Biochem Test 4 Sample Questions Flashcards

Which of the following regarding glycogen phosphorylase activity is true?

Which of the following regarding glycogen is not true?

When glycogen synthase adds glucose units onto a glycogen granule, what molecule serves as the substrate and direct source of the glucose unit?

Glycogen granules are limited in size to approximately 40 nm because:

How does caffeine affect how epinephrine regulates both glycogen synthesis and glycogen breakdown.

The main function of the pentose phosphate pathway is to:

In a tissue that metabolizes glucose using the pentose phosphate pathway, C-1 (carbon #1) of glucose would end up primarily in:

Which of the following is not required for the formation of Acetyl CoA using pyruvate?

They pyruvate dehydrogenase complex consists of multiple copies of three different proteis, E1, E2, and E3. For each, identify a coenzyme which is not free to dissociate from the protein and match each with one activity listed at right.

Identify and name an enzyme in the citric acid cycle that is both positively and negatively regulated. Name one activator and one inhibitor of this enzyme.

Oxaloacetate uniformly labeled with 14C (i.e. equal amounts of 14C in each of its carbon atoms) is condensed with unlabeled Acetyl CoA. After a single pass through the citric acid cycle back to oxaloacetate, which fraction of the original radioactivity will be found in the oxaloacetate?

The standard reduction potentials for the following half reactions are given:
fumurate + 2H + 2e = succinate Eo = +.031 V
FAD + 2H + 2e = FADH2 Eo = -.219 V
If you mixed succinate, fumurate, FAD, and FADH2 together, each at 1 M concentration and in the presence of succinate dehydrogenase, which of the following would initially occur?

Most of the molecular oxygen (O2) that you consume by breathing is converted to:

In an animal cell, electron transport occurs primarily:

For each of the following complexes found in the Electron Transport System (ETS) provide the name of the electron donor, electron acceptor, and the number of protons pumped across the membrane for every 2 electrons that pass through each complex. Indicate the oxidation state of the e- donor and e- acceptor. Note that the complexes are not necessarily in order.

In a cell that only metabolizes glucose using both the oxidative and nonoxidative branches of the pentose phosphate pathway, the C-1 (carbon #1) of the glucose would end up primarily in:

Two glucose molecules pass through the oxidative branch of the pentose phosphate pathway. Identify how many of the following are generated by this process.

The glycogen-branching enzyme catalyzes:

Which of the following molecules is a substrate for the enzyme glycogen synthase?

Which of the following limits the size of glycogen particles in the liver?

An increase in cellular (cAMP) in the liver would:

Which of the following molecules is not required for the PDH-catalyzed oxidative decarboxylation of pyruvate to form Acetyl CoA?

One of the coenzymes involved in the PDH reactions is not listed in the above problem. Which coenzyme is missing?

Identify the chronological order in which these 5 coenzymes participate in the PDH-catalyzed conversion of pyruvate to Acetyl CoA

The methyl carbon of Acetyl CoA is labeled with 14C as it enters the citric acid cylce. After one complete pass of the cylce (back to oxaloacetate), what percentage of the original 14C is lost as CO2?

In the next cycle (2nd pass), a 2nd, unlabeled Acetyl CoA (no 14C) enters and a second complete cycle is finished. What percentage of the orginal 14C is lost as CO2?

The proton motive force results from the combination of which two potential energies?

For each of the following complexes found in the mitochondrial Electron Transport System (ETS), provide the name (or acronym) of the electron donor, electron acceptor and the number of protons pumped across the membrane for every 2 electrons that pass through each complex. Be sure to indicate the oxidation state of the electron donors and acceptors. Read carefully! note that the complexes are not necessarily in chronological order.

If proton channels were opened across the typical inner mitochondrial membrane, into which compartment would protons flow?

If proton channels were opened across the typical inner mitochondrial membrane, how much energy would be released per mole of protons that flowed across this membrane (down the protein gradient)?

Which of the following ATP synthase subunits is known to spin?

Sodium cyanide and sodium azide are effective poisons that block mitochondrial function. Which of the following protein complex activity is significantly inhibited in the presence of these two poisons?

How many protons flow through the F1F0 ATP synthase for every ATP synthesized and released?

How many ATP are synthesized for every full 360* spin/turn made by the ATP synthase?

How many ATP are synthesized for every NADH that passes electrons in the ETS?

We spent nearly a month describing the complete catabolism of glucose to the end products of CO2 and H20. Please fill in the blanks for the balanced equation given in class for the typical animal cell.

