Biochemistry exam 3

Which molecule controls the rate of the pentose phosphate pathway?

NADP+/NADPH

The glycolysis pathway is shown. Place the enzymes used in each of the ten labeled steps of the pathway. Be sure to scroll down completely until pyruvate is formed

Reaction Enzyme Glucose to glucose-5-phosphate Hexokinase Glucose-5-phosphate to fructose-6-phosphate Phosphohexase Isomerase Fructose-6-phosphate to fructose-1,6-biphosphate Phosphofructokinase-1 fructose-1,6-biphosphate to dihydroxyacetone phosphate and glyceraldehyde-3-phosphate Aldolase dihydroxyacetone phosphate and glyceraldehyde-3-phosphate interconversion Triose phosphate isomerase glyceraldehyde-3-phosphate to 1,3-bisphosphoglycerate Glyceraldehyde-3-phosphate dehydrogenase 1,3-bisphosphoglycerate to 3-phosphoglycerate Phosphoglycerate kinase 3-phosphoglycerate to 2-phosphoglycerate Phsophoglyero mutase 2-phosphoglycerate to phosphoenolpyruvate Enolase phosphoenolpyruvate to pyruvate Pyruvate kinase

Which compound accepts electrons from NADH, producing a compound that can pass through the inner membrane?

oxaloacetate or malate

Scientists can use mutants to study metabolic pathways. These organisms have a mutation in a gene encoding a metabolic pathway enzyme that results in the inactivation of that enzyme. Saccharomyces cerevisiae (a yeast species) mutants are available that grow on fructose, but not glucose. This growth defect results from a mutation in the gene encoding what enzyme? phosphoglycerate mutaseenolase pyruvate kinase phophoglucose isomerase (phosphohexose isomerase or glucose-6-phosphate isomerase) phosphoglycerate kinase

phophoglucose isomerase (phosphohexose isomerase or glucose-6-phosphate isomerase)

Which direction is ADP3− transported during times of active oxidative phosphorylation?

into the mitochondrial matrix

Gluconeogenesis is the conversion of pyruvate to glucose. This metabolic pathway needs several cofactors to complete the conversion. 1) Complete the unbalanced equation to generate one equivalent of glucose. 2) Predict the positions of the glucose molecule that would become labeled from 1-14C Pyruvate (the label in the carboxyl group of pyruvate).

1) 2 pyruvate + 2 NADH +4ATP +2 GTP → 1 glucose +2NAD+ +4ADP +2GDP +6Pi 2) CARBONS 3 AND 4

Galactosemia can result from a deficiency of either galactokinase or UDP‑glucose: galactose 1‑phosphate uridylytransferase (transferase). Although a deficiency of either enzyme will cause gastric discomfort after milk ingestion, transferase deficiency also results in liver, kidney, spleen, and brain dysfunction, and in some cases, death. 1) Select the statements that correctly link each type of enzyme deficiency with the metabolites that accumulate in the blood and tissues. 2) Which result from a galactosemia study in an animal model will implicate galactose 1‑phosphate as the toxic agent in a transferase deficiency?

1) A galactokinase deficiency will cause an accumulation of galactose. Transferase converts galactose 1‑phosphate to UDP‑galactose; therefore, a transferase deficiency will cause an accumulation of galactose 1‑phosphate. 2) Affected animals given a galactokinase inhibitor do not experience toxicity.

1) Complete the reaction, which is part of the electron transport chain. The abbreviation Q represents coenzyme Q. Use the appropriate abbreviation for the product. 2) The reactant that is reduced is 3) In complex III, electrons are transferred from coenzyme Q to cytochrome c, which contains iron. QH2+2cyt c(Fe3+)⟶Q+2cyt c(Fe^x)+2H+ Determine the oxidation number for iron on the right side of the reaction arrow (x=?)

1) FADH2​+Q→FAD+QH2​ 2) Q 3) x=+2

Reactive oxygen species (ROS) are unstable oxygen‑containing molecules that can cause damage to enzymes and membranes. Cells can defend against damage by converting these ROS to harmless species. Complete the reactions. 1) 2O2 + 2H+ ----> __________________________ + O2 2) What is the enzyme or enzyme type that catalyzes this reaction? 3) ___________________ + 2GSH -----> 2 H2O + GS-SG 4) What is the enzyme or enzyme type that catalyzes this reaction?

1) H2O2 2) superoxide dismutase 3) H2O2 4) glutathione peroxidase

Under aerobic conditions, extramitochondrial NADH must be oxidized by the mitochondrial electron‑transfer chain. Consider a preparation of rat hepatocytes containing mitochondria and all the cytosolic enzymes. A mixture of [4-3H]NADH and [7-14C]NADH is added to the preparation. Mitochondria are isolated and assayed for radioactivity. 1) What do you predict will be the result of this experiment? 2) What system transports the electrons from the extramitochondrial NADH to the mitochondrial electron‑transfer chain?

