1. Negative transcriptional regulation of the lac operon is accomplished by a protein known as the lac repressor. It binds the operon's operator region and inhibits transcription.
2. In the absence of inducer molecules, the lac repressor tightly binds to the operator and inhibits transcription of the operon. When inducer molecules are present, they bind to the lac repressor and change its shape and reduce its ability to bind the operator, thus allowing the RNA polymerase to bind the promoter and start transcription.
3. CAP (also called CRP) must bind to cAMP in order to function. When CRP binds cAMP, its affinity increases for the lac operon adjacent to the RNA polymerase binding site (-68 to -55). This binding facilitates transcription of the lac operon by stimulating the binding of RNA polymerase to begin transcription.
4. When both CAP and the lac repressor are bound to the lac operon, the repressor 'wins', shutting down transcription of the operon.
5. In eukaryotic cells, DNA is wrapped up (coiled up) with basic proteins called histones. Histone sequences are strongly conserved from yeast to humans.
6. Four histones form a core around which DNA is wrapped. This core contains two copies each of histones H2A, H2B, H3, and H4. This core of proteins is called an octamer.
7. The appearance of chromatin DNA is that of beads on a string, with the octamer wrapped with DNA composing the beads and the DNA strand coated with histone H1 (and H5) composing the string.
8. Histones of the octamer have strong structural similarity to each other.
9. Wrapping of DNA around the histone octamer provides only partial compression of the length of a DNA molecule. Additional compression occurs as a result of coiling of octamer/DNA complexes as well, forming higher order structures.
10. Enhancer sequences are bound by enhancer proteins and are found only in eukaryotes. Multiple enhance sequences may be present before the start site of a particular gene. Binding of enhancer proteins to enhancer sequences allows for tissue specific expression of genes if the enhancer proteins themselves are expressed tissue specifically. Enhancer proteins help to "clear" out the histones from a region of a chromosome to allow transcription to occur.
11. Nuclear hormone receptors, such as the estrogen receptor, have DNA binding domains and ligand binding domains. The binding of the estradiol (and estrogen) ligand to the estrogen receptor causes a conformational change in the protein, but does not change the binding of the protein to DNA. Binding of the estradiol DOES appear to activate the protein and thus activate transcription of the genes that the receptor binds to the promoter of.
12. The key to action of the nuclear hormone receptor that binds estradiol is that binding of estradiol favors binding of the receptor to co-activator proteins. These co-activator proteins help to turn on transcription of the relevant genes. Binding of co-activator proteins by transcriptional factors, such as the estrogen receptor is called recruitment.
13. An antagonist of the estrogen receptor is the drug tamoxifen. Antagonists bind proteins and prevent them from acting. Binding of tamoxifen by the estrogen receptor stops the receptor from activating transcription of genes that it normally activates.
14. Tamoxifen appears to act by binding the estrogen receptor (I use the terms estrogen receptor and nuclear hormone receptor here as the same thing), with a part of the molecule extending into the region of the protein that normally binds to co-activators. Thus, tamoxifen acts by stopping recruitment by the receptor of co-activators. Tamoxifen is used to treat tumors that are stimulated by the binding of estrogens to the receptor.
15. Altering chromatin structure is an essential function for transcriptional activation in eukaryotes. Co-activator proteins appear to play a role in this process by catalyzing the acetylation of lysine residues in histones. Acetylation of histone lysines neutralizes their positive charge, changing the affinity of histones for DNA and changing the nature of their interaction with DNA, thus allowing more proteins to be able to gain access to the DNA where the acetylation has occurred.
16. Proteins involved in transcriptional control often have bromodomains. These regions of protein recognize and bind to acetylated lysine residues in histones.
This course in general biochemistry is intended to integrate information about metabolic pathways with respiration (respiratory control) and initiate the student into a microscopic world where blueprints are made of deoxyribonucleic acids, factories operate using enzymes, and the exchange rate is in ATPs rather than Yens or Euros. Beyond explaining terms, and iterating reactions and metabolic pathways, this course strives to establish that the same principles that govern the behavior of the world around us also govern the transactions inside this microscopic world of the living cell. And by studying and applying these principles, we begin to understand cellular and bodily processes that include sensory mechanisms.
1. Lipids, Membranes and Transport
2. Electron Transport, Oxidative Phosphorylation and Mitochondrial 3. Transport Systems
3. Lipid Metabolism
4. Nucleotide Metabolism
5. DNA Replication