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 to mRNA 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 Both miRNAs 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 more specific 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 a polypeptide chain needs to be exported or sent to the surface of the cell it begins with a signal sequence and once the ribosome moves towards one end of the cytoplasm that signal sequence is recognized by a protein called the signal recognition participle SRP At this point the ribosome and the growing polypeptide chain docks and the SRP directs it to a growing protein channel that leads into the RER 3 Does gene expression end with translation That is are all proteins active as synthesized How does 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 further modified in the RER This is important for the genotype phenotype relationship because certain proteins 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 proteins from one and ubiquitination tags them for destruction 4 Give 2 examples of post translational modifications and how they might affect a protein 1 2 3 4 5 6 It can be cleaved into smaller polypeptides This can result in multiple hormones coming from the same protein Additionally many enzymes are purposefully made inactive and they only activate once they are chopped up so that way the cell has time to prepare a substrate for them to even act on It can have sugars added to it glycosylation This results in glycoproteins which determine blood type It can have PO4 groups added to it phosphorylation This activates proteins so they can be used in other parts of the cells It can have ubiquitin added to it ubiquitination This tags the proteins so the proteasome can break them down if they need to It can have an acetyl group added to it acetylation This is important for epigenetics which is the practice of altering gene expression without changing the DNA 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 for the START anticodon and is no longer needed 5 What are the different levels of protein structure How are they interrelated Do all proteins show all levels of structure What are motifs and domains and how are they related to protein structure The primary level is the actual sequence of amino acids determined by the mRNA and DNA The secondary level is the shape taken on by the peptide backbone of the amino acids and it encompasses both alpha helices a coiled structure made of rigid rods and beta sheets parallel arrays 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 level determines all future levels of the proteins Not all proteins share the same levels of structure because 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 structural units 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 disulfide bridges 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 between these 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 is that 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 of the secondary and tertiary structures but leaves the primary structure intact put them back in their original environments and they renaturate back to the secondary and tertiary structures This proves that primary structure always results in the proper secondary and tertiary structure