Cell Structure & Function Exam #3

Extra Credit Question: 1) The experience of working with the RCC1 protein during his Ph.D. program made Dr. Azuma feel like a ? 2) Protein kinases in the Ras signaling pathway was discovered and named by a ? scientist.

1) 3D-looser 2) Japanese

Would the following process occur via endocytosis or exocytosis? A) A cell releases a hormone into the extracellular space B) A macrophage engulfs a bacterial cell

A = Exocytosis B = Endocytosis (specifically phagocytosis)

Can you tell me what each of these portions of the endomembrane system are?

A = Nuclear Envelope B = Endoplasmic Reticulum C = Golgi Apparatus - Can you tell me which side is cis and which is trans? (cis is closest to ER, trans faces Plasma membrane) D = Early Endosome E = Late Endosome F = Lysosome Now quiz yourself on the function of each of these organelles. Try to talk your way through the process moving outward and inward of what would be happening to the cargo inside of one of these vesicles.

Short Answer: Vesicle Formation in a Tube The budding of clathrin-coated vesicles from eukaryotic plasma membrane fragments can be observed when adaptins, clathrin, and dynamin are added to the membrane preparation. What would you expect to observe if you failed to add: A) Adaptins? B) Clathrin? C) Dynamin?

A) Without adaptins, there would be no vesicles formed. This result occurs because clathrin coats cannot assemble in the absence of adaptins that link the clathrin to the receptors and membrane. B) Without clathrin, you would expect to observe adaptins still bound to the receptors in the membrane, but no clathrin coat can form and thus, no clathrin-coated pits or vesicles are produced. C) Without dynamin, you would expect to observe deeply invaginated clathrin-coated pits forming on the membrane, but these pits do not pinch off to form closed vesicles

Label The Mitochondria

A: Inner Mitochondrial Membrane B: Outer Mitochondrial Membrane C: Mitochondrial Matrix D: DNA E: Ribosomes F: Inter-Membrane Space G: Cristae

Label the Following Parts of the Chloroplast:

A: Thylakoid Membrane B: Stroma C: Outer Membrane D: Inner Membrane E: Grana

Which of the following statements about vesicle budding from the Golgi is FALSE? A) COPII can initiate vesicle budding on Golgi membrane. B) Some vesicles budded from Golgi membranes move towards ER. C) Once vesicle budding is completed, clathrin molecules are released from the vesicle. D) Clathrin molecules act at the cytosolic surface of the Golgi membrane.

ANSWER: A COPII can initiate vesicle budding on Golgi membrane.

Which of the following statements about molecular switches is FALSE? A) Phosphatases are responsible for removing the phosphate from GTP on GTP-binding proteins for turning them off. B) Protein kinases transfer the terminal phosphate from ATP onto a protein to phosphorylate a protein. C) GTPase activating protein can turn activated small GTPase off. D) A GTP-binding protein exchanges its bound GDP to GTP for its activation by the help of its GEF.

ANSWER: A Phosphatases are responsible for removing the phosphate from GTP on GTP-binding proteins for turning them off.

When a signal needs to be sent to most cells in the multi-cellular organism the signaling molecule most suited for this is a ___________________. A) Neurotransmitter B) Hormone C) Dissolved gas. D) Plasma membrane anchored ligands.

ANSWER: B Hormone.

Which of the following statements is FALSE? A) The signal sequences on mitochondrial proteins are first bound to translocator on outer membrane after translation. B) Most mitochondrial proteins are not imported from the cytosol but are synthesized inside the mitochondria. C) Chaperone proteins in the mitochondria facilitate the movement of proteins across the outer and inner mitochondrial membranes. D) Mitochondrial proteins cross the membrane in their unfolded state.

ANSWER: B Most mitochandrial proteins are not imported from the cytosol but are synthesized inside the mitochondria.

Which of the following statements is TRUE? A) MAP kinase activates MAP kinase by phosphorylating it. B) PI 3-kinase phosphorylates a lipid in the plasma membrane at cytosolic side. C) Activated Ras binds to Adenylyl cyclase to produce cyclic GMP. D) Second messenger molecular only increases the strength of signal but not provide diversity of the signals.

ANSWER: B PI 3-kinase phosphorylates a lipid in the plasma membrane at cytosolic side.

Which of the following statements about signal transduction is FALSE? A) Ca2+ concentration in the cytosol will increase when PLC (Phospholipase C) is activated by a signal. B) Cyclic GMP is made in smooth muscle cells when they receive NO signal. C) SH2 domain containing proteins is expected to bind to inactive RTK (not binding to ligand). D) Ligand binding to RTK promote dimerization of the RTK.

