10303 Comprehensive Fil True/False Indicate whether the statement is true or false. ‘True (A) or False (B): Enzymes lower the overall AG of a reaction. a. True b. False True (A) or False (B): The molecular defects in cancer cells can be different in different cell types. a. True b. False True (A) or False (B): Rigor mortis illustrates the fact that, in the sarcomere, myosin headgroups remain bound to actin filaments when no ATP is available. a. Tre b. False ‘Muttiple Choice Identify the choice that best completes the statement or answers the question. 4. Which of the following is a property shared by eukaryotic and prokaryotic cell types? a. membrane-bound nucleus membrane-bound organelles ¢. usually 5-10 microns or larger 4. molecular structure of plasma membrane and genetic information e. cells are non-motile Why might cystic fibrosis patients be less susceptible to cholera? a. CF patients have a defective membrane protein, CFTR, that is unable to secrete choride and fluids in the intestine in response to cholera toxin b. CF patients have a defective membrane protein, CFTR, that is hyperactive and secretes more choride and fluids in the intestine than normal in response to cholera toxin ©. CF patients have a defective cytoplasmic protein, CFe, that sequesters choride in the intestinal cells in response to cholera toxin 4. cholera toxin activates heterotrimeric G-proteins, but these G-proteins are mutated to loss-of-function in most CF patients €. cholera toxin activates heterotrimeric G-proteins, but these G-proteins are already consitutively active in most CF patientsName: Which of the following is/are examples of covalent bonds? hydrophilic interactions between water and lipid head groups hydrogen bonds between molecules in the aqueous cytoplasm phosphorylation of proteins by kinases in a signal transduction cascade interactions between amino acids that result in secondary structures like alpha helices ¢. transcription factors bound to DNA during transcription Phosphatidylcholine, phosphatidylserine, and sphingomyelin are all examples of a. amphipathic membrane lipids 4. lipids with 24-carbon fatty acid tails b. hydrophobic membrane lipids ¢. phosphoinositol signaling components . major signaling molecules You have discovered a novel protein and use the amino acid sequence (303aas) to generate a hydrophobicity plot. You find 5 significantly hydrophobic regions: 2 are about twenty amino acids long, 2are ten amino acids long, and 1 is five amino acids long. From this data, how many transmembrane domains would you predict the protein to have? a 0 a4 b& 1 e 5 e 2 Which of the following statements about light microscopy is FALSE" a. Fluorescent light microscopy can be used to observe living cells. b. The maximal resolution obtainable by light microscopy is determined by the lenses used (numerical aperture), the media between the specimen and objective, and the wavelenght of light. ¢. The maximal resolution obtainable by light microscopy is determined by the lenses used (numerical aperture), the polarizers, and the thickness of the specimen. 4, The maximal resolution obtainable by light microscopy is about 200nm ©. Light microscopy is a good method for identifying where a particular protein is localized within the cell, if the protein can be labeled with a tag or by antibody. With respect to the Na+/K+ ATPase, which of the following is TRUE? a. This pump stores energy in the form of electrochemical gradients that is only required for nerve activation. b. Ions move more slowly through a pump than a channel because the movement of 3 Na+ and 2K+ molecules can only occur once per ATP hydrolysis instead of continuously. ¢. Ion movement via the Na+/K+ ATPase is an example of passive transport. d. The crystal structure of this molecule has yet to be determined. ¢. The Na*/K+ ATPase is unique in that itis the only ion pump that moves ions against a concentration gradient.Name: 14, For the reaction A + B <-> C+D, with AG* spontaneously proceed to the right? Recall the equation AG = AG%+ (1.4kcal/mol ) log ({C}[0]/IAI(81) (and recall that log 10 = 1, log 1= 0, and log 0.1 = -1 ) 1.0 kCal/mol, under what conditions will this 4. [A]={8]=[C], [A] = 10, [0] = 100 €. none of the above . An important aspect of transport by facilitated transporters and pumps is... a. they are always active 4. alpha-helices b ymational changes €. beta-pleated sheets ¢ ty {Cl-] inside a cell is usually about 10mM and [Cl-] outside a cell is about 100mM, If you discover a new Cl- channel that is voltage-gated, in which direction(s) will the Cl- ions flow