Week of 3.30.16 Notes
Week of 3.30.16 Notes CELL-1010-01
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This 11 page Class Notes was uploaded by Nina Kalkus on Monday March 14, 2016. The Class Notes belongs to CELL-1010-01 at Tulane University taught by Vijayaraghavan, Meenakshi in Fall 2015. Since its upload, it has received 152 views. For similar materials see Intro to Cell & Molec Biology in Business at Tulane University.
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Date Created: 03/14/16
Free Energy Change: Per glucose: Per cycle ATP NADH FADH2 Glycolysis 2 2 0 Pyruvate oxidation 0 2 0 Kreb’s Cycle 2 6 2 Total ATP yield: 38 2(used by NADH to move= 36 6(from adjustments)= 30 Yoshida and Kinosita demonstrated that the gamma subunit of the ATP synthase spins: Scientists were skeptical that a protein could have a subunit that was stationary and another subunit that moved Important subunits in ATP synthase: gamma and beta Gamma moves in clockwise direction to synthesize ATP Experiment: removed gamma subunit with alpha and beta cup Purified and attached microfilaments Applied ATP Caused gamma subunit to move in counterclockwise direction (breaking ATP) Cancer cells usually favor glycolysis: Cancer: increase in rate of division, inadequate oxygen Hypoxia: causes increase in rate of glycolysis 3 enzymes used for diagnosis of tumors: Glyceraldehyde 3 phosphate dehydrogenase Enolase Pyruvate kinase VHL: VHL syndrome= having several cancer of different kinds all at once Found mutation in regulatory gene (VHL gene) Other organic molecules: Carbohydrates, fats, and proteins also used for energy Carbohydrates feed directly into glycolysis Fats and proteins enter into cell respiration pathways at different points Anaerobic metabolism: Inorganic compounds receive electron Anaerobic: NADH made by glycolysis goes directly to Electron Transport Chain Fermentation: Fermentation by itself: NO ATP PRODUCED Muscle Yeast glycolysis→ 2 pyruvate (electron glycolysis → 2 pyruvate (electron acceptor) acceptor) pyruvate→ Lactic acid pyruvate → acetaldehyde (organic Enzyme: lactic acid compound) dehydrogenase CO2 removed NADH + H+ → NAD+ + 2H+ Acetaldehyde → ethanol +2e NADH + H+ → NAD+ + 2H+ +2e Secondary metabolism: Increases rate of survival, not necessary Camouflage capacity 4 Categories Phenolics Antioxidants with intense flavors and smells benzoic/phenolic ring Flavinoids, tannins, lignins Flavinoids: protect against herbivores Tannins: oxidized over time, also protect from herbivores Lignins: secondary cell wall component Alkaloids: Bitter tasting molecules for defense Caffeine, nicotine, atropine Target nerves Terpenoids: Intense smells and colors Cinnamon, fennel, cloves Highly volatile 5 carbon isoprene units Pigments Polyketides: Derivatives of acetyl and propionyl groups Chemical weapons, cancer cure Antibiotics Chapter 8: Photosynthesis Trophic organization: Heterotroph: must eat food, organic molecules from their environment, to sustain life Autotroph: make organic molecules from inorganic sources Photoautotroph: use light as a source of energy (light energy → chemical energy) Plants, algae, cyanobacteria Photosynthesis: Energy within light is captured and used to synthesize carbohydrates Highly endergonic (energy from light drives reaction) CO2 is reduced, H2O is oxidized 6CO2 + 12H2O + light energy → C6H12O6 + 6O2 + 6H2 18 ATP and 12 NADPH used → glucose Important players: Chloroplasts, Light and the electromagnetic spectrum, pigments, NADP+ (coenzyme) Cells generate ATP by photophosphorylation Biosphere: Regions on the surface of the Earth and in the atmosphere where living organisms exist Largely driven by the photosynthetic power of green plants Cycle where cell use the organic molecules for energy and plants replenish those molecules using photosynthesis Plants also produce oxygen Aerobic photosynthesis → speciation Chloroplast: Organelles in plants and algae that carry out photosynthesis Stoma: H2O and O2 out, CO2 in (leaf pore) Thylakoid membrane: light reactions Thylakoid lumen: O2 is produced Mesophyll tissue→ lots of chloroplasts Pigments: Chlorophyll a, chlorophyll b, carotenoids A vs. B: A has methyl group, B has aldehyde group Drawing is chlorophyll Tail anchors pigments in thylakoid membrane 2 Stages of Photosynthesis: Light reactions (light dependent) Take place in thylakoid membranes; produce O2, ATP, NADPH O2: thylakoid lumen ATP & NADPH: stroma Calvin Cycle (light independent) Occurs in stroma Uses ATP and NADPH to incorporate CO2 into organic molecules Light Energy: Shorter wavelength= Higher energy Photosynthetically Active Region (PAR): 380740 nm Photosystem I and II Photosystem II: Comes first 19 proteins; 250 chlorophyll pigments Reaction center= P680 (maximum absorbance/action at 680 nm) Photosystem I: Comes second 13 proteins; 130 pigments Reaction center= P700 (maximum absorbance/action at 700 nm) **insert diagram, including Z scheme Cyclic vs. noncyclic Noncyclic Electrons begin at PSII and eventually transfer to NADPH Linear process produces ATP and NADPH in equal amounts Cyclic photophosphorylation Electron cyclin releases energy to transport H+ into lumen driving synthesis of ATP Happens when there’s not enough ATP Ferredoxin takes electron back to plastoquinone b (pump until enough ATP is made) Absorption vs. Action Spectrum Absorption spectrum: range of wavelength with which it has max absorption Action spectrum: wavelength with maximum photosynthetic output Chlorophyll a: peak between violet and blue, and far red Chlorophyll b: peak at blue and red Betacarotene: peak at blue/green NADPH: energy intermediate NADP+: coenzyme (can help enzyme by accepting electron) NMP: accepts electron AMP: core structure (2nd phosphate connected to 2nd carbon, very rare) Calvin cycle: Dark reactions occur in stroma Reduce CO2 oxidize H2O All plants have C3 cycle (carbon fixation) Primary source of CO2 in plants: mitochondrial respiration (but also from atmosphere from stomata) Variations in photosynthesis: Light intensity Temperature Water availability Rate of photosynthesis should max at 3pm, actually at 12 noon bc transpiration (close stomata) RubisCO Carboxylase and oxygenase If there is less CO2, oxygen will bind with Rubisco RuBP + O2 → 3PG + phosphoglycerate (2C) → Glycolate → CO2 Happens when there’s a high rate of photosynthesis C4 Plants: Tropical/Subtropical Desert Stomata close Malate stored in vacuole Proteins Carbs Fat (6Carbon) 4.3 kcal 4.3 kcal 9 kcal Made of amino acids Glycolysis 2X Beta oxidation NH2 is kicked out Pyruvate oxidation Each time, use 1 ATP, (deamination) KC get 1 NADH and 1 FADH2 Left with metabolites ETC Gaining 8 ATP, 2 that Alanine can go are used right pyruvate Gives you 3 acetyl CoA oxidation Gives you 3 spins of Krebs Glutamate can Cycle go right into 30 ATP KC (becomes Total 36 ATP alphaketo glutamate) Asortic acid becomes oxaloacetate, goes into KC Anaerobic metabolism: Electron acceptors: sulfur, nitrate Electron transport chain, along plasma membrane Bacteria also have a cell wall Hydrogen gradient builds up between cell wall and plasma membrane Only 4 proteins Pumps are NADH dehydrogenase and ubiquinone Aerobic resp Anaerobic resp Oxygen Nonoxygen, electronegative 5 proteins 4 proteins 3 pumps 2 pumps Ubiquinone: carrier Ubiquinone: pump *reductase never pump *reductase never pump Fermentation: No deenergized electron, just electron Used when no oxygen Muscle Yeast Glucose Glucose Gives 2 pyruvate Gives 2 pyruvate Gives 2 ATP and 2 NADH Gives 2 ATP and 2 NADH Get lactic acid Acealdehyde By lactic acid dehydrogenase CO2 removed Also gives you NAD+ Ethanol NADH is removed, gives NAD+ *NADH is toxic in high quantities, that’s why fermentation happens Can act as a free radical Secondary metabolites: Not essential for survival, increase rates of survival Chapter 9: Cell Communication Why do cells need to respond to signals: Helps them survive Phototropism: plants leaning towards the sun Auxin (signal) is sent by cells on light side to cells on dark side Dark side cells stretch, get weaker, bend towards light Signals relayed between cells: Differences have to do with distance Autocrine: same cell produces and receives signal Can also bind to cells of same cell type Used during cell division Paracrine: Localized signaling (very small distance) Short halflife signals → water soluble Sent via circulatory fluid When neurons, sent thru synaptic gap Never a selfsignal Endocrine: signal= hormones Long distances between signal cell and target cell Long halflife → mostly lipid soluble (some water soluble) Ethylene: hormones in plants that cause them to ripen Contactdependent: Signaling molecule must move to target cell Direct intercellular: Signal moves through very small pathways linking cellst 3 Stages of Cell Signaling Receptor activation, signal transduction, Cellular response Receptor is activated when it undergoes conformational change (once signal connects with receptor) Not always growth: specialization, development (puberty) Ligand : Signaling molecule Noncovalent Very specific Short binding time Cell Surface receptors: Enzymelinked receptors, Gprotein coupled receptors (GCPR), Ligand gated ion channels Enzyme linked GPCR Ligandgated ion channel Both receives a signal Receptor cannot Transport proteins and acts as an enzyme function on its own Noncovalently (often kinase) Gprotein: lipid binding Normally single pass anchored (traverses membrane Gprotein (after once) signal and receptor When acting as an conformational enzyme, can do 1 of 3 change): things: 1) release 1) hydrolyze GDP, bind ATP, add the with GTP phosphate to 2) split into itself alphaGTP 2) hydrolyze and ATP, ᵳᵮdimer phosphorylate (either part another protein can be 3) hydrolyze involved in ATP, pass further phosphate onto activation, another depends on compound nature of (enzyme will be signal/cell) named by amino Gprotein always acid it associated with: phosphorylates) GDP (inactive, not bound to receptor) GTP (active) When signal is lost: 1) alpha recognizes loss of signal 2) hydrolyze GTP 3) binds with GDP 4) recruit ᵳᵮdimer back 5) now inactive Gprotein Intracellular receptors: Nucleus Cytoplasm Signal Transduction: Growth factors → mitotic division → epidermal growth factor EGF EGF receptors usually paired → dimerizes when activated → phosphorylate tyrosine
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