ANSWER: C SH2 domain containing proteins is expected to bind to inactive RTK (not binding to ligand).

Which of the following statements about what happens when a G-protein-coupled receptor activates a hereto trimeric G protein is TRUE? A) The Beta subunit exchanges its bound GDP for GTP. B) The GDP bound to the the Alpha subunit is phosphorylated to form bound GTP. C) The Alpha subunit exchanges its bound GDP for GTP. D) It activates the Alpha subunit and inactivates the Beta Gamma complex.

ANSWER: C The Alpha subunit exchanges its bound GDP for GTP.

Which of the following mechanisms is utilized by cells for inactivating a signal transduction pathway? A) Phosphorylation of the receptor by kinase to inhibit binding to signal transducer. B) Recruiting inhibitory molecules by its own initiated signals, such as RasGAP recruitment on the membrane by Inositol phosphorylation. C) Removal of the receptor from the plasma membrane by endocytosis. D) All of the above.

ANSWER: D All of the above.

Different glycoproteins can have a diverse array of oligosaccharides. Which of the statements below about making glycoproteins on plasma membrane is TRUE? A) Extensive modification of oligosaccharides occurs in the extracellular space. B) Initial oligosaccharide chains are made by the addition of one sugar at a time onto the protein in the lumen of the ER. C) Each layer of Golgi membrane structures contains identical modification enzymes for modifying sugar chain on proteins. D) ER lipids can be modified by sugar chain, which can be transferred to the proteins in ER lumen.

ANSWER: D ER lipids can be modified by sugar chain, which can be transferred to the proteins in ER lumen.

Typically, members of the steroid hormone receptor family _______________. A) Are cell-surface receptors. B) Do not undergo conformational changes by binding to their ligands. C) Are found mainly in the nucleus when ligands is not available. D) Interact with signal molecules that diffuse through the plasma membrane.

ANSWER: D Interact with signal molecules that diffuse through the plasma membrane.

Which of the following statement is FALSE? A) Not all peroxisomal proteins are synthesized on the ER. B) Enzymes that transfer sugar chains from the lipid to transmembrane proteins in the ER is expected to have ER retention signals to remain in the lumen of ER. C) The signal recognition particle (SRP) for ER signal sequence is in the cytosol. D) SRP receptor is located at the ER membrane and its SRP binding site faces into the ER lumen.

ANSWER: D SRP receptor is located at the ER membrane and its SRP binding site faces into the ER lumen.

Which of the following protein family is involved in directing transport vesicles to the target membrane? A) SNAREs B) Rabs C) tethering proteins d) all of the above

ANSWER: D all of the above

Fill blanks in the RTK signal transduction pathway in below from the provided list of molecules in correct order. Ligand-RTK- ? - ? - Ras - ? - ? - MAP kinase

Adaptor Protein Ras-GEF MAPKKK MAPKK

Modern eukaryotes depends on mitochondria to generate most of the cell's ATP. How many molecules of ATP can a single molecule of glucose generate in a cell? A) 30 B) 2 C) 20 D) 36

Answer: A 30

Which of the following statements is true? A) All transport vesicles in the cell must have a v-SNARE protein in their membrane B) Transport vesicles only deliver lipids to the cell surface C) Clathrin remains on the outside of a vesicle for its entire journey from origin to destination D) Vesicle fusion to its destination organelle requires adaptin molecules on the vesicle to bind to Rab on the destination membrane

Answer: A A is CORRECT: Must have a v-SNARE and t-SNARE for docking to occur B is INCORRECT because transport vesicles can deliver lipids and proteins C is INCORRECT as the clathrin coating will come off of a vesicle once the vesicle is formed. Without removing the clathrin coat, proper docking could not occur via v- and t-SNARES D is INCORRECT as vesicle fusion is mediated by v-SNARE and t-SNARE. Adaptin is important for vesicle formation. Rab is important for the initiation of docking of vesicles and is located on the vesicle.

Which of the following statements is TRUE? A) Carbon fixation can be described as a process by which gaseous carbon-containing molecules are captured and incorporated into biological hydrocarbon molecules B) The electron-transport proteins, utilized in Stage 1 of photosynthesis, reside in the inner membrane of the chloroplast C) Both photosystem 1 and photosystem 2 extract electrons from H2O then generate O2 D) Stage 2 photosynthesis (dark reactions) involves a cycle of reactions that uses the energy directly derived from sunlight.

Answer: A Carbon fixation can be described as a process by which gaseous carbon-containing molecules are captured and incorporated into biological hydrocarbon molecules

Indicate whether the following statement is FALSE: A) Two carbons supplied in the citric acid cycle as acetyl CoA are converted to CO2 in the subsequent reaction cycle. B) Acetyl CoA has a high-energy thioester bond. C) Extracted energy by oxidation of carbon during a citric acid cycle is stored as a high energy electron in the compounds including NADH. D) The pyruvate dehydrogenase complex catalyzes three different, but linked enzymatic reactions.

