BCMB 8020 Exam III 100 points total April 1 2008 Name True False 0 5 point each 10 points total 1 Regarding integral membrane proteins they typically have transmembrane segments that are 10 nm in width they typically constitute 25 of the genes in a typical genome 2 Regarding naturally occurring fatty acids they typically have an even number of carbon bonds they typically have trans double bond configurations when unsaturated they are relatively insoluble in water 3 Regarding prokaryotic protein secretion the Sec system translocates unfolded proteins the signal sequence targeting proteins to the Sec system is retained on secreted proteins Gram positive prokaryotes make extensive use of Type III systems for infection 4 Proteins with a PDZ domain typically bind a phosphorylated target interact with the N termini of proteins that are modified by the methionine aminopeptidase 5 In terms of protease mechanisms an aspartic protease forms an acyl intermediate with its substrates the N terminal product produced by all 4 proteolytic mechanisms would be radiolabeled in the presence of 18O H2O 6 Regarding protease inhibitors PMSF inhibits elastase chymotrypsin and trypsin TLCK inhibits chymotrypsin 7 GPI linked proteins are found in single celled parasites on the extracellular face of the plasmamembrane are anchored in plasma membranes because of their conjugation with a sphingolipid 8 On the topic of protein channels they can be either gated or ungated the aquaporin channel is 5 8 in diameter at its narrowest 9 Regarding the 4 types of transport ATPases discussed in class they can all be manipulated to hydrolyze ATP the P type ATPases represent the largest transporter gene family Multiple Choice 2 points each 28 points total one correct answer per question 10 Which of the following biological membranes does not actively restrict ion movement across it A endoplasmic reticulum B nucleus C peroxisome D plasma membrane BCMB 8020 Exam III Name 11 Which of the following amino acids is not a part of glutathione A cysteine B glutamate C glycine D serine 12 Which of the following is the best source of dietary docoahexanoeic acid A beef B fish C leafy vegetables D nuts and seeds 13 The polar head group on cholesterol is derived from which functional group A an amine B a hydroxyl group C a phosphate group D a sulfhydryl group 14 Cholesterol is similar in size to a fatty acid of which length A C12 B C14 C C16 D C18 15 What is the relative abundance of docosahexaenoic acid in the plasma membranes of neurons by weight relative to other lipid components A 50 B 33 C 25 D 10 16 Approximately what percentage of medically relevant drugs target membrane proteins A 50 B 33 C 25 D 10 17 Which of the following is the binding target of the FYVE domain A PI 3 P B PI 3 4 P2 C PI 4 5 P2 D PI 1 4 5 P3 more commonly known as IP3 18 The FYVE domain requires which ion cofactor A Ca2 B Fe2 C Mg2 D Zn2 2 BCMB 8020 Exam III Name 19 Which of the following is not known to be nucleophile in proteolytic mechanisms A cysteine B histidine C serine D water 20 Which of the following eukaryotic organelle membranes is not known to have an associated ABC transporter A endoplasmic reticulum B lysosome C nucleus D plasma membrane 21 Which of the following typically exists in monomeric form in biological membranes A ABC type ATPase B aquaporin channel C OmpF general porin D P type Ca2 ATPase 22 Based on class discussion which of the following amino acids is least likely to be at the interfacial region of a porin or channel ionophore A His B Phe C Trp D Tyr 23 Which of the following does not contribute to the selectivity of the aquaporin channel A desolvation filter B dipole filter C proton filter D size filter Short Answer These can be answered using one or two keywords lists diagrams and or a few sentences 1 4 points each 31 points total 9 12 24 Using the stick figure method draw the chemical structure of a naturally occurring 18 2 acid 4 points fatty 3 BCMB 8020 Exam III Name 25 Transmembrane segments of which type of secondary structure are not readily identified by existing computer algorithms 1 point 26 What is the common over the counter name for dietary docoahexanoeic acid 2 points 27 List the predominant sequence features and or protein domains of a prokaryotic protein that is destined for secretion via the autotransporter mechanism 3 points 28 List two protein interaction domains that were discussed in class that function similarly to the FYVE domain 2 points 29 What two types of proteases are generally required for production of peptide hormones such as adreno corticoprophin horomone ACTH and endorphin 2 points 30 Why is palmitoylation not an accurate descriptor for this type of lipid based protein modification 2 points 4 BCMB 8020 Exam III Name 31 List the types of lipid modified proteins that do not have a free carboxylic acid at the C terminus 3 points 32 Which lipid is typically found conjugated to mammalian retroviral Gag polypeptides such as HIV Gag 2 points 33 What new paradigm i e pathway did Dr Schmidt describe that expands the known paradigms for mediating signal transduction across biological membranes 2 points 34 List any four of the six domains that make up the Ca2 P type ATPase 4 points 35 List the two types of energy potential used to drive ATP synthesis 2 points 36 What bacterially derived reagent was essential for the experiments used in determining that the translocon channel was open and continuous with the exit channel of translocating ribosomes 2 points 5 BCMB 8020 Exam III Name Long Answer answer the following questions using several sentences highly descriptive diagrams and or highly descriptive lists in the case of the experimental diagram just fill in the appropriate banding pattern 4 8 points each 31 points total Use sufficient detail to convey your knowledge of the material do not use one word responses or diagrams without labels 37 As discussed in class in what two major ways do diagrams cartoons of biological membranes typically deviate from reality 4 points 38 Using the blank template provided diagram the results of a protease protection experiment that you would expect for a plasma membrane PM localized integral membrane protein having an extracellular N terminus Assume that you are using whole cells not microsomes as the source material for the experiment and that your detection assay is based on the immunoblot Western technique 4 points Location of reporter TX 100 Prot K N term C term PM