Biochemistry First Aid- Metabolism Part 1 (98-106) Flashcards
name four major metabolic processes that take place in the mitochondria
fatty acid oxidation (beta oxidation), acetyl CoA production, the TCA cycle, and oxidative phosphorylation
what major metabolic processes occur in the cytoplasm (try to name 6)
glycolysis, HMP shunt, fatty acid synthesis, protein synthesis (RER), steroid synthesis (SER), cholesterol synthesis
name three metabolic processes that occur both in the mitochondria and in the cytoplasm
heme synthesis, urea cycle, gluconeogenesis
define the term kinase
an enzyme that uses ATP to phosphorylate a substrate
define the term phosphorylase
an enzyme that phosphorylates a substrate without using ATP
define the term dehydrogenase
an enzyme that catalyzes redox reactions
define the term hydroxylase
an enzyme that adds a hydroxyl group to a substrate
define the term carboxylase
an enzyme that transfers CO2 groups with the help of biotin
define the term mutase
an enzyme that relocates a functional group within a molecule
what is the rate limiting step of glycolysis and what enzyme catalyzes it?
conversion of F6P to fructose-1,6-bisphosphanate
catalyzed by phosphofructokinase-1 (PFK-1)
what molecules promote or inhibit phosphofructokinase-1 activity?
promote: AMP and fructose-2,6-bisphosphate
inhibit: ATP and citrate
what enzyme catalyzes the rate-limiting step of gluconeogenesis? what is the rxn?
fructose-1,6,-bisphosphatase, which converts fructose-1,6,-bisphosphate to F6P
what molecules positively and negatively regulate fructose-1,6,-bisphosphatase?
positive: ATP and acetyl-CoA
negative: AMP and fructose-2,6-bisphosphate
what is the rate limiting reaction and enzyme of the TCA cycle?
conversion of isocitrate to alpha-ketoglutarate catalyzed by isocitrate dehydrogenase
what molecules positively and negatively regulate isocitrate dehydrogenase?
positive: ADP
negative: ATP and NADH
what is the rate limiting reaction and enzyme of glycogenesis?
addition of UDP-glucose to glycogen catalyzed by glycogen synthase
what are the negative and positive regulators of glycogen synthase
positive: G6P, insulin, cortisol
negative: epinephrine, glucagon
what is the rate limiting reaction and enzyme of glycogenolysis?
release of glucose-1-phosphate from glycogen catalyzed by glycogen phosphorylase
what are the positive and negative regulators of glycogen phosphorylase?
positive: epinephrine, glucagon, AMP
negative: G6P, insulin, ATP
what is the rate limiting reaction and enzyme of the HMP shunt?
conversion of G6P to 6-phosphogluconolactone catalyzed by G6PD
what molecules are the positive and negative regulators of G6PD?
positive: NADP+
negative: NADPH
what is the rate limiting reaction and enzyme for de novo pyrimidine synthesis
glutamine + CO2 conversion to carbamoyl phosphate catalyzed by carbamoyl phosphate synthetase II
what is the rate limiting enzyme for de novo purine synthesis
PRPP amidotransferase
what are the negative regulators of PRPP amidotransferase
AMP, inosine monophosphate (IMP), GMP
what enzyme catalyzes the rate limiting step of the urea cycle
carbamoyl phosphate synthetase I
what molecule upregulates the urea cycle
N-acetylcysteine
what enzyme catalyzes the rate limiting step in the fatty acid synthesis pathway
Acetyl-CoA carboxylase (ACC)
what molecules positively and negatively regulate fatty acid synthesis?
positive: insulin, citrate
negative: glucagon, palmitoyl-CoA
what enzyme catalyzes the rate limiting step of fatty acid oxidation
acetyl-CoA acyltransferase I
what molecule negatively regulates fatty acid oxidation?