This compound is formed in the pentose phosphate pathway. According to the lecture, the next step would directly involve:

Six glucose molecules pass completely through both the oxidative and nonoxidative branches of the pentose phosphate pathway. Identify how many of the following are generated when this process is complete. Molecules that are generated and then consumed do not count.

Circle all that apply. The glycogen debranching enzyme catalyzes:

During glycogen degradation, glucose-1-phosphate is generated. Which of the following molecules participate directly in the conversion of glycogen to glucose-1-phosphate? Circle all that apply.

Explain briefly why glycogen particles in muscle and liver are limited in size.

Pyrophosphate plays a role during glycogen synthesis. The fate of pyrophosphate during this synthetic pathway is most likely:

Caffeine affects glycogen metabolism by binding to and directly:

Illustrate the multi-step PDH-catalyzed oxidative decarboxylation of pyruvate.

The carbonyl carbon of Acetyl CoA is labeled with 14C as it enters the citric acid cycle. After one complete pass of the cycle (back to oxaloacetate), what percentage of the original 14C remains in the oxaloacetate?

In the next cycle (2nd pass), a 2nd, unlabeled Acetyl CoA (no 14C) enters and a second complete cycle is finished. What percentage of the original 14C remains in the resulting oxaloacetate?

Name one citric acid cycle enzyme that is inactivated directly by Succinyl CoA.

Name on citric acid cycle enzyme that is actived directly by NAD+.

Name the two citric acid cycle intermediate that are used to synthesize most of the 20 amino acids.

The following diagram represents the mitochrondrial Electron Transport System. Supply all the molecules that donate to or accept electrons from each of the complexes; fill in all 14 blanks. Be sure to indicate the oxidation state of the acceptors and donators.

For every two electrons, how many protons are pumped into the mitochondrial matrix by each of the following electron transport complexes?

Identify the specific mitochondrial target of cyanide (CN-1)poisoning and explain why it shuts down operation of the mitochondria F1F0 and ATP synthase.

Which of the following F1 sphere subunits (found in the F1F0 ATP synthase) spin during normal operation of the enzyme?

How many ATP are generated in the mitochondria for every glucose that is completely oxidized to CO2?

How many protons flow through the ATP synthase for every ATP generated?

When protons flow through the ATP synthase, into which specific compartment of the cell or organelle do they flow?

Part of the gluconeogenic pathway in liver cell involves the production of cytosolic phosphoenolpyruvate (PEP) starting with cytosolic lactate. Illustrate this conversion by identifying all the intermediates by name. Include key small molecules such as ATP, CO2, NADPH, etc. Enzyme names and metabolite structures are not necessary.

The molecule, AMP, is a reciprocal regulator of the glycolytic and gluconeogenic pathways. This means that:

For each hexose that feeds into the oxidative branch of the pentose phosphate pathway, there is a yield of one carbohydrate and two high energy molecules. Indentify these molecules:

The nonoxidative branch of the pentose phosphate pathway can convert pentoses into glycolytic intermediates. Identify these intermediates and indicate which and how many high energy compounds are consumed per pentose converted to these intermediates.

a-1,6-Glucosidase is active during glycogen degradation. One substrate for this enzyme is the glycogen polymer. The second substrate is:

Which molecule is a substrate for the enzyme glycogen synthase?

Circle all that apply. Phosphorylation of glycogen synthase by protein kinase A (PKA) will:

Imagine that a mouse line has been genetically modified so that it can no longer produce the protein glycogenin. Without this protein you would expect the following to occur in the liver and muscle cells of the mutant mice. Circle all that apply.

Insulin stimulation of a liver cell would be expected to have which of the following effects? Circle all that apply

The methyl carbon of Acetyl CoA is labeled with 14C as it enters the citric acid cycle. After one complete pass of the cycle (back to oxaloacetate), an unlabeled Acetyl CoA (no 14C) enters a second complete cycle is completed. What percentage of the original 14C remains in the oxaloacetate after the second cycle?

In the next cycle (3rd pass), a 3rd, unlabeled Acetyl CoA (no 14C) enters and a third complete cycle is finished. What percetage of the original 14C remains in the resulting oxaloacetate?

A number of citric acid cycle enzymes are regulated. Listed below are some allosteric effectors of some of these enzymes. Indicate whether or not the effector acts as an activator, inhibitor, or acts to activate one enzyme in the cycle while inactivating a 2nd enzyme in the same cycle.

