Moving into the final week of the semester, I feel far more confident in myself that previously throughout the semester. The quizzes have not gotten any easier, however the flow of material seems to come with time spent on reviewing right after class or re-reading. I’m typically a visual learner, and will almost always have trouble if I can’t close my eyes and visualize everything from a cell to cell bridge, down to a subunit binding a regulator ligand. Images in the book, and 3D videos on YouTube continue to help me improve my arsenal of visualizations so that I can recall their movements when the necessary time comes. Although not necessarily “difficult” I am still having trouble answering simpler questions such as is the molecule being oxidized or reduced, as opposed to questions asking how the pathway will be affected by removing one enzyme. Going from a large pathway and removing one, I’m able to see what the effects could be. It strikes me when I can’t figure out if the cofactor was reduced, or if anything even did happen to the cofactor, since I put more emphasis on placing the enzymes in the right order.

This week mentioned different types of cell signaling, however the G-protein cascade is a major concept that has been discussed outside of cellular biology class. In biochemistry we talked about the cascade system in terms of reactions vs. studying the pathway. I now am able to decipher that 7TM domain stand for 7 Trans-Membrane proteins due to the 7 connected alpha helices imbedded in the membrane. I know that the B-adrenergic receptors were 7TM receptors found in the muscle or liver cells, and that it was a tetramer composed of an alpha, beta and gamma subunit. The inactive state was the tetramer, however after exchanging a GDP for GTP, the alpha subunit dissociates from the other subunits and becomes active. Further conversation in cellular biology allowed me to learn that the beta-gamma complex is active as well and binds to its own target enzyme or channel, whereas in Biochemistry the alpha subunit was the only part studied in great detail. Furthermore, the cellular biology lecture allowed me to see where exactly cyclic AMP bound protein kinase A, regions on the two regulatory subunits, something seemingly ignored in Biochemistry. The topic of regulation seemed to match the most between the two courses, since there were different levels that the cascade must be “shut-down” at.

Looking into possibilities for my second disease project, I remember lightly looking into Sturge-Weber syndrome a year or two ago. The syndrome affects the development of blood vessels in a newborn, resulting in abnormalities as they grow up. One key staple in identifying this disorder is red “port-wine” marks on the face or limbs, as well as risk of seizures.

The article discusses the effects of Levetiracetem, the generic version of Keppra, an anticonvulsant medication. The article summarizes what happens in the human body during a epilepsy, and the medication’s mechanism of action. The medication binds to the SV2A synaptic vesicle proteins found in the brain. They are characterized by “almost complete absorption, minimal insignificant binding to plasma protein, absence of enzyme induction, absence of interactions with other drugs, and partial metabolism outside the liver.” Connecting back to the originally mentioned syndrome, the blood vessels in the individual develop in such a way that there is random pressure on the trigeminal nerve, causing random episodes of seizures. Following the mechanism of Levetiracetem, how does that properly offset this problem?

The answer is I don’t think it does. The article is a published journal on the effects of Levetiracetem on treatment of Epilepsy. The article mentions how the medication works, and the positive effects, however it does point out that half of patients fail the initial antileptic drug, and 35% are refractive to medical therapy. This means that there is much room for studying and finding more effective ways to deal with convulstion, especially in rare scenarios like Sturge Weber Syndrome.

Abou-Khalil B. (2008). Levetiracetam in the treatment of epilepsy. Neuropsychiatric disease and treatment, 4(3), 507–523. https://doi.org/10.2147/ndt.s2937

Briefly mentioned in class, the p53 gene is responsible for about 50% of all cancers. It was originally believed to be an oncogene due to its presence in cancer cells inducing transformation in gene assays. They have been correctly identified as a tumor suppressor gene. The provided article is collective source material with information about the p53 gene. The article identifies its purpose in the abstract and details the models for p53 activation, p53 effector functions, and a large section on context dependence. Since there are many different circumstances in which p53 causes different effects, there is an implication that context dependence is affected by the type of cell, genetic background of the cell, cell environment, and amount of stress applied on the cell.

The source is reliable and helpful in understanding this concept. The source uses several other articles in PubMed Central, the free archive of biomedical and life sciences academic journals. There is no “opinion” presented, however the conclusion does note that despite the vast amounts of information, “the next imperative duty is to unravel the mechanisms that dictate the biological outputs of the p53 network.” The source accepts that more understanding is necessary to help in treating cancers or other related disorders.

