Term
|
Definition
| Pyruvate dehydrogenase component |
|
|
Term
| How many chains does E1 have? |
|
Definition
|
|
Term
| What is the prosthetic group on E1? |
|
Definition
| TPP (thiamine pyrophosphate) |
|
|
Term
| What reaction does E1 catalyze? |
|
Definition
| Oxidative decarboxylation of pyruvate |
|
|
Term
|
Definition
| Dihydrolipoyl transacetylase |
|
|
Term
| How many chains does E2 have? |
|
Definition
|
|
Term
| What is the prosthetic group on E2? |
|
Definition
|
|
Term
| What reaction does E2 catalyze? |
|
Definition
| Transfer of acetyl group to CoA |
|
|
Term
|
Definition
| Dihydrolipoyl dehydrogenase |
|
|
Term
| How many chains does E3 have? |
|
Definition
|
|
Term
| What is the prosthetic group on E3? |
|
Definition
|
|
Term
| What reaction does E3 catalyze? |
|
Definition
| Regeneration of the oxidized form of lipoamide |
|
|
Term
| List the steps of the conversion from pyruvate to acetyl CoA. |
|
Definition
| Decarboxylation -> Oxidation -> Transfer to CoA |
|
|
Term
| Describe pyruvate dehydrogenase and its transacetylase (E2) core. |
|
Definition
The core is transacetylase (E2), made up of 8 trimers (alpha3).
Just outside the core is pyruvate dehydrogenase (E1), made up of 6 tetramers (alpha2beta2).
On the outside is dihydrolipoyl dehydrogenase (E3), made up of 6 dimers (alphabeta).
There is a lipoamide domain, a domain interacting with the E3 component, and finally the transacetylase domain in each E2 subunit. |
|
|
Term
|
Definition
|
|
Term
| What does TPP do during the decarboxylation by E1 step of acetyl CoA formation? |
|
Definition
| The positively charged ring acts as an electron sink, stabilizing the carbanion. |
|
|
Term
| In the formation of acetyl CoA from pyruvate, during the oxidation and transfer to lipoamide by E1, what energy-rich bond is formed? |
|
Definition
|
|
Term
| In the formation of acetyl CoA through oxidation and transfer to lipoamide by E1, what is the oxidant? |
|
Definition
|
|
Term
In the oxidation of dihydrolipoamide by E3, __ electrons are transferred to the ___ of E3.
Next, FADH2 is oxidized by ____. |
|
Definition
|
|
Term
| Beriberi was originally identified as resulting from a dietary deficiency of ____ (vitamin ___). |
|
Definition
|
|
Term
| What enzymes does beriberi affect? |
|
Definition
TPP requiring enzymes: pyruvate dehydrogenase, alpha-ketoglutarate dehydrogenase (TCA cycle), and transketolase (PPP)
-transfer active aldehyde group |
|
|
Term
| What symptoms does beriberi cause? |
|
Definition
| Neurologic and cardiac: PNS damage presents as pain in limbs, muscle weakness, and enlarged heart with insufficient cardiac output |
|
|
Term
| What type of poisoning is similar to beriberi? |
|
Definition
| Mercury or Arsenite poisoning |
|
|
Term
| Mercury and arsenite can cause poisoning because they both _____. They are treated with _____. |
|
Definition
have high affinity for neighboring sulfhydryls
sulfhydryl reagents |
|
|
Term
| The type of reaction that takes oxaloacetate + acetyl CoA and makes a citryl CoA intermediate is ______ |
|
Definition
|
|
Term
| The type of reaction that takes a citryl CoA intermediate and makes citrate is _____ |
|
Definition
|
|
Term
| ________ forms citrate from oxaloacetate and acetyl CoA. |
|
Definition
|
|
Term
|
Definition
| enzyme catalyzing a synthetic reaction in which two units are joined without the direct participation of ATP |
|
|
Term
| What drives the reactions in the synthesis of citrate from oxaloacetate and acetyl CoA? |
|
Definition
| hydrolysis of the high energy thioester bond |
|
|
Term
| Substrate binding to citrate synthase induces _____ |
|
Definition
