Bio303finaExam

You have identified a new protein that you suspect is an integral membrane protein with a single transmembrane domain. Which of the following characteristics do you look for in the amino acid sequence to determine if it has a transmembrane domain?

• A stretch of 20 polar amino acids

• A stretch of 20 amino acids that form a beta sheet

• A stretch of 20 hydrophobic amino acids that form an alpha helix

• A stretch of 20 amino acids that form an amphipathic alpha helix

• It is not possible to identify a transmembrane domain with only the amino acid sequence

Which of the following signals targets proteins to the lysosome?

• a hydrophobic amino acid sequence at its N-terminus

• a stretch of basic amino acids

• phophorylation of a tyrosine residue at the C-terminus

• the addition of a mannose-6-phosphate moeity

• the KDEL sequence

A temperature-sensitive mutation in the yeast gene SEC17 causes the accumulation of transport vesicles in the cell at the restrictive temperature. What does this indicate about the role of the Sec17 protein in the cell?

• Sec17 promotes vesicle fusion with the Golgi complex

• Sec17 is important for protein translation at the rough ER

• Sec17 promotes vesicle budding from the rough ER

• Sec17 is important for the formation of the rough ER

• there is not enough information to determine the function of Sec17

Based on its predicted role in mRNA processing, you expect Pro3500 to localize to the nucleus, however you need to determine this experimentally. Which of the following techniques would be the best, most direct method to determine the localization of Pro3500?

• SDS-PAGE and western blotting using an antibody to Pro3500

• fluorescence microscopy using an antibody to Pro3500

• performing a genetic screen to identify temperature senstive mutations in Pro3500

• chromatography followed by mass spectrometry

• flow cytometry

You identify a potential nuclear localization signal (NLS) in Pro3500 that has the following sequence: N-...Pro-Lys-Lys-Lys-Lys-Arg-Lys-Val...-C You generate point mutations within this potential NLS to determine the role of each residue in the nuclear localization of Pro3500. You decide to mutate the third Lys residue of the sequence to a series of different amino acids. Which of the following mutations is LEAST likely to result in Pro3500 becoming localized to the cytoplasm?

• proline

• arginine

• valine

• glutamine

• aspartic acid

Your analysis of the amino acid sequence of Pro3500 identifies a potential nuclear localization signal (NLS), and you perform the appropriate experiments to determine if this sequence is necessary for the import of Pro3500 in to the nucleus. Next, you would like to address whether this sequence is sufficient to act as a signal for nuclear import. Which of the following experiments would show that the identified NLS is sufficient for nuclear import?

• Fuse the Pro3500 NLS sequence to a normally cytosolic protein and observe that it enters the nucleus

• Add additional copies of the Pro3500 NLS sequence to a protein that is normally nuclear and observe that it stays in the nucleus

• Delete the region of Pro3500 containing the NLS and observe that it is cytoplasmic

• Delete the region of Pro3500 that contains the NLS and observe that it stays in the nucleus

• Mutate a single amino acid in the NLS of Pro3500 to lysine and observe that it is cytoplasmic

You predict that Pro3500 has a function during mRNA processing. Which of the following processes is Pro3500 LEAST likely to be involved with?

• 5’ methylguanosine cap addition

• mRNA export from the nucleus

• polyadenylation

• splicing

• co-translational translocation

Which of the following mechanisms is used by cells to ensure that proteins are correctly localized?

• all proteins encode a signal sequence, such as a nuclear localization signal (NLS), to target them

• after translation, most proteins are transported by binding to chaperones in the cytosol, which actively transport them

• proteins are usually synthesized by ribosomes that are pre-localized to the place the protein will be needed

• new proteins are often contained within vesicles/compartments that have a coating or signal on their membrane; these special coatings are recognized by acceptor compartments to permit vesicle fusion

• proteins become glycosylated in the rough ER and Golgi and only proteins with sugar modifications are transported to their correct subcellular location

Metabolic pathways are a series of chemical reactions that occur in cells to generate molecules required for normal cellular function. What strategy is used by the cell’s metabolic pathways to ensure that the appropriate molecules are generated when they are needed by the cell?

• enzymes that lower the Gibbs free energy of metabolic reactions are used

• metabolic pathways are driven by reactions that are at or near equilibrium

• only chemical reactions that are energetically favorable occur in the cell

• energetically unfavorable chemical reactions are coupled to energetically favorable chemical reactions

• only chemical reactions that are irreversible occur in the cell

Vesicle fusion is a complex process involving many types of proteins, including small G proteins, tethering proteins such as Rabs, v-SNARES and t-SNARES. If you consider just the protein-protein interactions that occur during this process, which of the following types of bonds is LEAST likely to be involved in the interactions between different proteins?

• covalent bonds

• hydrogen bonds

• ionic bonds

• van der Waal’s forces

• hydrophobic interactions