Biochemistry Practice Exam 1 – Metabolism

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What is Catabolism?
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1. Is the degradation of biomolecules for energy 2. Is the degradation of carbohydrates,lipids & proteins. 3. Either from the environment or energy reserves in the cell. 4. Either released and used directly to drive photosynthesis, transport, etc 5. Conserved in the form of ATP.
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What is Anabolism?
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Biosynthesis of nucleic acids, proteins and polysaccharides, lipids from simple building block precursors. (Which requires energy furnished by catabolism)
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In a eukaryotic cell, where do most catabolic reactions occur?
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Mitochondria (Mic)
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In eukaryotic cell, where do most anabolic reactions occur?
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Cytosol (AC)
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What is Feedback Inhibition?
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A product (usually final) of a pathway controls the rate of its own synthesis (By inhibition of an early step) – If enough Product is formed – Pathway down-regulates – Is Product is depleted – More can be made.
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For FEEDBACK INHIBITION, what is the advantage of a metabolic LATE in a metabolic pathway inhibiting a reaction EARLY in a pathway? Reason 1.
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1. Inhibition of an early step prevents needless synthesis and accumulation of intermediates. (saves resources)
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For FEEDBACK INHIBITION, what is the advantage of a metabolic LATE in a metabolic pathway inhibiting a reaction EARLY in a pathway? Reason 2.
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2. Inhibition of the protein/enzyme that synthesized that product if the step before yields a substrate for another pathway.
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What is FeedForward Activation? For FEEDFORWARD ACTIVATION, what is the advantage of a metabolic EARLY in a metabolic pathway activating a reaction LATE in a pathway?
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An early metabolic (intermediate) activates an enzyme further down the pathway. This will increase the flux through the pathway.
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(Match Cofactor with the Cycle) Acyl Carrier Protein
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Fatty Acid Biosynthesis
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(Match Cofactor with the Cycle) Coenzyme A
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Fatty Acid Oxidation
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(Match Cofactor with the Cycle) Cytochromes
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Electron Transport
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(Match Cofactor with the Cycle) Pyridoxal Phosphate
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Amino Acid Metabolism
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(Match Cofactor with the Cycle) NAD(H)
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Glycolysis (NAD+)
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(Match Cofactor with the Cycle) NADP(H)
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Fatty Acid Bio Synthesis
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(Match Cofactor with the Cycle) THF (Tetrahydrofolate)
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Nucleotide Biosynthesis
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(Match Cofactor with the Cycle) Ubiquinone
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Electron Transport.
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When a reaction is @ Equilibrium….
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Delta(G) = 0 Delta(G’) = -RTLnK(eq) Q = K(eq)
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Reactions are spontaneous when….
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Delta (G) < 0 Q < K(eq)
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Equilibrium favors the products when…..
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Delta (G) 1
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If Delta(G) rxn = Delta(G’) + RTln([C]^c[D]^d)/[A]^a[B]^b) for aA + bB —> cC + dD what does ([C]^c[D]^d)/[A]^a[B]^b) equal @ Equilibrium?
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K(eq)
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________________________________ is a measure of how far a reaction is from equilibrium.
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Delta(G)
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________________________________ is a measure of where the equilibrium of a reaction or system lies.
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Delta(G’)
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Delta (G)
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1. How far a reaction or system lies from equilibrium 2. Determines Spontaneity 3. All reaction want to go towards to equilibrium.
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-Delta(G)
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Spontaneous (and moves on without an external source)
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+Delta (G)
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Not Spontaneous (Would require energy and Reverse RXN is favored)
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Delta(G) = 0
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Reaction is at Equilibrium
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Delta(H)
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Measure of heat (- value is favored)
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Delta(S)
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Measure of Order/Disorder(+ Value is favored)
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STUDY Delta(G) = Delta(H) – TDelta(S) equation values.
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STUDY Delta(G) = Delta(H) – TDelta(S) equation values.
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When ATP is utilized for it’s energy, is it hydrolyzed to AMP&PPi or ADP&Pi but not Adenine and PPPi, because the first 2 are more stable than Adenine and PPPi? Why are AMP and PPi or ADP and Pi more stable than Adenine and PPPi?
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AMP&PPi or ADP&Pi – Require more energy in order for their bonds to cleave (Bond Cleavage DeltaG’ = -30 kJ/mol) Adenine and PPPi – Phospdiester Bond Cleavage – DeltaG’ = -14kJ/mol
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3 REASONS WHY AMP and PPi or ADP and Pi more stable than Adenine and PPPi?
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1. Electrostatic Repulsion of P-P-P > P-P or P 2. Products of Hydrolysis more stable – The e’s on terminal oxygens are more delocalized than on binding oxygens hydrolysis creates in new termini. 3. Products are better solvated – Ions electrically shielded from one another
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Why is ATP, of relative intermediate energy, the main energy molecule of the cell instead of a higher energy molecule such as phosphocreatine?
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The intermediate can be synthesized and utilized as needed. Thermodynamically it is well suited as the phosphoric carrier.
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Where does energy come from to make ATP
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1. Substrate Phosphoralyzation – Hydrolysis of a high energy compound to form ATP 2. Oxidative Phosphoralyzation – Proton gradient generated by the electron transport chain produces the energy needed to make ATP.
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Where (in what pathway) is ATP produced under ANAEROBIC conditions?
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Under ANAEROBIC Conditions 1. ATP comes directly/exclusively from glycolysis. Reactions under these conditions will regenerate NAD+ (which is necessary for glycolysis)
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Where (in what pathway) is ATP produced under AEROBIC conditions?
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Glycolysis = 1st step for producing ATP for energy (Net gain of ATP’s) Ultimately the ATP’s produced by oxidative phosphoralyzation. (Many more than 2 are made but these are the most important)
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How is NAD regenerated under Anaerobic conditions? In other words, write out one of the pathways.reactions showing the substrates, enzymes, coenzymes and products where NAD is generated.
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3-P-Glyceraldehyde ————————-> 1:3bisPglycerate Double arrows (Pi, NAD+ NADH) 1.2.1.12 (Oxidoreductases – Glyceraldehyde 3 Phosphate dehydrogenase)
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Glycolysis Which are the reactions with the large negative G values?
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1. Glucose to Glucose6P (-33.5) 2. PEP to pyruvate (-33.4) 3. F6P to FBP (-22.2)
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Glycolysis Which are the largely spontaneous reactions?
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Q < Keq and Delta(G) < 0 Largely spontaneous with be ones with a greater negative value. 1. Glucose to Glucose 6P 2. PEP to Pyruvate
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Glycolysis Which are the regulated reactions?
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Steps 1,3,10 All points of regulation Delta(G) and Delta(G’) will be – 1. Glucose to Glucose6P 2. Fructose6P to Fructose1,6diphosphyte 3. 2 phosporyl pyruvate to 2 pyruvate
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Glycolysis Points
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10 Enzymatic Steps Energy Investment (2ATP’s used) Energy Generation (4ATP’s made) Results in a Net of +2 ATP
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Which enzyme, Phosphofructokinase 1 or Phosphofructokinase 2 has a lower apparent Km (binding affinity) for fructose 6 phosphate? (Illustrate by drawing a graph of velocity as a function of substrate concentration for both enzymes)
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PFK2 activated when [Fructose-6-P] goes up PFK2 higher Km for Fructose 6-P than PFK1 Therefore PFK2 active only when [Fructose-6-P] high (Illustration – [Fructose-6-P] vs V PFK1 above PFK2)
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What happens to the apparent Km (becomes smaller, larger, or remains the same) for fructose 6 phosphate in Phosphofructokinase 1, as the concentration of fructose-2,6-bisphosphate increases? (Illustrate this by drawing a graph of the velocity as a function of substrate concentration in both the absence and presence of fructose 2,6 bisphosphate.)
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Fructose 2,6 bisphosphate activates PFK1 once a lot of fructose 6P converted to fructose 2,6 bisphosphate. PFK1 activated to make fructose 1,6 bisphosphate instead. (Illustration – [Fructose-6-P] vs V PFK1 above PFK2 and draw F26BP in the middle)
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Why does excessive sucrose and fructose yield a fatty liver?
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Most fructose that comes from sucrose or fructose from fruit is converted to fructose 1-P which enters glycolysis after conversion of fructose 6P to fructose 1,6-bisP, thus bypassing PFK-1 regulation. Over production of pyruvate, causes over synthesis of fat and cholesterol.
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Why is the first point of regulation NOT the main regulatory step in Glycolysis?
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PFK1 converts Fructose 6P to Fructose1,6bisP PFK not Hexokinase = major regulatory enzyme BECAUSE glucose from glycogen reserves enters the pathway @ glucose 6P not glucose, the control only beings after this point and not before.
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In glycolysis reaction, the reaction of dihydroxyacetone phosphate to glyceraldehyde-3-phosphate is a non spontaneous reaction when isolated in vitro. What drives it forward in the glycolysis pathway?
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Step 5. Triose phosphate isomerase converts Dihydroxyacetone-P to Glyceraldehyde-3-P Only glyceraldehyde is consumed in the next RXN. this drives the reaction forward even though Delta(G) is + the back reaction is favored (in a vacuum/isolated condition).
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What is a Negative Regulator?
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Inhibitor
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What is a Positive Effector?
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Activator
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Glycolysis AMP
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ACTIVATOR (Fructose 6P+ATP–> fructose 16bisP+ADP+H+)
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Glycolysis ATP
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INHIBITOR (Fructose 6P+ATP–> fructose 16bisP+ADP+H+)
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Glycolysis Citrate
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ACTIVATOR/INHIBITOR (Fructose 6P+ATP–> fructose 16bisP+ADP+H+)
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Glycolysis Acetyl CoA
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INHIBITOR (PEP —>Pyruvate) Pk Top and ADP–>ATP bottom
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Glycolysis Glucose 6 Phosphate
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INHIBITOR (Glucose– Glucose6P)
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Glycolysis Fructose2,6bisphosphate
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ACTIVATOR (Fructose6P–>Fructose2,6bisphosphate)
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Pentose Phosphate Pathway – (Purpose is to make biosynthesis Precursors) What are 2 metabolites and in what pathway are they formed?
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1. 2NADPHs formed from 2NADP+’s (NADPH needed for biosynthesis of fatty acids and sterols) 2. 1-Ribose-5-phosphate is formed (Needed for biosynthesis of nucleotides—> DNA to RNA)

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