Bioenergetics Flashcards
What are some characteristics of the TCA cycle?
A biochemical hub of the intermediary metabolism
Oxidizing carbon fuels for harvesting high energy e-
It is amphibolic and a source of precursors of biosynthesis
Takes place inside mitochondria
Acetyl CoA is the activated form of what?
Acetate
What are the three energy nutrients that acetyl CoA is obtained from?
Carbs, lipids and proteins
How is acetyl CoA obtained from carbs?
Glucose –> oxidation –> 2 pyruvate –> 2 acetyl CoA
How is acetyl CoA obtained from lipids?
TAG –> FAs –> acetyl CoA (beta oxidation)
Oxidation of KBs –> acetyl CoA
How is acetyl CoA obtained from proteins?
Breakdown into various amino acids –> acetyl CoA
Which form of PDC is active and what enzyme activates it?
Dephosphorylated form which is catalyzed by pyruvate dehydrogenase phosphatase (PDP)
Which form of PDC is inactive and which enzyme inactivates it?
Phosphorylated form which is catalyzed by pyruvate dehydrogenase kinase (PDK)
What three enzymes made up the pyruvate dehydrogenase complex (PDC)?
E1 (pyruvate decarboxylase), E2 (dihydrolipoyl transacetylase) and E3 (dihydrolipoyl dehydrogenase) which are all derived from vitamin B derivatives
What are the 5 coenzymes needed by PDC?
Thiamine pyrophosphate (TPP), lipoic acid, FAD, CoA and NAD+
Which 3 conenzymes of PDC act as prosthetic groups and are permanently bound to PDC?
TPP, lipoic acid and FAD
Which 2 coenzymes of PDC act as co-substrates and associate with PDC temporarily?
CoA and NAD+
Which vitamin is TPP derived from?
B1 (thiamine)
Which vitamin is CoA derived from?
B5 (pantothenic acid) (PENTothenic acid)
Which vitamin is lipoic acid derived from?
None
Which vitamin is FAD derived from?
Vitamin B2 (riboflavin)
Which vitamin is NAD+ derived from?
Vitamin B3 (niacin)
List factors that activate PDC activity
Its substrates and low energy signals (elevated [NAD] and [ADP])
High insulin concentrations in adipose
Ca2+ and Mg2+ via allosteric activation
ADP, CoA, NAD and pyruvate via inhibition of PDK
List factors that inhibit PDC activity
Its end products and high energy signals (elevated NADH and ATP)
Fasting conditions where acetyl CoA and NADH are high due to oxidation of FAs via activation of PDK
Arsenite by binding to lipoic acid in E2
What reaction is catalyzed by PDC?
Pyruvate + NAD + CoA –> Acetyl CoA + CO2 + NADH + H+
What occurs in a phosphatase deficiency?
PDC is always in its phosphorylated inactive form
Glucose made into lactate instead of acetyl CoA resulting in lactic acidosis (high lactatic acid in the blood)
CNS is mostly affected
Alanine intake should be restricted due to pyruvate accumulation and a ketogenic diet may be recommended
Describe how PDC is affected in the tissues
Ca released during muscle contraction activates PDC
Cardiac muscle Ca may inhibit PDK thus activating PDC
PDP is a Mg dependent enzyme and in adipose tissue insulin may activate the enzyme by lowering the Km for Mg
Describe pyruvate dehydrogenase deficiency (neonatal lactic acidosis)
May be due to PDC defects specifically in E1 (TPP)
Males more affected bc gene for E1 is on the X chromo
Pts will have high serum pyruvate and lactate
Tx: vitamin B1 (replaces deficient E1 subunit), lipoic acid (stimulates activity of PDC), or biotin (metabolizes pyruvate by the alternate enzyme pyruvate carboxylase)
Dicholoracetate (inhibits PDK) or ketogenic diet may also be suggested
How does arsenite (derived from aresenic) affect lipoic acid?
Arsenite irreversibly binds to two SH groups on lipoic acid subunit (E2) and limits its availability
This affects PDC, alpha-KG dehydrogenase and branched chain keto acid dehydrogenase which rely on lipoic acid
What is Beriberi?