| a large conformational change |
|
|
Term
| What substrates (and in what order) bind to citrate synthase? |
|
Definition
| Oxaloacetate followed by acetyl CoA |
|
|
Term
| Why does oxaloacetate bind to citrate synthase first? |
|
Definition
| Its binding induces a conformational change that creates an acetyl CoA binding pocket. |
|
|
Term
| What happens after the citryl CoA intermediate is formed? |
|
Definition
| Additional conformational changes in citrate synthase seal off the active site and bring residues that catalyze hydrolysis of the ester into position (induced fit). |
|
|
Term
| What 3 important residues are involved in the citrate synthase mechanism? |
|
Definition
|
|
Term
| In the citrate synthase mechanism, how is the enol intermediate formed? |
|
Definition
| His274 donates a proton to the carbonyl oxygen while Asp375 removes a proton. |
|
|
Term
| How is oxaloacetate activated in the citrate synthase mechanism? |
|
Definition
| proton transfer to its carbonyl oxygen |
|
|
Term
| Citrate synthase mechanism: Acetyl CoA ___ attacks ______ to form a new carbon-carbon bond while ______ proton pulled off by ____ in a concerted fashion. |
|
Definition
enol
carbonyl carbon
hydroxyl
His |
|
|
Term
| His acts as a ____ donor to hydrolyze the citryl CoA ______ |
|
Definition
|
|
Term
| In the isomerization of citrate by aconitase, what type of reaction takes citrate into cis-Aconitate? |
|
Definition
|
|
Term
| In the isomerization of citrate by aconitase, what type of reaction takes cis-aconitate into isocitrate? |
|
Definition
|
|
Term
| The isomerization of citrate by aconitase is an ______ reaction (delta Go' = ?). |
|
Definition
|
|
Term
| What drives the isomerization of citrate by aconitase? |
|
Definition
| other exergonic reactions in the cycle |
|
|
Term
| Aconitase contains a _____ cluster. |
|
Definition
|
|
Term
| What enzyme comes in cytoplasmic and mitochondrial isoforms? |
|
Definition
|
|
Term
| Name two common features between the cytoplasmic and mitochondrial aconitase isoforms. |
|
Definition
-Both enzymatically active; catalyze conversion of citrate to isocitrate
-Both have metastable 4FE-4S clusters than can lose an Fe (3Fe-4S) under low Fe conditions and become inactive |
|
|
Term
| What is IREBP-1 and what enzyme is it associated with? |
|
Definition
Iron response element binding protein 1
Cytoplasmic aconitase |
|
|
Term
| What happens to cytoplasmic aconitase under low iron conditions? |
|
Definition
IREBP-1 binds iron to iron responsive elements (IREs) within mRNAs whose expression is regulated by iron (ie: Fe transport proteins).
IRE binding stabilizes mRNA resulting in increased translation.
Increased levels of iron transporters increase the uptake of Fe. |
|
|
Term
| What does mitochondrial aconitase do? |
|
Definition
-Associated with protein-mTDNA complexes called nucleiods
-Serves to stabilize mtDNA
-Couples energy metabolism and mitochondrial gene expression |
|
|
Term
| _____ is a suicide inhibitor of aconitase. |
|
Definition
|
|
Term
| What plant has fluoroacetate? |
|
Definition
|
|
Term
| What are the symptoms of fluoroacetate poisoning? |
|
Definition
Nausea, vomiting, abdominal pain
Sweating, confusion, agitation
Cardiac related conditions
Neurological effects
Sublethal dose damages tissues with high energy needs--brain, gonads, heart, lungs, fetus |
|
|
Term
| Treatments/antidotes for fluoroacetate? |
|
Definition
|
|
Term
| Why is fluoroacetate so toxic? |
|
Definition
| It poisons aconitase and all subsequent TCA intermediates |
|
|
Term
| What enzyme takes fluoroacetate and makes fluoroacetyl-CoA (which eventually becomes fluorocitrate)? |
