Biochemistry Final Exam =) Flashcards
- What are the substrates and products of pyruvate oxidation? What enzyme catalyzes this step? What cofactors are required? What are the regulators of pyruvate oxidation? What is the cellular location of pyruvate oxidation? Which of these cofactors are vitamin derivatives?
- What are the substrates and products of pyruvate oxidation? What enzyme catalyzes this step? What cofactors are required? What are the regulators of pyruvate oxidation? What is the cellular location of pyruvate oxidation? Which of these cofactors are vitamin derivatives?
Substrates: Pyruvate (3C), NAD+, Coenzyme A
Products: Acetyl CoA, NADH, H+, CO2
Enzyme: Pyruvate dehydrogenase
Regulators: Activators - CoA, NAD+, pyruvate & AMP (Low E state), Ca2+ (exercise!)
Inhibitors: Acetyl CoA, NADH, ATP, fatty acids (we have enough fatty acids… Acetyl CoA produces synthesis of FA, so this is signal that we don’t need it…)
Requirements: Thiamine pyrophosphate (Vit. B1 derivative)
lipoic acid (not a vitamin!)
coenzyme A (Vit. B5)
NAD+ (niacin)
FAD (riboflavin)
The pyruvate dehydrogenase complex
A. Function: PDH provides a link between glycolysis and the Krebs cycle
B. Location: PDH is located in the mitochondrial matrix
Reaction: Several enzymatic activities are associated with the overall reaction
Pyruvate oxidation occurs in the inner membrane of the mitochondria.
This process is a source of acetyl-CoA molecules for the citric acid cycle.
Pyruvate oxidation occurs in three easy steps.
First, the pyruvate is oxidized (it goes from 3C to 2C acetyl. CO2 is released as a result).
Secondly, NAD+ is reduced to NADH
Finally, the pyruvate dehydrogenase complex attaches CoA to acetyl.
The total energy yield for this process is 2NADH’s.
- The 4 pathways to which pyruvate connects are _____..
- The 4 pathways to which pyruvate connects are _____.
anaerobic glycolysis
kreb’s cycle
gluconeogenesis
amino acid synthesis
- Identify the principal substrates and products of the Krebs cycle. What is the cellular location of the Krebs cycle? Name each of the intermediates of the Krebs cycle in the correct sequence. Match the reaction type to the appropriate step in the cycle.
- What are the regulatory enzymes of the Krebs cycle? What substances activate these regulatory enzymes? What substances inhibit these enzymes? Are any vitamins (vitamin derivatives) used in the Krebs cycle?
- Identify the principal substrates and products of the Krebs cycle. What is the cellular location of the Krebs cycle? Name each of the intermediates of the Krebs cycle in the correct sequence. Match the reaction type to the appropriate step in the cycle.
Citric acid (Kreb’s cycle) is the final common pathway for oxidation of metabolic fuels.
Location: mitochondrial matrix
Amphibolic pathway: Intermediates can be used for biosynthesis or in catabolic reactions
In total: Kreb’s cycle forms 3 NADH, 1 ATP, and 1 FADH2 for each Acetyl CoA (which is converted from pyruvate through pyruvate oxidation)
Net reaction: 1. 2 carbons enter the cycle as acetyl CoA and 2 carbons leave as CO2
- 3 NADH and one FADH2 are formed in electron transfer reactions
- One high energy phosphate bond is generated
II. REactions of the Kreb’s cycle:
A. Acetyl CoA and oxaloacetate are linked to form citrate
- Enzyme: Citrate Synthase
- Description: condensation reaction
- Regulation: A. inhibitors: citrate, ATP, NADH, succinyl CoA. B. Activators: ADP
B. citrate to isocitrate
- Enzyme: Aconitase
- Description: Isomerization
C. Isocitrate to alpha-ketoglutarate and CO2
- Enzyme: isocitrate dehydrogenase
- Description: oxidative decarboxylation, NADH formed
- Regulation: a. Inhibitors: ATP, NADH
B. Activators: ADP
D. alpha-ketoglutarate and CoA to succinyl CoA
- Enzyme: alpha-ketoglutarate dehydrogenase
- Requirements: TPP, lipoamide, FAD, NAD, pantothenic acid
- Description: oxidative decarboxylation, succinyl CoA is energy rich thioester, NADH formed
- Regulation: a. inhibitors: ATP, NADH, succinyl CoA
B. activators: Ca 2+
E. Succinyl CoA + GDP + Pi to succinate, + GTP + CoA
- Enzyme: succinyl CoA synthetase
- Description: substrate level phosphorylation, ATP formed
F. Succinate to fumarate
- Enzyme: Succinate dehydrogenease, assoc with inner mitochondrial membrane
- Description: dehydrogenation reaction, FADH2 formed
G. Fumarate to malate
- Enzyme: Fumarase
- Description: hydration reaction
H. Malate to oxaloacetate
- Enzyme: Malate dehydrogenase
- Description: dehydrogenation, NADH formed
- The electron transport chain is a series of _____. What are the sources of electrons for electron transport? How is the energy of these electrons used by the electron transport system? How are electron transport complexes believed to set up an H+ gradient in response to electron flow? What is the “respiratory chain”? What is the final electron acceptor for electron transport? What is the major source of body heat?
- The electron transport chain is a series of coupled oxidation-reduction reactions! What are the sources of electrons for electron transport? How is the energy of these electrons used by the electron transport system? How are electron transport complexes believed to set up an H+ gradient in response to electron flow? What is the “respiratory chain”? What is the final electron acceptor for electron transport? What is the major source of body heat?