at the activating voltage? a. inward ¢. equally in both directions b. outward cell junctions For the following 3 questions, refer to this schematic of cell junctions. What kind of cell is depicted in the schematic? a. hematopoietic stem cell 4d. migratory cell b. neuron ©. myocyte c. epithelial cellName: 15 Which of the junetions in the schematic depicts molecules that can bind to fibronectin and are known for inside-out signaling as well as outside-in signaling? a A d D b. B €. two of the above . C Refering to the schematic, which junction depicts cadherin molecules in an adherens junetion? a A dD b. B €. two of the above « C ‘The extracellular matrix provides tensile strength to tissues such as the skin, and also acts as a cushion or gel. Which of the following ECM components act as a gel in animal tissues, largely by association with water? a, glycosaminoglycans and proteoglycans b. collagen and laminin cc. keratins and integrin 4. cellulose and pectin ¢. glycolipids and cholesterol Microscopic beads are coated with dynein and subjected to an in vitro mobility assay. In what direction and along what cytoskeletal element are they seen to move? toward the plus end of the microtubule toward the minus end of the microtubule toward the plus end of the microfilament toward the minus end of the microfilament ¢. toward the plus end of the intermediate filament A paper published this month from the Jensen laboratory (Pilhofer et al) in PLoS Biology describes what the authors call “bacterial microtubules (bMTs)”, which they argue evolutionariliy preceded eukaryotic microtubules. Unlike FtsZ which is one molecule that polymerizes into filaments, bMTs are comprised of heterodimers of tubulin A and B molecules. Pilhofer et al show that bMTs polymerize in the presence of GTP and have 5 protofilaments arranged in a hollow tube. Which of these characteristics of bMTs makes them different from eukaryotic microtubules? a, heterodimers instead of polymers of one subunit using GTP instead of ATP the hollow tube the number of protofilaments all of the above aegeName: ‘A primary paper published this month in PLoS Biology examines actin dynamics in newly-possible detail. Use these figures from Jegou et al (2011) to answer the following 2 questions. A mete 8 i is : I io “oe ee i $ aM ® = ~ ~~ 10uM : ‘80uM +. age of F-actin) © peceeennene e Facin lone 016=007 S804 "0.0068=00021 with saraating 47=04" —$14229" 6103" 00065-00006" prot ok259224 4M forthe binding of profin to MgADP-Phactin at the barbed ond. Pk.=28.125.1 uM forthe binding of profi to MgADP-actin at the barbed end, steosured at 100 uM oof, do 10.137 journal pie-1001161:001 Precisely how the Actin binding protein Profilin functions is unclear. Panel B shows the reciprocal of the velocity of actin depolymerization as a function of time (age of actin filaments) for 3 different concentrations of Profilin: 5, 10, and 80 micromolar. At what concentration of Profilin is actin depolymerization fastest, and what (approximately) is the resulting highest depolymerization velocity?” a. 80, 0.025 d. 5,15 b. 80,40 © 5,017 ce. 10, 0.12 Panel C diagrams the reactions of dephosophorylation of Actin subunits and subsequent depolymerization of the filaments. According to the data in table E, does Profilin have a higher affinity for binding actin-ADP with or without the inorganic phosphate? a. with ¢. no difference b. withoutName: 22. 23. How does the kinetochore function to prevent chromosomal abnormalities? a, proteins at the kinetochore act in the G1-S checkpoint to block cell division until all kinetochores are associated with spindle tubulin fibers b. proteins at the kinetochore act in the G1-S checkpoint to block sister chromatid separation and cell division until all kinetochores are associated with spindle tubulin fibers ©, proteins at the kinetochore act during cytokinesis to block cell division until all kinetochores are associated with spindle tubulin fibers 4, proteins at the kinetochore act in the spindle assembly checkpoint to block sister chromatid separation and cell division until all kinetochores are associated with spindle tubulin fibers e. all of the above Using the generalized “cartoonish” diagram of an universal eukaryotic cell shown on the last exam page, answer the following 5 questions: Where can ATP be synthesized ° (be sure to include all possible locations) a a8 b. #o+HS c. #5 d. #il e #5+#11 ‘Where do the steroid receptors “act”/function in the classical steroid hormone signal transduction pathway after they bind their specific steroid hormone? a #4 b. 4s c #8 a 49 e #1Name: 25. Most of the proteins that end up in structure #5 are initially synthesized in structure # ? a #4 b. 4S c. H6 a #8 e #il 26. Which process is shown in region #7 in Zone D ? a. exocytosis b. endocytosis apoptosis 4. COPI induced vesicle formation €. COP Il induced vesicle formation 27. The addition of N-linked oligosaccharides to new glycoproteins begins in Zone _? and is completed in Zone a CD b. DC © GC d. D:D e BC 28. The main and immediate “purpose” of electron transport in mitochondria a. to synthesize ATP b. to oxidize pyruvate to CO; and H,0 €. to create a proton gradient across the inner membrane 4. to transport electron across the inner membrane to the matrix compartment €. toneutralize the positive charge present in the mitochondria matrix.Name: 29. ‘The sequence and structure of the carbohydrate “bushes” on glycosylated proteins is determined: 30, 31 32. a b, ©, 4. e by a specific amino acid “signal” in the nascent protein. by the sequence of the amino acids in the nascent protein acting as a template. by the complex which “edits” the information initially found in the precursor mRNA. by the nature of the glycosyl-transferases and their substrates. by particular membrane proteins which “flip” the bush attached to dolichol. Membrane phospholipids are synthesized: in the cytoplasmic leaflet of ER membranes and then distributed to other membranes and. leaflets. in the cytoplasmic leaflet of all membranes, and then some are “flipped” to the other leaflet. in the cytoplasm and then moved to all membranes by specific lipid carriers. in the golgi membranes and then distributed to other membranes via vesicles and carriers. in specialized “lipidsomes” and then distributed to other membranes, Movement of large proteins across the Nuclear Envelope into the nucleus involves clathrin-dependent endocytosis. involves energy-dependent diffusion through the nuclear pore complexes. involves ATP-dependent “molecular motors” to move them across involves the use of signals which are covalently attached to the macromolecules by specific enzymes. involves the use of “carriers” which diffuse across the pore complexes, releasing the protein in the presence of RanGTP. In terms of protein trafficking through a human cell after synthesis, the “default” pathway for a protein with no coded “signal a. to stay in the cytosol. b. toenter the nucleus. ¢. toenter the mitochondria. 4. toenter the rER system €. tobe secreted.Name: 33 34, 35 36. ‘One of the most important functions of the “proteasome” in human cells is: ‘a, tobe the site of modifications (such as glycosylation) of newly synthesized proteins bb. to be the site of destruction of cytoplasmic proteins. c. tobe the storage site for newly synthesized proteins destined for future secretion. 4. tobe the complex that is transported through the nuclear envelope. , to synthesize proteins. If you destroy your SER in your liver by drinking too much alcohol, what might happen? a, the metabolism of your steroid hormones affecting your sexual characteristics would now be defective. b. you would become diabetic because your liver cells could no longer generate ATP from glucose. ¢. nothing much since the liver rER is partially redundant with the liver SER. d. your liver would actually be able to detoxify molecules more efficiently €. nothing, since this is a “trick” question -- liver does not have sER; only your gonads, kidneys, and hormone synthesizing tissues of your brain have sER, ‘The importance of “clathrin” protein in eukaryotic cells is that a, its the important coat protein required for endocyt b. itis an important protein required for the docking and fusion of exocytotic vesicles with the plasma membrane. . itis an important coat protein for the movement of material from the ER to the Golgi. 4d. it has the enzymatic properties needed for vesicles to “pinch off” from the plasma membrane. . it is the receptor that binds specific proteins in “receptor mediated endocytosis”. ‘The major function of lysosomes in eukaryotic cells is 1, toact like a “garbage disposal” for the destruction of cytosolic proteins “tagged” with ubiquitin. b, to digest all types of macromolecules that enter the cell via endocytosis. . to serve as the “sorting station” where the cells “decides” which molecules are to be later digested and which molecules are to be sent to the plasma membrane. 4d. to.use its internal acidic high concentration of protons to synthesize ATP. €. to serve as one of the cell’s sites of protein glycosylationName: 37, 38, 39. 