Answer: A Two carbons supplied in the citric acid cycle as acetyl CoA are converted to CO2 in the subsequent reaction cycle.

Which of the following statements is true? A) Proteins destined for mitochondria and chloroplasts must translocate across two membranes, requiring close proximity of the two membranes during this process B) Proteins destined for the nucleus are marked by a nuclear localization signal which binds in the cytosol to the nuclear basket C) Nuclear import is powered by the hydrolysis of GDP to GTP D) The signal recognition particle binds to the mitochondrial signal sequence and enables proteins to embed in the membrane

Answer: A Proteins destined for mitochondria and chloroplasts must translocate across two membranes, requiring close proximity of the two membranes during this process B is INCORRECT. Proteins destined for the nucleus do have a nuclear localization signal but are bound to the nuclear import receptor in the cytosol. The nuclear basket is within the nucleus, not the cytosol, so that should also be an indicator that this response is incorrect. C is INCORRECT. Nuclear import is powered by the hydrolysis of GTP to GDP. GDP cannot be hydrolyzed into GTP. D is INCORRECT because the signal recognition particle is involved in ER protein transport, not mitochondrial protein import.

Which of the following statements is true? A) GTP-binding proteins are active when bound to GTP, and inactive when bound to GDP B) GDP is phosphorylated to form GTP by a GAP in order to activate GTP-Binding proteins C) GEFs promote hydrolysis of GTP to GDP D) Protein phosphatases add phosphate groups to protein

Answer: A A is CORRECT B is INCORRECT because GDP is removed and replaced (exchanged) with GTP by a GEF. C is INCORRECT because GAPs stimulate hydrolysis of GTP to form GDP D is INCORRECT because protein phosphatases remove phosphate groups - kinases add phosphate groups.

Which of the following statements is true? A) Pinocytosis takes place in some specialized cell types, whereas phagocytosis happens in all eukaryotic cells. B) Vesicles resulting from pinocytosis are small, whereas vesicles resulting from phagocytosis are relatively larger to accommodate large particles such as bacteria C) During constitutive exocytosis, selected proteins are diverted into secretory vesicles where the proteins are stored until an extracellular signal stimulates their secretion. D) Regulated exocytosis continually supplies the plasma membrane with newly synthesized lipids and proteins.

Answer: B A is INCORRECT - Pinocytosis takes place in all cell types, and phagocytosis takes place in some specialized cell types B is CORRECT C and D are INCORRECT as each describe the other type of exocytosis

The mitochondrial ATP synthase consists of several different protein subunits. Which subunit binds to ADP + Pi and catalyzes the synthesis of ATP as a result of a conformational change? A) F0 Base B) F1 ATPase head C) Peripheral Stalk D) Central Stalk

Answer: B F1 ATPase head

Steps 7 and 10 of glycolysis result in phosphorylation of the substrate. Which of the following best describes the reaction that occurred at Step 7 and 10. A) ATP is being hydrolyzed to phosphorylate the carbohydrate. B) High-Energy phosphate on carbon is transferred to ADP for the conversion of ADP to ATP. C) Two successive phosphates are transferred, first to AMP, then to ADP, finally forming ATP D) The substrate is hydrolyzed using ATP as an energy source.

Answer: B High-Energy phosphate on carbon is transferred to ADP for the conversion of ADP to ATP.

Which of the following statements is TRUE? A) Mitochondrial DNA codes all proteins required for mitochondrial function. B) Mitochondrial targeting signal on the proteins is recognized by a receptor on the outer membrane to initiate translocation of the protein. C) Proteins whose destination is in the mitochondrial matrix start folding once they have passed through the outer membrane. D) TIM complex is a translocator on the mitochondrial outer membrane.

Answer: B Mitochondrial targeting signal on the proteins is recognized by a receptor on the outer membrane to initiate translocation of the protein.

The photosystem in chloroplasts contains hundreds of chlorophyll molecules, most of them are part of ...? A) Plastoquinone B) The antenna complex C) The reaction center D) The ferredoxin reductase complex

Answer: B The antenna complex

Which of the following statements is true about the role of enzymes in the oxidation of sugars: A) Without enzymes, the oxidation of sugar will produce AND capture the same amount of energy B) Enzymes allow reactions to proceed in a stepwise manner at appropriate temperatures for the cell C) An enzyme must be able to function in all steps of cellular respiration in order to be involved D) Enzymes lower the energy released from the reaction

Answer: B Enzymes allow reactions to proceed in a stepwise manner at appropriate temperatures for the cell

Which of the following compartments has a lower pH compared to other compartments and carries a positive charge along the membrane following oxidative phosphorylation? A) Mitochondrial Matrix B) Inter-Membrane Space C) Inner Mitochondrial Membrane D) Outer Mitochondrial Membrane

Answer: B Inter-Membrane Space Why? The H+ ions being pumped across the inner mitochondrial membrane are generating a lower pH than the matrix as well as a more positive charge along the inner mitochondrial membrane.

