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Exam 2 Study Guide

by: Ifeoma O'Gonuwe

Exam 2 Study Guide BIOL-L 312

Ifeoma O'Gonuwe
Cell Biology
Sapna Mehta

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Cell Biology
Sapna Mehta
Study Guide
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This 12 page Study Guide was uploaded by Ifeoma O'Gonuwe on Monday February 23, 2015. The Study Guide belongs to BIOL-L 312 at Indiana University taught by Sapna Mehta in Spring2015. Since its upload, it has received 134 views. For similar materials see Cell Biology in Biology at Indiana University.


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Date Created: 02/23/15
LECTURE 7 QUESTIONS Where is Na concentrated 0 Outside the cell Where is K concentrated 0 Inside the cell What is a major complication of cholera 0 Massive loss of body uid Why does a major loss of body fluid occur 0 Diarrhea and dehydration How does fluid move to and from the ECF inside of the cell to the lumen inside of the gut 0 The body will move solutes and the water will follow property of osmosis Which ion is most important in regulating water secretion 0 Chloride How is chloride transported into the cell 0 Cotransporter What type of transport is necessary to transport chloride into the cell 0 Active transport What are the three ways to drive active transport 0 Coupled transport 0 ATPDriven pump 0 Lightdriven pump What mediates secondary active transport 0 Established ion gradient 0 Transport proteins How does secondary active transport 0 The transport of one solute against the concentration gradient is coupled downhill the concentration gradient of another solute What does it mean if the direction of travel for two solutes is the same 0 Symporters or cotransporters What does it mean if the direction of travel for two solutes is the opposite 0 Antiporters or exchangers After chloride ions leave what follows 0 Sodium ions are attracted to the Cl39 ions so they leave the cell for the lumen as well What happens when the solutes leave the cell 0 Water is drawn into the lumen Which bacteria causes cholera 0 Vibrio cholera What does vibrio cholera do 0 Secrete a toxin that results in the chloride ion channel to stay open How is glucose transported across the membrane of the intestine 0 Sodium glucose cotransporter symporter What is a cotransporter symporter 0 A transporter that couples two solutes going in the same direction What is oral rehydration therapy 0 A solution with a fixed ratio of salts and water to help stop dehydration from occurring What does oral rehydration therapy solution contain 0 Water 0 Sodium 0 Glucose 0 Potassium 0 Other electrolytes Why does ORT contain water 0 To rehydrate tissues Why does ORT contain sodium 0 To replace Na lost from the epithelium of the intestine Why does ORT contain glucose 0 To stimulate the uptake of Na from the intestine Why does ORT contain potassium 0 To replace K Why does ORT contain other electrolytes 0 To prevent electrolyte imbalance What pressure must the oral rehydration solution be 0 Isotonic What would happen if the solution has higher concentration of salts than normal maintained by body 0 Types of ATP driven pumps 0 Ptype pump 0 ABC transporter 0 Vtype proton pump 0 Ftype ATP synthase Where are Ftype pumps found 0 Bacteria and inner membrane of mitochondriathylalltoid proteins How do Ftype pumps work 0 They use H gradient across a membrane to synthesize ATP from ADP and phosphate What do ABC transporters do 0 Pump small molecules across cells What is an ATP binding cassettes 0 An ATPase domain that transports lipids metabolic products sterols drugs What do you use Xray crystallography 0 It allows you to see the 3D structure of a macromolecule What is the first step to using xray crystallography 0 Obtaining a crystal of a purified protein What does the NaK Pump do 0 Pump out 3Na ions for every 2K ions How does the Na K Pump work 1 Pump is open to the cytoplasmic side of the cell 2 3 Na molecules bind to specific affinity sites 3 ATP is hydrolyzed 4 Phosphate is added to the cytoplasmic side of the protein 5 Conformational change 6 Extracellular release of Na 7 2 K molecules bind to high affinity sites 8 Release the phosphate group 9 Conformational change 10 Opens the pump to allow release K inside the cell What do ABC transporters have 0 Multidrug resistant proteins OOOOOOOOOO What enables trans cellular transport of nutrients 0 Asymmetric distribution of the transport proteins in the epithelial cell Which direction does glucose travel 0 From intestinal lumen to the extracellular fluid What pump is glucose pumped through 0 Na powered glucose symporter How does glucose pass out of the cell 0 Down the concentration gradient via passive movement What keeps intracellular Na concentration low 0 NaK pump What type of pump is the Na K pump 0 Ptype ATPase What does the Na K pump regulate 0 The pH 0 Osmolarity What does the Na K pump drive 0 Transport of nutrients How can Na K pump mallte ATP 0 Driving ions down their electrochemical gradients LECTURE 8 