1) Only H3 will be found in the mitochondrial matrix. 2) the malate-α‑ketoglutarate transporter

In the presence of saturating amounts of oxaloacetate, the activity of citrate synthase from pig heart tissue shows a sigmoid dependence on the concentration of acetyl‑CoA. When succinyl‑CoA is added, the curve shifts to the right and the sigmoid dependence is more pronounced. 1) Choose the statements that are reasonable explanations for the right‑ward shift of the velocity curve caused by succinyl-CoA. Citrate synthase is regulated by another metabolite that has the opposite effect (i.e., stimulates citrate synthase). 2) Choose the description of a condition where a positive regulator activates citrate synthase

1) Succinyl‑CoA binds at a regulatory site other than the active site. Succinyl‑CoA competes with acetyl‑CoA for binding at the active site. 2) Low [ATP/ADP] ratio. ADP is an allosteric activator of citrate synthase.

The abbreviations DHAP and G3P represent dihydroxyacetone phosphate and glyceraldehyde-3-phosphate, respectively. 1- Which of these is the galactose derivative that enters the glycolytic pathway? 2- Which of these is the mannose derivative that enters the glycolytic pathway?

1) glucose-6-phosphate 2) fructose-6-phosphate

When considering free energy change, biochemists define a biochemical standard state, ΔG∘′, which differs from the chemical standard state, ΔG∘ . A similar distinction must be made with reduction potentials. 1) In contrast to the chemical reduction potential, Δ𝐸∘ , the biochemical standard reduction potential, Δ𝐸∘′... 2) Why might the standard reduction potential for a reaction differ from the reduction potential found in a cell?

1) specifies a pH of 7 2) Concentrations in the cell might not be 1 M.

In the first step of glycolysis, the given two reactions are coupled. reaction 1: glucose + pi->glucose 6 phosphate +h20 G=+13.8 reaction 2: ATD + H20 -> ADP + Pi G=-30.5 Answer the four questions about the first step of glycolysis. 1) Is reaction 2 spontaneous or nonspontaneous? 2) Complete the net chemical equation. 3) Calculate the overall ΔG for the coupled reaction. 4) Is the first step in glycolysis spontaneous (favorable)?

1) spontaneous, delta G is negative 2) glucose + ATP --> glucose-6-phosphate + ADP 3) Delta G= 13.8-30.5 = -16.7 4) Yes

The path of carbon through the glycolytic pathway is shown in the figure. Answer four questions about the steps in this pathway. 1) Which step of the pathway is the main control point? 2) What negative effector inhibits the enzyme in this step? 3) What positive effector activates the enzyme in this step? 4) Select every irreversible reaction step.

1) step 3 2) ATP and citrate 3) ADP and AMP 4) steps 1,3, and 10

The reactions of the citric acid cycle are shown in the image. As labeled in the diagram, reactions 1, 3, and 4 are regulation points in the citric acid cycle. 1) Which molecules inhibit reaction 1? 2) Which molecule or ion inhibits reaction 3? 3) Which molecules or ions activate reaction 3? 4) Which molecules inhibit reaction 4? 5) Which molecule or ion activates reaction 4?

1) succinyl‑CoA, NADH, citrate 2) NADH 3) ADP, Ca2+ 4) succinyl‑CoA, NADH 5) Ca2+

Why is MgATP2, instead of ATP4, a substrate for the hexokinase reaction? Select two correct phrases. 1- Mg2shields the negative charges of two of the phosphate oxygen atoms of ATP. 2- Mg2+ makes the 𝛾(terminal) phosphorus atom of ATP more accessible to nucleophilic attack by a glucose OH group. 3- Mg2+ prevents ATP hydrolysis. 4- Mg2+ makes the 𝛾(terminal) phosphorus atom of ATP more accessible to electrophilic attack by a glucose -OH group. 5- Hexokinase cannot bind ATP when it is not complexed with Mg2+

1, 2

Select true statements about the pentose phosphate pathway. 1) Glucose‑6‑phosphate is common to glycolysis and the pentose phosphate pathway. 2) Pentose phosphate pathway activity is high in rapidly dividing cells. 3) Products of the pentose phosphate pathway contribute to reductive biosynthesis reactions. 4) Glucose‑6‑phosphate is reduced to ribulose‑5‑phosphate in this series of reactions.