malonyl-CoA
what enzyme catalyzes the rate limiting step in ketogenesis
HMG-CoA synthase
what enzyme catalyzes the rate limiting step in cholesterol synthesis
HMG-CoA reductase
what molecules upregulate and downregulate cholesterol synthesis
upregulate: insulin and thyroxine
downregulate: glucagon and cholesterol
how many net ATP molecules does aerobic metabolism produce in the heart and liver?
in the muscle?
in heart and liver via malate-aspartate shuttle: 32
in muscle via glycerol-3-phosphate shuttle: 30
how does arsenic affect energy production?
arsenic causes glycolysis to produce zero net ATP (also uncouples oxidative phosphorylation)
how many ATP molecules are produced by anaerobic glycolysis
2 net ATP per glucose
what are CoA and lipoamide carriers of
acyl groups
what general rxn does biotin carry out
carboxylation
what do tetrahydrofolates carry
1-carbon groups
what does S-adenosyl methionine (SAM) carry
methyl groups
what does thiamine pyrophosphate (TPP) carry
aldehydes
NADP+ is generally used in _________ processes while NADPH is used in _________ processes
NADP+ is generally used in catabolic processes (to accept reducing equivalents) while NADPH is used in anabolic processes to supply reducing equivalents
what major processes use NADPH
anabolic processes, respiratory burst, cytochrome P450, glutathione reductase
differentiate hexokinase from glucokinase in terms of location, affinity, Vmax and insulin induction
hexokinase: in most tissues, but not liver nor beta cells of pancreas, lower affinity for glucose, lower Vmax, not induced by insulin
glucokinase: in liver and beta cells, higher affinity for glucose, higher Vmax, induced by insulin
is hexokinase or glucokinase feedback inhibited by G6P
hexokinase
is hexokinase or glucokinase gene mutation associated with the maturity-onset diabetes of the young
glucokinase
list the reactants and products of the glycolysis net reaction
Glucose + 2Pi + 2ADP+ NAD –>
2 pyruvate + 2ATP + NADH + 2H+ + 2H2O
which steps of glycolysis require ATP
glucose—> G6P (catalyzed by hexo/glucokinase)
F6P—> F-1,6-BP (catalyzed by PFK-1)
which steps of glycolysis makes ATP
1,3-BPG —> 3-phosphoglycerate (catalyzed by phosphoglycerate kinase)
PEP —> pyruvate (catalyzed by pyruvate kinase)
list the the molecules in the steps of glycolysis
glucose—> G6P —> F6P —> F-1,6-BP —> Glyceraldehyde-3P and DHAP (DHAP gets converted to Glyceraldehyde-3P) —>
1,3-bisphosphoglycerate —> 3-phosphoglycerate —> 2-phosphoglycerate —> phosphoenolpyruvate (PEP) —> pyruvate
what’s the relationship between FBPase-2 and phosphofructokinase-2
FBPase-2 and phosphofructokinase-2 are parts of the same bifunctional enzyme. Which activity the enzyme performs depends on phosphorylation by protein kinase A.
how is F2,6-BP regulate glucose in the fasting state
increased glucagon –> increased cAMP –> increased PKA –> increased FBPase-2 –> decreased PFK-2, leading to less glycolysis and more gluconeogenesis
what two metabolic pathways does pyruvate dehydrogenase complex link
glycolysis and TCA cycle
what are the reactants and products in the reaction catalyzed by pyruvate dehydrogenase complex
pyruvate + NAD + CoA —> AcetylCoA +NADH + CO2
what are the 5 cofactors that are needed for the pyruvate dehydrogenase complex to function
- pyrophosphate (TPP from thiamine aka B1)2. FAD (from riboflavin aka B2)3. NAD (from niacin aka B3)4. CoA (from panthenate)5. Lipoic acid
what stimulus upregulates activity of the pyruvate dehydrogenase complex and via what molecular changes
exercise causes increased NAD/NADH ratio, increased ADP, and increased calcium (stimulators of pyruvate dehydrogenase complex activity)
the pyruvate dehydrogenase complex is similar to what other enzyme
alpha-ketoglutarate dehydrogenase (they have the same cofactors, similar substrate and similar mechanism of action)
what inhibits lipoic acid
arsenic
what are the symptoms of arsenic poisoning
vomiting, rice-water stools, garlic breath
what molecules build up as a result of pyruvate dehydrogenase complex deficiency
pyruvate buildup leads to shunting to lactate (via LDH) and alanine (via ALT)
what is the clinical presentation of pyruvate dehydrogenase complex deficiency
neurologic defects, lactic acidosis, increased serum alanine starting in infancy
how is pyruvate dehydrogenase complex deficiency treated
increased intake of ketogenic nutrients (i.e. high fat content or increased lysine and leucine, which are the only purely ketogenic amino acids)
explain the four different ways that pyruvate can be metabolized
- into alanine catalyzed by alanine amintransferase (cofactor=B6)2. into oxaloacetate catalyzed by pyruvate carboxylase (cofactor=biotin)3. into acetyl-CoA catalyzed by pyruvate dehydrogenase (cofactors=B1,B2,B3,B5,lipoic acid)4. into lactic acid catalyzed by lactate dehydrogenase (cofactor=B3)
what is generated as a result of the TCA cycle (per acetyl-CoA molecule)how many ATP molecules does this eventually translate into
3 NADH, 1 FADH2, 2 CO2, 1 GTP (per acetyl CoA molecule)==> 10 ATP (per acetyl CoA molecule)
list the enzymes in the TCA cycle from right after entry of Acetyl-CoA until completion of a cycle
acetyl-CoA–> citrate–> isocitrate –> alpha-ketoglutarate –> succinyl-CoA –> succinate –> fumarate –> malate –> oxaloacetate
name three enzymes in the TCA cycle that catalyze irreversible reactions
isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase, citrate synthase
how do NADH electrons from glycolysis enter the mitochondria
via the malate-aspartate shuttle or via the glycerol-3-phosphate shuttle
to what complex in the inner mitochondrial membrane are NADH electrons transferred?what about FADH2?
NADH at complex 1FADH2 at complex 2
explain how the electron chain and oxidative phosphorylation drive ATP production (briefly summarize the pathway)
electrons from NADH and FADH2 are transferred to complexes 1 and 2 in the inner mitochondrial membrane leading to a build up of protons in the intermembrane space; protons rush into the mitochondrial matrix via complex 5 and this movement of H+ down its gradient is coupled to phosphorylation of ADP to make ATP
ATP produces how many ATP per NADH?how many per FADH2?
2.5 ATP per NADH1.5 ATP per FADH2
name four inhibitors of electron transport chain;how do they work?
rotenone, cyanide, antimycin A and CO directly inhibit electron transport leading to low proton gradient and low ATP synthesis
what electron transport complex does rotenone inhibit and therefore what electron carrier is directly affected
complex 1; transfer of electrons from NADH is blocked
what electron transport complex is blocked by antimycin A
Complex 3
what molecules inhibit complex 4 of electron transport chain
cyanide and CO
what molecule directly inhibits mitchondrial ATP synthase;what happens to the proton gradient across the inner mitochondrial membrane as a result
oligomycin;H+ gradient increases (causing electron transport to stop)
what are some uncoupling agents and how do they work
2,4-dinitrophenol, aspirin, thermogenin in brown fat;they increase the permeability of the inner mitochondrial membrane leading to lower proton gradient and higher O2 consumption –> ATP synthesis stops, but electron transport continues (produces heat instead)