QUESTIONS Describe the structure of an aquaporin 0 Four monomers with aqueous hourglass pores lined with one face of hydrophilic amino acids form a tetramer Where can you find aquaporins 0 In cells that require a large movement of fluid 0 Kidney sweat and exocrine glands What is transported through aquaporins 0 Single file of water molecules Can H travel through an aquaporin and why 0 No 0 H usually jumps from oxygen to oxygen of water when water is single filed 0 In an aquaporin oxygen binds to asparagines amino acid in the structure so H can t relay across the water molecules Describe an ion channel 0 Proteins with hydrophilic pores 0 Involved in passive transport down the electrochemical gradients 0 They have ion selectivity 0 They are gated not continuously open Name the types of gated ion channels 0 Voltagegated 0 Ligandgated 0 Mechanically gated 0 Phosphorylation regulated What opens voltagegated ion channels 0 Change in voltage across the membrane What opens ligandgated channels 0 Ligand binding intracellularly or extracellulary Give examples of ligands in ligandgated channels 0 Neurotransmitters 0 Nucleotides 0 Ion What opens a mechanically gated ion channel 0 Mechanical pressure Give examples of mechanical pressure 0 Sensory 0 Hearing 0 Touch 0 Blood pressure Explain the Venus fly trap 0 Leaves snap shut in less than half a second after mechanical stimulation 0 Ion channels open that set off an electrical signal I rapid change in turgor pressure Name the distinct biophysical properties of gated ion channels 0 Channels that open and close quickly 0 Channels that open quickly but close over long periods of time 0 Channels that open slowly and remain open 0 Channels that only allow ions to flow in one direction Is the K channel selective for K because of size 0 No Na is smaller than K so selectivity isn t just through size How do K ions enter through the K channel 0 In a single file in which they are separated and pushe by their mutual repulsion How does a K channel select for K 0 Negatively charged amino acids at the cytosolic entrance to attract cations 0 Selectivity filter of carbonyls that forms favorable interactions with K Na is too small How does the K channel open 0 Via movement of the helices that either obstructs or frees the path for ion movement Describe simple diffusion o D Describe facilitated transport 0 Transport requiring specific proteins 0 Example Describe active transport 0 Transport requiring specific proteins 0 Transport in which the solute is transported against its gradient 0 Transport coupled to ATP hydrolysis Describe co transport 0 Transport driven by movement of a cotransported ion down its gradient Describe the parts of a nerve cell 0 Cell body 0 Dendrites 0 Axon 0 Terminal branches of an axon How do neurons transmit signals 0 Action potential voltage difference What does the patchclamp technique enable researches to do 0 Study the flow of ions through a single channel How does the patchclamp work 0 1 It measures the ions that pass while the clamp is attached to the membrane 0 2 it measures the ions that pass through the channel when the patch is detached from the membrane and put in a solution of ions What is the net result of the Na K pump 0 Net positive charged is pumped out of the cell What is a K leallt channel 0 A pump that keeps intracellular potassium levels high K is conducted 10000 fold better than Na What are the steps of action potential 0 1 Stimulus I membrane depolarization I sodium channels open with less negative membrane self propagating positive feedback loop I 40mV 0 2 All sodium channels are closed with inactivation once the membrane potential and concentration gradient for Na is equal and opposite 0 3 Slow to open K channels are beginning to open 0 5 Hyperpolarization slow to close K channels pump to continue pump out K even past the membrane potential essentially making the cell more negative that it needs to be 70mV of the cell in actually about 90 mV 0 6 K diffuses back into the cell until the resting potential is back at 70 to uninactivate sodium 39 Creates an electrochemical gradient of zero Define depolarization 0 A decrease in potential difference between the inside and the outside of the cell What does a neuron nerve cell do 0 Receives conducts and transmits signals What are the parts of a neuron 0 Cell body dendrites and axon What are dendrites 0 Extensions from the cell body that provide a large surface area to receive signals from the axons of other neurons What are the three conformations of voltagegated Na channel 0 Closed 0 Inactivated 0 Open How can the voltagegated Na channel be inactivated and not closed 0 The Na channel has two gates inactivation and closed gate 0 In order to be inactivated a molecule binds to the inactivated gate and closes the channel by binding to the closing gate How can you increase the speed of action potential propagation 0 Myelination What does the excitatory synapse do 0 Activated by an excitatory synapse 0 Creates an influx of Na that depolarizes the membrane 0 Increases likelihood