1, 2, 3

Select the statements that accurately describe the electron transport chain. 1-Electron transfer in the ETC is coupled to proton transfer from the matrix to the intermembrane space. 2- The outer membrane of mitochondria is readily permeable to small molecules and hydrogen ions. 3- Electrons generated by the citric acid cycle in the mitochondrial matrix enter the ETC. 4- Electron carriers are organized into four complexes of proteins and prosthetic groups. 5- The reactions of the ETC take place in the outer membrane of mitochondria. 6- Electron carriers in the mitochondrial matrix include ubiquinone (coenzyme Q), FMN , and cytochrome c. 7-Prosthetic groups, such as iron-sulfur centers, are directly involved with electron transfer.

1, 2, 3, 4, 7

Identify all statements that accurately describe the structure of the pyruvate dehydrogenase (PDH) complex. 1- A regulatory kinase and phosphatase are part of the mammalian PDH complex. 2- The complex contains multiple copies of E2 and single copies of several other enzymes. 3-E2 contains three domains. 4-Several copies each of E1 and E3 surround E2 . 5-The core of the complex is made up of several copies of E2 .

1, 2,3, 5

Select the statements that explain why the addition of n‑butylmalonate causes a decrease in ATP synthesis. Inhibiting the malate-α‑ketoglutarate transporter will prevent the regeneration of NAD+ by the malate-aspartate shuttle in the cytosol, thus forcing the kidney cells to switch to anaerobic glycolysis via lactate fermentation. Blocking the malate-α‑ketoglutarate transporter will dissipate the electrical gradient across the mitochondrial membrane, thus uncoupling ATP synthesis from the respiratory chain. Blocking the malate-aspartate shuttle prevents the transport of reducing equivalents from cytosolic NADH to the mitochondrion, thus inhibiting oxidative phosphorylation. Inhibiting the malate-α‑ketoglutarate transporter will limit the amount of malate available for the citric acid cycle, thus slowing down oxidative phosphorylation. Inhibiting the malate-aspartate shuttle will result in the accumulation of NADH in the cytosol. High levels cytosolic NADH will initiate gluconeogenesis.

1, 3

Select the true statements about the citric acid cycle . 1- The citric acid cycle is an aerobic process. 2- Two molecules of coenzyme A are produced per turn of the citric acid cycle. 3- The major reactants in the citric acid cycle are acetyl CoA, NAD+, GDP, and FAD. 4- The citric acid cycle occurs in the mitochondria of the cell. 5- In the citric acid cycle, pyruvate is degraded to produce acetyl CoA.

1, 3, 4

Which of these actions regulate oxidative phosphorylation under hypoxic conditions? HIF‑1 replaces a subunit of Complex IV of the electron transport chain with a subunit that is more efficient under hypoxic conditions. High pyruvate concentrations increase pH above 6.8, stabilizing the inhibitory IF1 dimer and preventing ATP hydrolysis. The protein inhibitor IF1 binds two ATP synthase molecules and inhibits their ATPase activity. Pyruvate dehydrogenase (PDH) kinase phosphorylates PDH, inactivating it and reducing the availability of electron carriers to the electron transport chain. ATP synthase converts ATP to ADP, raising [ADP] to increase the rate of oxidative phosphorylation.

1, 3, 4

Select the reasons why the absence of cytochrome oxidase eliminates the Pasteur effect. Without cytochrome oxidase, the respiratory chain will be inhibited and the mutant yeast cells will be unable to transfer electrons from NADHNADH to oxygen. In the absence of an active respiratory chain, yeast cells will continue to regenerate NAD+NAD+ for glycolysis via fermentation. Without cytochrome oxidase, the mutant yeast cells will be unable to regenerate NAD+,NAD+, thus inhibiting glycolysis. When glycolysis is inhibited, cells will continue to break down glucose at a much faster rate via fermentation. In the absence of cytochrome oxidase, the last step in the respiratory chain will be inhibited, thus reducing the amount of ATP produced by oxidative phosphorylation. The mutant cells with compensate for the decrease in ATP production by generating ATP via fermentation. In the absence of cytochrome oxidase, oxidative phosphorylation will be inhibited and ATP production will decrease drastically. Low ATP levels will maintain the high rate of glucose consumption in the mutant yeast cells. In the absence of cytochrome oxidase, the respiratory chain will be inhibited and NADHNADH will accumulate. Since NADHNADH is a substrate for glycolysis, high NADHNADH levels will maintain the high rate of glucose consumption.1,

1, 4

Select the true statements about the electron transport chain. Coenzyme Q and cytochrome 𝑐 are components of the electron transport chain. In the electron transport chain, a series of reactions moves electrons through carriers. The major reactants in the electron transport chain are O2 and either NADH or FADH2 The electron transport chain is an anaerobic process. The electron transport chain produces two ATP.