The electrons for electron transport come from the NADH & FADH2 (which come from glycolysis, the citric acid cycle, pyruvate oxidation, fatty acid oxidation). The electrons are transferred due to an increase in reduction potential from one carrier to the next. The electron transport complexes are beleived to release hydrogen into the intermembrane space in response to electron flow. The final electron acceptor is H20.
Also note:
NADH–>forms 3ATPs
FADH2—>Forms 2ATP
In ETC, 10 NADH form 30 ATP
2 FADH2 form 4 ATP
4 ATP from glycolysis
….38 ATP produced from 1 molecule glucose!
- Indicate whether you expect to find each of the following molecules or functions (1) in the matrix, (2) the inner membrane, (3) the outer membrane, (4) the inter-membrane space, or (5) not in the mitochondrion.
a. co-enzyme A
b. co-enzyme Q
c. malate dehydrogenase
d. succinate dehydrogenase
e. conversion of lactate to pyruvate
f. ATP synthase
g. accumulation of a high hydrogen ion concentration
- Indicate whether you expect to find each of the following molecules or functions (1) in the matrix, (2) the inner membrane, (3) the outer membrane, (4) the inter-membrane space, or (5) not in the mitochondrion.
a. co-enzyme A: mitochondrial matrix (Pyruvate dehydrogenase complex)
b. co-enzyme Q: The inner membrane (ETC!)
c. malate dehydrogenase: matrix & not in mitochondrion
d. succinate dehydrogenase - inner mitochondrial membrane (only enzyme of Kreb’s Cycle not in the matrix =).
e. conversion of lactate to pyruvate: cytosol (not in matrix)
f. ATP synthase: inner membrane (ETC!)
g. accumulation of a high hydrogen ion concentration: intermembrane space
- What are the regulatory enzymes of the Krebs cycle? What substances activate these regulatory enzymes? What substances inhibit these enzymes? Are any vitamins (vitamin derivatives) used in the Krebs cycle?
- What are the regulatory enzymes of the Krebs cycle? What substances activate these regulatory enzymes? What substances inhibit these enzymes? Are any vitamins (vitamin derivatives) used in the Krebs cycle?
A. Acetyl CoA and oxaloacetate are linked to form citrate
- Enzyme: Citrate Synthase
- Description: condensation reaction
- Regulation: A. inhibitors: citrate, ATP, NADH, succinyl CoA. B. Activators: ADP
B. citrate to isocitrate
- Enzyme: Aconitase
- Description: Isomerization
C. Isocitrate to alpha-ketoglutarate and CO2
- Enzyme: isocitrate dehydrogenase
- Description: oxidative decarboxylation, NADH formed
- Regulation: a. Inhibitors: ATP, NADH
B. Activators: ADP
D. alpha-ketoglutarate and CoA to succinyl CoA
- Enzyme: alpha-ketoglutarate dehydrogenase
- Requirements: TPP, lipoamide, FAD, NAD, pantothenic acid
- Description: oxidative decarboxylation, succinyl CoA is energy rich thioester, NADH formed
- Regulation: a. inhibitors: ATP, NADH, succinyl CoA
B. activators: Ca 2+
E. Succinyl CoA + GDP + Pi to succinate, + GTP + CoA
- Enzyme: succinyl CoA synthetase
- Description: substrate level phosphorylation, ATP formed
F. Succinate to fumarate
- Enzyme: Succinate dehydrogenease, assoc with inner mitochondrial membrane
- Description: dehydrogenation reaction, FADH2 formed
G. Fumarate to malate
- Enzyme: Fumarase
- Description: hydration reaction
H. Malate to oxaloacetate
- Enzyme: Malate dehydrogenase
- Description: dehydrogenation, NADH formed
- Which intermediates of the Krebs cycle are referred to as “anaplerotic”?
- Which intermediates of the Krebs cycle are referred to as “anaplerotic”?
Kreb’s cycle intermediates can be used as precursors for biosynthetic reactions
>>>Pyruvate and amino acids can be sources of carbons for anaplerotic reactions which replace Kreb’s intermediates.
- What are the regulatory enzymes of the Krebs cycle? What substances activate these regulatory enzymes? What substances inhibit these enzymes? Are any vitamins (vitamin derivatives) used in the Krebs cycle?
- What are the regulatory enzymes of the Krebs cycle? What substances activate these regulatory enzymes? What substances inhibit these enzymes? Are any vitamins (vitamin derivatives) used in the Krebs cycle?
Regulatory Enzymes:
- Citrate Synthase (Condensation) (between Acetyl CoA & Citrate)
>>Activator: ADP, Inhibitors: Citrate, ATP, NADH, Succinyl CoA
- Isocitrate dehydrogenase (oxidative decarboxylation, between Isocitrate & alpha ketoglutarate).
>>Activator: ADP, Inhibitor: ATP, NADH
- Alpha ketoglutarate dehydrogenase (oxidative decarboxylation)
>>Activator: Ca2+, Inhibitors: ATP, NADH, Succinyl CoA
Vitamins used in the Kreb’s cycle: CoA (Vit. B5), NAD+ (niacin, Vit. B3), FAD (riboflavin, Vit. B2),
- Unlike NAD+, the coenzyme FAD tends to be tightly associated with the dehydrogenase enzymes that use it as an electron source. Why?