of firing action potential What does an inhibitory synapse do 0 Activated by an inhibitory transmitter 0 Creates an influx of C1 or K that keeps the membrane polarized 0 Decreases the likelihood of firing an action potential What are examples of excitatory neurotransmitters 0 Glutamate and acetylcholine What are examples of inhibitory neurotransmitters 0 GABA and glycine What is the natural charge of a cell 0 Negative due to the organic molecules 0 Cations K are used to offset the negativity of the cell Describe the electrochemical gradient of K 0 K is high inside of the cell I flows out of the cell down concentration gradient 0 K moving out of the cell makes the inside of the cell more negative positive charge leaves 0 K will continue to move out of the cell until the membrane potential reaches a value that balances the effect of the concentration gradient I electrochemical gradient of zero What is a synapse 0 A specialized site of contact between cells 0 Region between nerve and target What occurs in the synapse 0 Where the electrical message is converted to a chemical message Where are neurotransmitters located 0 Stored in vesicles at the axon terminal When are neurotransmitters released 0 Once the electrical potential reaches the end of the axon it triggers release of neurotransmitters via exocytosis Once the neurotransmitters are released via exocytosis what happens 0 They diffuse across the synapse to the postsynaptic cell Once the neurotransmitters bind to the postsynaptic cell what happens 0 They are quickly removed reuptallte by the presynaptic cell to be recycled for the next action potential triggered release How is the propagation of a signal unidrection 0 Because the Na channels are inactivated depolarization does not spread backwards 0 Depolarization will open the closed channels not the inactivated channels How do neurotransmitters binding to the postsynaptic cell create a membrane potential 0 The synapse is insensitive to membrane potential and can t selfamplify the signal 0 Changes of membrane potential are graded and once there is enough signal then the local voltage gated channels are activated When the nerve impulse reaches the nerve terminal and depolarizes the plasma membrane of the terminal what happens next 0 Voltagegated Ca2 channels are opened Opening voltagegated Ca2 channels does what 0 Release Ca2 to flow down the electrochemical gradient into the nerve terminal Ca2 flowing down the electrochemical gradient into the nerve cell does what 0 Triggers the local release of acetylcholine into the synaptic cleft Once acetylcholine has been released into the synaptic cleft what happens 0 It binds to the acetylcholine receptors in the muscle cell plasma membrane The binding of acetylcholine to acetylcholine receptors in the muscle cell plasma membrane does what 0 Opens the cation channels associated with acetylcholine receptors The opening the cation channels associated with acetylcholine receptors does what 0 Causes an influx of Na that depolarizes the membrane I action potential Generalized depolarization of the muscle cell membrane does what 0 Activates voltagegated Ca2 channels The activation of voltagegated Ca2 channels does what 0 Releases the Ca2 stored in the sarcoplasmic reticulum into the cytosol The release of the Ca2 stored in the sarcoplasmic reticulum into the cytosol does what 0 Causes myofibrils in the muscle cell to contract LECTURE 9 QUESTIONS What are the three distinct mechanisms by which organelles import proteins 0 1 Gated Transport I Cytoplasm I nucleus via nuclear pores 0 2 Transmembrane transport translocation I Cytoplasm I organelles by protein translocators in the membrane 0 3 Vesicular transport I ER I organelles via vesicles What makes gated transport specific 0 Nuclear pore complex serves as a selective gate to transport specific macromolecules and macromolecular assemblies What makes transmembrane transport specific 0 It directly transports a membrane into a topologically distinct space 0 The protein must unfold to snallte through the translocator Where are newly synthesized polypeptides sent by default 0 Cytoplasm How does a polypeptide become synthesized to a location other than the cytosol 0 It must have a targeting sequence Where does a major sorting step occur 0 At the level of free versus membranebound polysomes Where do proteins synthesized in free ribosomes in the cytosol go 0 Nucleus mitochondria chloroplasts and peroxisome Where do proteins synthesized in membranebound ribosomes go 0 Plasma membrane secretory vesicles lysosomes Describe the structure of the endoplasmic reticulum 0 A rich morphology of flattened sacs cisternae reticular and tubular elements What does the endoplasmic reticulum do 0 Lipid and protein biosynthesis 0 Store of intracellular Ca2 How does one study ER function 0 By using homogenization to create rough and smooth microsomes 0 The microsomes are placed in an environment with a gradient of sucrose concentration What is a microsome 0 A microsome is a synthetic that behaves like ER When smooth