# Shared Flashcard Set

## Details

Test 2 Cards Schempke
Eek
215
Biochemistry
02/21/2011

Term
 Synthesis or degradation of molecules involves a change in what?
Definition
 Energy
Term
 Thermodynamics
Definition
 Study of the energy changes
Term
 What determines direction of a reaction?
Definition
 Free energy, delta G (G prod-Greact)
Term
 Gibbs Free Energy equation
Definition
 DeltaG=DeltaH -TDeltaS
Term
 DeltaG' (o)
Definition
 Under very artificial conditions25 degreesC,All reactants/product @ [1M]ph=7
Term
 What is Delta G' useful for?
Definition
 When comparing 2 or 3 reactions
Term
 If energy cannot be created or destroyed, what happens when - free energy?
Definition
 Released in the form of heat or work
Term
 Delta G an also =
Definition
 Q+W (heat+work)
Term
 Work can be
Definition
 Motion, formation, [gradient], chemical work, etc.
Term
 Second law of thermodynamics
Definition
 For any reaction or process, then enropy of the universe increases
Term
 Entropy Equations
Definition
 DeltaSuniv=Sfinal-Sinitial (>0)DeltaSuniv=DeltaSsystem+DeltaSsurrounding
Term
 According to the second law of thermodynamics, can cells decrease their entropy?
Definition
 Yes, only if their surroundings increase entropy by a greater extent
Term
 What drives diffusion by concentration gradient?
Definition
 Entropy
Term
 If gibbs free energy is -
Definition
 Energy decreases, favorable reaction, spontaneous.Exergonic reaction
Term
 Gibbs free energy is +
Definition
 Energy is absorbed by the reaction, + deltaGEndergonic reactionDoesn't occur
Term
 Does a -33 reaction proceed faster than a -16 reaction?
Definition
 Not necessarily, just know it is spontaneous
Term
 DeltaG and the equilibrium constant:
Definition
 DeltaG=DeltaG'+RTln([C]^c[D]^d)/([A]^a[B]^b)
Term
 What is deltaG @ equilibrium?
Definition
Term
 DeltaG'=Equation
Definition
 RT*lnKeq
Term
 The farther the reaction is from equilibrium, what is deltaG?
Definition
 Low, (larger A,B values)
Term
 Values of deltaG and deltaG' when system NOT @ equilibrium?
Definition
 Not equal. Farther from equilibrium = more - reaction
Term
 Coupled reactions
Definition
 Occur simultaneously One endergonic and exergonic
Term
 What "drives" coupled reactions?
Definition
 Negative -G of summed reactions.
Term
 What compounds can transfer phosphate's?
Definition
 Compound w/ more - deltag(hydrolysis) can transfer to a one w/ more +
Term
Definition
 PEP, 1,3 BPG, Phosphocreatine,and phosphoarg
Term
Definition
 Glucose 1 P; Glucose 6 P; Glycerol 3 P
Term
 High energy compounds and phosphate transfer
Definition
 Want to transfer Pi; down hill
Term
 Low energy compounds and phosphate transfer
Definition
 Don't donate phosphate, uphill
Term
 What provides free energy to drive most endergonic reactions?
Definition
Term
 What is the primary energy currency of cells?
Definition
 ATP
Term
 Catabolism
Definition
 Degredation of nutrients, releases energy which is captured and stored as ATP
Term
 What happens in catabolism?
Definition
 releases energy which is captured and stored as ATP
Term
 Anabolism
Definition
 Building up of nutrients (biosynthesis) ; Uses energy of ATP to do transport and mechanical work
Term
 What happens during anabolism?
Definition
 Uses energy of ATP to do transport and mechanical work
Term
 Metabolism definition
Definition
 Set of all reaction used by living organism to break down molecules necessary for energy (catabolism) and synthesize biomolecules from simple precursors (anabolism)
Term
 What type of reaction is catabolism?
Definition
 Exergonic
Term
 What is characteristic of catabolism?
Definition
 Oxidation, Hydrolysis, and conversion of biomolecules ->CO2, H20, and NH3 (urea)
Term
 Energy released from oxidation is stored how?
Definition
Term
 What type of reaction is anabolism?
Definition
 Endergonic
Term
 What characterizes anabolism?
Definition
 Reduction, Hydration, Conversion of small molecules to complex biomolecules
Term
 How is energy for anabolism supplied?