|
Definition
|
|
Term
| The oxidative decarboxylation of isocitrate is sufficiently ______ (delta G*'=?) |
|
Definition
| exergonic (favorable), -8.4 kJ/mol |
|
|
Term
| When is the first NADH produced in the TCA cycle? |
|
Definition
| during the oxidative decarboxylation of isocitrate by isocitrate dehydrogenase |
|
|
Term
| Which step is important in determining the overall rate in the TCA cycle? |
|
Definition
| the oxidative decarboxylation of isocitrate by isocitrate dehydrogenase |
|
|
Term
| What complex is structurally homologous to the pyruvate dehydrogenase complex? |
|
Definition
| alpha-ketoglutarate dehydrogenase complex |
|
|
Term
| When is the second NADH formed in the TCA cycle? |
|
Definition
| during the oxidative decarboxylation of alpha-ketoglutarate by alpha-ketoglutarate dehydrogenase complex |
|
|
Term
| Formation of ___ from an activated phosphate group covalently linked to an active ___ in succinyl CoA synthetase |
|
Definition
|
|
Term
| GDP requiring enzyme (mammals) |
|
Definition
| Succinyl CoA synthetase in tissues where anabolic reactions predominate (eg: liver) |
|
|
Term
| Which enzyme is believed to operate in a reverse direction to generate succinyl CoA? |
|
Definition
| Succinyl CoA synthetase, GDP requiring in mammals |
|
|
Term
| Succinyl CoA is a precursor for... |
|
Definition
|
|
Term
| ADP requiring enzyme (mammals, plants, bacteria) |
|
Definition
| Succinyl CoA synthetase found in tissues with high rates of cellular respiration (skeletal and heart muscle) |
|
|
Term
| What type of mechanism is the proposed mech for succinyl coA synthetase? |
|
Definition
| Ordered Ter-Ter mechanism |
|
|
Term
| Succinyl CoA synthetase contains common protein motifs such as a(n) ____ in the alpha subunit and a(n) _____ in the beta subunit |
|
Definition
|
|
Term
| When is the first FADH2 formed in the TCA cycle? |
|
Definition
| During the conversion of succinate to fumarate by succinate dehydrogenase |
|
|
Term
| When is the third NADH formed in the TCA cycle? |
|
Definition
| During the conversion of malate to oxaloacetate by malate dehydrogenase |
|
|
Term
| FAD is usually the ____ in oxidations removing two hydrogen atoms |
|
Definition
|
|
Term
| Succinate dehydrogenase is a(n) _____ |
|
Definition
| iron sulfur protein (2Fe-2S, 3Fe-4S, 4Fe-4S) |
|
|
Term
| Succinate dehydrogenase is located where? |
|
Definition
| Embedded in the inner mitochondrial membrane |
|
|
Term
| What enzyme from the TCA cycle is directly associated with the electron-transport chain? |
|
Definition
|
|
Term
| Describe the behavior of FADH2 related to succinate dehydrogenase. |
|
Definition
| FADH2 does not dissociate from the enzyme; electrons transferred to its iron-sulfur clusters then to coenzyme Q. |
|
|
Term
| Fumarase only forms _-_____ because... |
|
Definition
L-malate
OH- always adds to the same side of the double bond |
|
|
Term
| What enzyme catalyzes the conversion from succinate to fumarase? |
|
Definition
|
|
Term
| What enzyme catalyzes the conversion from fumarate to malate? |
|
Definition
|
|
Term
| What enzyme catalyzes the conversion from malate to oxaloacetate? |
|
Definition
|
|
Term
| Complete equation for conversion of oxaloacetate to citrate |
|
Definition
Acetyl CoA + oxaloacetate + H2O -> citrate + CoA + H+
Citrate synthase |
|
|
Term
| Complete equation for conversion of citrate to cis-aconitate |
|
Definition
Citrate <-> cis-aconitate + H2O
Aconitase |
|
|
Term
| Complete equation for conversion of cis-aconitate to isocitrate |
|
Definition
cis-Aconitate + H2O <-> isocitrate
Aconitase |
|
|
Term
| Complete equation for conversion of isocitrate to alpha-ketoglutarate |