40. ‘An important property of X chromosomes in human: ‘a. one of the pair of X chromosomes in females never “decondenses” and so remains inactive in each cell. b. since it is a “sex” chromosome it has a different structure. c. the observation that they are missing in males. 4. that their nucleosomes do not condense into 30 nm chromatin fibers. €. they have a special set of histone proteins, The reversible modification of histones (“histone code”) is important because: a, itis involved in the regulation of transcription of specific genes. b. it is required for the structure of nucleosomes. a result of the histones being processed in the rER after th I synthesis. 4. they determine the replicon origins in chromatin. . they are present in cells undergoing meiosis and gamete formation instead of mitosis ‘Telomeres are: a. found in cells ranging from bacteria to plants and animals. b, involved in the control of the cell cycle. ¢. one of the transducers in a specific human signal transduction pathway. d, unusual in their mode of synthesis because containing a “built-in” RNA template. wolves a reverse transcriptase activity €. important in determining the location of the kinetochore. ‘The “signal hypothesis” (actually more than an “hypothesis includes the concept that: since itis supported by lots of experimental data) a. part of the amino acid sequence of a protein determines its fate or ultimate cellular location. b. it is important for eukaryotic cells and not for prokaryotic cells which do not need it c. the transduction of the “information” of the signal is used to activate effectors such as adenyl cyclase. 4d. glycosylation occurs in both the ER and the Golgi ¢. for most cytosolic proteins in eukaryotic cells, cotranslational synthesis is involved.Name: al. 43 44, ‘The signal that is found in lysosomal proteins that is used in the sorting within the Golgi is: . an amino acid sequence at the N-terminal end of the protein. b, an amino acid sequence surrounding an asparagine in the middle of the protein. ‘¢aphosphate group on a serine amino acid in the protein 4. a phosphate group on a tyrosine amino acid in the protein. ‘¢. a phosphate group on a sugar group on the protein. ‘The initial “transducer” in the signal transduction pathway that results in the activation of Protein Kinase A is: a. the plasma membrane protein receptor. b. the tracellular protein receptor that activates protein kinase A. ¢. the plasma membrane enzyme that catalyzes the formation of the intracellular messenger. 4. cyclic AMP molecules. ©. the protein that activates the enzyme that makes CAMP. In the RAS signaling transduction pathway (often mutated in human cancers), how is RAS actually activated ? a. it binds a GTP, stimulated by the SOS protein acting as a GEF. b._ithydrolyzes GTP, since RAS is a GAP. c. it is phosphorylated by the tyrosine kinase receptor (dimerized) 4. itis stimulated by the Ca++ ions released from the ER by IP3 . the inhibitor bound to inactive RAS is “removed” (no longer binds) when phosphorylated by MAPKKK, What would happen iffan eukaryotic organism had a mutation that prevented the synthesis of dolichol phosphate? a, all protein synthesis would be blocked. b. all transcription would be blocked. ‘c. the cotranslational movement of proteins destined for the rER lumen would be blocked. d. receptor mediated endocytosis would be blocked. €. protein glycosylation would be blocked.Name: 45 46. 47. 48. “High energy” electrons are donated to the electron transport system of mitochondria by: a. highly reduced Co2 b. NADH c. FAD d. 02 NAD+ Which of the following is NOT a “second messenger” whose cellular level is affected by binding of an extracellular messenger/hormone/ligand to eukaryotic cells? a. diacylglycerol b. cyclic AMP ©. cyclic GMP 4d. nitric oxide €. growth factor What drives the rotation of the axle in the F head of ATP Synthase in “happy” functioning mitochondria ? a. proton movement from intermembrane space to the matrix bb. proton movement from the matrix to the intermembrane space ©. ATP hydrolysis 4. ATP synthesis €. movement of electrons down the electron transport chain The interaction between almost all hormones and their receptors involves which common characteristic? The hormones move through the plasma membrane and then bind specific proteins. b. There is a covalent bond formation between the hormone and its receptor ©. the hormones bind to protein receptors and are then endocytosed into the cytoplasm where they act 4. There is a low affinity non-covalent interaction between them e. The a high affinity non-covalent interaction between them.Universal E UKargotic Cer(