For every two electrons that pass through, how many protons are pumped across the membrane by each of the following electron transport complexes?

If the pH on the matrix side of the inner mitochondrial membrane is pH 6.0, you would expect the pH on the intermembrane space side of the membrane would be closest to:

Identify the specific mitochondrial target of cyanide (CN-1) poisoning and explain why it shuts down operation of the mitochondrial F1FO ATP Synthase.

According to the lecture, how does fermentation differ from mitochondrial respiration?

Which of the following statements regarding the function of the mitochondrial F1F0 ATP synthase is/are correct? Circle all that apply.

Describe how spinning of the F1F0 ATP synthase is coupled to synthesis of ATP.

We spent a long time discussing how glucose can be completely oxidized to CO2 and how all the resulting high energy molecules can be transformed into ATP equivalents. Assuming that these events take place in a eukaryotic cell, balance the following equation.

In the final step of gluconeogenesis, glucose-6-phosphate is converted to glucose by the following enzyme in the appropriate cellular compartment.

The molecule, citrate, is a reciprocal regulator of the glycolytic and gluconeogenic pathways. This means that:

All of the following molecules are associated with gluconeogenic metabolism within liver mitochondria. One or more of these molecules can not pass easily across the inner mitochondrial membrane due to lack of a specific transporter or translocase. Identify the molecule(s).

The oxidative branch of the pentose phosphate pathway (PPP) generates which of the following molecules?

The nonoxidative branch of the pentose phosphate pathway can convert ribulose-5-phosphate into two glycolytic intermediates which in turn can enter the glycolytic or gluconeogenic pathways. Identify these two intermediates.

One substrate for glycogen phosphorylase is the glycogen polymer. The second substrate is:

Which of the following would be expected to result in increased glycogen phosphorylase activity? Mark all that apply

Which molecules function as substrate(s) for the enzyme glycogen synthase?

Each glycogen particle within the liver is limited in size to ~40 nm. This size restriction results directly from the:

The enzymatic conversion of pyruvate to Acetyl CoA is a multi-step process. In which eukaryotic subcellular compartment does this process occur?

The enzymatic conversion of pyruvate to Acetyl CoA is a multi-step process. Which coenzyme visits (binds to) all three active sites (E1, E2, & E3)?

The enzymatic conversion of pyruvate to Acetyl CoA is a multi-step process. Which coenzyme serves as the terminal (final) electron acceptor?

The carbonyl carbon of OAA (arrow) is labeled with 14C as it enters the citric acid cycle with unlabeled Acetyl CoA. After one complete pass of the cycle (back to oxaloacetate), what percentage of the original 14C remains in the oxaloacetate?

After two more complete cycles using unlabeled Acetyl CoA, what percentage of the orginal 14C remains in the resulting oxaloacetate?

Listed below are some allosteric effectors of some citric acid cycle enzymes. Indicate whether or not the molecule acts as an activator, inhibitor or acts to activate one enzyme in the cycle while inactivating a 2nd enzyme in the same cycle.

Which high energy molecule donates electrons to Complex I of the mitochondrial electron transport system?

Ubiquinone is routinely reduced by which mitochondrial electron transport complexes?

Mitochondrial cytochrome c(Fe+3) routinely accepts how many electrons at a time from which molecular species?

For every two electrons that pass through, how many protons are pumped across the membrane by each of the following mitochondrial electron transport complexes?

What is the indentiy of the mitochondrial terminal electron acceptor?

If the pH of the intermembrane space side of an active mitochondrian is pH 6.0, you would expect the pH on the matrix side of the membrane would be closes to:

Identify the specific mitochondrial target of cyanide (CN-1) poisoning and explain why it shuts down operation of the mitochondrial F1F0 ATP synthase.

In class we calculated how many protons were required to generate ATP in mitochondrial oxidative phosphorylation based on the total number of 'c' subunits in the ATP synthase. If the total number of c subunits was modified to be 6 but all else remain the same, how many protons would flow through the machine for every ATP generate?

Spinning the y-subunit (gamma) of the intact F1F0 ATP Synthase results in:

Which of the following is true regarding lactate metabolism during strenuous exercise in an adult human?

Shown to the right are three enzyme-catalyzed steps from the glycolytic pathway.
Glucose->Glc-6-P (1)
Glc-6-P -> Frc-6-P (2)
Frc-6-P -> Frc-1,6-BP (3)
Identify which of the glycolytic enzymes shown, if any, would be shared by the gluconeogenic pathway.

