Biology Final Exam: Dec 7- prokaryotes have operons which are a group of related structural genes and their controlling elements. - Lactose operon- an inducible operon that is normally off. The way it is normally off is there is another gene that is not part of the operon called a regulatory gene (transcribed into mRNA and then the mRNA is translated into a protein).o Protein is called a repressor protein- as soon as it is produced by translating the mRNA, binds to the operator. If it is bound to the operator, transcription is stopped and the entire operon is off.- It has 3 structural genes and controlling elements:o Promoter- where RNA polymerase binds and if it is allowed to, it will transcribe all 3 genes of the operon at the same time. So then 1 large mRNA molecule is produced and it is translated into 3 enzymes. o Operatoro Terminator- terminates transcription- Operon is turned on if lactose is available. You don’t want to have the operon on and go through the expense of making these enzymes if there is nothing for the enzymes to do. o If lactose is available, it can bond to the repressor protein. The repressor protein has a site that bonds to the operator, but it also has an allosteric site. The allosteric site is 3 dimensionally designed so it can bond to lactose. o If lactose is available, it fits into the allosteric site and if it does that, it changes the conformation of the repressor protein. In the new conformation, the repressor protein can’t bind to the operator. o Therefore, RNA polymerase can go ahead and transcribe the genes of the operon, which are then translated to form the enzymes. When these enzymes are available, the bacteria can now use lactose as an energy source to make ATP.- There is an isomer of lactose, which is uncommon, called allolactose. o Technically it is the isomer of lactose that bonds to the repressor protein. - Cotabolite repression- a cotabolism is the type of metabolism where you break something down (glycolysis).o A cotabolite is a molecule that is involved in or that is going to be broken down. Example: glucose is broken down in glycolysis, so it is a cotabolite Lactose can also be broken down and the energy that is released when it is broken down can be used to make ATP.o If you are one of these bacteria, lactose can turn on the lactose operon,but what happens if in addition to lactose, you also have plenty of glucose? It is better for the bacteria to eat glucose rather than lactose. The enzymes of glycolysis are always present, so if glucose is there, then the bacteria can use glucose, break it down and use the chemical bond energy to make ATP.  If the bacteria were to use lactose, you would have to spend a lot of energy and resources to make those enzymes necessary to use lactose as a cotabolite.  This is called cotabolite repression- if glucose is available, then the lactose operon is repressed because it is better for the bacteria to use glucose than lactose. - Involves a protein called CAP (cotabolite activating protein)- it has an allosteric site. If a molecule called cyclic AMP is available, the cAMP bonds to the CAP at the allosteric site.- ATP can be converted by adenylate cyclase into cyclic AMP.o Enzyme that breaks 2 phosphates off, and the 3rd phosphate, and then it bonds to another position on the sugar. - If cAMP is available and if it can bond to CAP, the CAP will then bond to the promoter, allowing transcription of the genes of the operon. - cAMP binds to CAP at allosteric site, CAP can bind to thepromoter, RNA polymerase can transcribe the genes of the operon.- If glucose is around, it inhibits adenylate cyclase. If this happens, then there won’t be any cAMP, meaning CAP’s allosteric site will be vacant. Then CAP can’t bind to the promoter, and RNA polymerase won’t transcribe the genes of the operon. - CAP regulates the amount of transcription that occurs. Ifit has cAMP, there will be a lot of transcription, but if it doesn’t, there won’t.o One other type of operon in bacteria: trp operon (tryptophan)- is one of the 20 amino acids Is a repressible operon meaning it is normally on and can be turned off. The operon has 5 genes that all share the same controlling element.- Terminator- Promoter- Operator Not part of the operon is the regulatory gene- always on, transcribed with the mRNA, and translated into a repressor protein. The repressor protein has an allosteric site and another site that can bind the operator- Is normally inactive when it is first produced. This operon allows the bacteria to make tryptophan. If bacteria is living in an environment where the tryptophan is already there, the tryptophan will bond to the allosteric site of the repressor protein and changes the conformation of the repressor protein so that it can bond to the operator and block transcription.- Eukaryote gene regulation- eukaryotes have about 18,000 genes. These are genes that can be transcribed and translated into proteins. All of your cells contain the same 46 chromosomes, that means that with a few exceptions, allof the cells in your body have the same genes.o The difference between liver cells and eye ball cells is that, in liver cells there is one set of genes that is turned on and one that is turned off. In eyeball cells, a different set of genes is being turned on. o Background of DNA packaging: every one of your cells has about 6ft ofDNA. How does cell manage the very long, slinky molecule? The DNA is divided into separate chromosomes.  After that, they are able to manage it by packaging the DNA using histones- Example: if you go out to fly a kite and the string is just in a big pile, you take a stick and you wind the kite string on the stick.- 8 histones are used to form a bead and the DNA wraps around the beads (nucleosome). Then these strands of DNA coilo Chromatin modification- chromatin is what chromosomes are made of. It is made of DNA and histone proteins. The histone proteins have an unusual shape with a fiber part that sticks out, called the N-Terminis.  The N-terminis has a lot of basic amino acids. A base is a proton acceptor, so protons are going to bind to the N-terminisof the histone proteins. The DNA molecule has a phosphate sugar backbone. And the phosphates have a negative charge, so the basic amino acids onthe histones are positive, while the phosphate is negative. There are 2 types of chromatin in the nucleus of our cells (mostcalled euchromatin) -