How Genes Transmit Information

Why Do Fireflies Glow?

Fireflies glow in order to attract mates. Males and females flash signals to each other to let each other know that they are interested. Males will compete to make the best flash. Fireflies each have a distinct flash depending on their species. After a female firefly is impressed by a male she answers with her best flash. The flash also helps warn predators not to eat fireflies. Fireflies taste bad because they contain chemicals called lucibufagens. Predators then associate the glow with a bad taste and stay away.

The light is made through a complex process. First an enzyme called RNA Polymerase, located in the nucleus, finds a LUC gene located in the firefly DNA. This gene codes for a sequence of amino acids that make up the luciferase enzyme.

Next in a process called transcription, the RNA Polymerase copies, or 'transcribes,' information from the LUC gene into

messenger RNA (mRNA). The mRNA then moves from the nucleus to the cytoplasm. In the cytoplasm, the cell's ribosome's recognizes the mRNA and, in a process called translation, produces a string of Amino acids that was specified by the LUC gene. The amino acids then bend and fold into a 3-D shape and become a functioning Luciferase enzyme.

These enzymes then bind to a chemical called luciferin and speed up the reaction of combining an oxygen molecule with the luciferin to produce Oxyluciferin. Thousands of enzymes bind to thousands of luciferin molecules at once and catalyze (speed up) the reaction. This reaction releases energy in the form of light and causes a firefly to glow.

Alkaptonuria

Archibald Garrod was a scientist who believed that alkaptonuria, a disease that turns urine black, was an "inbron error of metabolism." He believed that there was a mutation in a gene that led to a defect in the pathway for elimination of liquids from the body.

Alkaptonuria is a recessive trait, thus a person must have two mutated genes in order to have this disease. The mutation in the genes causes urine to turn black. The disease also causes a build of a dark pigment in the cartilage and skin. People who have this disease usually develop arthritis in their spine and larger joints. Other symptoms include darkening of the ear and dark spots on the eye. It can also cause heart problems, kidney stones and prostate stones.

Alkaptonuria is caused by a defect in the HGD gene. The mutation in this gene causes problems within the body and you are unable to break down certain amino acids (tyrosine and phenylalanine). Due to this, a toxic substance called homogentisic acid builds up in your tissues. When the acid leaves the body (when you pee) it mixes with the air and causes urine to turn black. Overtime, the buildup of this acid causes arthritis and heart problems (since the acid has been deteriorating your veins and arteries). Fortunately, it only affects 1 out of every 250,000 people worldwide.

The official name for the HGD gene is

homogentisate 1,2-dioxygenase. It is located on the long arm of chromosome 3 at position 13.33; more specifically, it is located from base pair 120,347,014 to base pair 120,401,417 on chromosome 3.

The HGD is what provides the instructions for producing the enzyme homogentisate oxidase. The enzyme helps break down two amino acids (phenylalanine and tyrosine) when they are

present in excess quantities. However, when the gene is mutated (specifically a substitution of the amino acid valine for the amino acid methionine at one position in the polypeptide), the homogentisate oxidase changes its structure and becomes inactive. Due to the enzyme being inactive, phenylalanine and tyrosine are not broken down and build up in the body, causing one to develop alkaptonuria.

Homogentisate oxidase (H.O.) works very similarly to the way fireflies create light. In order to break down phenylalanine and tyrosine (which, in their combined form, are called homogentisic acid), H.O. adds two oxygen atoms to the molecule, much like the firefly did. Adding the oxygen atoms changes the H.O. into another molecule called maleylacetoacetate, just like the luciferin was changed to Oxyluciferin. The maleylacetoacetate is then broken down by the body.

Beadle and Tatum

The central dogma of biology is a framework that describes the flow of genetic information from DNA to RNA to Protein. However, it took a long time for this to be proven. One of the first pieces of evidence came from Beadle and Tatum's experiments with Neurospora, a fungi that was a haploid (it only had one set of chromosomes). It was important for the Neurospora to be a haploid so that they didn't have to worry about dominant and recessive traits.

The Neurospora grew well on a minimal media made in the laboratory. This meant that the Neurospora had enzymes(that game from genes)

that were able to change these substances into the vitamins and amino acids needed for growing. Thus, if the genes were mutated, then the enzymes wouldn’t be made and the Neurospora would not be able to grow unless the substance missing was added. The Neurospora was mutated by exposure to X-rays and left to grow on complete media that contained all the things the Neurospora needed to grow. Then the cultures of Neurospora were tested on minimal media. Most of the cultures grew on the minimal media, but the 299th culture did not. Thus, the 299th culture was mutated and then Beadle and Tatum started

growing this culture on minimal media supplemented with either amino acids or vitamins. The culture only grew on the media supplemented with vitamins, thus it was concluded that the Neurospora was not able to make a vitamin. This culture was then tested with specific vitamins and it only grew when supplied with B6. Thus a gene had been mutated and was not able to make the enzyme that produced the B6 vitamin.