and rough microsomes are placed in a gradient of sucrose concentration where would you find them and why 0 Smooth microsomes in low sucrose concentration I Low density 0 Rough microsomes in high sucrose concentration I High density How do you use microsomes to determine if import of proteins occurred 0 Proteaseprotection assay Describe a proteaseprotection assay 0 1 Put protein in the IVT mix that will be translated 0 2 Add protease 0 3 If the protein was imported the protease will not be able to chew up the protein because the lipid bilayer creates barrier 0 4 If the protein wasn t imported by the protein it was chewed up by the protease 0 5 Run SDSPAGE What did early SDSPAGE experiments tell about proteaseprotection assay 0 Protein in the tissue was smaller than the protein from the IVT mix How did they fix the problem of experiment shown by SDSPAGE 0 Have mRN A make the protein in the presence of the microsomes I The protein migrated on the SDSPAGE just like the one from the tissue I Protease protection assay showed that it was imported Why did the solution of the experiment work 0 Because microsomes have functional translocons and signal peptidase What is the signal sequence for ER 0 1530 residues often basic residues with 912 residues of a hydrophobic core residing at the N terminus that directs a protein to the ER LECTURE 10 QUESTIONS Where does protein synthesis occur 0 Ribosomes What brings a protein to the ER 0 Signal recognition particle SRP How does a SRP recognize a protein meant for the ER 0 The signal sequence Where does an ER bound protein go 0 Protein translocation channel translocon What cleaves the signal peptide 0 Signal peptidase What is SRP 0 A ribonucleoprotein complex that cycles between the ER membrane and cytosol 0 Six protein subunits bound to a small RNA molecule Y shaped secondary structure 0 A large hydrophobic poclltet rich in methionines What are the two roles of SRP 0 1 Translational arrest 0 2 Targeting and release of the newly synthesized polypeptide chain to the ER translocon complex How does SRP pause protein synthesis 0 Its translational pause domain blocks the elongation factor binding site between the large and small ribosomal units thus halting protein synthesis Where does SRP bind and describe it 0 The SRP binding site 0 An integral membrnae protein complex imbedded in the rough ER What is the protein translocation channel translocon in eukaryotes called 0 Sec61 Describe the structure of Sec61 0 Heterotrimer 2 essential and conserved subunits alpha and gamma and a less conserved beta subunit 0 Contains an aqueous pore gated by a short helix that moves once bound by a ribosome to allow the newlysynthesized polypeptide to come through What are the steps required for polypeptides to enter the ER 1 Polypeptide is fed through channel 2 Translocon opens laterally 3 Signal peptidase cleaves signal peptide 4 Protein translated and released in lumen What are the types of transmembrane proteins 0 Single pass multipass with cterminal in cytosol multipass with aminoterminal in What determines the arrangement of a transmembrane protein in the lipid bilayer 0 Start and stop signals How many times is a signal sequence recognized and describe them 0 Twice I 1 First by the SRP in the cytosol I 2 By a binding site in the pore of the protein translocator as a starttransfer signal How does the single pass transmembrane protein integrate into the membrane 0 1 Recognized by SRP in the cytosol I brought to the ER 0 2 Recognized by a binding site in the pore of the protein translocator as a starttransfer signal 0 3 N terminal signal sequence initiates translocation 0 4 An additional hydrophobic segment serves as a stoptransfer signal How does the multipass transmembrane protein integrate into the membrane 0 1 Polypeptide chain passes back and forth across the lipid bilayer 0 2 Internal signal sequences serve as starttransfer signals until it encounters a stop transfer sequence 0 Another start transfer sequence reinitates translocation further down the polypeptide chain 0 This process leads to asymmetry What does a stoptransfer signal do 0 Anchor the protein in the membrane after the ER signal sequence is released and cleaved off What determines the orientation of transmembrane proteins arising from internal sequences 0 The charge of the residues on either side of the first transmembrane domain When it comes to the orientation of transmembrane proteins which side will be cytosolic and why 0 The side with positive amino acids I Because it will form interactions with the negative cytosol How do transmembrane helices of membrane proteins become incorporated into the hydrophobic 0000 environment while maintaining their topology 0 D Which directions can the translocation open 0 1 Open to allow protein to mass through the open pore 0 2 Open to allow the protein to pass into the membrane by opening the seam Protein translocation is often cotranslational but is it always 0 No it can be posttranslational Where does protein glycosylation start 0 Upon entering the ER lumen