sanger sequencing

November 7-11

On Monday in molecular biology, Dr. Peng discussed translation in bacteria and eukaryotes. The third test in that class was on Wednesday and covered site-specific recombination and translocation of DNA, transcription mechanisms, RNA splicing, and translation.

In biochemistry on Tuesday and Thursday, we learned about lipids’ roles in membranes, including the phospholipid bilayer of biological membranes and the fluid mosaic model. In bacterial physiology, we began with the structure of microbial communities, particularly biofilm formation. We continued with cell-to-cell communication systems, such as quorum sensing, which allows bacteria to sense how many of their own kind are in the population. Quorum sensing is used to coordinate varied activities such as competence, virulence, biofilm formation, sporulation, and bacteriocin production. We also discussed symbiosis such as mutualism, cooperation, commensalism, predation, and parasitism.

On Friday, the bacterial genetics lab met in the computer lab to analyze the Sanger sequences of the RFLP assay. The data did not work out as well as expected, probably because the PCR product was not incubated long enough with the restriction enzyme and the enzyme did not cut all the sequences. We have the final test for the lab next week, and then the class will be completed.

October 24-28

On Monday and Wednesday in molecular biology, Dr. Peng lectured on RNA splicing mechanisms and RNA editing. He reviewed important proteins and nucleic acids in the spliceosome such as snRNPs (small nuclear RNA paired with protein). He also went over the three ways of splicing an RNA – nuclear pre-mRNA, group I introns, and group II introns. We then moved on to alternative splicing and RNA editing such as site-specific deamination and RNA-directed uridine insertion/deletion.

On Tuesday and Thursday in biochemistry, Dr. Popescu began the chapter on carbohydrates and glycobiology. We started with basic structures of monosaccharides including open chain and ring forms and moved to disaccharides formed via glycosidic bonds, before looking at structures and metabolism of common polysaccharides including glycogen, starch, cellulose, and chitin. We concluded the chapter discussing the biological function of glycoconjugates – glycolipids, glycoproteins, and proteoglycans. In bacterial physiology, we concluded the section on metabolism by learning about the tricarboxylic acid cycle (TCA cycle), the electron transport chain, oxidative phosphorylation, and the 5 types of fermentation in bacteria (lactic acid, ethanol, butyric acid, mixed acid, and propionic acid fermentation).

On Friday in bacterial genetics lab, we performed plasmid preparation to separate the plasmids from the E. coli and chromosomal DNA and proteins. Dr. Brown also lectured on Sanger sequencing in preparation for analysis of our sequences.