Week 11: Gluconeogenesis, Pyruvate Dehydrogenase Complex, Citric Acid Cycle Flashcards
The reduced form of _____ is an indirect source of high-energy compounds.
NADH
Lipoic acid is associated with dihydrolipoyl transacetylase. It accepts a _______ from hydroxyethyl TPP, oxidizing the group to an _____. It delivers this _____ to coenzyme A. It then is oxidized by NAD+, so it acts as a _____ agent.
hydroxyethyl group, acetyl
acetyl group
reducing
A condensation reaction is one in which a new ______ is formed. The reaction of ______ and ______ to form citrate involves the formation of such a ______.
carbon-carbon bond
acetyl-CoA, oxaloacetate
C-C bond
What type of reaction is catalyzed by isocitrate dehydrogenase and α-ketoglutarate dehydrogenase?
An oxidative decarboxylation
Both dehydrogenases are involved in redox reactions in which a CO2 is abstracted from a substrate. In both cases NAD+ is reduced while the other substrate is oxidized. Thus, both of these enzymes catalyze oxidative decarboxylations.
The reactions that act as control points in the citric acid cycle are those that have the most ______ in the cycle, i.e. these are the most ____ reactions. These control points are allosterically regulated by ATP and NADH. Other regulators also allosterically regulate each of the enzymes catalyzing these reactions.
_______ and ________ are some examples of enzymes that catalyze control point reactions in the citric acid cycle.
negative free energy changes, favorable
Isocitrate dehydrogenase, α-ketoglutarate dehydrogenase
______ and _____ inhibit all four of the enzymes that are the ________ in the citric acid cycle. Succinyl-CoA inhibits two of the control points, citrate synthase and α-ketoglutarate dehydrogenase.
Acetyl-CoA inhibits pyruvate dehydrogenase. Citrate inhibits citrate synthase. ADP and NAD+ stimulate isocitrate dehydrogenase.
ATP and NADH, control points
The reactions of glycolysis occur in the ______ of the cell. The citric acid cycle, which is found only in _____, occurs in the _______.
cytoplasm
eukaryotes, mitochondrial matrix
How can the synthesis and breakdown of fructose-2,6-bisphosphate be controlled independently?
The concentration of fructose-2,6-bisphosphate synthesis depends on the balance between its synthesis and its breakdown. Its synthesis is catalyzed by _________ , while its breakdown is catalyzed by _________. Both of these enzymes are regulated by __________ mediated by kinases and phosphatases.
phosphofructokinase, fructose-1,6-bisphosphatase
phosphorylation and dephosphorylation
Fructose-2,6-bisphosphate is an allosteric effector in glycolysis and in gluconeogenesis.
In glycolysis, it activates ______ and is a ______ allosteric effector in the glycolysis pathway.
In gluconeogenesis, it inhibits _____.
phosphofructokinase
positive
fructose bisphosphate phosphatase
Most gluconeogenesis reactions take place in the _____, but there are some reactions that occur in the ______.
cytoplasm, mitochondria
When the body ______, carbohydrates are broken down via _____. When ______, glucose can be synthesized from the intermediates of the glycolytic and citric acid pathways by ______.
needs energy, glycolysis
energy is not needed, gluconeogenesis
Gluconeogenesis proceeds in reverse order from glycolysis, and many of the glycolysis enzymes also catalyze gluconeogenesis. However, at _____ points there are unique enzymes that catalyze only gluconeogenesis, making it a distinct pathway.
four points
Gluconeogenesis is NOT the only carbohydrate biosynthetic pathway.
Carbohydrates are synthesized by ______ in plants, by the gluconeogenesis process, and when glucose is used to synthesize other hexoses and hexose derivatives.
photosynthesis
If one were to introduce a pulse of acetyl CoA with the two carbons in acetyl CoA labeled with a radioactive tag, followed by unlabeled acetyl CoA, what would be the ultimate fate of the two carbons?
The carbonyl carbon from the acetyl CoA will be lost as CO2 during the second round, while the methyl carbon becomes incorporated in the core of the circulating compounds (e.g., the 2,3 positions of succinate and fumarate) and are only lost through dilution.
How many oxidation-reduction steps are found in one turn of the cycle?
Four
There are four steps: the isocitrate dehydrogenase, α-ketoglutarate dehydrogenase, succinate dehydrogenase, and malate dehydrogenase steps.
If one NADH generates 3 ATPs through oxidative phosphorylation and 1 FADH2 generates 2 ATPs through oxidative phosphorylation, how many ATPs can be generated from the products of one cycle through the TCA pathway?
Twelve ATPs can be generated: 9 from the 3 NADHs, 2 from the FADH2, and 1 directly generated by the combination of succinyl-CoA synthetase and nucleoside diphosphate kinase (reaction 5).
Gluconeogenesis:
- The synthesis of ____ from _____.
- The major site of gluconeogenesis is the ____,
although gluconeogenesis can occur in the ____. - Gluconeogenesis is especially important during
_____, as glucose is the primary fuel
for the brain and the only fuel for red blood cells.
glucose, pyruvate
liver, kidney
fasting or starvation
The beginning: The Conversion of Pyruvate into Phosphoenolpyruvate
* Requires two enzymes,
* First: ______ (in _____)
catalyzes formation of ______.
* Second: _____________ (in ______)
pyruvate carboxylase, mitochondria
oxaloacetate
phosphoenolpyruvate carboxykinase, cytoplasm
Pyruvate carboxylase requires the ______ as a cofactor.
* The formation of oxaloacetate by pyruvate carboxylase occurs in ____ stages.
vitamin biotin
three
The formation of oxaloacetate by pyruvate carboxylase occurs in the ______. (Step 1)
- Oxaloacetate is reduced to ____ and transported into the cytoplasm, where it is _____ to oxaloacetate with the generation of _______.
- PEP is then synthesized from oxaloacetate by
phosphoenolpyruvate carboxykinase. (Step 2)
mitochondria
malate, reoxidized
cytoplasmic NADH
Step 11: Glucose-6-Phosphatase
* Glucose 6-phosphate is transported into the lumen of the endoplasmic reticulum.
* Glucose 6-phosphatase, an ______ on the inner surface of the endoplasmic reticulum, catalyzes the formation of ______ from ______.
integral membrane
glucose, glucose 6-phosphate
What barrier prevents glycolysis from simply running in reverse to synthesize glucose?
How is this barrier overcome in gluconeogenesis?
3 irreversible steps of glycolysis (Steps 1, 3, 10)
4 new enzymes of gluconeogenesis.
Since G6P is a ______ effector for Hexokinase since…
G6P is a ____ effector for Glucose-6-phosphatase in glucogenesis
negative, build-up of G6P would stop hexokinase and halter glycolysis
positive
Lots of glucose, ATP needed –>
Glucose scarce and needed –>
Glycolysis
Gluconeogenesis
If cell needs energy, [AMP] ______, therefore AMP is a ______ effector of phosphofructokinase (PFK)
AMP is a _____ effector of fructose-1,6-biphosphate in gluconeogenesis
increases, positive
negative
If you have plenty of energy [ATP] ______, therefore ATP is a _____ effector of phosphofructokinase (PFK)
increases, negative
Higher [H+] means ____ pH.
H+ is a ____ effector of glycolysis to..
lower
negative, to keep enzymes from being damaged
Citrate is a ______ effector of glycolysis and a ______ effector of gluconeogenesis
negative, positive
In the liver, the rates of glycolysis and gluconeogenesis are
adjusted to maintain _______ levels.
- The key regulator of glucose metabolism in the liver is
_______. Fructose 2,6-bisphosphate _____ phosphofructokinase and ____ fructose 1,6-bisphosphatase. - The kinase that synthesizes fructose 2,6-bisphosphate
(phosphofructokinase 2) and the phosphatase that
hydrolyzes this molecule (fructose bisphosphatase 2) are
located on the same polypeptide chain. Such an
arrangement is called a ________.
blood-glucose
fructose 2,6-bisphosphate
stimulates, inhibits (positive affector for glycolysis, negative affector for gluconeogenesis)
bifunctional enzyme
Fructose 2,6-Biphosphate different names depending on the direction it is catalyzing.