Identify which of the glycolytic enzymes shown, if any, would be reciprocally regulated with respect to the corresponding gluconeogenic enzyme. Identify one reciprocal regulator molecule that would inhibit gluconeogenesis.

During active use of the Cori Cycle, you would expect which of the following to best represent the early steps of gluconeogenesis in liver cells?

Using the oxidative branch of the pentose phosphate pathway (PPP), glucose -6-P undergoes conversion to 6-phosphogluconate. Which carbon(s) were oxidized in this conversion?

Using the oxidative branch of the pentose phosphate (PPP), glucose-6-P undergoes conversion to 6-phosphogluconate. Which of the six carbons will be further oxidized in the conversion of 6-phosphogluconate to ribulose-5-phosphate?

The nonoxidative branch of the pentose phosphate pathway can convert ribulose-5-phosphate into two glycolytic intermediates which in turn can enter the glycolytic or gluconeogenic pathways. Identify these two intermediates.

Glycogen synthesis and degradation is strictly regulated within the cells of your liver. What effect do high levels of insulin have on glycogen degradation?

Glycogen synthesis and degradation is strictly regulated within the cells of your liver. What regulates the total number of glycogen particles found in a particular cell?

What limits the size of the glycogen particles to 40 nm?

Which of the following would be expected to result in increased glycogen synthase activity?

Which of the following is considered an inhibitory pseudosubstrate of the protein kinase A (PKA) catalytic subunit?

The enzymatic conversion of pyruvate to Acetyl CoA is a multi-step process requiring multiple enzymes (E1, E2, and E3) and multiple coenzymes. Which coenzymes physically interact with or bond to the pyruvate and/or acetyl group?

Which coenzyme, if any, visits (binds to) all three active sites (E1, E2, and E3)?

Which coenzyme serves as the terminal (final) electron acceptor for the PDH complex?

Which of the above enzymes would be classified as a lyase?

The methyl carbon of acetyl CoA is labeled with 14C as it enters the citric acid cycle with unlabeled oxaloacetate. After one complete pass of the cycle (back to oxaloacetate), what percentage of the original 14C remains in the oxaloacetate?

After one more complete cycle using unlabeled acetyl CoA, what percentage of the original 14C remains in the resulting oxaloacetate?

Listed below are some potential allosteric effectors of some citric acid cycle enzymes. Indicate whether or not the molecule should act as an activator or inhibitor or acts to activate one enzyme in the cycle while inactivating a 2nd enzyme in the same cycle.

Which molecule donates electrons directly to Complex III of the mitochondrial electron transport system?

Which electron transport system (ETS) complex is also known as succinate dehydrogenase?

The reduced form of mitochondrial cytochrom c routinely donates how many electrons at a time to which molecular species?

For every single electron that passes through, how many protons are pumped across the membrane by each of the following mitochondrial electron transport complexes?

What is the identity of the human mitochondrial terminal electron acceptor?

If the pH of a mitochondrion's matrix was measured to be 7.0, you would expect the pH of the intermembrane space to be closest to:

Identify the specific mitochondrial target of cyanide (CN-1) poisoning and explain why it shuts down operation of the mitochondrial F1F0 ATp synthase.

When operating normally, part of the F1F0 ATP synthase spins or turns. After one complete revolution of 360*, what are the expected quantities of each?

Spinning of the y-subunit (gamma) of the intact F1F0 ATP synthase results in:

An O2-free ATP generating pathway where carbon compounds are the electron donors and acceptors is known as:

Gluconeogenesis and glycolysis are reciprocally regulated pathways. As described in class, identify the one glycolytic enzyme and one gluconeogenic enzyme that are truly reciprocally regulated. Identify one allosteric effector that acts on both enzymes and indicate whether it activates or inhibits enzyme activity.

During active use of the Cori cycle, lactate is moved from the muscle to the liver. Answer the following as they would apply to active use of the Cori Cycle in humans. Identify the metabolite that moves from the liver to the muscle:

Identify the metabolite that enters the mitochondria of the liver:

The conversion of one lactate to one oxaloacetate in the liver requires what cost in terms of high energy compounds?

Which molecule served as the oxidant during the first step of PPP?

The nonoxidative branch of the pentose phosphate pathway can convert ribulose-5-phosphate into two glycolytic intermediates. What is the cost in terms of high energy compounds consumed to convert three ribulose-5-P into the glycolytic intermediates?

