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Lecture

BIOC212 - Teacher 1.docx

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Department
Biochemistry
Course Code
BIOC 212
Professor
Thomas Duchaine

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Entropy -spontatenous rxns drive for disorder-however despite this universal effect, the cells are organized… -This is because of energy that is used -This energy is taken from Catabolic pathways which breakdown stuff into monomers -These monomers are used to build back polymers and build an organized cell The energy is used to build polymers and ALSO used to organize the cell -organization is achieved through building of polymers! Second Law of thermodynamics: There’s an unstoppable increasing trend of disorder of the universe Entropy = S = is degree of disorder -If Delta S(change in Entropy) is positive, then reaction is Spontaneously favored! -High Entropy(high disorder) is spontaneously favored -Organizing against spontaneous disorder requires energy input -To be organized Entropy is translated into release of heat to the surroundings… thus to stay organized the cell sacrifices heat ! -organization is achieved through building of polymers! -As the polymer gets larger, the further reactions that it needs to go through are NOT ALWAYS spontaneously favored(some are, Some not)…these reactions are made possible through Enzymes Enzymes don't change thermodynamics and does NOT create energy… they just accelerate enzymes hold shit closer for rxn to occur faster COUPLING -using a rxn that releases energy, to couple with another rxn that absorbs energy(endergonic), where this endergonic rxn absorbs less energy than that released by the other rxn -Allowing a NON-spontaneous rxxn(like polymerization) to occur becus it is coupled with another rxn! -no reaction is independent, they all work together… First Law of Thermodynamics : the energy of the universe is constant: can be transferred and transformed but not created nor destroyed. Enthalpy(H) is the energy stored in chemical bonds(not only covalent bonds…even non-covalent bonds) If change in Enthalpy is positive, then the rxn is NOT Spontaneously favored! [where its more bonds, more order, thus not favored spontaneously] -If Y(reactant) has higher energy than X(product) then it means the rxn is spontaneously/thermodynamically favored Enzyme lower the activation energy without altering the change in energy... as shown in the diagram [Catalysis DOES NOT CHANGE The Thermodynamics]  the overall change in energy is NOT AFFECTED by the change in the Activation energy an enzyme will contribute with its side chains into the reaction…e.g. covalent bond -an enzyme is not consumed by the rxn.. they are restored -it will orient the molecule to continue the reaction… Catalysis SPEEDS up the rxn -Some Equations can be used to predict whether a rxn will occur spontaneously or not. -Gibbs Energy(G) is a measure of whether a reaction is favored energetically or not -If Change in Gibbs energy Is negative, then rxn is spontaneously favored, thus the greater the ‘G’ will mean that there is less of a chance that the reaction will occur on its own. a rxn will occur to bring Change in G lower than zero (negative) the Delta G is a DIRECT MEASURE of how far a rxn is from Equilibrium recall: Delta G equation can be used to predict whether a rxn will occur spontaneously or not T: temperature H: Enthalpy S:Entropy G = H - TS COUPLING: THIS is  the Gibbz free energies being additive a reaction with positive G will use the energy given off by a favored rxn that has Negative G making the overall rxn favorable!!!  coupling is addition of free gibbs energy! -- Gibbs change in energy has two components: 1)Properties of molecule like amount of bonds and shit 2)Concentration of molecules free gibbs energy change equals zero K= the equilibrium constant which is the ratio between the product&Reactant At equialibrium, the free gibbs energy(NOT THE STANDARD) will equal zero (0) DeltaG=0 at equilibrium To chek if a rxn will work, and check the reactant concentration at the end of the rxn, u equate the standard gibbs energy to zero. For POSITIVE free energy, we have hundred/thousand times greater equilibrium constantand will result in 100,1000,… more PRODUCT than Reactant For NEGATIVE G-free energy we have smaller K constant and thus result in more substrate than product… A rxn can go both ways, but one direction will be more likely… The relative 1)concentration of the molecules will depend on their 2)properties(bonds…) 1)2) are listed above as factors of Gibbs energy change. e.g. generating protein is not energetically favored because high energy bonds need to be formed, This process is coupled by a difernt rxn that has a strongely negative free gibbs energy a rxn with +5 Gibbs energy, will require a rxn that has -5 or higher negative free gibbs energy.. this transfer is done through nucleotides you can also have a series of events that are all positive Gibbs energy/unfavorable rxns.. where they are in the presence of another rxn or set of rxn that can accommodate to the amount of positive Gibbs energy! Thermodynamics Lecture #2 If a rxn XY has –ve Gibbs energy, then it is favorable If same rxn XY has +ve Gibbs energy, then it is NOT favorable.. rather the opposite is favorable YX You can breakdown the Equation into: Concentration dependant Entropy Concentration Independent ________ Standard free gibbs energyStandardizing…. Rule out components of Disorder(e.g.Temperature, Pressure,etc…) and focuses on the properties and structure(e.g. bonds in the rxn),,, AND takes into account the concentration factor K=equilibrium constant = its determined by the difference in concentration of X & Y (Product & Reactant) K=[X]/[Y] if free energy is negative, then K= 10+ so there is MORE Product than Reactant [X]/[Y] … When the products are favored, the products will accumulate until Equilibrium…Equilibrium is when both products and reactants are moving towards eachother at the same rate Equilibrium is when the “forward rxn = Reverse rxn” [however, note that a rxn is ALWAYS slightly away from equilibrium] -the spontaneous direction is because of the Nature of the bonds that are favoring it -the other direction is because of Concentration When a rxn reaches equilibrium, Mathematically the free gibbs energy is equal to zero, but in reality, the rxns are ALWAYS slightly away from Equilibrium, so the free gibbs energy is never at exactly zero… Activated Carrier Molecules Activated carrier molecules capture packages of stable energy and transfer it to rxns that are NOT favored Major Activated Carrier molecules is ATP-11 to -13kCal/mol they are grabbed from catabolism rxns, and used for Anabolism rxns This is for free gibbx energy change.. not Standardized?? If you were to normalized, you would end up with a value that is fixed?? -a reason for the ATP’s hydrolysis is because its full of highly negative bonds that are repelling eachother, and this favors the hydrolysis too… makes it easier on the molecule -As the Phosphate is being transferred, it becomes lower in energy ~ -3 depending on the molecule -but then when rxn proceeds, the phosphate is cleaved off.. the phosphate it only added to favor the rxn: Note: the two steps: 1)Activation step 2)Condensation step Here basically you make an intermediate that is higher, then you relax it… NADPH /NADH Activated Carrier: Couples Electrons as source NADP captures electrons +H from Glucose NADPH is mostly used in the Biosynthesis of metabolites(e.g. glucose, fatty acids,etc…) NADPH is used reduce metabolites.. and oxidizes Electrons and transfers is somewhere else by reducing The only difference form NADPH and NADH is a phosphate group The phosphate group on the NADPH is not reactive at all!!! The phosphate group only defines specificity.. allows different enzymes to recognize them The H+ that is reactive is on the other end of the carrier NADP and NAD have similar structure to ATP!!! Because they contain Adenine and Ribose[the RNA world left remnants through this molecules] NADH is for creating energy through respiration in the mitochondria NADPH is for biosynthesis of metabolites BOTH have same mech, where they bring an intermediate to a higher state then relaxes it to its final form The activated carriers above ALSO contain Adenine and Ribose!![also remnants of the RNA world] -CoA carrier attaches itself onto a Acetyl through a thioester bond forming intermediate then relaxes by letting go of the intermediate…just like the other carriers -Many polymerization rxns require carriers,, even Polysaccharide, Protein, Nucleic acids -When two monomers polymerize they let go of an H20 molecule(an OH and H) -while this occur, one of the monomer is brought into an intermediate state through ATP -ATP only contributes to -11 to -13kCal per mol… This is NOT ENOUGH.. so for ALL of these polymerization processes(Polysaccharide, Protein, Nucleic acids) YOU NEED an enzyme that cleaves off TWO phosphates off an ATP to make AMP…This releases 26kCal per mole Thermodynamics FIND OUT WHAT ARE THE RATE LIMITING STEPS!!! Lecture #3 Glycolysis, starts with a 6-carbon sugar and leaves off a 3-carbon molecule called pyruvate Two investment of ATP molecules -First phosphorylation allows the molecules to become polar and be captured to go thru glycolysis process since the negative charge prevents the passage across the PM, thus keeping it in the cell to go thru glycolysis -isomerase step to convert glucose hexose into a fructose pentose -Second phosphorylation prepares the fructose to be cleaved in two. After making Fructose-1,6,- biphosphate, the Phosphate intermediate, you’re ready to go thru Cleavage: -this creates TWO glyceraldehyde-3-phosphate …these have a strong phosphate bond which are targeted easily for oxidation (step6) generating NADH EACH… &&&(step7) generating ATP EACH (after an addition of inorganic phosphate)  Also later step(10) there is another generation of ATP EACH ( from the first phosphate that was on G-3-P) NOTE: You overall invest 2 ATP and you recover 4 ATP Net products from Glucose to Pyruvate are 2 ATP and 2 NADH Net from the Phosphate intermediate(biphosphate-fructose) to pyruvate 4 ATP and 2 NADH Net from Glyceraldehyde-3-phosphate to pyruvate is 2 ATP and 1 NADH Energy investment: uses 2 ATP Energy payoff: makes 4 ATP Glycolysis is divided into 10 steps 1)Glucose uses ATP through hexokinase  G-6-P 2)G-6-P reacts with Phosphoglucose isomerase, to switch to its isomer Fructose-6-P (F-6-P) 3)F-6-P uses another ATP through PFK, to form Fructose-1,6- Biphosphate (F-1,6-P) 4) F-1,6-P splits due to Aldolase enzyme  giving glyceraldehyde-3-phosphate (G-3-P) and it’s isomer 5) its isomer reacts with an isomerase to convert to G-3-P leaving two G-3-P to go on 6) 2NAD+ react with the G-3-P’s taking off 4H and forming 2NADH + 2H (dehydrogenase oxidizes the G-3-P) The energy released is coupled to attach ANOTHER Phopsphate on each of the 2 G-3-P’s 7) The P’s that attached on the Two G-3- biPhosphate’s are unstable andPhosphoglycerate kinase, takes a phosphate from each G-3-biphosphate to stabilize it…. The phosphate is transferred to 2 ADP forming 2 ATP altogether from both G-3- biPhosphate1.(exergonic) 8)enzymes rearranges the molecule’s OH 9) dehydration forms a double bond 10) the next P on the molecules substrate-level phosphorylate ADP’s forming 2ATP’s Many of the steps occur because they are close to equilibrium, Step1 is Far away from equilibrium, so hexokinase enzyme uses ATP Step2 Phosphoglucose isomerase, then will change the conformation of Glucose-6-phosphate into Fructose-6-phosphate Step 3 Phosphofructose kinase(PFK) then uses the second ATP to convert fructose-6-phosphate into fructose-1,6-biphosphate Glycolysis is regulated through this step via regulation of the enzyme phosphofructokinase(PFK)… Note: there is an enzyme called biphosphatase that removes this phosphate! this burning of phosphate, provides heat for other processes depending on the condition of the animal Metabolic adaptation (Allows bees to fly fast) The enzyme Fructose 1,6-biphosphatase reverses the activation of Fructose 6-phosphate Allosteric regulation of PFK/biphosphatase certain ligands cause a change in the enzyme making is less accesible to the substrate, and Also change it in a way making it more easily accessible ligands alter the energy of activation? ADP binds the PFK and positively modifies the speed of the enzyme PFK is positively stimulated by AMP and ADP and Fructose-2,6-bi….YES its 2,6  Negatively by ATP NOTE: PFK reaction’s end products POSITIVELY FEEDBACK on it through allosteric regulation to stimulate it even further!  Biphosphatase, is instead stimulated by ATP and negatively by AMP and ADP and Fructose-2,6-bi These two enzymes are regulated by the same Ligands, but in the opposite manner This is another way how a cell stays a little bit away from equilibrium… recall: if the cell processes reach exactly equilibrium they die! Step4 Aldolase will perform the cleavage the backbone to form two 3-carbon molecules , but ONLY glyceraldehyde-3-phosphate can proceed into glycolysis right away immediately.. Step5 the other 3-carbon molecule, the dihydroxyacetone is modified into another Glyceraldehyde-3-phosphate Basically the fructose1,6-biphosphate gives out two glyceraldehye-3-phosphate Step 6 The two glyceraldehye-3-phosphate are oxidized by dehydrogenase & the electrons are packaged into NADH and a phosphate grou p is added on the glyceraldehyde to replace the H+ Step 7 -The following step is mediated by Phosphoglycerate kinase, which removes the phosphate that was just added and MAKES ATP this enzyme phosphorylates ADP into ATP -Note: that the energy given off the oxidation rxn allows an overall negative free gibbs energy Total energy change from Step 6 and Step 7 is a favorable rxn -3kcal/mole STEP 6&7 DETAILS the dehydrogenase 1)oxidizes and 2)binds the aldehyde(glyceraldehy1)transfering energy to reduce NADNADH… ANDDDDD , 2) this energy allows the dehydrogenase ENZYME to bind and make a high-energy thioester covalent bond, through its OWN Cystein side chain’s thiol group(-SH) onto the glyceraldehyde-3-phosphate -An inorganic phosphate displaces the Thioester high-energy bond of the enzyme and attach itself(the P) onto the oxidized phosphoglyceraldehyde(phosphoglycerate) to make it back into another phosphate intermediate (like biphosphofructose phosphate intermediate.. biphosphoglycerate) which has an anhydride bond… -This phosphate intermediate biphosphoglycerate relaxes down and allows phosphoglycerate kinase enzyme to generate ATP -Note: the high-energy bond that was displaced by the phosphate is transferred to ADP to form ATP Mini summary: the phosphoaldehyde becomes oxidized(generating NADH) into phosphoglycerate which gets another phosphate becoming a phosphate intermediate(biphosphoglycerate, which has an Anhydride bond) which then relaxes down and generates ATP , and becomes a Carboxylic Acid energy released from the conversion of Aldehyde to the Carboxylic acid, is the energy that is stored into ATP and NADH Step 8 Isomerization of 3-phosphoglycerate to 2-phosphoglycerate by phosphoglycerate mutase, Step 9 Dehydration of 2-phosphoglycerate to phosphoenolpyruvate by enolase, Step 10 Transfer of the phosphate group from phosphoenolpyruvate to ADP by pyruvate kinase, to make ATP. The following is a list of Phosphate Carriers: Just note that each have their own amount of free gibbs energy -IN THE MUSCLE….Creatine kinase takes phosphate from Creatine phosphate to make ATP -Creatine kinase will act accordingly, depending on the requirement, when requiring energy, it will burn it and vice versa… the rxns are slightly off equilibrium and can change anytime… Fermentation-Anaerobic -occurs when there is not much access to oxygen -Uses NADH to regenerate NAD+ which will then be used in glycolysis There are many types of fermentation where they differ in end-products formed from pyruvate. Two common are Lactic Acid fermentation and alcohol fermentation. LACTIC ACID FERMENTATION Note: Pyruvate can enter the mitochndria in livr cell and complete cellular respiration, instead of fermentation too… but here is what happens to pyruvate in fermentation: 1)-in Humans Pyruvate converts to Lactate and uses NADH Occurs After glycolysis which produces 2ATP and 2 NADH, in the First Step Pyruvate is reduced directly by NADH to form lactate to giving NAD+ for glycolysis to continue. (this is the ONLY STEP to make lactate from pyruvate!!! Uses NADH for each Pyruvate) Human Muscles make ATP by lactic acid fermentation when oxygen is insufficient -In Humans, The excess lactate is carried away by the blood to the liver/kidneylungs…The Lactate is converted back to pyruvate, at this point when oxygen is available… -In yeast, which are unicellular have no organs for the Lactate… the Pyruvate will instead lead to excretion of CO2 & alcoholCHECK BELOW Note: 2 pyruvate made from glycolysis leads to 2 Lactate, in Humans Note: 2 pyruvate made from glycolysis leads to 2CO2 + 2ethanol, in Yeasts CHECK BELOW ALCOHOL FERMENTATION Pyruvate is converted to ethanol in two steps. Pyruvate will be first converted to Acetaldehyde(yields CO2) then second be converted to ethanol -First step releases carbon dioxide(CO2) from pyruvate that is converted to 2x acetaldehyde(2-C each) -Second step the acetaldehyde is reduced by NADH to ethanol. This regenerates the NAD+ that glycolysis uses!!!!(just like Lactic acid fermentation!) -Note: NAD+ is required for glycolysis to drive ATP synthesis in Glycolysis… (Recall: 2NAD+ reacts with the two G-3-P fo
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