Which of the following statements is true? A) All receptors are located on the cell surface of a target cell B) Ion-Channel-Coupled Receptors are often found on neurons and muscle cells C) G-Protein coupled receptors only bind to monomeric G proteins D) All Enzyme-Coupled receptors must bind to an associated enzyme to become activated

Answer: B A is INCORRECT as there are some intracellular receptors - especially those that are activated by hormone signaling B is CORRECT C is INCORRECT - typically G-protein coupled receptors bind to trimeric GTP-binding proteins D is INCORRECT - Many enzyme-coupled receptors have their own enzyme activity

Which is the following statements is true? A) G-Protein-Coupled Receptors are typically coupled to monomeric GTP-Binding proteins B) G-Protein-Coupled Receptors are typically seven pass transmembrane proteins C) G-Protein-Coupled Receptors activate their associated G proteins by phosphorylating GDP to create GTP D) G-Protein-Coupled Receptors will act directly on calcium channels to open them

Answer: B A is INCORRECT because G-Protein-Coupled Receptors are typically coupled to TRIMERIC GTP-Binding Proteins (called G proteins) B is CORRECT - GPCRs are often also called 7TM proteins C is INCORRECT because GPCRs activate G proteins by conformational changes that promote EXCHANGE of GDP for GTP. It's important to remember for all GTP-Binding proteins that GDP is always exchanged for GTP and that GDP is not phosphorylated to become GTP in these cases D is INCORRECT as GPCRs will activate G proteins, which will then act on ion channels and membrane bound enzymes

Which of the following molecules is a common second messenger in cell signaling pathways that regulate early development as well as key functions of nerve, muscle, and secretory cells? A) Na+ B) K+ C) Ca2+ D)Acetycholine

Answer: C

Glycolysis generates more stored energy than it expends. What is the net number of the activated carrier molecules produced in this process (number and type of molecules produced minus the number of those molecules used as input)? A) 6 ATP, 2 NADH B) 4 ATP, 4 NADH C) 2 ATP, 2 NADH D) 4 ATP, 2 NADH

Answer: C 2 ATP, 2 NADH

Which of the following statements is true? A) All enzyme-coupled receptors are receptor tyrosine kinases B) Receptor tyrosine kinases remove phosphate groups from the tyrosine amino acids of proteins C) Receptor tyrosine kinases often dimerize upon binding of their ligand, resulting in their activation D) Receptor tyrosine kinases often activate Ras directly by exchanging its GDP for GTP

Answer: C A is INCORRECT because not ALL enzyme-coupled receptors are RTKs, just some. B is INCORRECT because RTKs phosphorylate tyrosines of proteins - they do not remove them. C is CORRECT D is INCORRECT because RTKs activate indirectly. RTKs bind to adaptor proteins that will recruit a Ras-GEF. The Ras-GEF will exchange GDP for GTP to activate Ras.

Which of the following is an example of endocrine cell signaling? A) A neurotransmitter binding to a receptor on a target cell at a synapse B) A secreted signal acts locally in the extracellular fluid to influence nearby cells C) A secreted signal is available to interact with cells in the whole body via the bloodstream D) A membrane-bound signal molecule binds to a receptor on a neighboring cell

Answer: C A is INCORRECT because that is neuronal signaling B is INCORRECT because that is paracrine signaling C is CORRECT D is INCORRECT because it is contact-dependent signaling

Which of the following statements DOES NOT correctly describe the similarity between mitochondria and chloroplast? A) Converting available energy to create a proton gradient across the membrane B) Produce ATP by ATP synthase with the use of a proton gradient C) Both of them use NADPH as a proton carrier molecule D) They both contain unique circular DNA

Answer: C Both of them use NADPH as a proton carrier molecule

In anaerobic conditions, skeletal muscle produces... A) Lactate and CO2 B) Ethanol and CO2 C) Lactate Only D)Ethanol Only

Answer: C Lactate Only

Which of the following statements about electron transport in the mitochondria is FALSE? A) initial electron is provided from NADH. B) Ubiquinone and cytochrome c are used as electron carriers C) Oxygen is consumed at the first step in electron transfer D) nElectron carrier molecules can carry hydrogen ion (proton) when they receive an electron

Answer: C Oxygen is consumed at the first step in electron transfer

Which of the following statements is FALSE? A) The burning of sugar for complete oxidation will release the same amount of energy as stepwise oxidation of sugar in cells. B) Addition of Malonate to inhibit Citric Acid Cycle reaction proves the reaction is "Cycled" C) Sugar is the only source to provide Acetyl CoA for Citric Acid Cycle D) Some products during glycolysis can be used to produce amino acids.

Answer: C Sugar is the only source to provide Acetyl CoA for Citric Acid Cycle

Most proteins destined to enter the endoplasmic reticulum... A) are transported across the membrane after their synthesis is complete. B) are synthesized on free ribosomes in the cytosol. C) begin to cross the membrane while still being synthesized D) keep binding to signal recognition particle (SRP) while their translation is completed.

Answer: C begin to cross the membrane while still being synthesized

Which of the following is an ancient enzyme that was likely an early development in the evolution of energy-generating systems? A) Rubisco B) Pyruvate Dehydrogenase C) ATPase D) 3-Phosophoglycerate Transferase

Answer: C ATPase A is INCORRECT as rubisco is part of the carbon-fixation cycle and photosynthetic cells evolved after our first living cells B is INCORRECT because pyruvate dehydrogenase is the large enzyme responsible for converting pyruvate into acetyl CoA, and part of aerobic respiration, which came about much later in the evolution of energy-generating systems C is CORRECT D is INCORRECT as this enzyme is also involved in the carbon-fixation cycle, just like answer A.

Which of the following is true of photosynthesis? A) Electrons transferred along with Photosystem II and then Photosystem I are eventually donated to O2 as the final step. B) Photosynthesis takes place in the inner chloroplast membrane C) Photosynthesis takes place in two stages: The Light Reactions and The Light-Independent (or dark) reactions D) ATP and FADH are products of Stage 1 of photosynthesis, which go on to be consumed in Stage 2 of photosynthesis.

Answer: C Photosynthesis takes place in two stages: The Light Reactions and The Light-Independent (or dark) reactions A is INCORRECT because, in photosynthesis, the final electrons are donated to NADP+ to create NADPH. O2 is the final electron acceptor in oxidative phosphorylation in mitochondria. B is INCORRECT as photosynthesis occurs in the thylakoid membrane. Oxidative phosphorylation occurs on the inner membrane of mitochondria. C is CORRECT D is INCORRECT because ATP and NADPH are the activated carrier products of Stage 1 that are consumed in Stage 2 of photosynthesis.

Where in the mitochondria would you find ATP synthase? A) Mitochondrial Matrix B) Outer Mitochondrial Membrane C) Cytosol D) Inner Mitochondrial Membrane

Answer: D

Which of the following processes do NOT take place in the mitochondria? A) Citric Acid Cycle B) Conversion of pyruvate to activated acetyl groups C) Complete oxidation of carbon to CO2 D) ATP production by transferring phosphate to ADP from phosphoenolpyruvate

Answer: D ATP production by transferring phosphate to ADP from phosphoenolpyruvate

Which of the following components of the electron-transport chain acts as a proton pump in the mitochondria? A) NADH dehydrogenase B) cytochrome c oxidase C) cytochrome c reductase D) all of the above

Answer: D All of the above

Several different classes of enzymes are needed for the catabolism of carbohydrates. Which of the following class of enzymes is not involved in glycolysis reactions? A) Kinase B) Mutase C) Isomerase D) Protease

Answer: D Protease

Which of the following statements about nuclear transport is FALSE? A) NLS on proteins bind to cytoplasmic NLS receptors that direct the proteins to the nuclear pore. B) Nuclear pore complex creates a gate structure on nuclear envelope that allows diffusion of proteins smaller than 45-60 kDa into the nucleus. C) A protein that contains an NLS and NES on its primary sequence can shuttle between the nucleus and the cytosol. D) Ran small GTPase is always located in the nucleus to facilitate nucleo/cytoplasmic transport.

Answer: D Ran small GTPase is always located in the nucleus to facilitate nucleo/cytoplasmic transport.

Which of the following statement is FALSE? A) Cells eliminate unwanted mitochondria by autophagy. B) The outer mitochondrial membrane is more permeable than the inner mitochondrial membrane. C) If a mitochondrion has more cristae, it can produce more ATP than mitochondria has fewer cristae. D) The inter-membrane space of the mitochondria is more basic than the matrix.

Answer: D The inter-membrane space of the mitochondria is more basic than matrix.

Which of the following statements is TRUE? A) The dark reactions of photosynthesis contain a carbon fixation cycle. B) Oxygen is generated from light reactions in photosynthesis. C) Rubisco is the enzyme that adds C02 to a five-carbon sugar and converts it into two three-carbon sugars. D) all of the above

Answer: D all of the above

Your friend works in a biotechnology company and has discovered a drug that inhibits Ran-Gef. What is the most effect of this drug on nuclear transport when you treat cells with this drug? A) Nuclear import receptors would be unable to bind cargo. B) Nuclear export receptors would be able to bind cargo. C) Nuclear import receptors would be able to release their cargo in the nucleus. D) mRNA would be accumulated in nucleus.

Answer: D mRNA would be accumulated in nucleus.

The ATP synthase found in chloroplasts is structurally similar to the ATP synthase in mitochondria. Given that ATP is being synthesized in the stroma, where will the F0 portion of the ATP synthase located? A) thylakoid space B) stroma C) inner membrane D) thylakoid membrane

Answer: D thylakoid membrane

Which of these is a process by which cells harvest the energy stored in food molecules; usually accompanied by the uptake of O2 and release of CO2? A) Glycolysis B) Photosynthesis C) Oxidative Phosphorylation D) Cellular Respiration

Answer: D Cellular Respiration

Which statement is true regarding mitochondria? A) Mitochondria remain in the same location throughout the life of the cell B) All cells have roughly the same number of mitochondria C) Mitochondria never divide or fuse D) Mitochondria can be either small and round in shape or long continuous tubules

Answer: D Mitochondria can be either small and round in shape or long continuous tubules A is INCORRECT because mitochondria can move - we saw that happen in the movie. B is INCORRECT because cells may have different numbers of mitochondria depending on their ATP needs. Remember the example of the cardiac muscle cell and the skin. C is INCORRECT because mitochondria can do both. D is CORRECT as we have seen in a variety of EM and fluorescence micrographs and videos.

Which of the following statements is true? A) Notch signaling is a pathway used in very few organisms B) Notch signaling requires the diffusion of an extracellular ligand from a distance and would be classified as endocrine signaling C) Steroid hormone-induced signaling pathways require the activation of a series of effector proteins and second messengers D) Steroid hormones move across the plasma membrane in order to bind to their receptors

Answer: D A is INCORRECT because Notch Signaling is a highly conserved signaling pathway - meaning that is is used in most animals we've studied and in many tissues and developmental processes B is INCORRECT as Notch Signaling takes place in a cell contact-dependent manner. The ligand is on the membrane of a direct neighbor cell of the cell expressing the Notch Receptor C is INCORRECT because steroid hormone signaling (and Notch signaling) do not require many intermediate steps. These signaling pathways involve binding to the receptor and then either all or part of the receptor directly affecting transcription of target genes. D is CORRECT

Which of the following choices reflects the appropriate order of locations for a protein destined for the plasma membrane? A) lysosome > endosome > plasma membrane B) ER > lysosome > plasma membrane C) Golgi > lysosome > plasma membrane D) ER > golgi > plasma membrane

Answer: D ER > golgi > plasma membrane

Experimental evidence supporting the ATP synthesis by proton gradient was gathered by using artificial vesicles containing a protein that can pump protons in one direction across the vesicle membrane to create a proton gradient. Which protein was used to generate the gradient in this experiment? A) cytochrome c oxidase B) NADH dehydrogenase C) cytochrome c D) bacteriorhodopsin

Answer: D bacteriorhodopsin

Which of the following statements is true? A) A nuclear localization signal at the 3' end of an mRNA, will trigger nuclear import of that mRNA B) An N-terminal NLS is necessary, but not sufficient to trigger protein sorting to the nucleus C) Stop-Signal Sequences for ER transport are cleaved off of a single-pass transmembrane protein once the protein is embedded in the membrane. D) Signal sequences governing protein transport can be as short as 3 amino acids long

Answer: D Signal sequences governing protein transport can be as short as 3 amino acids long A is INCORRECt because the NLS is located at the N terminus of a protein (action is not triggered by the mRNA) B is INCORRECT because an N terminal NLS is both necessary and sufficient to trigger protein sorting to the nucleus C is INCORRECT because Stop-Signal sequences for transmembrane proteins will remain within the protein and embedded within the membrane D is CORRECT - This is the case for peroxisome import

To make efficient ATP production in mitochondria by ATP synthase, functions of protein complexes (electron transfer complex and ATP synthase) on inner membrane are critical. What will be important in terms of location of those protein complexes on the inner membrane? Why do mitochondria that have more cristae structure produce ATP more efficiently?

Both electron transfer complexes and ATP synthase are need to be located on inner membrane forming cristae structure. Due to more permeable nature of outer membrane, proton gradient can be formed more efficiently at inter membrane space in cristae than inter membrane space between inner membrane and outer membrane. Electron transfer complexes needed to be in place a particular order so that electron career molecules effectively provided energy from higher state to lowest state. Because proton gradient can be formed at cristae, more cristae structure in a mitochondria will provide more efficient ATP production. (Key point is location of the complexes in inner membrane at cristae and reason of requirement of that. How to create proton gradient, which can be used by ATP synthase, and why that can be achieved at cristae.)

Which of the following observations support the theory that mitochondria are descendants of prokaryotic ancestors? A) Mitochondria have DNA based genomes B) Mitochondria have ribosomes C) Chemiosmotic coupling happens similarly in plasma membranes of mitochondria, bacteria, and archaea. D) Mitochondria are found within bacteria and archaea

Correct Answers: A, B, and C

From the discussion in class, if you analyze the primary sequence of a Notch protein, what kind of signal sequences determine the location of a protein and where will they be on its primary structure? Indicate where signal sequences will be located on the box diagram below. Indicate their role on Notch function with 2-4 sentences.

ER insertion (start insertion) on N-terminal, Stop transfer sequence after start insertion, then NLS at C-terminal side. Notch need to receive Delta ligand at plasma membrane, thus it needs to be directed plasma membrane. That require Start sequence of ER insertion. To make N-terminal part facing to extracellular side (ER lumen side), Stop insertion sequence need to be follow after Start signal then Start signal should be cut off. Once Notch receive Delta signal, cleavage of Notch protein at cytoplasmic side will release part of Notch can translocate to Nuclear where it acts as transcription regulator. To locate into nuclear, cytoplasmic side of Notch (C-terminal part) need to have NLS. ("Start insertion", "Stop insertion" and NLS are expected answer. If you add other information such as DNA binding motif, cleavage sequence, we took account for these case by case.)

Plasma membrane proteins are inserted into the membrane in the ? The address information for protein sorting in a eukaryotic cell is contained in the ? of the proteins. Proteins that remain in the cytosol do not contain a ?. Proteins are transported into the Golgi apparatus via ?. The proteins transported into the endoplasmic reticulum by ? are in their ? unfolded form.

Endoplasmic Reticulum Amino Acid Sequence Sorting Signal Transport Vesicles Protein Translocators Unfolded

Label the following diagram with these terms: Extracellular Signaling Molecule, Receptor, Target Cell, Intracellular Signaling Molecules

In Red = Extracellular Signaling Molecule Green = Receptor Grey Cell = Target Cell Small Blue Blob = Intracellular Signaling Molecule

Short Answer: Explain how the structure and function of GPCRs, G-Proteins, and membrane-bound enzymes and ion channels are linked during cell signaling. In other words, what about these proteins' structures and locations enables the reactions that will take place?

It's important to note that the GPCRs are seven pass transmembrane proteins - which are embedded in the membrane. Their extracellular domains bind to extracellular signals. Once that signal binds, a conformational change allows the GPCR to bind to G-Proteins. That binding promotes exchange of GDP for GTP, activating the G Protein. Importantly, two of the G-Protein subunits are linked to the membrane by lipid modifications. This membrane linkage is part of the structure that enables the G protein to be in the right place to function. The membrane-bound enzymes and ion channels are both also associated with the membrane, so again, will be in the right place to be activated by G-Proteins to do their jobs.

If a protein is being transported to this organelle, will it happen folded, unfolded, or mid-synthesis? 1) Nucleus? 2) Mitochondria? 3) Peroxisome? 4) Endoplasmic Reticulum?

Nucleus = Proteins Remain Folded Mitochondria = Proteins will need to be Unfolded Peroxisome = Proteins Remain Folded ER = Mid-Synthesis, Proteins are translocated into ER mid-synthesis

You isolated two mutant cells (Cell A and Cell B) which have a problem in their signal transduction pathway controlled by GPCR. Both cells show a response without the ligand, suggesting the signaling pathway has been constitutively activated by mutations. When you added compound that inhibits Adenylyl Cyclase in both cells, each cell showed the following result. Cell A: the signaling pathway was still active even without ligand. Cell B: the signaling pathway becomes inactive with the ligand. From these results; Q1) Which protein of the signaling pathway in Cell A might have the mutation? How does that mutation affect the function of that protein? Why do you think so? Q2) Which protein of the signaling pathway in Cell B might have the mutation? How does that mutation affect the function of that protein? Why do you think so?

Q1: Cell A does not require cAMP production thus the mutation activating the signaling is after cAMP production. The candidate protein mutated is PKA (Protein Kinase A). The mutation makes PKA constitutively active that does not require cAMP binding to be activated. Other possibility might be PKA-dependent transcription factor that usually require phosphorylation by PKA to become active transcription factor. If the transcription factor has mutation that become constitutively active without phosphorylation , same result might be observed. Q2: Cell B require cAMP production thus the mutation activating the signaling is before cAMP production. The candidate proteins mutated are GPCR or heterotrimeric G-protein. GPCR can be mutated to become ligand bound state without ligand that initiate signals. Heterotrimeric G-proteins also can be mutated to keep a-subunit stay as GTP bound form (constitutively active mutant). Both cases, inhibition of cAMP production can stop signaling.

Activation of small GTPases are determined by where their GEF (Guanine nucleotide Exchange Factor) are located. Therefore, location of GEF is critical for the cellular function of each small GTPase. Also, inactivating small GTPase controlled by its GAP (GTPase Activating Protein) can regulate where the small GTPase is inactivated. Explain how this mechanism control nuclear/cytoplasmic transport of the protein by RanGTPase. Indicate where GEF and GAP are located and how that control transport mechanism through nuclear pore complex. Draw a picture if it helps to explain.

RanGEF (RCC1) protein is located inside of nucleus and RanGAP is located cytoplasmic side of nuclear envelope. This separated distribution of enzymes makes uneven distribution of RanGTPase; RanGTP is in nucleus and RanGDP is at cytoplasm. RanGTPase can control complex formation of NLS/NLS-receptor complex and NES/NES-receptor complex. RanGTP promote complex formation of NES/NES-receptor in nucleus by binding to that, then once exported, cytoplasmic RanGAP convert RanGTP to RanGDP to dissociate the NES/NES-receptor/RAN complex thus NES containing proteins are discharged from NES-receptor at cytoplasm. NLS/NLS-receptor can be formed at cytoplasm, then after imported into nucleus RanGTP promote dissociation of that complex to discharge NLS containing protein from NLS-receptor in nucleus.

Unlike mitochondria, chloroplasts do not have a transporter that allows them to export ATP to the cytosol. How, then, do plant cells obtain the ATP that they need to carry out energy-requiring metabolic reactions in the cytosol?

Remember that plant cells also have mitochondria and the mitochondria and chloroplasts are working together as collaborators to address the cell's energetic needs. Mitochondria will produce ATP via oxidative phosphorylation. That ATP is able to be made because of the glyceraldehyde-3-phosphate that is made via photosynthesis in chloroplast. That sugar moves out of the chloroplast, into the cytosol and eventually will be used via the Citric Acid Cycle and oxidative phosphorylation to make ATP, which can be pumped out of the mitochondria into the cytosol of the plant's cell. So the cell is NOT using the ATP produces directly during photosynthesis, but is instead using ATP from mitochondria.

Name This Organelles and Tell Me Its Function

This is the rough endoplasmic reticulum Why is it rough? What is attached? Ribosomes And it's function is transport of proteins and lipids to their final destination whether that's another membrane-bound organelle or the plasma membrane.

Consider a protein that contains an ER signal sequence at its N-terminus and a nuclear localization sequence in its middle. What do you think the fate of this protein would be? In other words, what will happen to it and where will it end up? Explain your answer.

This protein would end up being translocated into the ER. With nuclear import, the protein is synthesized and folded at the time of import and the nuclear import receptor binds to the nuclear localization signal. But with proteins being sorted to the ER, the ER signal sequence gets bound by the signal recognition particle before the protein has even been fully synthesized. This difference in the timing is important especially when we remember from the question that the ER signal sequence is at the N terminus and the nuclear localization signal is in the middle. So before the NLS has even been made, the SRP will be binding to that polypeptide and ribosome and making sure that protein gets placed into the ER. With the ER signal sequence being at the N terminus, we also know that the signal peptide will be cleaved off and the protein will end up in the ER lumen. Once it's in there, the NLS won't be available for the nuclear import receptors in the cytosol to find it. So it will not be imported to the nucleus.

Yeast cells can proliferate both in the presence of O2 (aerobically) and in its absence (anaerobically). Under which of the two conditions could you expect the cells to proliferate better? Explain your answer.

Yeast cells will proliferate much better aerobically. But why? It's all about efficiency of ATP production. If the yeast cell is under aerobic conditions, it can utilize oxidative phosphorylation and produce 30 molecules of ATP per glucose molecule oxidized. If the yeast cell is under anaerobic conditions and can only perform glycolysis, it may only produce 2 molecules of ATP. A cell that is short on ATP or making ATP in a less efficient manner is not going to be able to perform its basic cellular functions as easily or quickly. Therefore the cells wouldn't grow and divide as easily or quickly.