Vitamin B1 (thiamine) deficiency (no TPP)
sx: weight loss, SOB, mental confusion, speech difficulties, pain, etc
tx: thiamine supplements along with water soluble vitamins
Leads to increased levels of pyruvate and alpha KG in the blood due to impaired action of PDC and alpha KG dehydrogenase which need TPP
Wet vs Dry Beriberi
Dry form involves peripheral neuropathy
Wet form affects cardiovascular function
Wenicke-Korsakoff syndrome
Form of vitamin B1 deficiency/Beriberi in alcoholics
Describe steps 1 and 2 of the TCA cycle
Condensation of Acetyl CoA and OAA to form citrate catalyzed by citrate synthase
Citrate then isomerized to isocitrate by aconitase
What regulates citrate synthase?
Activators: insulin, acetyl CoA, and OAA
Inhibitors: ATP, citrate, NADH and sucicnyl CoA
What is aconitase inhibited by?
Fluorocitrate (metabolic product of rat poison)
Describe steps 3 and 4 of the TCA cycle
Isocitrate oxidized and decarboxylated into alpha KG by isocitrate dehydrogenase (RLE)
Another oxidation and decarboxylation rxn catalyzed by alpha KG dehydrogenase converting alpha KG into succinyl CoA
What activates isocitrate dehydrogenase?
ADP (allosteric) and Ca2+
What inhibits isocitrate dehydrogenase?
ATP and NADH
What is the RLE of the TCA cycle?
isocitrate dehydrogenase
Describe step 5 of the TCA cycle
High energy thioester bond of succinyl CoA is cleaved to form succinate which is coupled to the substrate phosphorylation of GDP into GTP
Catalyzed by succinate thiokinase (succinyl CoA synthetase)
Describe steps 5-8 of the TCA cycle
Succinate oxidized into fumarate with the production of FADH2 catalyzed by succinate dehydrogenase
Fumarate converted to malate by fumarase
Malate converted to OAA by malate dehydrogenase with the production of NADH
Which enzyme is the only one in the TCA cycle that is located in the inner mito membrane?
Succinate dehydrogenase (complex II in ETC) and only one that generates FADH2
What competitively inhibits succinate dehydrogenase?
Malonate
What is malate dehydrogenase inhibited by?
NADH
Which three enzymes of the TCA cycle are highly regulated?
Citrate synthase, isocitrate dehydrogenase (RLE) and alpha ketoglutarate dehydrogenase
Which steps of the TCA cycle form NADH?
Isocitrate to alpha KG by the RLE
Alpha KG to succinyl CoA by alpha KG dehydrogenase
Malate to OAA by malate dehydrogenase
(first two also make CO2)
Which step of the TCA cycle makes FADH2?
Succinate to fumarate by succinate dehydrogenase
How many FADH2 and NADH are made in one turn of the TCA cycle?
3 NADH
1 FADH2
Which step of the TCA cycle forms GTP by substrate level phosphorylation?
Succinyl CoA to succinate by succinate thiokinase
also forms CoA
What differential effects does citrate have on RLE?
Capable of inhibiting PFK-1 (RLE of glycolysis) and ACC (RLE of FA synthesis)
Promotes storage of excess energy as fat and prevents further production of ATP which maintains the energy charge of the cell in the desired range
When cellular ATP is low the TCA cycle is
increased/stimulated
How does the rat poison, fluoroacetate, inhibit the TCA cycle?
Fluoroacetate reacts with CoA to form fluoroacetyl CoA instead of acetyl CoA and condenses to with OAA to form fluorocitrate
Fluorocitrate inhibits aconitase causing citrate to accumulate therefore inhibiting citrate synthase
Also allosterically inhibits PFK-1
What role does succinyl CoA play in heme synthesis?
Is condensed with aa glycine to form delta-ALA which is the first step in heme synthesis
Catalyzed by ALA synthase (RLE) which also requires pyridoxal phosphate as a cofactor (vitamin B6)
What are anaplerotic reactions and that are the two major types?
