRNA has, at its attachment site, a region called the anticodon, which is a three-nucleotide sequence that is perfectly complementary to a particular codon. For example, a codon that is AUU has an anticodon that reads UAA in the same direction. Each tRNA molecule carries an amino acid that is coded for by the codon that its anticodon matches up with. Once the tRNA's amino acid has been incorporated into the growing protein, the tRNA leaves the site to pick up another amino acid just in case its services are needed again at the ribosome. An enzyme known as aminoacyl tRNA synthetase makes sure that each tRNA molecule picks up the appropriate amino acid for its anticodon.

Uh-oh … there is a potential problem here. There are fewer than 50 different types of tRNA molecules. But there are more codons than that. Oh, dear … but wait! This is not a problem because some tRNA are able to match with more than one codon. How can this be? This works thanks to a phenomenon known as wobble, where a uracil in the third position of an anticodon can pair with A or G instead of just A. There are some tRNA molecules that have an altered form of adenine, called inosine (I), in the third position of the anticodon. This nitrogenous base is able to bind with U, C, or A. Wobble allows the 45 tRNA molecules to service all the different types of codons seen in mRNA molecules.

We have met all the important players in the translation process (see also Figure 11.6), which begins when an mRNA attaches to a small ribosomal subunit. The first codon for this process is always AUG. This attracts a tRNA molecule carrying methionine to attach to the AUG codon. When this occurs, the large subunit of the ribosome, containing the A site and the P site, binds to the complex. The elongation of the protein is ready to begin. The P site is the host for the tRNA carrying the growing protein, while the A site is where the tRNA carrying the next amino acid sits. Think of the A site as the on-deck circle of a baseball field, and P site as the batter's box. So, AUG is the first codon bound, and in the P site is the tRNA carrying the methionine. The next codon in the sequence determines which tRNA binds next, and that tRNA molecule sits in the A site of the ribosome. An enzyme helps a peptide bond form between the amino acid on the A site tRNA and the amino acid on the P site tRNA. After this happens, the amino acid from the P site moves to the A site, setting the stage for the tRNA in the P site to leave the ribosome. Now a step called translocation occurs. During this step, the ribosome moves along the mRNA in such a way that the A site becomes the P site and the next tRNA comes into the new A site carrying the next amino acid. This process continues until the stop codon is reached, causing the completed protein to leave the ribosome.

Practice problems for these concepts can be found at: Molecular Genetics Review Questions for AP Biology