_________ when adding a phosphate (glycolysis)
_________ when removing a phosphate (gluconeogenesis)
PFK-2, phosphofructokinase-2
FBPase2, Fructose biphosphatase
How does the enzyme know which domain should be active?
Synethesis and Degradation of Fructose 2,6-biphosphate is controlled by _________
Low blood glucose levels trigger pancreas to release the hormone ______.
Glucagon acts as a _____ in signal transduction pathway:
- Glucagon binds to a G-protein receptor
* The G-protein receptor activates adenylate cyclase
* Adenylate cyclase catalyzes formation of cyclic AMP
* CMP binds to protein kinase A and activates it
blood glucose sensitive hormones
glucagon
primary messenger
Alanine is a _____ effector of glycolysis
Acetyl CoA is a _____ effector of glucogeonegensis
negative
postive
What would be the effect on an organism’s ability to produce
glucose if there was an inability to produce adequate
quantities of pyruvate carboxylase?
Lack of pyruvate carboxylase would cause hypoglycemia.
Lactic acid could build up in the blood.
What would be the effect on an organism’s ability to use
glucose as an energy source if a mutation inactivated
glucose 6-phosphatase in the liver?
During the night, while fasting glucose levels would
drop to dangerously low levels.
The formation of acetyl CoA from pyruvate is ______ in animal cells.
* Acetyl CoA has two possible fates:
irreversible
metabolism by the citric acid cycle or incorporation into fatty acids.
The synthesis of acetyl CoA from pyruvate consists of three
chemical steps:
a decarboxylation, an oxidation, and the transfer to CoA.
Lipoamide, a coenzyme, is formed by the attachment of
the _______ to a ______ residue in another
enzyme in the complex, dihydrolipoyl transacetylase
(E2).
* The _____ linkages allow lipoamide to move between
different sites.
* The three enzymes of the pyruvate dehydrogenase
complex are structurally integrated, and the lipoamide
arm allows rapid movement of ________
from one active site of the complex to another.
vitamin lipoic acid, lysine
flexible
substrates and products
The Pyruvate Dehydrogenase Is Regulated by
Two Mechanisms
1. ________ of Enzyme E1. (deactivated when ______, activated when ______)
* There is a kinase associated with the E2 and E3 parts of the complex
* This kinase phosphorylates E1 at one of serine residues and inactivates E1 .
* This kinase is activated by glucagon when glucose is low. Want to save pyruvate to make glucose
* A phosphatase is also associated with the E2 and E3 parts of the complex
* This phosphatase removes the phosphate and thereby activates the enzyme
* The phosphatase is activated by different activators depending on cell type.
* Insulin, Ca 2+
Covalent modification
phosphorylated, not phosphorylated
- Allosteric regulation based on the ______ charge.
* _______ inhibit the complex.
* ______ stimulate the complex.
energy
ATP, acetyl CoA, and NADH
ADP and pyruvate
List some of the advantages of organizing the
enzymes that catalyze the formation of acetyl CoA
from pyruvate into a single large complex.
Reaction facilitated by close proximity (don’t have to wait for intermediate to diffuse out or float to another enzyme)
Lipoamide swinging arm (speeds up process, don’t have to wait for something to diffuse from one ACTIVE SITE to another)
Reactants don’t leave complex (reduces side reactions)
Enzymes are in correct ratio from the start
Regulatory enzymes part of complex
The CAC Consists of Two Stages:
- In the first stage of the citric acid cycle, ______ are introduced into the cycle by ______ of an ______ with a four-carbon compound, _______.
- The six-carbon compound formed (______) undergoes two ________, generating two molecules of ______ .
- In the second stage, _______ is regenerated.
- Both stages generate ______ that are used to power the synthesis of _____ in __________.
two carbons, condensation, acetyl group, oxaloacetate
citrate, oxidative decarboxylation, CO 2
oxaloacetate
high-energy electrons, ATP in oxidative phosphorylation
In step 2 of the CAC, Aconitase is a _____ because it adds ____ to break the C-C double bond.
lyase, H2O
In step 4, _________ complex is structurally and mechanistically similar to the ________ complex.
E3 same in both:
regenerates _____ and _______
a-Ketoglutarate dehydrogenase, pyruvate dehydrogenase
FAD, lipoamide
Step 5. Succinyl CoA synthetase
Cleavage of the _____ of succinyl CoA powers the formation of ______.
* Example of a ______ because succinyl phosphate, a _________ compound, donates a phosphate to ADP.
thioester, ATP
substrate-level phosphorylation
high-phosphoryl-transfer-potential
Oxaloacetate Is Regenerated by the _______ of Succinate
Oxidation
The two carbons released as CO2 in the 1st round of the citric acid cycle did NOT come from ________.
acetyl-CoA
The Citric Acid Cycle Produces:
* ______ Electrons
* an ______ (sometimes ______)
* _______
High-Transfer-Potential
ATP, GTP
Carbon Dioxide
Even though _____ is not a reactant in the CAC, it has to be present for the cycle to keep going
oxygen
Positive effectors of CAC:
Negative effectors of CAC:
ADP and Pyruvate
ATP, acetyl CoA, succinyl CoA NADH
Biosynthetic roles of the CAC
Citrate –>
a-Ketoglutarate –>
Succinyl CoA –>
Oxaloacetate –>
Citrate –> Fatty acids, sterols
a-Ketoglutarate –> amino acids, purines
Succinyl CoA –> heme
Oxaloacetate –> Aspartate, glucose
Which steps of glycolysis are irreversible? What bearing does this observation have on the reactions in which gluconeogenesis differs from glycolysis?
These reactions are _______ in gluconeogenesis; the reactions of gluconeogenesis differ from those of glycolysis at these points and are catalyzed by ______ enzymes.
bypassed, different
What is the role of biotin in gluconeogenesis?
Biotin is the molecule to which _______ is attached to the process of being transferred to ______. The reaction produces ______, which then undergoes further reactions of gluconeogenesis.
carbon dioxide
pyruvate
oxaloacetate
Fructose-2,6-bisphosphate is an allosteric _____ of phosphofructokinase (a glycolytic enzyme) and an allosteric _______ of fructose-1,6-bisphosphatase (an enzyme in the pathway of gluconeogenesis).
activator
inhibitor
Hexokinase can add a phosphate group to any of several _______, whereas glucokinase is specific for _____. Glucokinase has a lower affinity for glucose than does hexokinase. Consequently, glucokinase tends to deal with an excess of glucose, particularly in the liver. Hexokinase is the usual enzyme for phosphorylating six-carbon sugars.
six-carbon sugars
glucose
How does pyruvate from glycolysis get to the pyruvate dehydrogenase complex?
There is a ______ on the inner mitochondrial matrix that allows pyruvate from the ______ to pass into the ______.
transporter
cytosol
mitochondria
_____ and _____ are the primary electron acceptors of the citric acid cycle.
NAD+, FAD
What is the advantage to the organization of the PDH complex?
Five enzymes are all in close proximity for efficient shuttling of the ______ between molecules and efficient control of the complex by _______.
acetyl unit
phosphorylation
What are the similarities and differences between the reactions catalyzed by pyruvate dehydrogenase and a-ketoglutarate dehydrogenase?
The reactions proceed by the _____ mechanism and use the same ______. The difference is the initial ______, which is pyruvate or a-ketoglutarate. During the course of the reaction, pyruvate dehydrogenase shuttles an _______ through the reaction while a-ketoglutarate dehydrogenase shuttles a _______.
same , cofactors
substrate
acetyl unit , succinyl unit
In substrate-level phosphorylation, the energy of ______ of some compound provides sufficient energy to allow the ______ phosphorylation of ______ to take place.
hydrolysis
endergonic
ADP to ATP
Which steps of aerobic metabolism of pyruvate through the citric acid cycle are control points?
The reactions are catalyzed by pyruvate dehydrogenase, citrate synthase, isocitrate dehydrogenase, and a-ketoglutarate dehydrogenase.
PDH is controlled allosterically. It is inhibited by ______. In addition, it is subject to control by _______. When PDH kinase phosphorylates PDH, it becomes _____. Removing the phosphate with the PDH phosphatase ______.