- Unlike NAD+, the coenzyme FAD tends to be tightly associated with the dehydrogenase enzymes that use it as an electron source. Why?
Electron transfers involving FAD are one-electron transfers; unpaired electrons tend to be more reactive, leading to cellular damage
- For aerobic respiration a variety of substances must be in a state of flux across the inner mitochondrial membrane. Assuming a cell in which glucose is the sole energy source, for each of the following substances indicate whether you would expect a net flow across the membrane and in which direction the molecules are moving.
a. pyruvate
b. oxygen
c. ATP
d. water
e. Oxaloacetate
f. glycerol-3-phosphate
g. acetyl CoA
h. ADP
- For aerobic respiration a variety of substances must be in a state of flux across the inner mitochondrial membrane. Assuming a cell in which glucose is the sole energy source, for each of the following substances indicate whether you would expect a net flow across the membrane and in which direction the molecules are moving.
a. pyruvate in flow
b. oxygen in flow
c. ATP outflow
d. water outflow
e. Oxaloacetate no net flow
f. glycerol-3-phosphate no net flow
g. acetyl CoA no net change
h. ADP in flow
- Complete each of the following statements about the glycolytic pathway.
a. Although one of its reactions is an oxidation, glycolysis can proceed in the absence of oxygen because
b. If you bake bread or brew beer, you are dependent on glycolysis in yeast for
- Complete each of the following statements about the glycolytic pathway.
a. Although one of its reactions is an oxidation, glycolysis can proceed in the absence of oxygen because NAD+ is regenerated by the conversion of pyruvate to lactate.
b. If you bake bread or brew beer, you are dependent on glycolysis in yeast for generation of pyruvate which they then convert to alcohol and carbon dioxide. Carbon dioxide causes dough to rise and produces bubbles in beer.
Picture: Anaerobic glycolysis (pyruvate dehydrogenase catalyzed reaction)
- If the circulating blood is deoxygenated, heart muscle consumes glucose at a steady rate. When oxygen is added to the blood, the rate of glucose consumption drops dramatically, then, continues at the new, lower rate. Explain.
- If the circulating blood is deoxygenated, heart muscle consumes glucose at a steady rate. When oxygen is added to the blood, the rate of glucose consumption drops dramatically, then, continues at the new, lower rate. Explain.
In aerobic respiration the number of reducing equivalents produced is far greater, these in turn lead to more electrons passed along the e-transport chain and greater ATP production for each glucose metabolized.
- The concentration of glucose in human blood plasma is maintained at about 5 mM. The concentration of free glucose inside muscle cells is much lower. How is this concentration difference maintained?
- The concentration of glucose in human blood plasma is maintained at about 5 mM. The concentration of free glucose inside muscle cells is much lower. How is this concentration difference maintained?
By conversion of glucose to glucose- 6-phosphate
- Calculate the number of ATP produced from complete oxidation of glycerol?
- Calculate the number of ATP produced from complete oxidation of glycerol?
From Krebs cycle (after converting reducing equivalents) – 12 ATP
Pyruvate oxidation – 3 ATP
Glycolysis (when using the malate shuttle for NADH) – 7 ATP
Total - 22 ATP
- Is it possible to get a net synthesis of oxaloacetate by adding acetyl CoA to an experimental extract that contains only the enzymes and cofactors of the Krebs cycle?
- Is it possible to get a net synthesis of oxaloacetate by adding acetyl CoA to an experimental extract that contains only the enzymes and cofactors of the Krebs cycle?
No – 1 OAA enters the Krebs with acetyl CoA and one is generated at the end of Krebs sequence
- The electrochemical proton gradient consists of two components: a pH difference and an electrical potential. (true or false)
- The electrochemical proton gradient consists of two components: a pH difference and an electrical potential. (true or false)
TRUE!
- If no O2 is available, all the components of the mitochondrial electron transport chain will accumulate in their __________. (reduced form or oxidized form)
- If no O2 is available, all the components of the mitochondrial electron transport chain will accumulate in their __________. (reduced form or oxidized form)
REDUCED!
- At many steps in the electron-transport chain Iron (Fe) ions are used as part of heme or iron-sulfur clusters to bind the electrons in transit. Why do these functional groups that carry out the chemistry of electron transfer need to be bound to proteins?
- At many steps in the electron-transport chain Iron (Fe) ions are used as part of heme or iron-sulfur clusters to bind the electrons in transit. Why do these functional groups that carry out the chemistry of electron transfer need to be bound to proteins?
To limit electron leaking and to define the redox potentials of each carrier; to channel electrons along a defined path; to couple electron flow to H+ pumping.
- When the drug dinitrophenol (DNP) is added to mitochondria, the inner membrane becomes permeable to protons (H+). In contrast, when the drug nigericin is added to mitochondria, the inner membrane becomes permeable to K+.
a. How does the electrochemical proton gradient change in response to DNP?
b. How does the electrochemical proton gradient change in response to nigericin?
- When the drug dinitrophenol (DNP) is added to mitochondria, the inner membrane becomes permeable to protons (H+). In contrast, when the drug nigericin is added to mitochondria, the inner membrane becomes permeable to K+.
a. How does the electrochemical proton gradient change in response to DNP?
DNP reduces the size of the proton gradient by returning H+ to the matrix without passing through the ATP synthase/more heat production, less ATP production
b. How does the electrochemical proton gradient change in response to nigericin?