1,2,3

Which enzymes produce NADH as a product? Select all that apply. isocitrate dehydrogenase α-ketoglutarate dehydrogenase malate dehydrogenase succinate dehydrogenase

1,2,3

Which statements about the evolution of the citric acid cycle are consistent with existing knowledge? 1) The citric acid cycle may have originated from two pathways: a reductive pathway and an oxidative pathway. 2) Early organisms may have lacked the enzyme α‑ketoglutarate dehydrogenase. 3) The citric acid cycle may have evolved from two biosynthetic pathways in early life forms. 4) Although some organisms do not use the citric acid cycle under anaerobic conditions, they use a reductive pathway similar to the citric acid cycle to generate some larger molecules. 5) A reductive citric acid cycle can replenish oxidized cofactors such as NADH

1,2,3,4

Which enzymes produce coenzyme A as a product? Select all that apply. succinyl-CoA synthetase fumarase citrate synthase α-ketoglutarate dehydrogenase

1,3

Which enzymes produce carbon dioxide as a product? Select all that apply. isocitrate dehydrogenase succinate dehydrogenase malate dehydrogenase α-ketoglutarate dehydrogenase

1,4

Hexokinase catalyzes the first step of glycolysis, in which glucose is phosphorylated to form glucose‑6‑phosphate. Which of these statements are accurate? 1) Hexokinase consists of two domains, or lobes, that come together when glucose and the MgATP2-MgATP2- complex are bound. 2) Hexokinase is found in the mitochondrial membrane. 3) Hexokinase transfers the terminal phosphate of ATP to carbon 3 of glucose. 4) Kinases require the presence of a metal ion such as Mg2 or Mn2+, which forms a complex with ATP. 5) The conformational shift that occurs when glucose, but not water, enters the active site prevents water from hydrolyzing ATP. 6) Hexokinase is a type of phosphatase that catalyzes the transfer of a phosphoryl group from ATP to a hexose.

1,4,5

In the Cori cycle, when glucose is degraded by glycolysis to lactate in muscle, the lactate is excreted into the blood and returns to the liver. In the liver, lactate is converted back into glucose by gluconeogenesis. For each given enzyme, identify whether it is involved in the glycolysis pathyway, gluconeogenesis pathway, both pathways, or neither pathway. 1- The enzyme triose phosphate isomerase is involved in 2-The enzyme fructose‑1,6‑bisphosphatase is involved in 3- The enzyme alcohol dehydrogenase is involved in 4-The enzyme phosphoenolpyruvate carboxykinase is involved in 5-The enzyme phosphofructokinase‑1 is involved in 6-The enzyme enolase is involved in 7-The enzyme hexokinase is involved in 8-The enzyme pyruvate decarboxylase is involved in

1- both 2- gluconeogenesis 3- neither 4- gluconeogenesis 5- glycolysis 6- both 7- glycolysis 8-neither

Without using a textbook, predict the sequence of electron transport carriers (the sequence of participants in the redox reactions) in the electron transport chain. A table of standard reduction potentials is given for reference.

1. NAD+ 2. Coenzyme Q 3. Cytochrome b 4. Cytochrome c 5. Cytochrome a 6. O2

ATP synthase, shown in the image, uses the proton (H+) gradient to drive ATP synthesis. Put the steps of ATP synthesis in order from proton transport to the synthesis of ATP.

1. protons from the intermembrane space bind to proton binding sites on c subunits. 2. as the c ring rotates past the a subunit, c subunits release their protons into the matrix. 3. the gamma subunit rotates along with the c subunit. 4. the gamma subunit rotates and interacts with three alpha-beta subunit pairs, causing conformational changes in the beta subunits. 5. each beta subunit binds ADP and Pi, converts ADP+Pi to ATP, and releases ATP once during one turn of the gamma subunit.

Select the statements that describe amphibolic characteristics of the citric acid cycle. Catabolic pathways for several macromolecules involve the citric acid cycle. Oxaloacetate is a product of the citric acid cycle and an amino acid precursor. Both oxidation and reduction reactions occur. Both catabolic and anabolic processes occur. The citric acid cycle produces oxaloacetate, a substrate for gluconeogenesis.

2,4,5

Arsenate is structurally and chemically similar to inorganic phosphate, Pi, and many enzymes that require phosphate will also use arsenate. Organic compounds of arsenate are less stable than analogous phosphate compounds, however. For example, acyl arsenates decompose rapidly by hydrolysis. On the other hand, acyl phosphates, such as 1,3‑bisphosphoglycerate, are more stable and undergo further enzyme‑catalyzed transformation in cells. Predict the effects on the net reaction catalyzed by glyceraldehyde 3‑phosphate dehydrogenase and other reactions of glycolysis if phosphate were replaced by arsenate. 1) By substituting for phosphate in this reaction, the arsenate‑containing compounds would inhibit several downstream reactions. 2) The 1,3‑bisphosphoglycerate intermediate would decompose nonenzymatically, so no NADH would be formed in the reaction. 3)The 1‑arseno‑3‑phosphoglycerate intermediate would decompose nonenzymatically, so no ATP would be formed in the phosphoglycerate kinase reaction. 4) There would be no net conversion of ADP to ATP from the conversion of glucose to pyruvate during glycolysis. 5) Gluconeogenesis would be inhibited by arsenate because glyceraldehyde 3‑phosphate dehydrogenase is also an enzyme in that pathway.