ATP, acetyl-CoA, and NADH
phosphorylation
inactive
reactivates
What are the two most common inhibitors of steps of the citric acid cycle and the reaction catalyzed by pyruvate dehydrogenase?
ATP and NADH are the two most common inhibitors.
How does an increase in the ADP/ATP ratio affect the activity of isocitrate dehydrogenase?
If the amount of ADP in a cell increases relative to the amount of ATP, the cell needs energy (ATP). This situation not only favors the reactions of the citric acid cycle, which release energy, activating isocitrate dehydrogenase, but also stimulates the formation of NADH and FADH2 for ATP production by electron transport and oxidative phosphorylation.
How does an increase in the NADH/NAD+ ratio affect the activity of pyruvate dehydrogenase?
If the amount of NADH in a cell increases relative to the amount of NAD+, the cell has completed a number of energy-releasing reactions. There is less need for the citric acid cycle to be active; as a result, the activity of pyruvate dehydrogenase is decreased.
The citric acid cycle is less active when a cell has a high ______ ratio and a high ______ ratio. Both ratios indicate a high “energy charge” in the cell, indicating less of a need for the energy-releasing reactions of the citric acid cycle.
ATP/ADP , NADH/NAD+
Thioesters are “high-energy” compounds that play a role in group-transfer reactions; consequently, their ∆G of hydrolysis is ______ to provide energy for the reaction.
large and negative
The citric acid cycle is the ______ metabolic pathway and indirect producer of _____. It receives fuels from the other pathways at many points and generates reduced ______ that go into the electron transport chain. It is also involved in ______, as many of its intermediates can be drawn off to synthesize other compounds.
central, energy
electron carriers
anabolism
In oxidative decarboxylation, the molecule that is oxidized loses a _____ group as _____.
Examples of oxidative decarboxylation include the conversion of pyruvate to acetyl-CoA, isocitrate to -aketoglutarate, and a-ketoglutarate to succinyl-CoA.
carboxyl, carbon dioxide
PDH Complex Subunits Cofactors
E1:
E2:
E3:
E1: TPP –> oxidation decarboxylation of Pyruvate
E2: Lipoamide –> transfer acetyl group to CoA
E3: FAD –> regenerates oxidized form of Lipoamide
What primarily drives the formation of citrate from oxaloacetate and acetyl-CoA?
Cleavage of a thioester bond
What are the regulatory enzymes in the citric acid cycle?
α-ketoglutarate dehydrogenase
Isocitrate dehydrogenase
What is a potent activator of phosphofructokinase in mammalian liver cells?
Fructose-2,6-bisphopsphate
describe why two steps are needed to convert pyruvate to phosphoenolpyruvate in gluconeogenesis, compared to the single step that converts the phosphoenolpyruvate in glycolysis?
The glycolytic conversion of phosphoenolpyruvate to pyruvate is highly exergonic and cannot be easily reversed.
Sequence of events for gluconeogenesis:
Pyruvate
Carboxylation of pyruvate
Phosphorylation of 3-phosphoglycerate
Hydrolysis of fructose-1,6-bisphoshate
Hydrolysis of glucose 6-phosphate
Glucose
Glycolysis:
_______ is the key regulatory enzyme
Stimulated in response to _____
Acts to _____ blood glucose levels
Phosphofructokinase-1
insulin
decrease
Gluconeogenesis:
_________ key regulatory enzyme
Stimulated in response to _____
Acts to _____ blood glucose levels
Fructose-1,6-bisphosphatase
glucagon
increase
Which of the following statements best describes the concept of reciprocal regulation?
When one pathway is active, the other pathway is inhibited
Positive effectors of the pyruvate dehydrogenase complex:
Pyruvate, ADP
What is ∆G for most regulatory reactions in metabolic pathways?
∆G < 0
Regulatory steps of gluconeogenesis & associated enzymes:
Step 1: Pyruvate –> Oxaloacetate (Pyruvate Carboxylase)
Step 2: Oxaloacetate –> Phosphoenolpyruvate (Phosphoenolpyruvate carboxykinase)
Step 9: Fructose 1,6-biphosphate –> Fructose-6-phosphate (F-1,6-BPase)
Step 11: Glucose-6-Phosphate –> Glucose (Glucose-6-phosphatase)
Positive effectors for gluconeogenesis:
Negative:
Citrate, acetyl CoA
AMP, F-2,6-BP, ADP
The structure of the pyruvate dehydrogenase complex is fascinating. The complex is composed of 3 different
enzymes (E1, E2 and E3) and _____ coenzymes, 2 of which function as co-substrates.