Nigericin moves K+ into the matrix reducing the charge difference across the membrane/ one component of electrochemical gradient is reduced (electrical) so fewer ATP will be produced
- In muscle tissue, the rate of conversion of glycogen to glucose 6-phosphate is determined by the ratio of glycogen phosphorylase a (active) to glycogen phosphorylase b (inactive). What happens to the rate of glycogen breakdown if a muscle preparation containing glycogen phosphorylase is treated with
a. phosphorylase kinase and ATP
b. phosphorylase (a) phosphatase
c. epinephrine
- In muscle tissue, the rate of conversion of glycogen to glucose 6-phosphate is determined by the ratio of glycogen phosphorylase a (active) to glycogen phosphorylase b (inactive). What happens to the rate of glycogen breakdown if a muscle preparation containing glycogen phosphorylase is treated with
a. phosphorylase kinase and ATP promotes/accelerates glycogen breakdown
b. phosphorylase (a) phosphatase decreases glycogen breakdown
c. epinephrine promotes/accelerates glycogen breakdown
- 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.
a. How does succinyl CoA regulate the activity of citrate synthase?
b. Why is succinyl CoA an appropriate signal for regulation of Krebs cycle?
- 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.
a. How does succinyl CoA regulate the activity of citrate synthase?
Negative feedback/allosteric/shifts apparent Km to higher concentration of acetyl CoA
b. Why is succinyl CoA an appropriate signal for regulation of Krebs cycle?
Succinyl CoA targets the first step of Krebs cycle, signaling a reduced need for reducing equivalents and ATP production
- Avidin, a protein in egg white, has a very high affinity for biotin. Which of the following conversions would be blocked by the addition of avidin to a cell homogenate?
a. glucose ® pyruvate
b. glucose 6-phosphate ® ribulose 5-phosphate
c. oxaloacetate ® glucose
d. pyruvate ® oxaloacetate
e. ribose 5-phosphate ® glucose
- Avidin, a protein in egg white, has a very high affinity for biotin. Which of the following conversions would be blocked by the addition of avidin to a cell homogenate?
a. glucose ® pyruvate
b. glucose 6-phosphate ® ribulose 5-phosphate
c. oxaloacetate ® glucose
d. pyruvate ® oxaloacetate
e. ribose 5-phosphate ® glucose
DDDDD!! Oxaloacetate >>Glucose
Biotin = B7!!!
- How are electrons from the NADH generated in glycolysis transferred to the electron transport chain? What are the organ locations of the NADH shuttle systems?
Picture 1
- How are electrons from the NADH generated in glycolysis transferred to the electron transport chain? What are the organ locations of the NADH shuttle systems?
NADH is generated between G3P and 1,3 bisphosphoglyerate (1,3GPG). Electrons are shuttled to the electron transport chain through:
A. The glyercol-3-phosphatase shuttle moves reducing equivalents from the cytosol to the mitochondrial matrix. The equivalent of one ATP is requirement for this transfer.
B. The malate-aspartate shuttles moves reducing equivalents from the cytosol to the matrix without an energy requirement.
Picture: glycerol phosphate shuttle
- How are electrons from the NADH generated in glycolysis transferred to the electron transport chain? What are the organ locations of the NADH shuttle systems?
- How are electrons from the NADH generated in glycolysis transferred to the electron transport chain? What are the organ locations of the NADH shuttle systems?
NADH is generated between G3P and 1,3 bisphosphoglyerate (1,3GPG). Electrons are shuttled to the electron transport chain through:
A. The glyercol-3-phosphatase shuttle moves reducing equivalents from the cytosol to the mitochondrial matrix. The equivalent of one ATP is requirement for this transfer.
>>The glycerol-3-phosphate shuttle is a mechanism that regenerates NAD+ from NADH, a by-product of glycolysis. Its importance in transporting reducing equivalents is secondary to the malate-aspartate shuttle.
B. The malate-aspartate shuttles moves reducing equivalents from the cytosol to the matrix without an energy requirement.
Picture: malate shuttle
- What coenzymes and metal ions are among the components of the electron transport chain? What is the prosthetic group of a flavoprotein? What is the sequence of major complexes and electron carriers in the electron transport system? Are these carriers physically linked? What is the cellular location of the electron transport chain?
Components of ETC:
- Complex 1 (NADH Dehydrogenase) is a large complex that utilizes FMN and iron-sulfur proteins
- Coenzyme Q is embedded in the membrane via a lipid chian
- Complex II (Succinate Dehydrogenase) transfers electrons to CoQ
- Complex III (Cytochrome b-c1) contains heme and iron-sulfur proteins
- Cytochrome c is a small, mobile protein
- Complex IV (Cytochrome Oxidase) contains heme and copper complexes
- Complex IV receives molecular oxygen and generates water
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An electron transfer flavoprotein (ETF) is a flavoprotein and functions as a specific electron acceptor for primarydehydrogenases, transferring the electrons to terminal respiratory systems such as electron-transferring-flavoprotein dehydrogenase. ETFs are heterodimeric proteins composed of an alpha and beta subunit (ETFA and ETFB), and contain an FADcofactor and AMP.[2][3
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The ETC is located in the inner membrane of the mitochondria.
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In eukaryotes, an important electron transport chain is found in the inner mitochondrial membrane where it serves as the site of oxidative phosphorylation through the use of ATP synthase. It is also found in the thylakoid membrane of the chloroplast in photosynthetic eukaryotes. In bacteria, the electron transport chain is located in their cell membrane.
