Cell and Molecular Biology

Cell and Molecular Biology Final Name: Hadeel Binomar30 pts. Protein misfolding can be an aspect of several different human disorders, including cystic fibrosis, Alzheimer's disease, and atherosclerosis. Many times, the misfolded protein is a membrane protein. In fact, a type of diabetes insipidus results from a mutation in the G-protein-coupled vasopressin 2 receptor that prevents the protein from making it to the cell membrane A) Describe how this type of receptor would normally get targeted to the membrane (from the beginning of translation) and B) then propose one mechanism by which the mutation could cause a lack of proper targeting. One of the most important protein's target is G protein-coupled receptors, several signaling mechanisms depend on this type of receptor to change both internal and external stimuli to the intracellular responses. Basically, one of the G couple receptor subfamilies is G-coupled Vasopressin-2- Receptor (V2R), and this receptor is going through a strict quality control process at the endoplasmic reticulum, which presents the only correctly folded protein to gets through the secretory pathway. The primary function of the V2 receptor is to activate the attached G protein that bound to the ? subunit then phosphorylated to GTP. The G protein couple receptor then activates the enzyme adenylate cyclase that catalyzes the reaction in the ER and forms cAMP from ATP. After that, cAMP acts as a second messenger and activates a protein kinase that phosphorylates the integral membrane proteins on the cell surface. Moreover, the secretory pathway organelles' and the plasma membrane both are first introduced into the Endoplasmic reticulum, and the co-translationally proteins that can cross the ER are synthesized by the ribosome first then binds by chaperones to gets moves to the ER surface using GTP that allows them to move toward the receptor then release it. The soluble proteins and the integral membrane proteins as I mentioned above, can be targeted through the ER and then translocated by the same mechanism.Further, several mutations occurring in the transmembrane region which affect the structure of the protein. These are multiple mutation sites, such as mutations occurring in the amino acid residues which was acting as a causative agent for human disease. Also, there are other mutations occurring on the single site position that will affect the translation mechanism and cause many human diseases like: cystic fibrosis, Alzheimer's disease, and atherosclerosis that proves the function of V2R protein which plays important role in the translation during the protein folding process. One of the mechanism that may a reason for lacking the proper target protein is when the mutations of the CFTR gene occurring and affect the function of the chloride ion channels and cause defect in the protein sequences which lead to the production of diseases and misfolded of the proteins that are unable to recognize their functional destinations. Otherwise, Lack of the stop signals is another issue that prevents the protein from getting into the surface of the ER, also called the non-stop decay cellular pathway, because lack of this stop signals prevents mRNA from synthesis and translate the proteins, these consider as a point mutation that inhibits the essential stop codons. 30 pts. Describe the experiment shown in figure 3 from the paper we discussed in class (Miller et al, 2003). (A) In your description, consider the following questions: Why did they do it? How did they do it? What did they learn? (B) Diagram the results that you would expect to see in Lanes T, 1, 2, 3, and 4, if the amino acid signal DID in the protein Gap1p was mutated to random amino acids and tell why; and (C) Give two possible (different) results that might occur if the amino acid signal LxxLE in Bet1p was mutated to the amino acids DID (which are the signal in Gap1p). Diagram the results expected in Lanes T, 1, 2, 3, and 4 and explain why you predicted this result for each case.left20840701.A001.A4467225201739500The experiment was performed to study the role of cargo binding domain of Sec24p in the process of protein sorting. To perform this study, both mutant and wild types subunit Sec23/24p and Sec23/24L616W were harvested from microsomal membranes. The immunoblotting assay performed to quantify cargo molecules using radio-labeled secondary antibodies. Comparison of the mutant subunit with wild type illustrated omission of some molecules in mutant one, these molecules were cargo protein molecules. While some of them are packed in a way that similar to the wild-type. It meant that there were some signals that remained unaffected although mutation was there. Unexpectedly, it was found that in these unaffected molecules of mutation in Sec23/24p, packaging was better than the wild type. Further, they found the proteins that were highly affected had Bet1p and Gap1p/Sys1p chimera, because they completely depending on the Sys1p di-acidic of COPII vesicles. If the amino acid signal DID in the protein Gap1p was mutated to random amino acids, the resulting bands would be seen as in figure 1. A because the amino acids might be present in all the lanes. And Gap1p is required for di-acidic motifs to fuse together with the COPII vesicles at the mutated domain. Also, Sys1 peptide is not involved in Sec 23/24p hence its mutation is not contained in a di-acidic motif. If the signal LxxLE was mutated to the DID, the expected Bet1p packaging would be shown in figure 2. A as not be seen in lanes containing Bet1p because the amino acid signal LxxLE does not exit after mutating to amino acids DID. The second probability for the Bet1p would be expected to bind with the vesicle for packaging when it interacts with di-acidic motifs which is