3, 4

Consider a cell that requires much more ribose5‑phosphate than NADPH. The cell needs ribose 5‑phosphate but has a relatively high concentration of NADPH and a low concentration of NADP+.NADP+. These conditions may occur in rapidly dividing cells. What is the fate of glucose 6‑phosphate, glycolytic intermediates, and pentose phosphate pathway intermediates in this cell? 1) Under the given conditions, all triose phosphates are converted to pyruvate by the glycolytic pathway. 2) Most of the glucose 6‑phosphate enters the pentose phosphate pathway. 3) Most of the glucose 6‑phosphate enters the glycolytic pathway and is converted to fructose 6‑phosphate and glyceraldehyde3‑phosphate. 4) Conversion of glycolytic intermediates to ribose 5‑phosphate requires transketolase and transaldolase. 5) The oxidative pentose phosphate pathway reaction catalyzed by glucose 6‑phosphate dehydrogenase is slowed down. 6) Three molecules of glyceraldehyde 3‑phosphate and two molecules of fructose 6‑phosphate are used to generate five molecules of ribose 5‑phosphate.

3, 4, 5

Which enzymes have an α‑keto acid substrate? Select all that apply. fumarase malate dehydrogenase α-ketoglutarate dehydrogenase citrate synthase

3,4

A mitochondrial membrane complex consisting of ATP synthase, adenine nucleotide translocase (ATP-ADP translocase), and phosphate translocase functions in oxidative phosphorylation. Adenine nucleotide translocase, an antiporter located in the inner mitochondrial membrane, moves ADP into and ATP out of the matrix. Phosphate translocase is also located in the inner mitochondrial membrane. It transports H+ ions and phosphate H2PO− ions into the matrix. The energy derived from the movement of H+ ions down an electrochemical gradient from the intermembrane space into the matrix is used to drive the synthesis of ATP. How many H+H ions must be moved into the matrix for the synthesis of 1 ATP?

4

Determine which statements regarding aconitase are true. 1-An equilibrium mixture contains less than 10% citrate, but the isocitrate dehydrogenase reaction is exergonic, and draws the aconitase reaction to the left. 2-Aconitase contains the iron‑sulfur center Fe2S2 . 3-The iron of the iron-sulfur center forms a complex with the substrate that involves two hydroxyl groups from citrate. 4-Aconitase is stereospecific. 5-The reaction proceeds through the intermediate cis‑aconitate.

4,5

Which of the molecules is the major regulator of oxygen consumption during oxidative phosphorylation?

ADP

The succinyl CoA to citrate pathway of the citric acid cycle is shown. Identify the missing intermediates by placing the molecules to the appropriate position. Identify the missing cofactors.

Cofactor A is FAD Cofactor B is FADH2 Cofactor C is NAD+ Cofactor D is NADH + H+

The pyruvate dehydrogenase complex catalyzes the oxidative decarboxylation of pyruvate to form acetyl‑CoA. E1, E2, and E3are abbreviations for the enzymes of the complex. Classify the enzyme names, prosthetic groups, and reactions as E1 , E2 , or E3.

E1 = pyruvate dehydrogenase, TPP, decarboxylation of pyruvate, hydroxyethyl group transferred to lipoamide, formation of hydroxyethyl-TPP E2= dihydrolipoyl transacetylase, lipoamide, transfer of acetyl group to coenzyme A E3=dihydrolipoyl dehydrogenase, FAD, dihydrolipoamide is oxidized to lipoamide, transfer of electrons to FAD then NAD+

The net reaction catalyzed by malate dehydrogenase is malate + NAD+↽⇀ oxaloacetate+ NADH + H+ The standard reduction potentials for the half-reactions are given in the table. Oxidant Reductant 𝐸∘(V) oxaloacetate+2H+ malate −0.17 NAD++H+ NADH −0.32 Calculate Δ𝐸∘′for the given reaction. Calculate Δ𝐺∘′ for the given reaction.

E= -0.15 G= 28.95

Animals are not able to convert fatty acids into carbohydrates. The net synthesis of 1 mol of oxaloacetate from 2 mol of acetyl‑CoA by the citric acid cycle does not occur because 1 mol of oxaloacetate is used in the cycle for each one generated. Plants are able to convert 2 mol of acetyl‑CoA into 1 mol of oxaloacetate with only two additional enzymes not found in animals. This process is called the glyoxylate cycle, and it occurs in organelles called glyoxysomes. Identify the enzyme in each step of the glyoxylate cycle. Not all the enzyme names will be used.