Definition
Term
 Different forms of metabolic pathways:
Definition
 Cyclic; linear; Spiral; Reversible
Term
 Overall DeltaG (for multi-step)
Definition
 Sum of delta G for each step
Term
 What could multiple steps mean for energy?
Definition
 Small amounts of free energy change in each step. More feasible biological systems.
Term
 Good example of many steps, small change:
Definition
 Ethanol->Acetyl CoA
Term
 Ehtanol oxidized to acetyl reaction
Definition
 Ethanol->Acetaldyhyde->Acetate->Acetyl CoA
Term
 What oxidizes nutrients in catabolism?
Definition
Term
Definition
Term
 What happens when reduced cofactors are oxidized?
Definition
 Released energy is used to form ATP
Term
 What are small molecules converted to in anabolism?
Definition
 Larger, more energy rich products
Term
 What supplies energy to anabolism?
Definition
 ATP
Term
 Reducing equivalents in anabolism?
Definition
Term
Definition
Term
Definition
Term
Definition
 4/1ATP required for anabolism and other energy requiring rxns
Term
 Major carb pathway:
Definition
 Glucose->Phosphoenolpyruvate->2pyruvate->Acetyl CoA-> Citric acid cycle.
Term
 Is glucose->phosphoenolPyruvate reaversible?
Definition
 Yes. Depending on the needs of the cell
Term
 Gluconeogenesis
Definition
 Synthesis of glucose
Term
 Where does gluconeogenesis occur?
Definition
 Liver cells only
Term
 What cells can convert glucose->cycle?
Definition
 All cells
Term
 What cells use energy as an energy source?
Definition
 All cells
Term
 What cell can ONLY use glucose as an energy source?
Definition
 RBC-only glucoseNeuron- prefer glucose; can use others
Term
 Glycolysis
Definition
 Anaerobic oxidation of glucose to give two molecules of pyruvate and chemical energy in the form of ATP and NADH
Term
 GLycolysis Reaction
Definition
Term
 What type of reaction is glycolysis?Thermodynamicly and Oxygen requirement
Definition
 ExergonicAnerobic
Term
 What helps make glucose more reactive in glycolysis?
Definition
 ATP
Term
 Stages 1 and 2 of glycolysis?
Definition
 Energy inputEnergy output
Term
 How is energy released in glycolysis stage 2?
Definition
 As G3P converted to pyruvate.
Term
 What is the 1st step of glycolysis?
Definition
Term
 Why is glucose converted to glucose 6 phosphate?
Definition
 Glucose 6 phosphate cannot get out of the cell
Term
 What enzyme catalyzes Glucose->Glucose 6 phos?
Definition
 Hexokinase; glucokinase
Term
 What is the second step of glycolysis?
Definition
 Glucose 6 phos==Fructose 6 phos
Term
 What is the enzyme for the second step of glycolysis?
Definition
 Glucose 6 phosphate isomerase
Term
 Step 3 of glycolysis
Definition
 Add another phospho group to moleculeFructose 6 phos-> Fructose 1,6 biphos
Term
 Enzyme for 3rd step of glycolysis?
Definition
 Fructo-kinase 1
Term
 What is the committed step in stage 1 of glycolysis?
Definition
 3rd step.Fructose 1,6 Bisphos is formed
Term
 What regulates PFK-1?
Definition
 Allosteric effectors
Term
 Reaction @ PFK-1
Definition
 Irreversible
Term
 Glycolysis step 4
Definition
 Fructose 1,6 Bisphos cleaved to form Dihydroxy-acetone and glyceraldehyde
Term
 Step 4 of glycolysis begins what?
Definition
 First step of energy out stage
Term
 Enzyme in fourth step of glycolysis?
Definition
 Aldose
Term
 Glycolysis Step 5
Definition
 Interconversion of dihydroxyacetone to glyceraldehyde (from previous)
Term
 Enzyme for step 5 of glycolysis
Definition
 Triose phosphate isomerase
Term
 What happens after step 5?
Definition
 2 glyceraldehyde molecules.Each reaction happens 2 times :)
Term
 Reaction 6 of glycolysis (overall)
Definition
 phosphorylate G3P to form 1,3 Bisphosphoglycerate
Term
 What enzyme is used in step 6 of glycolysis?
Definition
 Glyceraldehyde 3 phosphate dehydrogenase
Term
 What two things happen in reaction 6 of glycolysis?
Definition
 Phosphorylation and Electron oxidation
Term
 Detail Reaction 6 of glycolysis?
Definition
Term
 What does G3P stand for?
