Consider the following fictitious reaction in the coco plant:

On one of the chromosomes of the coco plant is an area of DNA that codes for the enzyme chocholatase:

1. The first step is that the DNA splits (by an enzyme) at the part of the DNA that is going to eventually code for the protein that is to be made. That section of DNA that is going to code for a single protein is called a structural gene (a unit of information).
2. Appropriate RNA nucleotides complimentary bind to the exposed DNA nucleotides via random movement of molecules. The strand from which the information comes is called the coding strand (or sense strand or template strand) while the other strand is called the noncoding strand (or mis-sense strand).
3. The RNA nucleotides are bound together by RNA polymerase.
1. Prokaryotes have one RNA polymerase for all RNA's while eukaryotes have three known RNA polymerases.
2. The RNA polymerase recognizes the coding strand and the place to start by looking for a particular start sequence (promoter) on the DNA.
1. It needs the help of a "sigma" factor to find this initiation (promoter) spot.
2. The promoter site on the DNA often involves TATA, but as of yet it is not fully understood. It can be up rather long (40 nucleotides).
3. The RNA polymerase keeps working until it finds another unique sequence (terminator) that tells it to stop and fall off.
4. It needs the help of a "rho" factor to find this termination spot.
5. The termination site on the DNA is not yet fully understood.
6. Polymerases always work from the 3' to the 5' end of the coding strand of DNA (template); thus the antiparallel structure it is forming is going from the 5' to 3' direction.
7. The m-RNA is longer than the actual coding area because there is a leader sequence before AUG and a terminator sequence that follows the ribosomal stop codon.
4. The newly formed m-RNA leaves the DNA and the DNA becomes double stranded again.

1. In eukaryotes, a gene can be made up of sections that are never translated into a protein. The other sections are eventually expressed. The areas that are never translated are called intron parts of the gene, and the expressed areas are called exons.
2. It is known that the introns plus the exons are transcribed into a m-RNA molecule, but then the intron sections of the m-RNA are snipped out by enzymes (spliceosomes). What is left represents only the exon sections of the gene. ('SNURPS' Sci Am June 88).
3. Only after all of the intron sections are snipped out is the m-RNA allowed to leave the nucleus. Then this 'exon' m-RNA is translated into a protein.
4. There is no fully known function or cause for introns: Introns can be artificially removed from certain genes of DNA and replaced into cells. With pure 'exon' DNA (known as c-DNA), the protein can still be made without any apparent problems! Furthermore, introns do not exist in prokaryotes. What is this 'junk' DNA doing there??? Left over from viruses??? Gene control???

1. Have two subunits of which about 2/3 is r-RNA and 1/3 is protein
2. The two subunits are different sizes in prokaryotes versus eukaryotes.
1. Prokaryotic ribosomes are 70 S
1. Small subunit (30S) of E. coli has one molecule of m-RNA and a single molecule each of 21 different proteins.
2. The larger subunit (50S) has 2 r-RNA molecules and 34 proteins.
2. Eukaryotic ribosomes are 80S with a 40S subunit and a 60S subunit.
3. The two subunits are separately free in the cytoplasm before they come together and bind onto the m-RNA.
4. Apparently the smaller subunit has the binding site for m-RNA.

1. A small ribosomal subunit binds to the 5' end of the m-RNA then the large subunit.
1. If it is a prokaryotic cell one end of the m-RNA can bind to a ribosome before the other end is fully formed from the DNA!
2. If it is a eukaryotic cell, the fully formed m-RNA must leave the nucleus before it can find a ribosome in the cytoplasm. In the process the m-RNA itself may get altered! (processing of m-RNA).
2. In the meantime, a particular t-RNA with a particular anticodon binds a particular amino acid. This happens for several t-RNAs and proper corresponding amino acids in the cytoplasm. ATP is the energy source used to bind the amino acid to the t-RNA. Aminoacyl-tRNA synthetase is the enzyme that does the binding.
3. The appropriate t-RNA has its anticodon bind to the appropriate triplet codon on the m-RNA. (on the ribosome).
4. Another t-RNA with a particular anticodon and another appropriate amino acid binds to the next sequence of three nucleotides on the m-RNA.
5. The amino acid of the first t-RNA detaches and reattaches to the amino acid that is still bound to the second t-RNA. This new bond between the two amino acids is called a peptide bond. This is the first step in actually making a protein.
6. The first t-RNA, now that it no longer has the amino acid attached, floats away from the ribosome (and goes off and binds another amino acid).
7. The entire ribosome now moves, using the energy of GTP, down the messenger RNA exactly three nucleotides. The t-RNA that was in the second position on the ribosome now fills the first position because of the ribosomal movement. First position is called the P site (peptide) and the second position is called the A site (aminoacyl).
8. Another t-RNA-amino acid has its anticodon bind to the appropriate triplet codon on the m-RNA in the second slot on the ribosome.
9. The processes in I, J, and K are repeated and the amino acid chain grows in length. This happens until the end of the m-RNA is reached.
10. The end of the m-RNA is determined by one of the three "stop codes" (UAA, UGA, or UAG). When the end is encountered, the last amino acid with the attached chain releases from the last t-RNA and the protein is fully free. Also, the two halves of the ribosome disassociate and again become free in the cytoplasm.