Enzyme A is citrate synthase. Enzyme B is aconitase. Enzyme C is isocitrate lyase . Enzyme D is malate synthase. Enzyme E is malate dehydrogenase.

Although eukaryotic cells can use both glucose (C6H12O6)and hexanoic acid (C6H14O2) as fuel sources for cellular respiration, hexanoic acid yields more energy per gram when completely oxidized to CO2 and H2O Select the reasons why hexanoic acid releases more energy upon complete combustion to CO2 and H2O.

Hexanoic acid is more hydrogen rich than glucose, thus hexanoic acid is more reduced than glucose. Complete oxidation of hexanoic acid generates more reducing equivalents that can enter the respiratory chain than the complete oxidation of glucose.

The passage describes some glycolysis reactions. Select the appropriate term for each blank to complete the passage.

In the first reaction of glycolysis, glucose is converted to glucose 6-phosphate . The phosphate comes from ATP. A kinase is an enzyme that transfers the terminal phosphate of ATP to a substrate. The product of this reaction is then isomerized to Fructose-6-phosphate. Fructose 6 phosphate is then phosphorylated by a second kinase reaction, giving fructose 1,6-bisphosphate

The last step of glycolysis converts phosphoenolpyruvate to pyruvate. The Δ𝐺°' of the reverse reaction is +31 kJ/mol (+7.5 kcal/mol). Instead of reversing the pyruvate kinase reaction, the step is bypassed in gluconeogenesis. Several steps for the conversion of pyruvate to phosphoenolpyruvate via gluconeogenesis are given. Place the steps in the correct order. You will not place all of the steps.

In the mitochondrion, pyruvate carb converts Malate dehyd in the mito Malate dehyd in the cyto phosphoenelpyruvate

Which are coenzyme prosthetics?

Lipoamide FAD and TPP TDP

A researcher follows a protocol to test the activity of a mitochondrial extract containing all of the soluble enzymes of the matrix. Because the mitochondrial extract was dialyzed, the protocol lists low molecular weight cofactors that must be added to the extract in order to catalyze the oxidation of acetyl‑CoA to CO2.CO2. The list does not include lipoic acid, a known cofactor of the citric acid cycle. Why is lipoic acid omitted from the list of cofactors to add back to the extract?

Lipoic acid is covalently attached to the pyruvate dehydrogenase complex.

The pentose phosphate pathway is a two‑stage pathway that generates (1) which is a reductant in many biosynthetic reactions and takes part in detoxifying reactive oxygen species, and (2) which is a nucleotide (DNA and RNA) precursor. The substrate for the pentose phosphate pathway is (3) The (4) phase of the pentose phosphate pathway interconverts phosphorylated monosaccharides, some of which can feed into the (5) pathway.

NADPH ribose-5-phosphate glucose-6-phosphate nonoxidative glycolytic

Animals are not able to convert fatty acids into carbohydrates. The net synthesis of one mole of oxaloacetate from two moles of acetyl‑CoA by the citric acid cycle does not occur because one mole of oxaloacetate is used in the cycle for each one generated. Plants are able to convert two moles of acetyl‑CoA into one mole of oxaloacetate with only two additional enzymes not found in animals. This process is called the glyoxylate cycle, and it occurs in organelles called glyoxysomes. Classify the enzymes based on whether they are found only in plants or are found in both plants and animals.

Plants only: isocitrate lyase and malate synthase Plants and animals: everything else

Some cofactors participating in reactions of the citric acid cycle are given. Identify the position or positions each cofactor has in the cycle by selecting the appropriate letter or letters designating that position in the cycle diagram.

The co-factor NADH+H+ is present at positions B, D, J. The co-factor FADH2​ is present at position H. The co-factor GTP is present at position F.

The consumption of alcohol (ethanol), especially after periods of strenuous activity or after not eating for several hours, results in a deficiency of glucose in the blood, a condition known as hypoglycemia. The first step in the metabolism of ethanol by the liver is oxidation to acetaldehyde, catalyzed by liver alcohol dehydrogenase. CH3CH2OH+NAD+⟶CH3CHO+NADH+H+ How does this reaction inhibit the transformation of lactate to pyruvate and lead to hypoglycemia?

The conversion of lactate to glucose in the liver is inhibited. Lactate dehydrogenase competes with ethanol metabolism for NAD+NAD+ .