Complex II
In Complex II (succinate dehydrogenase; EC 1.3.5.1) additional electrons are delivered into the quinone pool (Q) originating from succinate and transferred (via FAD) to Q. Complex II consists of four protein subunits: SDHA, SDHB, SDHC, and SDHD. Other electron donors (e.g., fatty acids and glycerol 3-phosphate) also direct electrons into Q (via FAD). Complex 2 is a parallel electron transport pathway to complex 1, but unlike complex 1, no protons are transported to the intermembrane space in this pathway. Therefore, the pathway through complex 2 contributes less energy to the overall electron transport chain process.
===> Complex 1 –>releases 4 H+ into intermembrane space
>>>>Complex III releases 2 H+ into intermembrane space
>>>>Complex IV releases 4 H+ into intermembrane space
- How does the ATP synthase use the H+ gradient to produce ATP?
- How does the ATP synthase use the H+ gradient to produce ATP?
The Chemiosmotic model of ATP synthesis explains how electron transfer to oxygen is coupled to ATP synthesis.
Fomration of the H+ gradient: 1. The E flow from electron transport is used to form an H+ gradient across the inner mitochondrial membrane
- The large carriers act as H+ pumps
- The H+ gradient has an electrical and chemical component
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The ETC complexes are arranged in order of increasing redox potentials (increasing electron affinity). the increase in H+ in the intermembrane space causes a proton gradient (electrochemical gradient) to form, and the proton gradient provides E for synthesis of ATP! The E stored in the protonmotive forces drives the synthesis of ATP by the movement of protons down the electrochemical gradient through the ATP-synthase.
Electron transport chains in mitochondria
Most eukaryotic cells have mitochondria, which produce ATP from products of the citric acid cycle, fatty acid oxidation, and amino acid oxidation. At the mitochondrial inner membrane, electrons from NADH and succinate pass through the electron transport chain to oxygen, which is reduced to water. The electron transport chain comprises an enzymatic series of electron donors and acceptors. Each electron donor passes electrons to a more electronegative acceptor, which in turn donates these electrons to another acceptor, a process that continues down the series until electrons are passed to oxygen, the most electronegative and terminal electron acceptor in the chain. Passage of electrons between donor and acceptor releases energy, which is used to generate a proton gradient across the mitochondrial membrane by actively “pumping” protons into the intermembrane space, producing a thermodynamic state that has the potential to do work. The entire process is called oxidative phosphorylation, since ADP is phosphorylated to ATP using the energy of hydrogen oxidation in many steps.
- Account for the number of ATP theoretically synthesized from the complete oxidation of a molecule of glucose. Calculate the total ATP production from glycerol?
- Account for the number of ATP theoretically synthesized from the complete oxidation of a molecule of glucose. Calculate the total ATP production from glycerol?
Glycolysis preparation phase: -2 ATP (glucose>glucose 6P, fructose 6P>fructose 1,6 bisphosphate)
Glycolysis pay off phase: 4 ATP,
2 NADH: >>4-6ATP yield (since this requires that they are converted into ATP in the mitochondrial ETC out of the cytosol, which sometimes costs 2ATP or is free in other organisms)
pyruvate oxidation: 2 NADH = 6 ATP in ETC
Kreb’s cycle: 2 ATP, 6 NADH (=12 ATP in ETC), 2 FADH2 (=4 ATP in ETC)
- Why do the electrons carried by NADH potentially result in the synthesis of greater amounts of ATP than those carried by FADH2?
FADH2 makes less ATP because it enters the electron transport chain at a later stage than does NADH.
5. Why do the electrons carried by NADH potentially result in the synthesis of greater amounts of ATP than those carried by FADH2?
The electron transport chain is made of carrier molecules assembled into 3 protein complexes, and the passage of an electron through each complex generates enough energy to make roughly 1 ATP per complex. NADH enters the cycle at the first complex, so NADH produces 3 ATP. FADH2 enters the cycle at the 2nd complex, thus generating 2 ATP….gtp is feeds its electrons to the third, making only one atp
- Describe the consequences of inhibition of the electron transport chain. What is the purpose of thermogenin?
- Describe the consequences of inhibition of the electron transport chain. What is the purpose of thermogenin?
As described in a former post, the inhibitors of the Electron Transport Chain are substances that bind to some of the components of the ETC blocking its ability to change in a reversible form from an oxidized state to a reduced state.
This inhibition results in the accumulation of reduced forms before the inhibitor point, and oxidized forms of the components of the ETC downstream (ahead) the inhibition point.
Since energy is not released, the synthesis of ATP also stops.
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Thermogenin (called uncoupling protein (An uncoupling protein is a mitochondrial inner membrane protein that can dissipate the proton gradient before it can be used[clarification needed] to provide the energy for oxidative phosphorylation >>Oxidative phosphorylation is the metabolic pathway in which the mitochondria in cells use their structure, enzymes, and energy released by the oxidation of nutrients to reform ATP, such as ETC[1]))) by its discoverers and now known as uncoupling protein 1, or UCP1)[1] is an uncoupling protein found in the mitochondria of brown adipose tissue (BAT). It is used to generate heat by non-shivering thermogenesis.
UCPs are transmembrane proteins that decrease the proton gradient generated in oxidative phosphorylation. They do this by increasing the permeability of the inner mitochondrial membrane, allowing protons that have been pumped into the intermembrane space to return to the mitochondrial matrix. UCP1-mediated heat generation in brown fat uncouples the respiratory chain, allowing for fast substrate oxidation with a low rate of ATP production. UCP1 is related to other mitochondrial metabolite transporters such as the adenine nucleotide translocator, a proton channel in the mitochondrial inner membrane that permits the translocation of protons from the mitochondrial intermembrane space to the mitochondrial matrix. UCP1 is restricted to brown adipose tissue, where it provides a mechanism for the enormous heat-generating capacity of the tissue.
UCP1 is activated in the brown fat cell by fatty acids and inhibited by nucleotides. Fatty acids cause the following signaling cascade: Sympathetic nervous system terminals release Norepinephrine onto a Beta-3 adrenergic receptor on the plasma membrane. This activates adenylyl cyclase, which catalyses the conversion of ATP to cyclic AMP (cAMP). cAMP activates protein kinase A, causing its active C subunits to be freed from its regulatory R subunits. Active protein kinase A, in turn, phosphorylates triacylglycerol lipase, thereby activating it. The lipase converts triacylglycerols into free fatty acids, which activate UCP1, overriding the inhibition caused by purine nucleotides (GDP and ADP). At the termination of thermogenesis, the mitochondria oxidize away the residual fatty acids, UCP1 inactivates and the cell resumes its normal energy-conserving mode.
- What is meant by the term “gluconeogenesis”? What are the key substrates for gluconeogenesis?
gluconeogenesis is the synthesis of new glucose from non-carbon precursors. Precursors: lactate, pyruvate, glycerol, some amino acids (eg alanine). It is used to keep blood sugar levels from dropping too low (hypoglycemia).
Substrates for gluconeogenesis:
A. Lactate (the Cori cycle). A. Lactate derives from glyolysis in muscles. B. Lactate released into blood, taken up by liver. C. Liver converts lactate into pyruvate. D. Pyruvate converted into glucose, E. glucose released into blood.
B. Alanine. A. Muscle pyruvate can be converted into alanine. B. Alanine is released into blood. C. Liver converts alanine into pyruvate D. Pyruvate converted into glucose
C. Glycerol: A. Comes from breakdown of triglycerides. B. Enters blood and taken up by liver. C. Converted to glucose-3-phosphate D. 2 units converted to glucosek
- How is gluconeogenesis regulated?
- How is gluconeogenesis regulated?
Gluconeogenesis (synthesis of new glucose from non-carbohydrate precursors) is regulated by different inhibitors/activators:
1st bipass reaction: A. pruvate to PEP (phosphoenol pyruvate). Pyruvate carboxylation to oxaloacetate. Enzyme: pyruvate carboxylase. Requires: biotin, Mg2+, Mn2+. REGULATORS: Acetyl CoA is activator; inhibited by ADP. Location: mitochondrial matrix.
B. oxaloacetate (OAA) to malate in mitochondrial matrix; enzyme is malate dehydrogenase; OAA can’t cross mitochond. membrane. Membrane converted back to oxaloacetate in cytosol; also transfers NADH to cytosol. >>Oxaloacetate to PEP: Phosphoenolpyruvate carboxykinase (PEPCK). Requires MN2+, location: cytosol
- 2nd bipass reaction: fructose 1,6 bisphosphatase to fructose 6-phosphate. Enzyme: fructose 1,6-bisphosphatase (F1,6Bpase), MAJOR REGULATORY enzyme. Activators: citrate, ATP, Inhibitors: AMP, F2,6BP. GLUCAGON, EPINEPHRINE stimulate synthesis of bypass enzymes, insulin suppresses bypass enzyme synthesis, in the cytosol.
- 3rd bipass reaction: Glucose 6-phosphate to glucose. Enzyme: glucose 6-phosphatase. Location: Endoplasmic reticulum. Expressed only in gluconeogenic tissue.
- How many moles of high energy compounds are required to carry out synthesis of 1 mole of glucose via gluconeogenesis? What vitamin(s) and metal ions are required?
- How many moles of high energy compounds are required to carry out synthesis of 1 mole of glucose via gluconeogenesis? What vitamin(s) and metal ions are required?
Energetics: 1. 2 moles of pyruvate to 1 mole of glucose.
- Uses 4 moles of ATP and 2 moles GTP (equiv. to 6 ATP)
Gluconeogenesis (synthesis of new glucose from non-carbohydrate precursors) is regulated by different inhibitors/activators:
1st bipass reaction: A. pruvate to PEP (phosphoenol pyruvate). Pyruvate carboxylation to oxaloacetate. Enzyme: pyruvate carboxylase. Requires: biotin, Mg2+, Mn2+. REGULATORS: Acetyl CoA is activator; inhibited by ADP. Location: mitochondrial matrix.
B. oxaloacetate (OAA) to malate in mitochondrial matrix; enzyme is malate dehydrogenase; OAA can’t cross mitochond. membrane. Membrane converted back to oxaloacetate in cytosol; also transfers NADH to cytosol. >>Oxaloacetate to PEP: Phosphoenolpyruvate carboxykinase (PEPCK). Requires MN2+, location: cytosol
- 2nd bipass reaction: fructose 1,6 bisphosphatase to fructose 6-phosphate. Enzyme: fructose 1,6-bisphosphatase (F1,6Bpase), MAJOR REGULATORY enzyme. Activators: citrate, ATP, Inhibitors: AMP, F2,6BP. GLUCAGON, EPINEPHRINE stimulate synthesis of bypass enzymes, insulin suppresses bypass enzyme synthesis, in the cytosol.