proteins on Asn residues Nlinked What holds the precursor oligosaccharide in the ER lumen 0 Dolichol a lipid What transfers the precursor oligosaccharide to the emerging protein 0 OSToligosaccharyltransferase in a single enzymatic step Why is the ER in charge of quality control of proteins 0 All proteins that reside in membranes secreted pass through the ER How does the ER control quality of proteins 0 Depending on the state of the protein the protein is I 1 Retained in the ER for more folding attempts I 2 Export and maturation 39 3 Retrotranslocated for degradation What is used to mark the extent of folding 0 Glycosylation ensures that proteins leave the ER When properly folded What is the first phase of quality control in the ER 0 Trimming of 2 terminal glucose residues What undergoes folding while bound to chaperones 0 Protein with a single terminal glucose How does the protein bind to the chaperone 0 The chaperone recognizes the nlinllted oligosaccharides and helps them fold once they have been trimed What recognizes misfolded proteins from the ER 0 Protein translocator complex How are misfolded proteins taken out of the ER 0 Through an active process requiring ATP Once the misfolded protein leaves the ER Where does it go 0 Cytosol Once the misfolded protein is in the cytosol What happens 0 Glucoses are removed and ubiquitin molecules are added What does the addition of ubiquitin to misfolded proteins do 0 Ubiquitin is a death tag that is recognized and degraded by the proteosome LECTURE 11 QUESTIONS What are the subcompartments in the mitochondria 0 Outer membrane 0 Inner membrane 0 Intermembrane space 0 Matrix space Where are the enzymes involved in the oxidation of carbohydrates and fatty acids located 0 Matrix space Where is the electron transport chain the ATP synthase and transport proteins 0 Inner membrane What is the signal sequence for mitochondria 0 N terminal end of 2030 amino acids called a presequence What are the translocons in the mitochondria 0 TOM SAM TIM23 TIM22 and OXA Which of the mitochondria translocons are located in the outer membrane 0 TOM and SAM Which of the mitochondria translocons are located in the inner membrane 0 TIM 23 TIM 22 and OXA What does TOM do 0 Transfers proteins across the outer membrane Which proteins must go through TOM 0 All nucleus encoded mitochondrial proteins What does TIM 23 do 0 Transports some soluble proteins into the matrix and helps them insert others into the inner membrane What does TIM 22 do 0 Mediate the insertion of a subclass of inner membrane protein What does the SAM complex do 0 Helps fold betabarrel proteins in the outer membrane What does the OXA complex do 0 Mediates the insertion of inner membrane proteins synthesized within Does protein translocation into mitochondria require energy 0 Yes Where does the cell get the energy to do protein translocation into the mitochondria 0 ATP hydrolysis to release of unfolded proteins from hsp70 0 Electrochemical gradient to translocate a protein through TIM after having been bound to TOM What will satisfy hydrogenbonding requirements 0 Betabarrels What is the sequence needed for mitochondrial inner membrane transport 0 A hydrophobic sequence immediately after the first signal sequence What pulls the protein into the intermembrane space 0 TOM complex What mediates the insertion of IM proteins within the mitochondria 0 OXA complex When does OXA translocate the protein 0 After cleavage of N terminal sequence because it unmasllts the second signal How do multipass transmembrane proteins enter the mitochondria 0 TOM IIchaperone TIM22 What does TIM22 complex do 0 Insert them using membrane potential How is a protein imported into the mitochondria 0 1 Signal sequence of the mitochondria binds to the import receptors of the TOM complex 0 2 Interacting proteins are stripped off and the unfolded polypeptide chain is fed signal first into the channel 0 3 Protein passes through both membranes at the same time 0 4 Protein enters matrix space TQM and can move onto the inner membrane TIM When is ATP hydrolysis required during protein import 0 When the unfolded precursor protein associated with chaperone proteins interacts with import receptors of TOM complex When is membrane potential required during protein import 0 When the positively charged signal sequence protein is being translocated through the TIM complex What is Hsp70 used for 0 As a motor to pull the precursor protein into the matrix space Where is Hsp70 located 0 Matrix side of TIM23 complex What are porins 0 Betabarrel proteins How are porins imported into the membrane 0 TOM What keeps the porins from aggregating 0 Binding to specialized chaperone proteins What inserts porins into the outer membrane 0 Binding to a SAM complex in the outer membrane What prevents further translocation of intermembrane proteins across the membrane 0 A hydrophobic sequence after Nterminal signal sequence 0 Where is the signal sequence cleaved and What cleaves it 0 In the matrix by peptidase


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