|
Definition
Isocitrate + NAD+ <-> alpha-ketoglutarate + CO2 + NADH
Isocitrate dehydrogenase |
|
|
Term
| Complete equation for conversion of alpha-ketoglutarate to succinyl CoA |
|
Definition
a-ketoglutarate + NAD+ + CoA <-> succinyl CoA + CO2 + NADH
alpha-ketoglutarate dehydrogenase complex |
|
|
Term
| Complete equation for conversion of succinyl CoA to succinate |
|
Definition
Succinyl CoA + Pi + ADP <-> succinate + ATP + CoA
Succinyl CoA synthetase |
|
|
Term
| Complete equation for conversion of succinate to fumarate |
|
Definition
Succinate + FAD (enzyme bound) <-> fumarate + FADH2 (enzyme bound)
Succinate dehydrogenase |
|
|
Term
| Complete equation for conversion of fumarate to malate |
|
Definition
Fumarate + H2O <-> L-malate
Fumarase |
|
|
Term
| Complete equation for conversion of malate to oxaloacetate |
|
Definition
L-malate + NAD+ <-> oxaloacetate + NADH + H+
Malate dehydrogenase |
|
|
Term
| Delta G*' for acetyl CoA -> citrate |
|
Definition
| -31.4 kJ/mol (most favorable) |
|
|
Term
| Delta G*' for citrate <-> cis-aconitate |
|
Definition
|
|
Term
| Delta G*' for cis-aconitate <-> isocitrate |
|
Definition
|
|
Term
| Delta G*' for isocitrate <-> a-ketoglutarate |
|
Definition
|
|
Term
| Delta G*' for a-ketoglutarate <-> succinyl CoA |
|
Definition
|
|
Term
| Delta G*' for succinyl CoA <-> succinate |
|
Definition
|
|
Term
| Delta G*' for succinate <-> fumarate |
|
Definition
|
|
Term
| Delta G*' for fumarate <-> malate |
|
Definition
|
|
Term
| Delta G*' for malate <-> oxaloacetate |
|
Definition
| +29.7 kJ/mol (least favorable) |
|
|
Term
| Prosthetic group of aconitase? |
|
Definition
|
|
Term
| Prosthetic group of a-ketoglutarate dehydrogenase complex? |
|
Definition
|
|
Term
| Prosthetic group of succinate dehydrogenase? |
|
Definition
|
|
Term
| Reaction type for oxaloacetate -> citrate? |
|
Definition
|
|
Term
| Reaction type for citrate <-> cis-aconitate? |
|
Definition
|
|
Term
| Reaction type for cis-aconitate <-> isocitrate? |
|
Definition
|
|
Term
| Reaction type for isocitrate <-> a-ketoglutarate? |
|
Definition
| decarboxylation + oxidation |
|
|
Term
| Reaction type for a-ketoglutarate <-> succinyl CoA? |
|
Definition
| decarboxylation + oxidation |
|
|
Term
| Reaction type for succinyl CoA <-> succinate? |
|
Definition
| substrate-level phosphorylation |
|
|
Term
| Reaction type for succinate <-> fumarate? |
|
Definition
|
|
Term
| Reaction type for fumarate <-> malate? |
|
Definition
|
|
Term
| Reaction type for malate <-> oxaloacetate? |
|
Definition
|
|
Term
| The pyruvate dehydrogenase reaction is a major point of regulation because... |
|
Definition
| animals cannot convert acetyl CoA back into glucose; must either enter TCA cycle or be incorporated into lipid |
|
|
Term
| Key means of pyruvate dehydrogenase complex regulation in eukaryotes is ______ |
|
Definition
|
|
Term
| ______ inactivates the pyruvate dehydrogenase complex. |
|
Definition
| Phosphorylation of E1 by pyruvate dehydrogenase kinase I (PDK); kinase associates with E2 |
|
|
Term
| ____ reverses deactivation of the pyruvate dehydrogenase complex. |
|
Definition
| Pyruvate dehydrogenase phosphatase (PDP) |
|
|
Term
| Inactivation of pyruvate dehydrogenase? |
|
Definition
NADH (E3), Acetyl CoA (E2), and ATP inhibit
Promote phosphorylation |
|
|
Term
| Activation of pyruvate dehydrogenase? |
|
Definition
ADP and pyruvate activate by inhibiting kinase
Phosphatase is stimulated by Ca2+ |
|
|
Term
| Hormonal regulation of pyruvate dehydrogenase? |
|
Definition
Epinephrine in liver activates a-andrenergic receptor (increasing Ca2+), stimulating phosphatase.