needed as shown in figure 2.B290512515621000581025113030004781550412752.B002.B6286501346202.A002.A20 pts. Explain the experiment shown in Figure 5C from the Shen et al. (2018) paper on the phosphorylation of CDC25 that we discussed in class. In addition, be sure to also address the following: A) why did they do this experiment (the central issue); B) what did they learn; and C) what is another control experiment they could have done? D) Would these results change if you added a constitutively active form of LKB1 to the reaction? If so, how and why? A) Overall, the main purpose of this paper is to explain how the division of cells is highly regulated such that cells that fail to pass some specific stage-based tests cannot advance to the proceeding stages. In this particular experiment, HeLa cells were subjected to chemicals that are known to activate the enzyme AMPK. Also, the main catabolic processes that are involved to generate energy for cells to transition from G1/G2 were determined by the application of radiochemical approaches, the experiment required to approve how highly conserved cellular energy sensor can significantly delay mitosis entry and activation of AMP-activated protein kinase (AMPK). Further, Wee 1 family inactivates the cell cycle G2/M Phase which is controlled by Cdc3/cyclic B (mitotic cyclin-dependent kinase complex). They found that AMPK-dependents phosphorylation of CDC25C arranges a metabolic control point for the M-phase transition and the cell cycle phase G2. B) Also, they learned that suppression of Wee 1 or acute induction partially reinstates mitosis ingress in the circumstance of activated protein kinase (AMPK). This experiment showed that when Phosphorylates Cdc25 is in a distributive and disordered state, it results into ultra-sensitivity in protein phosphorylation. C) For another control experiment, they might try exposing the U2OS (cell line) clones conditionally exhibiting Cdc25A etoposide. That will help to test whether Cdc25A degradation is significant for the G2 control point or not.D) If they add an active form of LKB1 to the reaction, the results will not change, because in cells LKBI activity inhibits AMPK activation in response to different stimulations. Also, LKBI is lost upon consistent isolation and therefore no effects of phosphates observed.20 pts. Briefly describe the role of cyclin-CDK in the cell cycle and give an example of positive and negative control in this system. Also, describe how cell cycle regulation links to the stimulation of apoptosis at the molecular level. In the beginning, the cell cycle depends on many basic factors that control the regulation process starting from the signal transcription molecules, growth factors and the Cyclin Dependent Kinases enzymes include the checkpoints which control the transition process between the cell cycle phases by binding to the cyclin proteins CDKs then phosphorylate other proteins to transfer from one phase to another. The role of transcription factors is to turn on the signals for gene expression, DNA replication, and cell divisions. As an example of CDKs, cyclin-dependent kinase 1 CDK1 is a cell division cycle protein homolog 2, that has a primary role in human cancer cells because CDK1 rather than any types of CDKs is fatal to the mutated version of MYC- dependent cancer that leads to a depletion of oncogenes like (Fos and Jun) in human cancer cells. Fos and Jun are combined forms of the transcription factor called AP1 that activates the delayed response genes such as cyclin D and CDK4. Recent studies reveal that the reason for the MYC breast cancer cells duplation is targeting CDF1 exhibit any other CDKs cell lines. Also, CDK1 inhibition can control and target the cancer cells in human and both phosphorylation and expression of MYC during the cell cycle process. To initiate intracellular signaling pathways and stimulate the cell cycle entry, mitogens substance bind to the cell surface receptor with the activation form of GTPase Ras that activates MAP kinase cascade. That will lead to the expression of encoding gene of the transcription regulatory protein like MYC. Moreover, E2F transcription factor is a target for cyclin D and CDKs that stimulate proteins expression to initiate S phase, also E2F regulated by the tumor suppressor gene Rb (Retinoblastoma protein). At early G1 Phase, Rb protein combined with E2f to form the histone deacetylases protein that remains chromatic condensed, then cyclin kinase phosphorylates Rb protein, causing it to disassociate from E2F. That allows recruitment of histone acetylates, which decondense the chromatin and helps transcription complexes to form in G1 and S phase and to form a positive feedback. For the negative control, if there are no growth factors present to stimulate the synthesis of Cyclin D in the new cell, Rb phosphorylated will turn off, and Rb will rebind to E2F, then the cell cycle will stop and that will lead to many negative results like prevent it to bind with DNA, or DNA damage and cells will return to the G0 phase. Apoptosis is a consequence of DNA damage; if the damage is not repaired, the cell cycle will divert towards apoptosis, otherwise, if the cell has DNA defects and fail to undergo apoptosis, that will change to the cancer cell. G1 phase regulators such as P53 and E2F are essential to promote the cell regulations and eliminate any damage or abnormal changes during the cell cycle. P53 has a primary function to prevent any mutation in DNA during cell progression, so any defect in P53 will lead to cancer, and it's usually mutated in cancer cells. Further, Rb protein considers as a tumor suppressor and also promotes apoptosis. Additionally, most human cancers have inactive Rb protein, either mutated Rb or the non-phosphorylated (inactivated form) of Rb protein