Consider the fructose-1,6-bisphosphatase reaction. Calculate the free energy change if the ratio of the concentrations of the products to the concentrations of the reactants is 23.3 and the temperature is 37.0°C? Δ𝐺°′ for the reaction is −16.7 kJ/mol

The free energy change, Δ𝐺ΔG, can be calculated using the equation Δ𝐺=Δ𝐺°′+𝑅𝑇ln([products][reactants]) where Δ𝐺°′is the standard free energy change, 𝑅 is a constant equal to 8.3145J/(mol⋅K), and 𝑇 is the temperature in Kelvin. Δ𝐺°′ and the ratio of the products and reactants concentrations are given. The temperature must be converted from degrees Celsius to Kelvin. To match the units of Δ𝐺°′ the constant 𝑅 must be converted to kJ/(mol⋅K) = -8.5

Thiamine (vitamin B1) deficiency diseases have a lower prevalence now than in the past. However, they are seen as beriberi in some developing regions and in regions of crisis, and as Wernicke-Korsakoff syndrome in some alcoholics. One type of beriberi causes neurological symptoms such as weakness, fatigue, and loss of sensation. What is a possible explanation for these symptoms?

The metabolism of glucose provides most of the energy for the brain.

Suppose you discovered a mutant yeast whose glycolytic pathway was shorter because of the presence of a new enzyme catalyzing the reaction glyceraldehyde3‑phosphate+H2O+NAD+ ⟶ NADH+H+3‑phosphoglycerate Which of the changes would you expect to find in the growth and metabolism of the mutant yeast?

The mutant will not grow under anaerobic conditions. The formation of pyruvate from glucose will be energetically more favorable.

In yeast, ethanol is produced from glucose under anaerobic conditions. A cell‑free yeast extract is placed in a solution that contains 3.50×102 mmol glucose, 0.30 mmol ADP, 0.30 mmol Pi, 0.60 mmol ATP, 0.20 mmol NAD+ , and 0.20 mmol NADH. It is kept under anaerobic conditions. What is the maximum amount of ethanol (in millimoles) that could theoretically be produced under these conditions? Under the same conditions, what is the theoretical minimum amount of glucose (in millimoles) required in the solution to form the maximum amount of ethanol?

The net reaction is C6H12O6+2ADP+2Pi⟶2C2H5OH+2ATP+2H2O+2CO2 In order to determine the maximum amount of ethanol produced, the limiting reactants must be identified. In the conversion of glucose to pyruvate, NAD+ is not limiting because it is regenerated in the second step (fermentation). Therefore, the concentrations of ADP and Pi will limit pyruvate formation. Since the molar ratio of ADP and Pi to pyruvate is 1:1, 0.30 mmol ADP will result in 0.30 mmol0.30 mmol pyruvate. The maximum amount of ethanol that can be produced will be 0.30 mmol. One mole of glucose is converted to two moles of ethanol (a 1:2 ratio), so the minimum amount of glucose needed to form 0.30 mmol ethanol would be 0.15 mmol under these conditions (0.30 mmol ADP and Pi)

Predict what would happen when an uncoupling agent, such as 2,4‑dinitrophenol, is added to an actively respiring tissue preparation. 1) The rate of oxygen consumption 2) rate of ATP synthesis 3) The P/O ratio 4) Ingestion of uncouplers causes profuse sweating and an increase in body temperature. Explain this phenomenon in molecular terms.

The rate of oxygen consumption would increase. the rate of ATP synthesis would decrease. the P/O ratio would decrease. Energy from the increased rate of electron transport is converted to heat rather than to ATP.

Consider the malate dehydrogenase reaction from the citric acid cycle. Given the listed concentrations, calculate the free energy change for this reaction at energy change for this reaction at 37.0 ∘C (310 K). Δ𝐺∘′ for the reaction is +29.7 kJ/mol. Assume that the reaction occurs at pH 7. [malate]=1.29 mM [oxaloacetate]=0.180 mM [NAD+]=390 mM [NADH]=160 mM HINT: convert mM to M by moving the decimal to the left 3 spaces

To solve for the free energy change of this reaction, consider that Δ𝐺=Δ𝐺∘′+𝑅𝑇ln([oxaloacetate][NADH]/[malate][NAD+]) Add in the values for oxaloacetate, malate, NAD+, and NADH, as well as the temperature of the reaction in Kelvin and the Δ𝐺∘′ of the reaction. Δ𝐺=29.7 kJ⋅mol +(8.3145×10−3kJmol⋅K)(310 K)ln((0.000180 M)(0.16 M)/(0.00129 M)(0.39 M)) =29.7 kJ⋅mol^−1+(−7.44 kJ⋅mol^−1) =22.26 kJ⋅mol^−1