- 3rd bipass reaction: Glucose 6-phosphate to glucose. Enzyme: glucose 6-phosphatase. Location: Endoplasmic reticulum. Expressed only in gluconeogenic tissue.
- Which organs synthesize and store significant amounts of glycogen? What is the purpose of these glycogen stores? How long do liver glycogen stores last?
- Which organs synthesize and store significant amounts of glycogen? What is the purpose of these glycogen stores? How long do liver glycogen stores last?
Glycogen is a multibranched polysaccharide of glucose that serves as a form of energy storage in animals[2] andfungi. The polysaccharide structure represents the main storage form of glucose in the body.
Glycogen is the storage form of glucose. A. highly branched polymer of glucose molecules B. Exists in CYTOSOL as granules. C. granules contain enzymes of synthesis and degradation. D. stored in muscle and in liver; liver stores can be used to elevate blood glucose. E. Glycolysis (synthesis) and glycogenolysis (breakdown) occur via separate pathways.
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After a meal has been digested and glucose levels begin to fall, insulin secretion is reduced, and glycogen synthesis stops. When it is needed for energy, glycogen is broken down and converted again to glucose. Glycogen phosphorylase is the primary enzyme of glycogen breakdown. For the next 8–12 hours, glucose derived from liver glycogen is the primary source of blood glucose used by the rest of the body for fuel.
- What are the key enzymes in glycogen synthesis and degradation? Are coenzymes required by these enzymes?
- What is the form of activated sugar in glycogen metabolism?
- What are the key enzymes in glycogen synthesis and degradation? Are coenzymes required by these enzymes?
In glycogenesis (synthesis):
- Glucose 6-phosphate converted into glucose 1-phosphate
B. Glucose 1-phosphate is esterified w/ UTP by the enzyme UDP-glucose pyrophosphorylase.
C. UDP-glucose is activated form of glucose
D. Activated glucose units are transferred to glycogen by the enzyme glycogen synthase. . Alpha 1,4-glycoside bonds are formed.
E. Glycogen synthase is the key enzyme in glycogen synthesis (glycogenesis) .
F. Transferase activity: seven residue segments of amylose chain are transferred to form branch chains.
- Discuss the general scheme of glycogen synthesis and breakdown.
- Discuss the general scheme of glycogen synthesis and breakdown.
Glycogenolysis (breakdown):
A. alpha 1,4 glycoside bonds are broken by phosphorylytic cleavage, producing glucose 1-phosphate
B. glucose is removed 1 residue at a time
C. enzyme: glycogen phosphorylase
D. requires: pyridoxal phosphate (Vit. B6)
E. Debranching enzyme removes branch points.
In glycogenesis (synthesis):
- Glucose 6-phosphate converted into glucose 1-phosphate
B. Glucose 1-phosphate is esterified w/ UTP by the enzyme UDP-glucose pyrophosphorylase.
C. UDP-glucose is activated form of glucose
D. Activated glucose units are transferred to glycogen by the enzyme glycogen synthase. . Alpha 1,4-glycoside bonds are formed.
E. Glycogen synthase is the key enzyme in glycogen synthesis (glycogenesis) .
F. Transferase activity: seven residue segments of amylose chain are transferred to form branch chains.
- What are the metabolic purposes of the pentose pathway? What is the regulatory enzyme in the pentose pathway? What is the metabolite that governs flow through the pathway?
- What are the metabolic purposes of the pentose pathway? What is the regulatory enzyme in the pentose pathway? What is the metabolite that governs flow through the pathway?
Functions:
- NADPH for biosynthesis
- ribose 5-phosphate for nucleic biosynthesis
- pathway for conversion of pentoses into glycolytic intermediates
Glucose-6-phosphate dehydrogenase is the rate-controlling enzyme of this pathway. It is allosterically stimulated by NADP+.
>>>G6PD is enzyme between Glucose 6-phosphate to 6-phosphogluconolactone (In picture between G6P & Ribulose 5-phosphate). Descrption: In RBCs, pathway is required to maintain reduced glutathione; red blood cell integrity depends on reduced glutathione; hemolytic anemia if NADPH is insuficient. E. produces NADP
- What is meant by oxidative and non-oxidative segments of the pentose pathway?
- What is meant by oxidative and non-oxidative segments of the pentose pathway?
There are two distinct phases in the pathway. The first is the oxidative phase, in which NADPH is generated, and the second is the non-oxidative synthesis of 5-carbon sugars. For most organisms, the pentose phosphate pathway takes place in the cytosol; in plants, most steps take place in plastids.[1]
- What is the syndrome and enzyme associated with thiamine deficiency in the pentose pathway?
- What is the syndrome and enzyme associated with thiamine deficiency in the pentose pathway?
Key reactions:
- Transketolase catalyzes 2 reactions in pathway.
A. Requires thiamine pyrophosphate
B. Defective transketolase leads to Wiernicke-Korsakoff syndrome
What vitamin derivatives are required for the pentose pathway?
What vitamin derivatives are required for the pentose pathway?
Requires B1 & B3 (niacin, NADP+ for Glucose 6-phosphate to 6-phosphogluconolactone, & Thiamine pyrophosphate for Transketolase which catalyzes two reactions in the pathway)
- What are the two routes (and initial enzyme) by which fructose is catabolized? Compare the processing of fructose to that of glucose. How do glucose and fructose sbsorption and metabolism differ?
