An Introduction to Proteins

How proteins are made and what they look like

How are proteins made?

In order to learn how proteins are made you will have to familiarize yourself with the Central Dogma of molecular biology. The Central Dogma basically states that DNA provides the instructions for making RNA, and RNA then provides the instructions for making protein. The overall concept of protein synthesis is basic, but the details of this process are quite complex.

As we just learned in “An Introduction to DNA and Chromosomes,” DNA contains all of the instructions for life. It is present in each and every cell of the body, located in a compartment called the nucleus. DNA can be thought of as a blueprint to a house because it provides all of the instructions about the materials to be used and how it is to be built. Proteins can be thought of as some of the different materials used to build the house (wood, glass, bricks), as well as the people and devices that help put the house together. But before all this can happen, there must be a middleman between the DNA’s instructions and the actual protein. This middleman is called RNA.

RNA is actually rather similar to DNA. Just like DNA, it is made of nucleotide subunits that contain a sugar molecule, a phosphate group, and a nitrogenous base.

But unlike DNA, the RNA sugar molecule has an additional chemical group that makes it more reactive, but less stable, than DNA. The name RNA stands for ribonucleic acid, which comes from the name of the specific sugar molecule, ribose (remember that DNA has the sugar deoxyribose, which is why it is called deoxyribonucleic acid). Another difference is that while DNA is comprised of four bases - adenine (A), guanine (G), cytosine (C), and thymine (T) - RNA uses the first three, but substitutes the base uracil (U) for T.

While DNA is usually double-stranded, RNA is most often single-stranded (although there are exceptions). DNA never leaves the nucleus of complex cells, but RNA can be found both inside and outside of the nucleus. For a summary of these differences between DNA and RNA, see the table below.

Now that we know more about RNA, we can explore the first half of the Central Dogma. The first step involves going from DNA to RNA and is called transcription. In the process of transcription, one strand of DNA is used as a template to build the RNA strand. Normally only a small section of the DNA is transcribed. The specific section to be transcribed usually makes up one gene. Remember how DNA is double-stranded and all wound up like a spiral staircase? Well, in order to be able to use the DNA as a template, it first has to be unwound and separated from its partner strand. You can think about this separation as unzipping a zipper, which can then be zipped up again later. So far, this process is very similar tao DNA replication. (For a review of DNA replication click here .) The major difference is that instead of making a complementary strand of DNA, a strand of RNA is made. Once the bases of the DNA template strand are exposed, RNA nucleotides can begin to match up with their complementary pairs. Just as in DNA replication, C pairs with G and G pairs with C. However, since RNA uses U instead of T, it will match A to T, and U to A.

Once the entire section has been transcribed, the RNA strand separates from the DNA template, and what is left is the RNA transcript.

The RNA strand that remains is called messenger RNA (mRNA). This name is fitting because mRNA acts as the messenger between DNA and protein. After a few subtractions and additions to the strand, the mRNA transcript can exit the nucleus. You are now ready to explore the second half of the Central Dogma: translation. Translation is the process by which mRNA is used to create proteins. At this stage, mRNA serves as the blueprint for a protein product. The process of going from RNA to protein is called translation because we are, in effect, changing languages. The basic subunit of DNA and RNA is the nucleotide, while the basic subunit of protein is the amino acid. The translation is from the language of RNA (nucleotides) to the language of protein (amino acids).

In order to complete this translation, some important helpers are needed. One of these helpers is the ribosome, a small organelle located in the cytoplasm of the cell.

Another one of these helpers is transfer RNA (tRNA).

tRNA is made up of the same subunits as mRNA, but it has a very different function. tRNA can be thought of as the bilingual interpreter because it understands both the language of RNA and protein. One tRNA can bind to one of twenty different amino acids on one end, and to mRNA on the other end. tRNA binds to an mRNA codon by matching it to its own anticodon. Recall that a codon is simply a group of three bases. An anticodon is a sequence of three bases on the tRNA that is complementary to a codon on the mRNA (sometimes the anticodon is also referred to as just a codon). Each codon calls for a specific amino acid, although several different codons can call for the same amino acid. By being able to read a codon and match it up with the corresponding amino acid, tRNA plays an important role in translation.

Next we will discuss how we go from this one amino acid to the chain of amino acids that makes up a protein.

Now the different helpers must all work together to translate the mRNA into a protein. The ribosome has two main parts and the mRNA is held between them. The ribosome also has two binding sites. The first site, the A site, is where a new tRNA is accepted. At this point, the tRNA is bound to both its amino acid and the mRNA. This first tRNA is then pushed into the second binding site, the P site, pulling the mRNA along with it. P stands for peptide because this site is where the peptide bond is formed. A peptide bond is the link between two amino acids, and peptide is a word to describe two linked amino acids. (A chain of several linked amino acids is sometimes called an oligopeptide, a larger chain of amino acids is a polypeptide, and once the chain of amino acids is in its final shape it is called a protein.)

Once the first tRNA has been moved to the P site, the second tRNA can bind to the A site. The amino acid linked to the first tRNA is positioned close to the amino acid linked to the second tRNA, and a peptide bond is formed between them. The first tRNA can then release its amino acid, which is now linked to the amino acid on the second tRNA. The mRNA transcript is moved again, so that the second tRNA moves from the A site to the P site, and the first tRNA is moved out of the P site to the exit site, where it leaves the mRNA and ribosome. The process continues for each codon on the mRNA: a new tRNA binds to the codon matching its anticodon, attaches to the corresponding amino acid, and is moved into the A site of the ribosome. The growing amino acid chain is connected to the newest amino acid, and the tRNA is pushed into the P site and then out. For a pictorial description of translation, see figure 10a-c.

Figure P-10a

Figure P-10b

Figure P-10c

Once the entire mRNA transcript has been translated from nucleotide codons to a chain of amino acids, the polypeptide is cut free, and the ribosome-mRNA complex falls apart. The mRNA is soon degraded and the parts are recycled, and the ribosome goes on to translate other mRNA transcripts. We are left with the free amino acid chain, but we do not have a completed protein yet! You will find out how a protein is finished in the next section, part 3.

Last Modified: 02/12/2006

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