Zilfou, J. T., & Lowe, S. W. (2009). Tumor suppressive functions of p53. Cold Spring Harbor perspectives in biology, 1(5), a001883. https://doi.org/10.1101/cshperspect.a001883

I have spent an extended number of time isolated in my room. Missing out on labs before the quarantine started, followed by sickness throughout the first week or so of online classes has provided more than enough stress for a semester. Stress has been commonly associated with breaking out however no mechanism is ever explained in a typical news post. When stressed the body produces glucocorticoids in response, for example cortisol. If your mouth was swabbed during a stressful situation, the swab would indicate high concentrations of cortisol, given they are even capable of producing saliva in that moment. Cortisol receptors can be found everywhere, one of which causes the adrenal glands to produce more oil. This leads to more acne. I am experiencing this right now, as well as patches of eczema which can also be attributed to stress’ effect on the body during this pandemic.

Genetically-Modified Organisms: An organism that that contains genes that do not originate from the organism itself.

GMO’s can be found in all typical foods, since the FDA has no regulation on notifying consumers on the presence of GMOS.

pGLO/GFP: pGLO is a plasmid of genetic information that codes for many proteins one being GFP, green fluorescent protein which gives off said color when underneath UV light.

The pGLO plasmid is able to be inserted into bacterial cells, that will then grow colonies with the GFP.

Hydrophobic Interaction Column (HIC): A column filled with tiny bead like structures aimed to interact with proteins that show hydrophobic character, having them pass through the column with much more resistance than hydrophilic proteins.

This week’s highlight was in different cell signaling pathways. Usually a similarity in words would help me to understand the functions of different molecules. For example a hekokinase and pyruvate kinase both have similar functions in phosphorylating a molecule using ATP. Seeing the cell to cell adhesions and junctions has just been a confusing chapter. The table made during class was helpful to an extent, however active filaments and intermediate filaments give me the “same name” feel but I’m just almost always confused. Zonula occuldens has an actin filament cytoskeleton, but so does the zonula/macula adherens. Desmosomes are similar but have intermediate filament cytoskeletons. Despite that the zonula/macula adherens and desmosomes use the same transmembrane proteins. Mixing and matching these patterns has been difficult, and has been showing on early quiz attempts. Hardcore studying allows me to temporarily understand, yet forget in the short few hours afterwards.

Zonula occuludens: Tight junctions that act as a barrier, preventing water and ions from passing

The cytoskeleton protein that makes up the zonula occludens are actin filaments.

Zonula Adherens: A intermediate junction that keeps cells from being pulled apart.

This can be seen through cardiac muscle, where a tear could be catastrophic.

Gap Junctions: Regulated channels that allow small molecules and ions to pass through

Gap junctions use connexin in conjunction with complex AP-2.

Defects in IRE1 Enhance Cell Death and Fail to Degrade MRNAs Encoding Secretory Pathway Proteins in the Arabidopsis Unfolded Protein Response

The unfolded protein response is the body’s way to deal with misshaped proteins. Typically they are signaled to be reshaped or edited, in a similar mechanism to DNA when it creates a wrong base-pair. There are cofactors send to reshape the proteins, and if there comes a point where the protein is beyond saving, it will be programmed to undergo cell death.

According to the article, the IRE1 protein is one that catalyzes mRNA splicing of transcription factors as a way to induce the UPR. Essentially, IRE1 leads to UPR, and any errors with IRE1 should prevent this induced UPR. Data supported that IRE1 was involved in splicing bZIP60 mRNA, however the article’s data supports the idea that IRE1 mutants promoted cell death. This effect was not seen in mammals or bacterial cells, which have been previously researched. This increase in cell death is instead seen in the plant Arabidopsis. This suggests that IRE1 may have another function since it wouldn’t make sense that a defective protein had enhanced function.

The source is extremely well rounded noting the contradicting data found in literature, yet presenting the findings in an inconclusive way. The authors admit lack of knowledge and understanding, and implored the world to continue to research this mechanism to see how defective IRE1 could lead to an increase in cell death. Protein mutations could lead to an increased or decreased cell function, however the experiment notes that the IRE1 paralogs studied were just “defective” making this find all the more interesting.

Mishiba, K.-I., et al. “Defects in IRE1 Enhance Cell Death and Fail to Degrade MRNAs Encoding Secretory Pathway Proteins in the Arabidopsis Unfolded Protein Response.” Proceedings of the National Academy of Sciences, vol. 110, no. 14, 2013, pp. 5713–5718., doi:10.1073/pnas.1219047110.

Ran protein: A GTP-binding protein that works in conjunction with importins

RAN/GTP complexes bind to importins which causes disruption in the cargo/importin complex.

Karyopherin: A family of nuclear transport receptors that include importins and exportins

Examples of Karyopherin importins include Snurportin, Transportin, and Importin7.

Nuclear Localization Signals: a small stretch of amino acids that allow a protein to target the nucleus.

The first NLS mapped was by Alan Smith  in 1984.