My Science Box

Teacher Background
The process of turning DNA into protein is called the “central dogma of molecular biology” because it is the foundation of all modern genetics, biotech and pharmacology. There are 6 major players in the process.

1. DNA – the blue print for construction of specific proteins. A section of DNA that codes for a protein is called a gene. More on the structure of DNA can be found in the background section of the DNA Models activity.
2. RNA polymerase – an enzyme responsible for assembling a strand of RNA from a DNA template. It is formed from an assembly of several different individual proteins with various roles.
3. Messenger RNA – temporary courier of information that brings a copy of the information encoded in the DNA to the ribosome where the proteins are actually made. More on the differences between RNA and DNA can be found in the background section of the Secret Codes activity
4. Ribosome – a fairly complex organelle that is like a protein factory. It assembles a chain of amino acids using the messenger RNA as a template. More on the genetic code that governs which amino acids pair with what RNA sequence may be found in the background section of the Secret Codes activity.
5. Transfer RNA – a small length of RNA (less than a hundred base pairs long) that transfers a specific amino acid to the growing protein chain within a ribosome. Each transfer RNA has a site where an amino acid can bind and a special 3 nucleotide sequence celled the “anticodon.” The anticodon matches a 3 nucleotide sequence on the messenger RNA molecule called the “codon”.
6. Protein – the primary building material of cells. Proteins constitute most of the dry mass of a cell and execute nearly all cell functions. Proteins are long single stranded chains constructed of 20 different building blocks called amino acids.

Transcription and translation: Illustration from Radboud University NijmegenThere are 2 major steps in the protein synthesis process. The first is the synthesis of messenger RNA in a process known as transcription. This process is similar to DNA replication, except that only a tiny portion of one strand is copied and it is copied into a single-stranded RNA molecule, not a double stranded DNA molecule.

To start transcription, RNA polymerase binds to a specific DNA sequence known as a promotor. Promotors sequences are very diverse, however, generally are found in the stretch of DNA in front of the gene and contain a place for RNA polymerase to bind as well as a transcriptional start sequence that indicates where transcription should begin. They range in length from less than a hundred base pairs to several thousand base pairs. Many promotor sequences contain the sequence TATAAA, known as a TATA box by biologists. This TATAAA sequence is used in this activity to indicate where the RNA polymerase should bind and begin transcription.

Once, the RNA polymerase binds to the promotor, it follows along the DNA, unzipping the base pairs, reading one of the two DNA strands, matching an RNA nucleotide to each DNA nucleotide, and assembling a messenger RNA molecule. The RNA polymerase continues moving along the DNA until it reaches a specific terminator sequence, at which point it releases the messenger RNA and disassembles. Messenger RNA molecules may extend over 2 million bases in length. At this point, the messenger RNA travels out of the nucleus to the ribosome where proteins are actually made.

This second step of the protein synthesis process is known as translation. First, a ribosome assembles around the messenger RNA molecule. Translation always begins at the messenger RNA sequence AUG. The messenger RNA then feeds its way through the ribosome like a tape. As it proceeds, each codon on the messenger RNA is matched to a transfer RNA. The ribosome forms bonds between the amino acids carried by the transfer RNAs and the empty transfer RNA molecules detach and float away. Gradually, the amino acid chain grows longer and longer until a stop sequence (UAG, UAA, or UGA) is reached. At that point, the protein is released.

From here, the protein may go through many stages of further processing. Depending on the sequence of amino acids, some parts of the protein like water and some curl away from it. Thus, the protein will fold itself up to protect the water-hating parts of the protein from the surrounding cytosol. In addition, proteins may be cut, spliced, joined together, packaged and reshaped into a final functional protein.

Student Prerequisites
Some basic introduction to the protein synthesis process (see Secret Codes lesson).