- What are the two routes (and initial enzyme) by which fructose is catabolized? Compare the processing of fructose to that of glucose. How do glucose and fructose sbsorption and metabolism differ?
The major pathway of fructose catabolism is expressed in the liver
- Fructose to fructose 1-phosphate. A. Enzyme: fructokinase. B. Description: high affinity, high capacity for fructose
- Fructose-1-phosphate to DHAP + glyceraldehyde. A. Enzyme: aldolase B (fructose-1-phophate aldolase).
- B. Glyerceraldehyde to glyceraldehyde 3-PO4. Enzyme: triose kinase.
- Bypasses the major regulated step of glycolysis catalyzed by Phosphofructokinase.
- Additional catabolism of fructose occurs in the small intestine and proximal tubules of the kidneys.
- Small amounts of fructose can be converted to fructose-6-phosphate in other tissues.
A. Enzyme: hexokinase.
B. Extrahepatic isoforms have a low affinity for fructose.
Fructose…
Consequences of fructose catabolism
Fructose absorption is mediated by GLUT 5 (to enter) and GLUT 2 (to exit)
C.. Glucose improves fructose absorption in the small intestine.
D. Fructose does not stimulate an insulin response
E. Fructose may not stimulate satiety centers in the brain
F. Most of the fructose present in the portal circulation is extracted by the liver
Also, glucose outcompetes fructose (and is preferred over fructose as a nutrient)
- How many moles of high energy compounds are required to carry out synthesis of 1 mole of glucose via
gluconeogenesis? What vitamin(s) and metal ions are required?
- How many moles of high energy compounds are required to carry out synthesis of 1 mole of glucose via
gluconeogenesis? What vitamin(s) and metal ions are required?
Gluconeogenesis: Is a reversal of the glycolytic pathway; irreversible steps in glycolysis must be bypassed. Requires: biotin (B7!), MG2+, Mn2+,
It requires 4 molecules of ATP and 2 molecules of GTP to occur spontaneously
Big Picture: Dietary Carbohydrates & blood glucose
Big Picture: Dietary Carbohydrates & blood glucose
When glucose blood levels are ELEVATED, have uptake by tissues (insulin).
GLUT 4 (in fat, skeletal muscle, heart) -mediates insulin-stimulated glucose uptake. Increased glucose uptake w/ insulin causes more GLUT 4 transporters. Not every GLUT is the same…
When blood glucose levels are low, there is a release by gluconeogenic tissues (glucagon is a hormone of the fasting state!)
GLUT transporters: Quick Summary
When glucose blood levels are ELEVATED, have uptake by tissues (insulin).
GLUT 4 (in fat, skeletal muscle, heart) -mediates insulin-stimulated glucose uptake. Increased glucose uptake w/ insulin causes more GLUT 4 transporters. Not every GLUT is the same…
When blood glucose levels are low, there is a release by gluconeogenic tissues (glucagon is a hormone of the fasting state!)
GLUT 2 - Liver, pancreatic B cells - high capacity, low affinity. Km of 15 mM or higher.
What are the common names of the B vitamins and where are they found?!
Thiamine PP (B1) –> Required (along with lipoamide, FAD, NAD, & pantothenic acid>>B1,2,3,5 & lipoic acid) for conversion of alpha-ketoglutarate and CoA to succinyl CoA
riboflavin (B2) –> FMN, FAD In Citric Acid Cycle & ETC
Niacin (B3): NAD… Citric acid cycle, pyruvate oxidation, ETC
CoA (B5): pyruvate oxidation, TCA cycle. ALSO - pantothenic acid has B5!
Pyridoxal phosphate (B6) –> Required for glycogenolysis (not pictured)
biotin (B7): Required (along w/ MG2+ & Mn2+) for gluconeogenesis
NOTE: lipoamide = lipoic acid
What are the activators/inhibitors for glycolysis vs. gluconeogenesis?
What are the activators/inhibitors for glycolysis vs. gluconeogenesis?
Glycolysis: Hexokinase inhibited by G6P. PFK-1 activated by F6P, AMP, F2,6BP. Inhibited by glucagon, citrate, and ATP. Pyruvate kinase is activated by F1,6BP, and inhibited by ATP and cAMP.
Gluconeogenesis: 1st bipass reaction is activated by acetyl CoA, inhibited by ADP. Fructose bisphosphatase reaction is activated by glucagon & citrate, inhibited by AMP & F2,6BP!
Discuss the hormonal and metabolic regulation of glycogen synthesis and degradation in the liver
Discuss the hormonal and metabolic regulation of glycogen synthesis and degradation in the liver
Insulin - promotes glycogenesis
glucagon - activated enzymes that break down glycogen (glycogenolysis) =)
What are the intermediates into which galactose and mannose are converted? What is the major dietary source of galactose? How many ATP can be synthesized from the catabolism of galactose and mannose?
What are the intermediates into which galactose and mannose are converted? What is the major dietary source of galactose? How many ATP can be synthesized from the catabolism of galactose and mannose?
Lactose can be broken down into both galactose & glucose. As seen in the diagram below, galactose can be converted into UDP-galactose, and then UDP-glucose (to then be converted to G1P & then G6P and down through glycolysis). Mannose is converted to Mannose 6 phosphate, and then to Fructose 6 phosphate
mannose: 38 ATP (same as glucose!)
galactose:
