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Week 6: Membrane Transport and Metabolism

by: Marin Young

Week 6: Membrane Transport and Metabolism BIOL 3510

Marketplace > University of North Texas > Biological Sciences > BIOL 3510 > Week 6 Membrane Transport and Metabolism
Marin Young
GPA 4.0

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These notes cover membrane transport (from the substitute's lecture) and metabolism from glycolysis through the TCA Cycle. Biochemical details are included, and steps to memorize are separated from...
Cell Biology
Dr. Chapman
Class Notes
Cell Bio, Biology, metabolism, biochem
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This 8 page Class Notes was uploaded by Marin Young on Monday February 29, 2016. The Class Notes belongs to BIOL 3510 at University of North Texas taught by Dr. Chapman in Spring 2016. Since its upload, it has received 97 views. For similar materials see Cell Biology in Biological Sciences at University of North Texas.

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Date Created: 02/29/16
Week 6: Chapters 12, 14 | BIOL 3510 Notes by Marin Young Saturday, February 27, 2016 1:06 AM Transport Across Membranes: • Passive transport occurs in many ways without costing the cell energy ○ Simple diffusion is the passive movementof small and/or nonpolar molecules directly through the plasma membrane itself  Examples include dissolved gases (generally small and often nonpolar), fatty acids (largely nonpolar), and steroid hormones (nonpolar) □ No charged molecules can moveacross a membrane by simple diffusion  Moleculescan movein and out at the same time, but more move down the concentration gradient □ This creates a net movement towards lower concentration (whereverthere is currently less of that solute)  This includes osmosis, the diffusion of water □ Water moves down its concentrationgradient, from high concentrationof free water to low concentrationof free water  A certain amount of water molecules will always be "busy" solvating other particles, so high concentration of solutes means low concentrationof free (available) water  Put another way, water osmosesfrom low solute concentrationto high solute concentration □ Cells generally need to have higher solute concentrationsthan their environments,so more water will tend to diffuse into the cell, which can cause lysis (bursting) from being too full  Animal cells avoid this by having gel-like cytoplasmand maintaining an electrochemical gradient using ions, which we'll revisit later  Plant cells avoid this using turgor pressure, or physical pressure from the cell wall holding the cell to the correct volume  Protozoansavoid this using contractile vacuoles, which fill with water and then physically force it out of the cell by contracting the vacuole ○ Channel proteins form a gated aqueous pore that allows particles to pass through when open  They can change conformationfrom open to closed, and regulation affects whether they're open or closed (or, strictly speaking, whether they spend more time open or closed--theytend to open and close a bit randomly) □ Voltage-gated channels open and close according to membrane potential, or the accumulation of a charge difference across a membrane  A voltage-gatedchannel lets Ca enter a nerve cell, which relays a signal causing the release of neurotransmittersinto a synapse ◊ At neuromuscular junctions, acetylcholine vesiclesfuse with the membrane (and release acetylcholine) □ Ligand-gated channels open and close according to whether a ligand, like a hormone or neurotransmitter,is bound +  An acetylcholine-gatedchannel lets Na enter a (postsynaptic)nerve cell to depolarize the membrane (triggering many, many voltage-gatedNa channels to open and let in even more sodium ions--an action potential) ◊ This makes acetylcholine an excitatory neurotransmitter;inhibitory - neurotransmitterslike GABA and glycine open Cl channels to make depolarization even harder □ Stress-activatedchannels are literally pulled open by a mechanical stress  Hair cells in the ear (tilting bundles) bend in response to sound waves and open stress- activated ion channels to trigger a signal pathway  Channels do not change conformationwhen particles pass through them  Channels do not change conformationwhen particles pass through them □ This means many particles can pass at once, in single-file, like a line of people going through an open door  Channels can selectivelytransport molecules of a certain charge and size □ Moleculeswith the wrong charge are excluded by ionic repulsion: positively charged amino acid residues in a channel's pore will repel positively charged molecules □ Too-big molecules or ions don't fit □ Too-smallions can be excluded by failing to be stabilized + by the c+annel, like in the case of K channels  K is stabilized by its attraction to four δ- (partial negative) charged oxygen atoms  Na is too small to be stabilized by all four oxygens,so water moleculesfollow it and can't pass through  An important example of a channel protein is an aquaporin, or water pore □ When osmosisis too slow to allow water into the cell, aquaporins open to let water rush in □ "NPA regions" (sequences of N-P-A, or Asparagine-Proline-Alanine) help aquaporins stick together in tetramers/groupsof four fully functional aquaporin monomers(they're more stable this way) □ Remembertransmembranehelices? Each aquaporin has six ○ Carrier proteins, unlike channels, bind to a molecule,change conformation,and release it on the other side of the membrane  Know that these are called transporters in the textbook  They change conformations(open to cytoplasmor open to outside the cell) independently of whether the solute is there □ Solute simply binds to an available site and dissociates shortly after that □ If more solute is present on one side of the membrane, solute moleculeson that side are more likely to bind and cross the membrane  This causes a net movementtowards lower concentration,just like simple diffusion and channel-facilitated diffusion ○ The kinetics of simple diffusion and facilitated (channel-mediated and carrier-mediated)diffusion are very different  The rate of simple diffusion increases steadily with solute concentrationoutside the cell  The rate of facilitated diffusion follows Michaelis-Mentenkinetics □ There's a theoretical maximum rate (v max) representing an infinite amount of substrate, where the mediating protein itself is the limiting factor □ At a certain concentration,K ,mv is half of vmax □ K is a measure of the enzyme's affinity for the m substrate, or the carrier's affinity for the solute  A lower K imdicates higher affinity (lower concentrationof solute needed to get the same effect)  For example, glucose uptake proteins have much lower K valums for D-glucose than L- glucose because cells prefer D-glucose • The presence of electric charge is important to transport across membranes, especially active transport ○ Know that the Nernst equation relates resting membrane potential to charge balance and concentration  This determines the direction of the electrochemicalgradient, or the combinationof concentration gradient and charge gradient ○ The patch-clamp technique is used to isolate a piece of a cell membrane containing an ion channel and make it a sort of switch in a circuit  Ions travel through the channel due to the flow of electrons through the circuit  Changes in voltage are recorded and analyzed to measure the rate of ion flow • Active transport requires energy input in the form of coupled transport, ATP hydrolysis, or light absorption ○ Coupled transport involves transporting something down its gradient (which is favorable) to generate the energy to move something else up its gradient energy to move something else up its gradient  Symport movestwo solutes the same direction □ This requires that one is moving high to low and one is moving low to high □ An example is glucose uptake, which movesboth sodium ions (down the gradient/high to low) and glucose (up the gradient/lowto high) into the cell  The sodium ion-binding site is nearly always occupied due to the high sodium concentration,so the protein is likely to change conformationsas soon as glucose binds  This brings glucose from the intestine into the intestinal epithelium, and then passive uniport lets glucose continue into the bloodstream □ Many plant, protist, and prokaryotic cells use H instead of Na for symport  Antiport movestwo solutes in opposite directions  Coupled transporters can be occluded, or closed to both sides, if neither substrate is present ○ ATP hydrolysis powers transport via ATPases,or ATP-hydrolyzing enzymes(which, in this case, also pump solutes)  The Na /K ATPase is a very important example; know that it pumps 3 Na out for each 2 K in + □ Steps: binds Na from cytosol,hydrolyzes ATP to phosphorylateitself, changes conformation, + + + releases Na outside cell, binds K , loses phosphate, changes