Definition
 Glyceraldehyde 3 phosphate formed in 4/5
Term
 Step 7 of glycolysis?
Definition
 1,3 bisphosphoglycerate->3 phosphoglycerate
Term
 What happens for the first time in reaction 7?
Definition
 Transfer of a high energy phosphoryl groupADP->ATP
Term
 What is the enzyme for reaction 7?
Definition
 Phosphoroglycerate kinase
Term
 Glycolysis step 8
Definition
 Intramolecular phosphoryl group transfer3 phosphoglycerate->2phosphoglycerate
Term
 Enzyme for reaction 8 of glycolysis?
Definition
 Phosphoglycerate mutase
Term
 Glycolysis step 9
Definition
 Dehydration to form energy rich ester2 phosphoglycerate->phosphoenol pyruvate
Term
 Reaction 9 enzyme?
Definition
 Enolase
Term
 Glycolysis step 10
Definition
 Transfer of a high energy P group to ADP to yield ATPPhosphoenol pyruvate->Pyruvate
Term
 Enzyme of reaction 10 of glycolysis
Definition
 Pyruvate kinase
Term
 Fates of pyruvate:
Definition
 Conterted to ethanol (yeasts, alc. ferm)Lactate (in RBC and anaerobic musc.)Oxaloacetate (TXA- substrate for gluconeogenesis)
Term
 Energy of pyruvate
Definition
 High energy
Term
 What can cells with mitochondria do to pyruvate?
Definition
 Extract energy from it by converting it to acetyl CoA
Term
 Pyruvate fermintation reaction:
Definition
Term
 Where does pyruvate fermentation occur?
Definition
 Cells w/ no mitochondria. Ex. RBC or anaerobically muscle cells
Term
Definition
 Mitochondria (ox/phos)
Term
 Why does lactic acid make muscles sure?
Definition
 Acidic, inflammation
Term
 What converts pyruvate to ethanol?
Definition
 Yeasts
Term
 How do yeasts convert pyruvate -> ehtanol
Definition
 Pyruvate decarboxylase->Acetyl aldehydeAlcohol dehydrogenase ->ethanol
Term
 Where is pyruvate decarboxylase found?
Definition
 Only in bacteria and yeasts, if we had it we could hold our breath and get drunk ;)
Term
 How do you make 2,3 BPG for RBC?
Definition
 You take 1,3 BPG from step 6 and you use enzyme BPG mutase and get 2,3 BPG
Term
 ATP production of glycolysis (Stage 1, Stage2)
Definition
 2 steps in stage 1 use ATP gluctose->Glucose 6 phos Fructose 6 p->1,6 bisphos2 steps produce ATP in stage 3 Glycerate 1,3 bisP to 3-P glycerate PEP to pyruvateNet result=2 ATP/glucose
Term
 Which steps of glycolysis are irreversible?
Definition
 1,3,10Significantly negative delta G values
Term
 Overall glycolysis is endergonic or exergoinic?
Definition
 Exergonic
Term
 Where are the primary sites of regulation in glycolysis?
Definition
 Irreversible reactions. 1,3,10
Term
 Regulation of glycolysis
Definition
 3 allosteric enzymesHexokinasePFK-1Pyruvate Kinase
Term
 Hexokinase
Definition
 Step 1Inhibitor is Glucose 6 phos, ATPNo activator
Term
 PFK-1
Definition
 Step 3Activated by F2,5 bp, AMPInhibitied by Citrate, ATP
Term
 Pyruvate kinase
Definition
 Step 10Activated by F,1-6 BP, AMPInhibitied by Acetyl CoA; ATP
Term
 What can generate acetyl CoA?
Definition
 Many nutrientsProtein, Triglyceride, Glycogen
Term
 Where does oxidation of acetyl CoA occur?
Definition
 Mitochondria
Term
 What does oxidation of acetyl CoA provide?
Definition
 Vast majority of energy for aerobic cells
Term
 PDH
Definition
 Pyruvate Dehydrogenase
Term
 What does pyruvate dehydrogenase do?
Definition
Term
 Required cofactors for PDH
Definition
Term
 Coenzyme A contains what subgroups
Definition
 2 mercaptoethylamine, Pantothenate, ADP w/ 3' phosphate group.
Term
 How is CoA often written, why?
Definition
 As CoA-SH. All the chemistry happens @ SH group
Term
 Where is the high energy bond in acetyl CoA?
Definition
 Thio-ester bond which connects the two structures
Term
 Role of Coenzyme A?
Definition
 Carries acetyl group
Term
 Role of NAD in PDH cofactors?
