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Week of 3.30.16 Notes

by: Nina Kalkus

Week of 3.30.16 Notes CELL-1010-01

Marketplace > Tulane University > Business > CELL-1010-01 > Week of 3 30 16 Notes
Nina Kalkus

GPA 3.8

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About this Document

Notes from end of Chapter 7 into Chapters 8 and 9!
Intro to Cell & Molec Biology
Vijayaraghavan, Meenakshi
Class Notes
Cell, Biology
25 ?




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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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