5
When your body is low on glucose, the body will release the hormone ______.
glucagon
Glucagon activates a signaling cascade that _______ the PFK2/FBPase-2 enzyme. This results in the kinase domain
being ______ and the phosphatase domain being ______, ultimately lowering the amount of ______ in the cell.
phosphorylates
inactive, active
F-2,6-BP
When body is low on glucose, ______ would slow down and ______ would speed up due to the decreased amount of ______.
Glycolysis
gluconeogenesis
F-2,6-BP
When your body has high glucose, insulin will be released. Insulin starts a signaling cascade that will ultimately result in
the _______ of the bifunctional enzyme. This will activate the kinase domain and deactivate the phosphatase
domain, increasing the amount of _______ in the cell. This will activate ______ and inhibit _______.
dephosphorylation
F-2,6-BP
glycolysis
gluconeogenesis
Step 1: Citrate Synthase forms a bond between ______ and ______ to form _____.
Step 2: Aconitase performs an _______ on citrate to form _____.
**Step 3: Isocitrate dehydrogenase performs an ________ on isocitrate to form _______.
+NADH
**Step 4: alpha-ketoglutarate dehydrogenase performs an ______ to form _______
+NADH
Step 5: succinyl-CoA synthetase cleaves a ______ bond to form ______
+GTP
Step 6: succinate dehydrogenase performs an _______ on succinate to form _____ (formation of C=C bond)
+FADH2
Step 7: Fumarase ______ fumarate to form malate
Step 8: Malate dehydrogenase _____ malate to form oxaloacetate (formation of C=O bond)
+NADH
oxaloacetate
acetyl-CoA
citrate
isomerization
isocitrate
oxidative decarboxylation
alpha-ketoglutarate
oxidative decarboxylation
succinyl-CoA
high-energy thioester
succinate
oxidation
fumarate
hydrates
oxidizes
Step 1: ______ forms a bond between oxaloacetate and acetyl-CoA to form citrate.
Step 2: ______ performs an isomerization on citrate to form isocitrate
**Step 3: _______ performs an oxidative decarboxylation on isocitrate to form alpha-ketoglutarate
+NADH
**Step 4: _________ performs an oxidative decarboxylation to form succinyl-CoA
+NADH
Step 5: _______ cleaves a high-energy thioester bond to form succinate
+GTP
Step 6: _______ performs an oxidation on succinate to form fumarate (formation of C=C bond)
+FADH2
Step 7: ______ hydrates fumarate to form malate
Step 8: ________ oxidizes malate to form oxaloacetate (formation of C=O bond)
+NADH
Citrate Synthase
Aconitase
Isocitrate dehydrogenase
alpha-ketoglutarate dehydrogenase
succinyl-CoA synthetase
succinate dehydrogenase
Fumarase
Malate dehydrogenase
FAD ___ Oxidize _______ to sulfhydryl form so it can begin another cycle.
CoA E2 This coenzyme is attached to the acyl group and is important because the thioester bond it will form carries a lot of free energy. Thus, acetyl- CoA can go on to enter the citric acid cycle.
E3, lipoamide
NAD+ _____ Oxidize _____ to return it to _____ so that it can perform its function in E3.
Additionally, forms ______ to be used in ETC.
E3
FADH2
FAD
NADH
TPP ____ Involved in the _______ reaction of pyruvate and will become the first carrier of the ______
E1
decarboxylation
acyl group
Lipoamide _____ AKA lipoic acid, functions as an ‘arm’ that swings into E1 site to accept the _____ from TPP. Swings back into E2 to then _____ the acyl
E2
acyl group
attach
CoA ____ This coenzyme is _____ to the acyl group and is important because the ______ bond it will form carries a lot of free energy. Thus, acetyl- CoA can go on to enter the citric acid cycle.
E2
attached
thioester