Definition
 Carries reducing equivalents
Term
 Purpose of TPP as a PDH cofactor?
Definition
 Chemistry takes place at the R group. A possible R group, hydroxy ethyl, comes from pyruvate
Term
 Function of Lipoamide as a PDH cofactor?
Definition
 2 carbon fragment transferred here. Oxidation reaction. Reduced agent if Flavin (FAD->FADH2)2 forms
Term
 Lipoamide oxidized form?
Definition
 Disulfide bond
Term
 Lipoamide Reduced form?
Definition
 SH bond
Term
Definition
 Reduces to FADH2 as the oxidation reaction occurs @ the lipoamide. Puts enzayme back into reduced form
Term
 What are the 3 enzymes present in the reaction cataylzed by PDH?
Definition
 PDHDihyrolipoamide Acetyl transferaseDihyrolipoamide dehydrogenase
Term
 What is the structure of pyruvate referred to as?
Definition
 Alpha Keto acid
Term
 What is the function of NAD in PDH?
Definition
Term
 UQH2/U2 is similar to what?
Definition
Term
Definition
 Diffusable redox reactions
Term
Definition
 Enzyme bound. Non mobile
Term
Definition
Term
Definition
Term
Definition
Term
 Where does glycolysis occur?
Definition
 Cytosol of most cells
Term
 First step of TCA cycle?
Definition
 Pyruvate->Acetyl
Term
 Where do products of PDH go?
Definition
 Mitochondria, cannot leave there
Term
 Product that leaves mitochondria just before start of TCA cycle?
Definition
 Acetyl CoA
Term
 What is the primary use of NADH?
Definition
 Energy Production
Term
 What is the primary use of acetyl CoA
Definition
 Energy Production
Term
 How is the activity of the PDH controlled?
Definition
 By availability of pyruvate;rate of product use (energy status of the cell)
Term
 How is energy status of the cell determined?
Definition
Term
Definition
Term
 How is PDH activity regulated?
Definition
 Allosteric regulationPhosphorylation
Term
 What does acetyl CoA have negative feedback on?
Definition
 Dihydroliponamide acetyltransferase
Term
 In regulation of PDH what does NADH have negative feedback on?
Definition
 Dihydrolipoamide dehydrogenase
Term
 in regulation of PDH what does NAD have positive feedback on?
Definition
 Dihydrolioamide dehydrogenase
Term
 In regulation of PDH what does HS-CoA have feedbackon?
Definition
 Positive feedback, Dihydroliponamde acetyltransferase.
Term
 What do you have lots of if you are starved for energy?
Definition
Term
 What type of metabolic pathway is the TCA cycle?
Definition
 Cyclic
Term
 How does the TCA cycle form citrate?
Definition
 Combining acetyl CoA and oxaloacetate
Term
 What reduction reactions happen in the TCA cycle?
Definition
Term
 In what organisms is the TCA cycle found?
Definition
 Mostly aerobic organisms
Term
 Mutations in the TCA cycle?
Definition
 Few known, but they indicate critical function.
Term
 Citrate re-arranges when?
Definition
 After it's formed to make isocitrate
Term
 What happens to isocitrate in TCA cycle?
Definition
 It is oxidized to alpha keto glutarate
Term
 What oxidizes isocitrate?
Definition
 Isocitrase dehyrogenase
Term
 Where does the first CO2 come off in the TCA cycle?
Definition
 After oxidation of isocitrate.
Term
 When does the second oxidation reaction occur?
Definition
 4. alpha keto glutarate->Succinyl CoA
Term
 Alphaketoglutarate is oxidized and combines w/ what?
Definition
 CoA group. Forms succinyl CoA
Term
 Alphaketohydrogenase is similar to what?
Definition
 PDH.Same cofactors. B/c molecules are same class.
Term
 Where does second carbon leave?
Definition
 @ second oxidation. Oxidation of alphaketoglutarate
Term
 Thio-ester bond in succinyl coA?
Definition
 High energy bond, just like acetyl
Term
 What is hydrolysis of thio-ester bond associated with in the TCA cycle?
Definition
 High energy bond. Forms energy for GDP->GTP
Term
 Substrate level phosphorylation in TCA cycle?
Definition
 GDP->GTP
Term
 What reaction does succinyl CoA undergo in TCA cycle?
Definition
 Succinyl CoA synthetase oxidizes it.FAD as cofactor
Term
 What is cofactor of Succinate dehydrogenase complex in TCA cycle?
Definition
Term
 What does succinyl CoA synthetase do?
Definition
 Succinyl CoA -> SuccinateVia substrate level phosphorylation Release Hs-CoA
Term
 Succinate dehydrogenase complex in TCA cycle?
Definition
 Succinate->Fumarate
Term
 Fumarase in TCA cycle?
Definition
 Fumarate-> L-maleate
Term
 Maleate dehydrogenase in TCA cycle?
Definition
 Maleate -> OxaloacetateOxidation. NOT decarboxylation
Term
 What happens to the reduced cofactors of the TCA cycle?
Definition
 They enter the ox/phos pathway
Term
 Why does NADH goes to ETC?
Definition
 To get oxidized back to NAD, so the TCA cycle can function
Term
 Final reactions of ETC?
Definition
 H2O and water?
Term
 If no oxygen present, what happens to ETC?
Definition
Term
 What is the TCA cycle coupled to?
Definition
 ETC
Term
 Exergonic reactions of TCA cycle?
Definition
 Acetyl->CitrateIsocitrate->AlphaketoglutarateAlphaketoglutarate->Succinyl Coa
Term
 Which reactions in the TCA cycle are irreversible?
Definition
 1,3,4Release CO2Exergonic ones
Term
 Which reactions are sites of regulation in TCA cycle?Enzymes?
Definition
 1,3,41.Citrate synthase2.Isocitrate dehydrogenase3.Alphaketoglutarate dehydrogenase complex
Term
 What reactions drives the TCA cycle
Definition
 1,3,4
Term
 Other reactions we need to know:
Definition
 5,6,8Syccinyl-CoA synthetaseSuccinate dehydrogenase complexMalate dehydrogenase
Term
 Succinate dehydrogenase Reaction
Definition
 Oxidized succinate to fumerateComplex 2 of the ETC
Term
 Succinate dehydrogenase enzyme location
Definition
 Membrane bound enzyme (inner membrane of the mitochondria)
Term
 Succinate dehydrogenase enzyme function
Definition
 Takes reducing equiv. of succinate->FAD->QH2QH2 released. Donate e- to rest of ETC
Term
 Thio-ester high energy bond in the succinyl CoA synthetase provides energy for what?
Definition
 Substrate level phosphorylation
Term
 Malate dehydrogenase DeltaG'
Definition
 Positive
Term
 What is Delta Gactual of Malate dehydrogenase in cell?
Definition
Term
 Overall Delta G' for TCA cycle?
Definition
 -13.1 kcal/mol;-54.7 kj/mol
Term
 Since the Delta G of TCA is negative what happens?
Definition
Term
 What forms of energy storage are created by TCA cycle?
Definition
Term
 Other function of the TCA cycle?
Definition
 Intermediates for TCA cycle can be used as precursors for other metabolic pathways.
Term
 What substrates can be exported from TCA cycle?
Definition
 CitrateAlphaketoglutarateSuccinyl CoAAxaloacetate (gluconeogenesis)
Term
 What happens to TCA cycle when TCA cycle intermediates leave?
Definition
 Depletes oxaloacetate. Can eventually limit TCA cycle.
Term
 If oxaloacetate is low enough that TCA cycle is limited, what kind of energy state is the cell in?
Definition
 The cell is at a lower state of energy, so it doesn't need the TCA cycle. However, it can have a sudden need.
Term
 What happens if the cell needs energy quickly and not enough oxaloacetate?
Definition
 Run in reverse, to get oxaloacetate. Most important reaction is the first one (pyruvate+co2) make oxaloacetate
Term
 Pyruvate carboxylase
Definition
 Catalyzes Pyruvate+Bicarb=oxaloacetate
Term
 Anaplerotic Reaction
Definition
 Reaction running in reverse to get necessary products to form reaction
Term
 Most important Anaplerotic Reaction?
Definition
 Pyruvate Carboxylase
Term
 What stimulates pyruvate carboxylase reaction?
Definition
 Acetyl CoA
Term
 Where in the body can pyruvate carboxylase be found?
Definition
 High levels in the liver and neruon mitochondria.
Term
 Function of pyruvate carboxylase?
Definition
 To decrease the number of intermediates in the TCA cycle to allow it to function @ maximum level.
Term
 Regulation of TCA cycle
Definition
Term
 Glycolysis ATP numbers
Definition
 7 total (5 NADH, 2 ATP)
Term
 Pyruvate->Acetyl ATP
Definition
Term
 TCA cycle
Definition