The reversible interconversion reactions of the pentose phosphate pathway can operate either to convert pentoses to hexoses, when operating in an oxidative mode to generate NADPHNADPH , or to convert hexoses to pentoses, when operating in a non‑oxidative mode to generate pentoses for nucleic acid synthesis. Two key enzymes in these interconversion reactions are transaldolase and transketolase. Identify the products formed from the seven‑carbon sugar sedoheptulose‑7‑phosphate and glyceraldehyde‑3‑phosphate with each of these enzymes

Transaldolase products are erythrose-4-phosphate + F6P Transketolase products are ribose-5-phosphate + xylulose-5-phosphate

When the antibiotic valinomycin is added to actively respiring mitochondria, several things happen: the yield of ATP decreases, the rate of O2 consumption increases, heat is released, and the pH gradient across the inner mitochondrial membrane increases. Explain these observations by listing the causal order of events that occur beginning with the addition of valinomycin to the respiring mitochondria and ending with the release of heat. Some events listed do not occur and should not be placed.

Valinomycin binds to K+ Ions Valinomycin -K+ complex moves into the mitochondrial matrix. The electrical potential across the mitochondrial membrane decreases. Rate of ATP synthesis decreases. Rate of electron transfer and oxygen consumption increases The pH gradient across the mitochondrial membrane increases. Heat is generated.

In 1906, Harden and Young, in a series of classic studies on the fermentation of glucose to ethanol and CO2 by extracts of brewer's yeast, made the observations 1) inorganic phosphate was essential to fermentation; when the supply of phosphate was exhausted, fermentation ceased before all the glucose was used; 2) during fermentation under these conditions, ethanol, CO2, and a sugar phosphate accumulated; 3) when arsenate was substituted for phosphate, no sugar phosphate accumulated, but the fermentation proceeded until all the glucose was converted to ethanol and CO2 a) Which enzyme of glycolysis requires inorganic phosphate and, therefore, stops when no phosphate is available? b) What sugar phosphate accumulates under these conditions? c) Arsenate substitution for phosphate generated an acyl arsenate compound that immediately degraded. What glycolysis intermediate was a product of the spontaneous degradation of this acyl arsenate?

a) glyceraldehyde 3‑phosphate dehydrogenase b) fructose 1,6‑bisphosphate c) 3‑phosphoglycerate

Which enzyme has an overall net reaction as an isomerization?

aconitase

Which compound is transported across the inner membrane in exchange for malate?

alpha-ketoglutarate

Which of the following enzymes must all gluconeogenic tissues express?

fructose 1,6‑bisphosphatase glucose 6‑phosphatase phosphoenolpyruvate carboxykinase

Which reaction is influenced by the molecule in the first question? Choose the enzyme that catalyzes the reaction. (This is the major controlling step.)

glucose 6‑phosphate dehydrogenase

Pyruvate produced by glycolysis in the cytosol must first be transported into mitochondria if it is to be consumed by pyruvate dehydrogenase. is consumed by pyruvate dehydrogenase, which is also found in the cytosol. is small enough to cross the inner mitochondrial membrane by simple diffusion. is always converted to lactate before it can enter other pathways.

must first be transported into mitochondria if it is to be consumed by pyruvate dehydrogenase.

Complete the overall reaction catalyzed by the pyruvate dehydrogenase complex. Move the compounds and cofactors to the correct answer blanks. Two terms will not be used.

pyruvate + CoA + NAD + ---> AcetylCoA + NADH + H+ + CO2

ATP production in the flight muscle of the fly Lucilia sericata results almost exclusively from oxidative phosphorylation. During flight, 187 mL O2/hr⋅g of body weight is needed to maintain an ATP concentration of 7.0 μmol/g of flight muscle. Calculate the rate at which the ATP pool turns over. The O2 is at 25 ∘C and 1.00 atm. Determine the amount of time that it would take for the reservoir of flight muscle ATP to last in the absence of oxidative phosphorylation. The flight muscle comprises 20% of the weight of the fly. Assume that reducing equivalents are transferred by the glycerol 3‑phosphate shuttle and that one mole of glucose produces 30 moles of ATP.

rate: 2.12 time: 0.13

Identify the oxidation-reduction reactions of glycolysis. Use the step numbers from the glycolytic pathway shown.

step 6 only The sixth step of the glycolysis or the first step of the pay-off phase includes the redox reaction in which oxidation of Glyceraldehyde 3-phoaphate to 1, 3-bisphosphoglycerate takes place. In this step Glyceraldehyde 3-phosphate is converted to 1, 3-bisphosphoglycerate by taking one mole of inorganic phosphate. This reaction is catalyzed by the enzyme glyceraldehyde 3-phosphate dehydrogenase.

What would be the limiting factor for ATP production by glycolysis in a strenuously exercising muscle that lacks lactate dehydrogenase?

the supply of NAD+