Episode 1: Cracking the Genetic Code
Episode 1: Cracking the Genetic Code
The genetic code tells us how the information in DNA is used to make proteins. But before we get there, let's break it down. DNA is a type of molecule- a nucleic acid. It is made of a whole bunch of smaller molecules called nucleotides. One nucleotide is linked to another, which is linked to another, and another, and so on. A typical DNA strand in a cell consists of millions of linked nucleotides.
Each nucleotide is made of a sugar. In the case of DNA, the sugar is deoxyribose. That's where DNA gets its name: DeoxyriboNucleic Acid. Deoxyribose is a 5-carbon molecule, with each carbon bonded to one oxygen atom EXCEPT for one carbon, which we call the 2' carbon. That's what makes it "deoxy." It's missing one oxygen compared to normal ribose.
The sugar is connected to at least one phosphate group (PO4) on one end, and a nitrogenous base (A, T, C, or G) on the other end. Below is a typical depiction of double-stranded DNA, as well as a zoomed-in portion showing what each nucleotide looks like, and how the nucleotides in one strand bond to the nucleotides in the other.
OpenStax, CC BY 4.0 <https://creativecommons.org/licenses/by/4.0>, via Wikimedia Commons
Although DNA serves many functions (and some of it serves no function at all that scientists can tell), the part we're interested in is the part that encodes proteins. That DNA stores the necessary information telling the cell exactly what to do. When a cell gets a cue that it's time to make a certain protein, through a very complex process it tells a molecule called RNA polymerase to go to the relevant part of the DNA, from which it makes RNA, as shown.
Notice that there are two strands of DNA, but RNA polymerase only reads one of them at a time. Everywhere RNA polymerase sees a deoxyribonucleotide with an A, it will put down a ribonucleotide with a U (RNA uses uracil instead of thymine). Everywhere the DNA strand has a T, RNA polymerase will put an A. And G pairs with C. So the RNA that is made is complementary to one strand of the DNA, and nearly identical to the other (except that it has U instead of T, and it uses ribose instead of deoxyribose).
And here we are dealing with a specific type of RNA called messenger RNA, or mRNA. Only mRNA is used as the instructions for protein synthesis. The mRNA that is made leaves the nucleus and goes to the cytoplasm- the sort of "soup" that makes up most of the cell. There, it interacts with a huge molecule called a ribosome.
The ribosome begins reading sets of 3 nucleotides, which we call codons. Basically, the ribosome slides along the mRNA one codon at a time. As each codon enters the ribosome, another type of RNA called transfer RNA, or tRNA, is also allowed to enter. The tRNA is attached to an amino acid. If the tRNA is complementary to the current codon, its amino acid will be added to the growing protein. So if the codon is CUC, then a tRNA that has GAG in the right position, called the anticodon, enters the ribosome and puts down its amino acid.
pluma, CC BY-SA 3.0 <https://creativecommons.org/licenses/by-sa/3.0>, via Wikimedia Commons
Then the ribosome slides along to the next codon, the next tRNA comes in, and the next amino acid is added. So what's an amino acid? Well, it's just the building block of proteins in the same way that nucleotides are the building blocks of DNA and RNA. You stick two amino acids to each other, and then you stick another one on to that, and another and another. This makes a peptide or a protein- the difference is subjective and it depends who you ask, but usually a protein is around 50 amino acids long or longer. They can be thousands of amino acids long. Here is the basic structure of an amino acid:
The ball labeled "R" is what we call the side chain. In theory it could be anything, but in the proteins found in nature, there are 20 different side chains to choose from, shown here in red:
In the podcast, I described a series of experiments that led researchers to figure out which codons correspond to which amino acids. Remember, there are 20 amino acids but 64 possible codon. Every codon corresponds to either a single amino acid or is a stop codon that tells the ribosome the protein is done. Even though each codon corresponds to one amino acid, most amino acids correspond to multiple codons. For instance, phenylalanine is encoded by both UUU and UUC. The full genetic code is shown here:
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