In molecular biology on Monday and Wednesday, Dr. Peng lectured about translation in prokaryotes and eukaryotes. He discussed the structure of tRNAs as well as tRNA charging by class I and class II aminoacyl-tRNA synthetases. We also learned about ribosome structure and translation initiation, elongation, and termination.
In biochemistry on Tuesday and Thursday, Dr. Popescu discussed lipids, including sections on the biological roles of lipids and structure and properties of storage, membrane, and signaling lipids. We learned about all 6 classes of lipids – fatty acids, triacylglycerols, wax esters, glycerophospholipids, sphingolipids, and isoprenoids. On Tuesday in bacterial physiology, we learned about bacterial two-component signaling systems such as the Arc, Nar, Che, Pho, Bvg, Agr, Spo, PhoQ/PhoP, and EnvZ/OmpF systems. We also began to discuss microbial communities and environmental stresses such as heat shock response, SOS response, and oxidative stress responses.
Bacterial genetics lab was cancelled on Friday because the Sanger sequencing results weren’t ready. We had planned to do computer analysis of the results.
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.
The Monday before fall break, I had a test in molecular biology on DNA mutability and repair, homologous recombination, site-specific recombination, and transposition of DNA. The Monday and Wednesday after fall break, Dr. Peng reviewed transcription mechanisms in bacteria and eukaryotes.
In biochemistry on Tuesday, we had a review for the test on Thursday. The test covered protein metabolism, enzymes, nucleotides and nucleic acids, regulation of gene expression, and DNA-based technologies. In bacterial physiology, Dr. Roberts reviewed bacterial metabolism, including the Embden–Meyerhof–Parnas (EMP) pathway, the Entner–Doudoroff (ED) pathway, and the pentose phosphate pathway (PPP), focusing on key intermediates, enzymes, and regulators.
In bacterial genetics lab on Friday, we prepared a restriction fragment length polymorphism (RFLP) assay on our PCR products.
In molecular biology on Monday, Dr. Peng discussed site specific recombination of DNA. We learned the mechanism of both tyrosine and serine recombinases, as well as examples of each. On Wednesday we reviewed the two classes of transposable elements and their mechanism of mobilization (cut-and-paste vs. long terminal repeat mobilization). Finally, we went over V(D)J recombination, which is essential in the development of a functional vertebrate immune system. B cell and T cells undergo V(D)J recombination to provide immunity to a wide range of potential toxins.
Last week in biochemistry, we discussed protein metabolism, starting with an overview of the genetic code, such as codon and amino acid pairing. Next, Dr. Popescu talked about the mechanism of protein synthesis. On Thursday, we talked about antibiotics that target translation as well as protein targeting and degradation. In bacterial physiology, we took Test 2 on Tuesday, and began a new section on Thursday on metabolism. The first part was on regulation patterns such as feedback inhibition. We discussed the trp operon as an example of positive regulation and the lac operon in E. coli as an example of negative regulation.
In genetics lab we ran a restriction length polymorphism analysis on colonies selected last week. The results will be compared across the class to see which groups started with the same organisms.
In molecular biology on Monday and Wednesday, Dr. Peng discussed DNA damage and repair mechanisms including nucleotide excision repair, non-homologous end joining, and translesion synthesis. For the honors paper in this class, I decided to write about the molecular biology of preeclampsia, as I have previously researched the pathophysiology of the disease. In biochemistry, Dr. Popescu reviewed DNA technologies beginning with the mechanisms of cloning. On Thursday, she continued with reviews of polymerase chain reaction amplification of DNA, electrophoresis separation of DNA, and DNA genotyping. The second part of the lecture was about eukaryotic gene expression in bacteria.
In bacterial physiology on Tuesday, Dr. Roberts handed back quizzes and midterm grades, answered any questions about any lecture material, and listed important topics for the test on Tuesday. On Thursday, four groups presented papers titled Antimicrobial effects of silver nanoparticles, Capsule switching and antimicrobial resistance acquired during repeated Streptococcus pneumoniae pneumonia episodes, Effects of fermented sumach on the formation of slime layer of Staphylococcus aureus, and Membrane lipoteichoic acid of Streptococcus pyogenes and its stabilized L-form and the effect of two antibiotics upon its cellular content. These papers in addition to all the others presented in class will be on the test on Tuesday, so I have read through the papers again during my studying for the test.
In bacterial genetics lab on Friday, we selected colonies that had the recombinant plasmid. The microbial DNA, if taken into the plasmid, would have disrupted the gene for X-gal utilization. When transformed into E. coli that were plated on an agar with X-gal, the E. coli with non-recombinant plasmids would grow into blue colonies, since they could utilize the X-gal. The E. coli with recombinant plasmids, since they could not utilize X-gal, grew into white colonies. My lab partner and I had fewer colonies than the rest of the class, so we selected all our colonies, while the rest selected white colonies.
This week began with a review in molecular biology in preparation for the first test on Wednesday. The test included DNA and RNA structure, the genome structure and organization, and techniques used in molecular biology labs. On Tuesday morning, I had another review in biochemistry I for the first test on Thursday. Needless to say, I spent a lot of this week studying for both of these tests.
On Tuesday afternoon, two of my bacterial physiology classmates and I presented a PowerPoint summarizing a research paper. We were the first group to present, and I am relieved that I don’t have to worry about doing that later in the semester when there is more going on in other classes. Our paper was titled “Inhibition of Bacterial Cell Division Protein FtsZ by Cinnamaldehyde.” On Thursday, Dr. Roberts started a lecture on membrane bioenergetics, though we only got part way through the lecture on transport through bacterial cell membranes.
I took the two tests on Wednesday and Thursday, and finished up the week in bacterial genetics lab and communications on Friday. In the lab, we ran a gel electrophoresis to visualize the DNA we amplified last week. We also prepared our samples to run in a nested PCR, which will amplify only parts of the genes that were amplified last week. This is sometimes necessary because, while the 18S RNA genes are highly conserved between species, there can still be some differences that interfere with amplification of the gene.
This week began with discussion of the genome in molecular biology. Dr. Peng lectured first on the structure of the genome which involves DNA wrapped around histone proteins to form chromatin. We then learned how the chromatin is regulated to allow access to the DNA that is to be transcribed into RNA.
In bacterial physiology, we finished the lectures on microbial growth and reproduction, focusing on ways to measure growth, the physiology of growth, cell division, and growth kinetics. One of the things I found most interesting in this lecture was the Min system, which works with other regulatory systems to regulate the location of cell division. Min proteins oscillate between the cell poles, blocking the access of FtsZ, a protein which forms a ring at the division site. Since the Min proteins are focused on the cell poles, FtsZ is free to start the septum at the middle of the cell, resulting in two similarly sized daughter cells. The first test in this class was on Thursday, so I spent the first part of the week preparing for it.
On Friday, I went to my bacterial genetics lab, where we began with a brief discussion of PCR primer design before extracting DNA from unknown amoebas. Friday afternoon consisted of scientific communications followed by an extra band rehearsal for the football game on Saturday.