1. Transcription is the process where RNA is made using DNA as a template. Students should ABSOLUTELY not mix up or misuse the terms DNA Replication, Transcription, and Translation.
2. RNA polymerization requires an enzyme called RNA polymerase. It can start a chain without a primer, incorporates nucleotides into a growing chain in the 5' to 3' direction using phosphodiester bonds, and uses ATP, GTP, CTP, and UTP as starting compounds. The product of RNA polymerization is called a transcript.
3. The 5' -most nucleotide in RNA has three phosphates on it. All other nucleotides in RNA have only the single phosphate of a phosphodiester bond. Synthesis of the phosphodiester bond arises from nucleophilic attack of the 3' oxygen on the internal phosphate (closest to carbon 5 of the ribose) of the incoming 5' nucleotide.
4. Cells have three main types of RNA - mRNA (carries message to be translated into protein), tRNA (carries amino acids to ribosomes for incorporation into protein), and rRNA (components of ribosomes).
5. In E. coli, all of the RNAs are made by a single polymerase, known as RNA Polymerase. Eukaryotic cells have three RNA polymerases - RNA Polymerase I (rRNAs), RNA Polymerase II (mRNAs and snRNAs), and RNA Polymerase III (tRNAs).
6. E. coli RNA Polymerase has five distinct polypeptide subunits we discussed in class - alpha, beta, beta prime, and sigma.
7. Footprinting is a technique for determining where on a DNA molecule a protein is bound. The figure I gave in class explains the technique better than I can here in words.
8. Promoters in E. coli (RNA polymerase binding sites adjacent to genes) function with widely varying rates of efficiency - some stimulating initiation of transcription every few seconds, others only one or twice per life cycle. One way for a promoter to control such events is via variation in conserved sequences. E. coli genes have two conserved sequences - one at -10 relative to the transcription start site (TATAAT) and another at -35 relative to the transcription start site (TTGACA).
9. The more closely a given promoter's sequence matches the consensus sequence of the -10 sequence, the more active the promoter is at initiating transcription. RNA Polymerase slides along the DNA and when the sigma subunit identifies a promoter site, it stops.
10. Different sigma factors (such as the one made during heat shock) allow the cell to turn on sets of genes with different sequences in the -10/-35 sequences as needs arise.
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