Reactions that replenish TCA cycle intermediates
Degradation of aa and carboxylation of pyruvate are the two major types
Describe how degradation of aa can replenish TCA cycle intermediates
Replenishes OAA, alpha KG, succinyl CoA and fumarate
Occurs via transamination runs, deaminations, and oxidation of aromatic rings
Describe how the carboxylation of pyruvate can replenish TCA cycle intermediates
Replenishes OAA
ATP consuming rxn catalyzed by pyruvate carboxylase (requires biotin) and is stimulated by acetyl CoA
Occurs under glucose deprived conditions resulting in the OAA being used for gluconeogenesis
Which aa can form OAA?
Asparagine –> Aspartate –> OAA
Which aa can form alpha KG?
Glutamine, proline, histidine, arginine
Which amino acids can be used to form propionyl CoA which can then form succinyl CoA?
Threonine, methionine, isoleucine and valine
What amino acids can form fumarate?
Phe, tyrosine and aspartate
What anabolic functions do intermediates of the TCA cycle serve?
Several intermediates serve as precursors for anabolic pathways that synthesize biomolecules such as glucose, lipids and amino acids
What are the three biomolecules that can be formed by TCA cycle intermediates and how?
OAA contributes to synthesis of glucose
Citrate contributes to synthesis of lipids
OAA and alpha KG contribute to aa synthesis
What is pyruvate carboxylase deficiency?
Mutations in the pyruvate carboxylase gene that alter the activity of this enzyme leading to this deficiency
Causes more pyruvate to be converted to lactic acid instead of OAA which accumulates in the blood
sx: appear shortly after birth and include seizures, muscle weakness (hypotonia) and uncontrolled muscle movements (ataxia)
More prevalent among Algonkian Indian tribes in eastern Canada
autosomal recessive
Describe 2-oxoglutaric acid aciduria
Sx: chronic metabolic acidosis, severe microcephaly, mental retardation, variable urinary excretion of 2-oxoglutarate and fulmaric acid, hypoketonic hypoglycemia
Lethal w/in first 10 years of life
What are the similarities between 2-oxoglutaric acid aciduria and fumarase deficiency?
Both are rare disorders w/ global developmental delay and serve neurologic problems in infants
sx in common: hypotonia, spasticity, developmental delay and extrapyramidal sx
Diagnosis established by clinical features, metabolic findings and biochemical enzyme activity w/ molecular testing
No curative tx
Describe fumarase deficiency
Characterized by severe neurological impairment
Fatal outcome w/in first 2 years of life
sx: encephalomyopathy, dystonia, increased urinary exertion of fumarate, succinate, alpha KG and citrate
Autosomal recessive
Mutation in fumarase gene contains Q319E
Describe succinyl CoA synthetase (SCS) deficiency
Associated with mutations in 2/3 subunits for the enzyme in the SUCLA2 and SUCLG1 genes
Recognizable pattern of dystonia, deafness syndrome, mild methylmalonic aciduria, altered mtDNA maintenance
Diagnosis made w/ direct genetic testing
Recently discovered
What are oncometabolites?
Key components of the communication b/w mitochondria and nucleus
Accumulation results in the cell eliciting oncogenic signaling cascades leading to cancer
Studies have found several mutations in TCA cycle enzymes in human tumors which demonstrates a connection b/w TCA and cancer occurrence
What is mitochondrial depletion syndrome associated with?
Profound hypotonia, progressive dystonia, muscular atrophy and several sensory neural hearing impairment
What are free radicals?
Generated during the respiratory burst in response to invading microbes
Oxygen is converted by NADPH oxidase to superoxide which is then able to be further converted to the bacteria killing agents H2O2 and hypercloride (bleach)
What is an example of signaling molecule that is used to kill invading microbes?
NO is capable of acting as a signaling molecule which uses cGMP as its 2nd messenger
What is an example of a cellular response to invading microbes?
In X linked G6PD deficiency erythrocytes are susceptible to rupture by oxidative stress caused by oxidant drugs or fava beans containing oxidizing agents
What are the four major antioxidants?
Superoxide dismutase, Catalase, glutathione peroxidase, vitamin E and C
Where is the Cu/Zn form of SOD found (SOD1)?
Cytosol
Where is the Mn/Zn form of SOD found (SOD2)?
Mitochondria
