1. Initiation of replication in E. coli occurs at a specific site on the E. coli genomic DNA, known as OriC, in the cell's circular chromosome. The OriC site contains three repeats of an AT rich sequence near some sequences bound by the DNA A protein.
2. Replication initiation begins with binding of the several copies of the DNA A protein to the OriC site. Bending and wrapping of the DNA around DNA A proteins causes the AT-rich sequences noted above to become single-stranded.
3. Next, the DNA BC complex binds the DNA B protein (helicase) to each of the single strands in opposite orientations. The DNA C protein is released in the process. Next, SSB and primase bind the exposed single-stranded regions and cause DNA A protein to be released. The primases begin synthesizing RNA primers (remember - 5' to 3' RNA synthesis only also) in opposite directions on each strand. The primases DO NOT require a pre-existing primer to function.
4. Note that replication is bi-directional - two replication forks pointed in opposite directions from the origin. They meet later at a termination site on the other side of the genomic DNA.
5. Eukaryotic DNA replication is coordinated tightly with the cell cycle. Checkpoints during the cell cycle ensure that progression through the cell cycle does not occur if there are problems with the DNA. When such conditions arrive, the repair process can be initiated and if repair cannot be performed, a series of events resulting in cellular death may start to occur.
6. Eukaryotic chromosomes differ from prokaryotic DNAs in being linear. The linear ends of the chromosomes are called telomeres. Telomeric sequences have thousands of copies of repeats of short sequences.
7. The enzyme that builds telomeres is called telomerase and is found predominantly in fetal and cancer cells, as well as fertilized eggs. Differentiated cells for the most part do not appear to have an active telomerase.
8. With each round of DNA replication, linear chromosomes in eukaryotes shorten. Thus, the more telomeric sequences a chromosome has, the more divisions it can undergo before the telomeres are "eaten up".
9. Telomerase is a reverse transcriptase - an enzyme that uses an RNA template (a circular RNA that it carries) to synthesize DNA. Other reverse transcriptases are found in retroviruses, such as HIV.
10. Damage to DNA can occur chemically (deamination of adenine to form hypoxanthine), by oxidation (creation of 8-oxo-guanine by reactive oxygen species reaction), by reaction with an aflatoxin metabolite, by reaction with a cross-linking reagent, such as psoralen, and by dimerization of adjacent thymines stimulated by ultraviolet light. These systems require repair - deescribed below. Another system requiring repair is DNA sliding, which can occur amid repeating sequences. Lack of a repair system for these leads to Huntington's disease.
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