This experiment was repeated for many different types of mutant Neurospora to confirm that the pathway went from gene to enzyme. One type of Neurospora did not grow unless supplemented with the amino acid arginine. However, it was known at the time that arginine is produced in a step-wise process that converts a Precursor molecule into Ornithine which is converted to Citrulline which is then converted to Arginine. If they were trying to prove that one gene makes one enzyme, they concluded that each step of this pathway must have a mutation.

They experimented with the Neurospora and found their assumption to be correct. There were three classes of mutant Neurospora that needed Arginine to grow. One class would grow if supplemented with any of the three molecules involved in the biochemical pathway of making Arginine (thus is would grow if supplemented with Ornithine, Citrulline or Arginine). This meant that these mutants were lacking the enzyme to transform the Precursor molecule to Ornithine. The second class of mutants would only grow if supplemented with Citrulline or Arginine, adding Ornithine to them would not help. This meant they were lacking the second enzyme, the one transforming Ornithine to Citrulline, thus explaining why adding Ornithine would not help. Finally, the last group of mutants only grew when supplemented with Arginine. This meant they were lacking the enzyme in the final step of the pathway, the one transforming Citrulline to Arginine. This explained why adding Citrulline or Ornithine (which was still successfully being transformed to Citrulline) would not help. Thus, with each mutated gene only one step of the pathway was affected, effectively proving that one gene is responsible for one enzyme.

Transcription & Translation

Transcription is the synthesis of RNA from a DNA template. It is three steps Initiation, elongation and termination. In initiation a RNA polymerase binds to a double-stranded DNA at a sequence called the promoter. The strand then beings to unwind. In elongation the RNA polymerase moves down the DNA from the 3' to 5' direction. It creates an RNA

transcript that elongates as the polymerase moves down the DNA. It does this through the covalent addition of nucleotides to the 3’ end of a polynucleotide chain. The nucleotides still follow the base pair rules, C always pairs with G and vice versa, but A always pairs with U (instead of T as in DNA) and vice versa. Finally in termination the transcription termination sequence is recognized and RNA polymerase is released. Transcription factors aid RNA polymerase in the process of transcription

in Eukaryotes only. Eukaryotes also contain a TATA box of certain nucleotides that beings the transcription. In Eukaryotes, before the mRNA can be sent to the cytoplasm for translation it must be "fixed." Transcription results in Pre mRNA which must their introns (segments of nonfunctional genes) removed. This is done through a protein called a spliceosome (which is made of small nuclear RNA or snRNA).

Translation occurs after transcription. Translation is a step in protein in synthesis in which genetic code carried by mRNA is deciphered and changed to produce the specific sequence of amino acids in a polypeptide chain. Translation occurs in the cytoplasm where the ribosomes are located and has four steps: activation, initiation, elongation, and termination. In activation, a specific amino acid is covalently bonded to a tRNA. Next in initiation, the small

subunit of a ribosome covalently bonds to a specific sequence on the mRNA chain. This occurs due to complementary base pairing between the ribosome binding site and the internal subunits. Next a special tRNA molecule, fMET, binds to an initiator codon and an initiation complex is formed. This process is helped by initiation factors (extra proteins). Then in elongation, an aminoacyl tRNA binds to the

mRNA passing through the acceptor site. The specific tRNA that binds to the mRNA is dependent on the mRNA codon. The tRNA contains anticodons that correspond to the codons on the mRNA. Next the ribosome goes through translocation which is triggered by elongation factors. In this process a ribosome moves three nucleotides towards the 3’ prime along the mRNA so the A site is available for the next aminoacyl tRNA. This process creates a polypeptide chain in the P site of a ribosome. In termination, translation comes to a halt when one stop codon, (UAA, UAG, or UGA) enters the A site of the ribosome. Release factors bind to the P site, catalyzing the release of the completed polypeptide chain and then causes the separation of the ribosome into its original small and large subunits. Many ribosomes can translate on mRNA at once to produce multiple polypeptides.

Eukaryotes and Prokaryotes

First off, Eukaryotes have bigger ribosomes (80S) than prokaryotes (70S). Secondly, the initiating amino

acid is methionine in eukaryotes while in prokaryotes it is N-formylmethionine. Still, both have Met-tRNA functioning in initiation. Also, Eukaryotes always use AUG as the starting codon. They don’t distinguish initiator AUGs by using a certain purine sequence on the 5’side as do prokaryotes. Eukaryotes can do this because they select the AUG closest to the 5’ end of mRNA as the starting site. Then a 40S (small) ribosome is attached to the 5’ end of mRNA and it looks for an AUG by moving towards the 3’ direction. This process is powered by helicases hydrolyzing ATP. Eukaryotes only have one start site which acts as a template for a single protein; prokaryotes have multiple start sites that act as a templates for the synthesis of several proteins. In prokaryotes, the mRNA is ready for translation immediately after transcription while in eukaryotes pre-mRNA must be processed( as described before) and then transported to the cytoplasm before translation takes place.