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Purdue BIOL 10200 - Focus Questions #4 (Protein Structure and RNAi)

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1. How can micro RNAs (miRNAs) affect gene expression? How can small interfering RNAs(siRNAs)? How do miRNAs and siRNAs differ?miRNAs can interfere in gene expression by getting “loaded into” the RISC and getting attached tomRNA, preventing the mRNA from being translated by the ribosome during translation.Alternatively, they can outright degrade the portion of the mRNA so it becomes unreadable.siRNAs are also loaded into the RISC, but they cleave the mRNA so it cannot be translated. BothmiRNAs and siRNAs are transcribed from portions of DNA.miRNAs are more versatile (one type of miRNA can silence or degrade many portions of the DNA)and they can silence portions of the mRNA far from where they originated. siRNAs are morespecific and only operate close to where they originated.2. Are ribosomes directly anchored to the RER? How do they get to the RER in the first place?How do proteins enter the RER?Ribosomes are not anchored to it. Instead, it is anchored to the RER. In the event a protein (aka apolypeptide chain) needs to be exported or sent to the surface of the cell, it begins with a signalsequence, and once the ribosome moves towards one end of the cytoplasm, that signal sequenceis recognized by a protein called the signal recognition participle (SRP). At this point, theribosome and the growing polypeptide chain docks, and the SRP directs it to a growing proteinchannel that leads into the RER.3. Does gene expression end with translation? That is, are all proteins active as synthesized? Howdoes this relate to the genotype phenotype relationship?No, it’s not the end, and not all proteins are active as synthesized; the protein chain is furthermodified in the RER. This is important for the genotype phenotype relationship because certainproteins that were coded for (genotype) might be different from what actually happened in the body(phenotype). For example, acetylation alters gene expression, cleavage makes multiple proteinsfrom one, and ubiquitination tags them for destruction.4. Give 2 examples of post-translational modifications and how they might affect a protein.1. It can be cleaved into smaller polypeptides. This can result in multiple hormones comingfrom the same protein. Additionally, many enzymes are purposefully made inactive and theyonly activate once they are chopped up, so that way the cell has time to prepare a substratefor them to even act on.2. It can have sugars added to it (glycosylation). This results in “glycoproteins,” whichdetermine blood type.3. It can have PO4groups added to it (phosphorylation). This “activates” proteins so they canbe used in other parts of the cells.4. It can have ubiquitin added to it (ubiquitination). This “tags” the proteins so theproteasome can break them down if they need to.5. It can have an acetyl group added to it (acetylation). This is important for epigenetics, whichis the practice of altering gene expression without changing the DNA.6. It can have the signal sequence removed, since it was only necessary for docking.7. It can have the N-terminal methionine removed, since that methionine was only needed forthe START anticodon and is no longer needed.5. What are the different levels of protein structure? How are they interrelated? Do all proteinsshow all levels of structure? What are motifs and domains and how are they related to proteinstructure?The primary level is the actual sequence of amino acids determined by the mRNA (and DNA). Thesecondary level is the shape taken on by the peptide backbone of the amino acids, and itencompasses both alpha-helices (a coiled structure made of rigid rods) and beta-sheets (parallelarrays of planar sheets). The tertiary level is the actual 3D shape that is taken on by a polypeptide.The quaternary level is the overall shape taken on by many different polypeptides. The primary leveldetermines all future levels of the proteins. Not all proteins share the same levels of structurebecause the quaternary level is absent in proteins with only one polypeptide.Motifs are the repeated units of the secondary structure, and domains are the repeated structuralunits of the tertiary structure.6. What factors contribute to stabilizing protein structure?● Hydrogen bonding stabilize the secondary structure● Electrostatic interactions (/ionic bonds) on the R-groups of the amino acids● Some protein groups have sulfhydryl (SH), and the sulfurs can bond together in disulfidebridges (S-S), which stabilizes protein structures● Van der Waals interaction (attraction of nonpolar groups to each other)● Hydrophobic exclusion (bury hydrophobic R groups in interior)7. Can we predict tertiary structure from primary sequence? Is there any relationship betweenthese levels of structure? Do we have any experimental evidence to support this?We cannot perfectly predict the tertiary structure from the primary structure, and a major reason isthat during folding, the protein enters a glob-like intermediate stage called molten globule.That being said, we do know the primary structure determines the secondary and tertiary structures.We’ve done experiments before where we denature proteins (which, again, destroys the shape ofthe secondary and tertiary structures but leaves the primary structure intact), put them back in theiroriginal environments and they “renaturate” back to the secondary and tertiary structures. Thisproves that primary structure always results in the proper secondary and tertiary


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