Glycogen synthesis and degradation is strictly regulated within liver and muscle. As described in class, which hormone(s) would act to activate glycogen degradation?

Hormonal stimulation of glycogen breakdown requires the activation of which enzymes?

Normal glycogen granules are never bigger than ~40 nm across. What prevents the synthase enzyme from making the granule bigger than 40 nm?

The carbonyl carbon of acetyl CoA is labeled with 14C as it enters the citric acid cycle with unlabeled oxaloacetate. After one complete pass of the cycle, the resulting oxaloacetate combines with unlabeled Acetyl CoA and continues to do so after every cycle. During which cycle is 100% of the 14 C loast as CO2?

Which enzyme in the citric acid cycle catalyzes the specific step that results in a four or five carbon compound with only 50% of the original 14C remaining?

Listed below are two potential allosteric effectors of some citric acid cycle enzymes. Indicate whether or not the molecule should act as an activator or inhibitor or acts to activate one enzyme in the cycle while inactivating a 2nd enzyme in the same cycle.

When succinate dehydrogenase feeds two electrons directly into the mitochondrial electron transport chain and the electrons are ultimately picked up by the terminal electron acceptor, protons are pumped across a membrane. Where are the protons pumped? Identify which ETS complexes pump protons as a result of these two electrons reaching the terminal electron acceptor. Where are the protons pumped?

Mitochondria use oxidative phosphorylation to synthesize ATP synthesis. Explain potions of this process in three distinct parts. Read carefully; it is possible to answer the 1st two questions succintly.
Part I: What is the direct energy source used to physically run the mitochondrial machine that makes ATP?

Part II: What is the name of the mitochondrial machine that makes ATP?

Part III: How is the gamma (y) subunit of this machine used to force the machine to release newly synthesized ATP?

When the Cori Cycle is operating in the human body, the biochemical conversion of lactate to pyruvate will be occurring in a specific tissue. This conversion to pyruvate requires the direct consumption of which of the following molecules?

In which tissue is this conversion of lactate to pyruvate most likely to occur?

Gluconeogenesis and glycolysis share some of the same enzyme-catalyzed steps. Listed below are several glycolytic enzymes. Identify which, if any, also operate in the gluconeogenic pathway:

Gluconeogenesis in a liver cell (hepatocyte) occurs in multiple subcellular compartments. Identify where each of the following conversions would most likely occur during this pathway in a liver cell.

What is the full name of the glucoeogenic enzyme that catalyzes the conversion of Glc-6-P to glucose?

The third step of the oxidative branch of PPP would best be characterized as:

The nonoxidative branch of the pentose phosphate pathway can convert 3 ribulose-5-phosphate molecules into glycolytic intermediates. Identify these glycolytic intermediates.

As written, what is the cost in ATP (hydrolyzed to ADP) to complete this conversion?

Glycogen degradation is strictly regulated within liver and muscle. When active, glycogen phosphorylase results in the cleavage of what bond?

Which small molecule attacks this bond in this catalyzed reaction?

Hormonal stimulation of a liver cell by insulin (following a holiday feast) would be expected to inhibit which of the following enzymes?

Normal glycogen granules are never bigger than ~40 nm across. What simple mechanism prevents the granules from becoming larger than 40 nm?

The enzymatic conversion of pyruvate to Acetyl CoA is a multi-step process requiring multiple enzyme active sites and multiple coenzymes. What is the full name of the coenzyme that visits all three active sites?

When lipoic acid visit the E2 active site, what reaction is catalyzed?

When lipoic acid visits the E3 active site, what reaction is catalyzed?

In two separate experiments, the #1 or #2 carbon of oxaloacetate is labeled with 14C as it enters the citric acid cycle with unlabeled Acetyl CoA. After one complete pass of the cycle, the resulting oxaloacetate combines with unlabeled Acetyl CoA and continues to do so after every cycle. During which cycle is 100% of the #1 carbon 14 C lost as CO2?

During which cycle is 100% of the #2 carbon 14C lost as CO2?

ATP and NADH are allosteric effectors of citrate synthase. You would expect these two effectors to act in the following manner on this enzyme:

One of the coenzymes described in lecture was ubiquinone. In a human cell, ubiquinone is confined to a very specific structure inside an organelle. Identify this structure.

What chemical feature of ubiquinone ensures that it stays confined to the structure identified in the inner mitochondiral membrane?

One metabolite attacked by TPP in an enzyme-catalyzed reaction is: