Lecture 3:Metabolism

Extra Credit: Oliver

9/12/2011 6:29:00 AM

Metabolism  Anabolism—synthesis and requires energy  Catabolism—focus, break down of substances to yield energy Amphibolic—pathways that are involved in both in anabolism and catabolism  anabolism—grow and divide  catabolism—housekeeping so it can make things it needs to grow and divide Enzymes  ABCD (each step requiring an enzyme or each arrow )  are able to measure the cells needs for different things, regulated by how much energy it needs at a particular time  activation energy is less when enzyme is present  some products and reactants that are oxidized and reduced  looking for the production of NADH and FADH2 (reduced forms) o oxidized forms being: NAD+, and FADH o occur in oxidized forms, and are reduced and utilmately responsible for the production of ATP o oxidized form interacts with the substrate thus reducing NAD+ and oxidizing the substrate  can also occur in a reversed process Energy  phosphoenolpyruvate (phosphorylates sugar across the membrane in prokaryotes) –energy equivalent to ATP    ADP and ATP have equal amounts of energy Low energy—AMP ATP (contains an a ribose sugar, beucase of the OH at the 2’ prime carbon) o adenine is attached to the first carbon o 3 phosphates are attached to the 5’

ATP equalivalents (after one high energy bond broken)  ATP  ATP  GTP ATP  PEPATP o the first phosphate bond to the 5’ carbon is a low energy bond o the cell is constantly able to measure the amt of energyit needs and constantly able to make it Enzyme Mediates Reaction  enzyme looks like a pacman.o squigel bonds are high energy bonds—most of the time it is the last phosphate is removed (high energy bond) (the second bond is also a high energy bond) o ATP. but as the substrate concentration increases there is a beter likely hood that the substrate will bind to the enzyme than the competitive inhibitor o allosteric activator/inhibitor o allosteric effector—an allosteric site is on the enzyme other than the active site where the allosteric effector binds  causes a change in the active site    an allosteric effector is an activator so that the active site changes so that the substrate can bind thus an allosteric inhibitor will change the active site so that the substrate cannot bind to the active site allosteric effectors are energy (ATP. GTP. and the substrate = missing piece  how the enzyme measure how much energy is needed that allows the enzyme to either progress or stop the reaction o inhibitor o competitive inhibitor—looks like the substrate so it can bind to the active site. AMP) or other things that will become energy (to tell the cell it has or doesn’t have enough energy) the way the cell measures energy needs***  . or PEP are all considered to be equilavent in energy when the first bond (last phosphate) is removed o actual vs. ADP.

PEP in the first step regulates other mechanisms in the cell which is why its needed in the first step. key point of control* --committed step (irreversible and specific to that particular pathway)        starts at glucose and goes to pyruvate yellow = requires energy (PEP and ATP) glucose  fructose-1.  activator tells the cell that the energy levels are low so that the reaction will create energy ATP will shut off the enzyme (allosteric inhibitor) Question from last time: sensing concentration along the microbe or is it sensing the concentration over time  deceptive because receptor is on one side of the organism and cascade goes to the other side to the flagella  over time—because the organism is so small that they cannot tell that there is a concentration gradient different from one side of the  organism to the other side the runs were longer if the organism was at all near the higher concentration Aerobic Respiration Glycolysis  each arrow correlates to an enzyme but most of the focus will be on. glucose  (PEP used/phosphotransferase system)  glucose-6P  .6 P ***1st step is phosphotransferase (ATP cross out and put PEP)!!!! different colors (stage 1 and stage 2) pink stage goes to pyruvate. pink because it is making ATP and NADH 6 carbon sugars—both have 6 carbons just the ring differs in being 5 or 6 carbons long <3 orgo PEP vs ATP. but not in the second step which is why ATP is used in the second step o PEP is only used in prokaryotes o in eukaryotes ATP is used for both steps yellow o 1.

and binds to the allosteric site to inhibit the reaction when there is a high concentration of ATP present in the cell PFKas—inhibited by ATP. for example if G6P builds up in the cell—product inhibition through allosteric inhibition meaning that G6P binds to some region of hexokinase and changes the enzyme’s active site feedback inhibition—also allosteric inhibition if there is a lot of aerobic respiration. multiple binding sites to indicate on or off  . is inhibited by the product of the reaction (G6P).6 PP(di/bi-phosphate) **key point of control  phosphorylation of the other side  the molecule is symmetrical requires energy to do so      so that the molecule can get cut in half in the next step 6 carbon sugar in a 5 carbon ring  cut in half from this step on energy is PRODUCED not USED ATP inhibits the reaction ATP is binding to the active site to only when there is a low concentration of ATP. fructose-6P  (ATP used/ phosphofructokinase)  fructose-1. the enzyme used in the reaction.     group tanslocation. not the same molecule hexokinase. (allosteric when ATP concentrations are high)  activated by AMP (adenine monophosphate) by allosteric. then G6P should not be building up  if energy is not needed then G6P will build up o 2. binding somewhere other than the active site and thus changing the active site to confer to the subtrate  ATP and AMP bind to different allosteric sites  enzymes with dimers. requires energy to bring sugar into the cell. glucose-6P  fructose-6P (6 membered ring becomes a 5 membered ring) o 3. but phosphorylates (using PEP) therefore not active transport.

key point of control* --committed step (irreversible and specific to that particular pathway ) .6 diphosphate tries to speed up/ make sure that phosphate kinase is producing pyruvate o in eukaryotes.6 diphosphate  allosteric activation when energy levels are low. phosphate kinase can be phosphorylated to make it less active or dephosphorylated to make the enzyme more active be able to differentiate between molecules used in the TCA cycle  and glycolysis  TCA Cycle  each arrow correlates to an enzyme but most of the focus will be on. ex ATPase and ATPsynthase both make ATP difference between eukaryotic and prokaryotic is that it occurs in the mitochondria vs. the cytoplasmic membrane PEP Pyruvate o 3 levels of control: o inhibition by ATP/ Alanine (amino acid).      when PEP loses a phosphate  pyruvate (uses the enzyme pyruvate kinase to do ) and phosphorylates the ADP to ATP enzyme = ends with –ase and the name often tells the action performed kinase generally = phosphorylation and phosphotase = dephosphorylation BUT most enzymes are reversible so kinases also dephosphorylate and phosphotase can phosphorylate.  alanine is an amino acid that is produced by the pyruvate products. feedback inhibition  allosteric inhibition o activation by fructose-1.6 diphosphate buildup because all being used to make pyruvate  fructose-1. no fructose-1.

      acetyl-CoA=2 carbons. FADH2 are all produced substrate level phosphorylation—something is phosphorylated directly versus going through the electron transport system. made from compounds shuttled out of this process ultimately have to have regeneration of some of the compounds to keep the cycle going: o pyruvate + CO2 + ATP + H2O (pyruvate carboxylaze) OAA+ ADP + Pi + 2H+ o separate reaction that keeps the cycle going o the reaction requires ATP and turns is into ADP + Pin only tends to operate under aerobic conditions. fumarate. citrate. oxalaacetate =6 carbons key point of control in TCA—pyruvate  acetyl Co-A (outside of TCA cycle. but still the key point of control) both molecules are outside of the cycle itself most important in terms of energy generation NAD(P)H. a-ketoglutarate = 5 carbons succinyl Co-A. hemes (protein component). aconitate. a variation than can occur under anaerobic conditions key point of control: pyruvate dehydrogenase (complex): pyruvate  Acetyl Co-A o the enzyme carries an oxidative decarboxylation o the process yields NADH and carbon dioxide o 3 carbons  2 carbons (which binds with oxalacetic acid to start the cycle)       . isocirate. succinate. phophorins. malate.\ o ATP and GTP are considered substrate level phosphorylation o GTP can give a phosphate to ADP to make ATP oxidative phosphorylation—most energy comes via this process o ATP made through the electron transport system from NADH o typically NADH  3 ATP and FADH2 2 ATP 34 ATP typically thought per glucose but can be lower than ten depending on the conditions in which the organisms lives in Amino acids. GTP more common in prokaryotes). GTP (or ATP in some molecules.

production of NADH or FADH2 o inhibited by ATP and activated by ADP (lower levels of ATP) o double whammy. 2FADH2  total NADH to ETS = 10 and total FADH2 = 4  34 ATP through oxidative phosphorylation & 4 ATP substrate level = 38 in prokaryotes  in eukaryotes 36 ATP (transport across membrane uses energy) **glycolysis: makes 4 ATP eq (1NADH & 1 ATP) but uses 2 (1 PEP & 1 ATP). but NADH and Acetyl Co-A are also inhibitors (fully inhibited if all three are present. 2 NADH  intermediate: 2 NADH  TCA: 2 GTP/ATP. 1FADH2. a little less if only 2 of the three. and even less if only one of the inhibitors are present o irreversible reaction Acetyl Co-A  citrate (citrate synthase) o allosteric o inhibited by ATP Isocitrate  a-ketogularate (isocitrate dehydrogenase) o allosteric o decarboxyalation. it can measure both ATP and ADP levels a-ketogularate  (a-KG dehydrogenase) succ-CoA o allosteric o inhibited by succinyl coA and NADH (products of the reaction) the TCA pathway yields the most energy o 4 NADH.  net = 2 (ATP eqv) anabolically important because products are shuttled out to make amino acids     . 1GTP per pyruvate (double for glucose) o ATP Equivalents: 4 NADH (12 ATP). 6 NADH.  o allosteric inhibitors: tend to see ATP. 1 GTP (1 ATP) = 15 ATP per pryvuate  GTP through substrate level phosphorylation  NADH. FADH2 through oxidative phosphorylation (ETS) o per glucose:  glycolysis: 2 ATP. 1 FADH2 (2 ATP).

soluble in lipids (sitting within the phospholipid bilayers) o responsible for carrying protons across the membrane o only complex that can do so? two things happening in the membrane: o 1) the proteins (non proteins) setting up the proton gradient o 2) ATP synthase (operates separately from process above  it synthesizes ATP but can also work backwards ( then called ATPase)  if a proton gradient is needed. then ATP can be degraded to allow protons to be shuttled across the membrane  F1 (hydrophilic) & F0 (hydrophobic) different functions  F0= channel through which  F1 = responsible for ATP production     *** READ EXPERIMENT. chemiosmotic theory  electron transport and ATP synthesis are two different entitities E. determining what cytochromes are in the organisms are helpful in determining what the organism is quinone—nonproteinaous.o what would have to happen to amino acid intermediates for it to replenish the intermediates o Electron Transport System  oxygen is the terminal electron acceptor ** determines whether aerobic or anaerobic  proton motive force—proton gradient across the membrane is used to make ATP (NADH and FAADH2 are shuttled in to create the gradient)  all organisms have variations of the molecules utilized in the ETS. Coli o FP Fe-SQcyt b cty o energy yirld is different dependent on organism and environment it was found in ATP synthase   .

water bath. o carbon monoxide—interacts with iron in cytochromes and prevents it from being able to carry oxygen. just shuttled through the uncoupling proteins o process occurs just prior to hibernation . increase synthesis in uncoupling proteins   o produces non-shivering heat  Anaerobic Respiration  Glycolysis o  TCA Cycle . vital in young infants found in inner mitochondrial membrane where ETS is the proton motive force is made but ADP is not phosphorylated  thernogenin becomes the shuttling protein to generate heat instead of getting shuttled through ATP synthase o uncouple the two systems  still get production of the protons. making the proton gradient o so when its inhibited  no proton gradient being produced o therefore no protons are shuttled into ATP synthase and ADP is not phosphorylated o cyanide.  found in brown fat or brown adpipose tissue. animals that hibernate or live in cold environment. o azide—lab setting. prevents algae growth Uncouplers are o dinitricphenol and o thernogenin (eukaryotic) (UPC1). o responsbilbe for controlled dispassion  oxidative phosphorylation o the protons are shuttled down its electrochemical gradient  phosphorylating ATP inhibition of the ETS are one mechanism o create proton motive force.

o no energy is formed acids are the byproducts. light and CO2 Anabolic Nature  a-KG  glutamate and oxalacetate  asparate  mostly amino acids Fermentation (green. they will die  this process does not make energy either  the purpose of fermentation is to recycle and reform NAD+ o NAD+ is necessary to be an electron acceptor for gylycolysis as well as for the TCA cycle o NAD+ is necessary for glycolysis and TCA cycle to occur.  end products for fermentation are also end products for the cell: lactate. Electron Transport System o the terminal electron is acceptor is something other than oxygen* Anaerobic Growth (Fermentation)  Gylcolysis  Fermentation   some organisms can use anaerobic respiration using other inorganic (NO3 and SO4) or organic electron accepts to produce ATP    proton motive force  S elemental chemolithotrophic--< start using an inorganic compound photoheterotroph—start with an organic compound (glucose). acetate. H2. (lactate. formate)  . the surrounding environement thus becomes more acidic. Stage III: Reduction)  absence of oxygen. CO2  if the cells live in an environment containing these waste products. ethanol.

9/12/2011 6:29:00 AM .

9/12/2011 6:29:00 AM .

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