conformation,and releases K into cell □ Ouabain blocks K binding and inhibits the entire cycle, which is toxic in large doses but may becomea heart disease drug eventually  The Ca ATPase pumps calcium ions out of the cytosoland into the sarcoplasmicreticulum (in muscle cells) or out of the cell □ This maintains a low concentration of calcium, which lets it efficiently act as a second messenger ○ Light-driven transport is most commonin prokaryotes  Bacteriorhodopsinchanges conformationwhen photon absorption isomerizesretinal □ The conformationalchange pumps protons out of the cell □ This creates a proton gradient used to power ATP synthesis  If an organism is modified to express a channel rhodopsin, stimulating that rhodopsin with a fiber- optic cable (delivering blue light straight to the channel) can trigger other signal pathways □ This has been used to cause crazy aggression via the mouse hypothalamus,which was…interesting □ It has promising applications for studying neural circuits Cellular Energy Extraction: This section can be approached two ways. You can learn what you need to learn by brute force, or you can look at the o chem and nomenclature that makes most of it make sense without rote memorization.Here, I'll facilitate both methods, or whatever combinationis best for you. The light orange column on the left contains everything you need to know on test day, while the light blue column on the right clarifies and explains with o chem and biochem background information. I strongly recommendat least reading it: no matter how much o chem you understand, at least some of the enzyme names will make more sense. 1) Hexokinase Energy investment phosphorylates both sides of the sugar to allow cleavage. 2) P-glucoisomerase Hexokinase phosphorylates a 6-C sugar. Phosphoglucoisomerase rearranges the 3) P-fructokinase product a bit. Phosphofructokinase adds the 2 phosphate. 4) Aldolase Aldolase cleaves the sugar to two trioses (3-C 5) Triose P Isomerase sugars) by the reverse of the aldol condensation reaction. Triose phosphate isomerase converts one of the two triose 6) G-3-P Dehydrogenase phosphates to the other. 7) PGlycerate Kinase Glyceraldehyde-3-phosphate dehydrogenase takes two hydrogens from the triose and generates NADH. P-glycerate kinase 8) PGlycerate Mutase generates an ATP, and P-glycerate mutase and enolase both rearrange the molecule a 9) Enolase bit so that pyruvate kinase can make another ATP. 10) Pyruvate Kinase Net gain 2 NADH, 2 ATP Bridging Step: Pyruvate Decarboxylase Complex Pyruvate (3 carbons) is split into an acetyl group (2 carbons) and CO (2 carbon). On this page and the next, ATPs, electron carriers, and byproducts are circled and color-coded. High-energy molecules are red, orange, and green, while carbon substrates are blue and byproducts are purple. For more chemical detail and structures, please refer to my attached biochem notes. Biochem Monday, February 15, 208:34 PM Citrate synthase is such a nice, logical name. Some of 1) Citrate Synthase Citrate (6) the others aren’t so clear-cut: Aconitase makes isocitrate 2) Aconitase Isocitrate (6) via an intermediate called 3) Isocitrate DHase α-ketoglutarate (5) aconitate. The four DHases are all 4) α-ketoglutarate DHase Succinyl-CoA (4) named for their substrates! 5) Succinyl-CoA Synthetase Succinate (4) Succinyl-CoA synthetase is named for its reverse reaction, turning succinate 6) Succinate DHase Fumarate (4) and CoA into succinyl-CoA. GTP is formed by cleaving an 7) Fumarase Malate (4) unstable thioester bond. Fumarase converts fumarate 8) Malate DHase Oxaloacetate (4) to malate! A few things to know here: DHase stands for dehydrogenase, Steps 6-8 just regenerate and succinyl-CoA is actually the only compound in the cycle to oxaloacetate and capture es. - include CoA. It gets attached to the substrate in step 4 and chopped off in step 5. Mnemonic for substrate order: Citrate Is Krebs’ Starting Substrate For Making Oxaloacetate (From A few final notes: Glycolysis happens in the cytoplasm, and then the TCA/Krebs Cycle happens in the mitochondrial matrix. The electron carriers NADH and FADH are u2ed in the mitochondria for oxidative phosphorylation, which reduces O to H O. Finally, be aware that all the various intermediate products like 2 2 malate and oxaloacetate are biosynthetic precursors, meaning they can be yanked out of these pathways and used to build up other important biomolecules.


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