1. The factor involved in factor dependent transcription termination in E. coli is called rho. It binds to the 5' end of an RNA being made and (using ATP energy) "climbs" the RNA until it reaches the RNA polymerase. There it destabilizes the RNA/DNA duplex, favoring the release of the RNA polymerase from the DNA and the RNA from the DNA, as well.
2. In prokaryotes, tRNAs are the most altered (processed) RNAs. Modifications start with their being cleaved from a larger RNA containing both tRNAs and rRNAs. Ribonuclease P is a ribozyme (catalytic RNA) that cleaves the 5' end of tRNAs from the larger RNA. Ribonuclease III catalyzes excision of rRNAs from the larger molecule.
3. Eukaryotes and prokaryotes differ significantly in the relationship between transcription and translation. Prokaryotes have no nucleus. In them, translation starts oftentimes WHILE a message is being transcribed. There are no significant modifications to mRNAs in prokaryotes.
4. In eukaryotes, transcription and translation are spacially separated. Transcription occurs in the nucleus, whereas translation occurs in the cytoplasm. In addition, eukaryotic mRNAs are modified at the 5' end (capping), the 3' end (polyadenylation) and even in the middle (editing and splicing).
5. Eukaryotes have 3 specialized RNA polymerases. They differ in their sensitivity to alpha-amanitin (a poison from some mushrooms). RNA polymerase II (makes mRNAs) is the most sensitive. RNA polymerase III (makes tRNAs and small rRNA) has moderate sensitivity and RNA polymerase I (makes large rRNAs) has low sensitivity.
6. Sequence elements that affect transcription of eukaryotic genes. They include the TATA box (positioned approximately -30 to -100), and a CAAT box and GC box (-40 to -150).
7. The TATA box is not found in front of all eukaryotic genes, but is essential for strong transcription.
8. The promoters for each RNA polymerase are different in structure. I will not hold you responsible for their structures.
9. Enhancer sequence elements are DNA sequences that about bound by enhance (transcription factor) proteins. Enhancer proteins act in this way to enhance transcription of genes located up to many thousands of base pairs upstream (ahead of), downstream (down from ) or even in the middle of genes.
10. RNA Polymerase II in eukaryotes differs from RNA polymerase in E. coli in not binding to the DNA directly, but rather, it must bind to another protein that binds to the promoter first.
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