Insulin stimulates phosphatase increasing formation of acetyl CoA (in liver and adipose tissue), which is the precursor for fatty acid synthesis |
|
|
Term
| Without phosphatase activity, pyruvate dehydrogenase is.... |
|
Definition
| phosphorylated and INACTIVE, causing shift to lactate |
|
|
Term
| Isocitrate dehydrogenase is stimulated by? |
|
Definition
| ADP; increases affinity for substrates |
|
|
Term
| Isocitrate dehydrogenase is inhibited _____ by? |
|
Definition
|
|
Term
| Isocitrate dehydrogenase is inhbited by ____ (displaces ____) |
|
Definition
|
|
Term
| Inhibition of isocitrate dehydrogenase leads to buildup of ____, which is transported to the cytoplasm. |
|
Definition
| citrate; inhibits PFK; source of acetyl CoA for GA metabolism |
|
|
Term
| a-ketoglutarate dehydrogenase is inhibited by... |
|
Definition
Succinyl CoA and NADH (rxn products)
ATP (high energy charge) |
|
|
Term
| Buildup of a-ketoglutarate is used as... |
|
Definition
| a precursor for some amino acids and purine bases |
|
|
Term
| Oxaloacetate can leave the TCA cycle and become... |
|
Definition
glucose
Aspartate -> other AAs, purines, pyrimidines |
|
|
Term
| Citrate can leave the TCA cycle and make... |
|
Definition
|
|
Term
| a-ketoglutarate can leave the TCA cycle and make... |
|
Definition
| glutamate -> other AAs -> purines |
|
|
Term
| Succinyl CoA can leave the TCA cycle and make... |
|
Definition
| porphyrins, heme, chlorophyll |
|
|
Term
| Oxaloacetate is replenished by... |
|
Definition
| carboxylation of pyruvate (gluconeogenesis) |
|
|
Term
| The TCA cycle is the ____ for the oxidation of fuel molecules. It also serves as a source of ______ |
|
Definition
final common pathway
building blocks for biosyntheses |
|
|
Term
| Most fuel molecules enter the TCA cycle as... |
|
Definition
|
|
Term
| The link between glycolysis and the TCA cycle is... |
|
Definition
| the oxidative decarboxylation of pyruvate to form acetyl CoA |
|
|
Term
| Where does the TCA cycle take place in eukaryotes? |
|
Definition
|
|
Term
| The TCA cycle operates only under ___ conditions because.. |
|
Definition
aerobic
it requires a supply of NAD+ and FAD. |
|
|
Term
| The irreversible formation of ____ from ____ is an important regulatory point for the entry of glucose-derived pyruvate into the TCA cycle. |
|
Definition
|
|
Term
| The activity of the pyruvate dehydrogenase complex is stringently controlled by... |
|
Definition
| reversible phosphorylation |
|
|
Term
| The electron acceptors are regenerated when.. |
|
Definition
| NADH and FADH2 transfer their electrons to O2 through the electron transport chain, with the concomitant production of ATP |
|
|
Term
| The rate of the TCA cycle depends on... |
|
Definition
|
|
Term
| In eukaryotes, the regulation of ____ and ____ also is important for control. |
|
Definition
| Isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase |
|
|
Term
| A ____ charge diminishes the activities of isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase. These mechanisms complement each other in reducing the rate of formation of ____ when the energy charge of the cell is ___ and when biosynthetic intermediates are ____. |
|
Definition
high energy
acetyl CoA
high
abundant |
|
|
Term
| When the cell has abundant energy, the TCA cycle can also provide building blocks for... |
|
Definition
| nucleotides, proteins, and heme groups |
|
|
Term
| When the TCA cycle needs to metabolize fuel, how are the intermediates replenished? |
|
Definition
|
|
Term
| The ____ cycle enhances the metabolic versatility of many plants and bacteria, allowing them to grow on acetate. |
|
Definition
|
|