what is 2,4-dinitrophenol used for
used illicitly for weight loss
name the irreversible enzymes of gluconeogenesis
(“pathway produces fresh glucose”) pyruvate carboxylase, phosphoenolpyruvate carboxykinase, fructose-1,6-bisphosphatase, glucose-6-phosphatase
what reaction does pyruvate carboxylase catalyze, where does it occur, and what is needed for the reaction to happen (cofactors and activators)
pyruvate –>oxaloacetate;occurs in mitochondria;requires biotin and ATP, activated by acetyl-CoA
what reaction does PEP carboxykinase catalyze;where does it occur;what is required
oxaloacetate –> PEP;takes place in the cytosol;GTP is required
what reaction is catalyzed by F-1,6-bisphosphatase; where does it occur;what upregulates and downregulates this reaction
F-1,6-BP–> F-6-P;occurs in the cytosol;upregulated by citrate, downregulated by F-2,6-BP
what reaction does G-6-phosphatase catalyze;where does it occur
G-6-P;occurs in the ER
where does gluconeogenesis predominantly occur and why
in the liver; to maintain euglycemia in states of fasting
besides the liver where else are enzymes of gluconeogensis found
kidney and intestinal epithelium
why can’t the muscle do gluconeogenesis
it lacks G-6-phosphatase
how can odd chain fatty acids get converted to glucose
odd chain fatty acids yield 1 proprionyl-CoA during metabolism which enters the TCA cycle as succinyl-CoA –> oxaloacetate and undergoes gluconeogenesis
why can’t even-chain fatty acids yield new glucose
even-chain fatty acids get metabolized to acetyl-CoA, which cannot enter the pathway for gluconeogenesis
what is the purpose of the HMP (hexose monophosphate) shunt
to use G-6-P to generate NADPH (used as a reducing agent i.e. for glutathione, fatty acid synthesis and cholesterol synthesis)
what are the end products of the HMP shunt
NADPH, ribose (can be used for DNA synthesis or glycolytic intermediates)
where does the HMP shunt take place (what cellular location)
in the cytoplasm
how much ATP does the HMP shunt use?how much ATP does the HMP shunt produce?
trick question!: none and none!
in what tissues of the body use the HMP shunt
lactating mammary glands, liver, adrenal cortex, RBC’s
what are the two phases of the HMP shunt and which phase is reversible
two phases: oxidative and nonoxidativethe nonoxidative phase is reversible
what are the reactants and products of the oxidative branch of the HMP shunt
G-6-P —–> CO2 + 2NADPH + ribulose-5-P
what enzyme catalyzes the rate limiting step of the oxidative branch of the HMP shunt
G-6-P dehydrogenase
what are the reactants and products of the nonoxidative branch of the HMP shunt
ribulose-5-P ——> ribose-5-P + G3P and F6P
explain the respiratory burst (steps)
within the phagolysosome of (neutrophils and monocytes) NADPH reduces oxygen; superoxide dismutase then converts radical oxygen to hydrogen peroxide; which gets combined with chloride to generate HOCl radical (hyperchlorite aka bleach) or gets shunted over to the HMP shunt to regenerate more NADPH
what is the purpose of respiratory burst
rapid release of ROS for immune response
what defect causes chronic granulomatous disease
NADPH oxidase deficiency
why are patients with chronic granulomatous disease at increased risk for infection by catalse positive species (i.e. S. aureus and aspergillus)
patients with CGD can use the hydrogen peroxide produced by pathogens (since they can’t generate their own), but when pathogens invade that can neutralize their own H2O2 (using catalase) there is no H2O2 for the patient’s immune system to utilize against infection
what molecule allows P. aeruginosa to kill competing microbes
pyocyanin
when lactoferrin is secreted how does it inhibit microbial growth
iron chelation
explain why NADPH is important
generates glutathione used by RBCs and other cells to detoxify free radicals
what are the two main categories of triggers for NADPH deficiency patients
drugs (i.e. sulfa drugs, primaquine, antimycobacterials, fava beans)infection (immune response triggers free radical release)
what is the inheritance of GDPD deficiency
X-linked
what benefit does G6PD deficiency confer
increased malaria resistance
what is seen on histology for G6PD deficiency
Heinz bodies (oxidized hemoglobin)Bite cells (partially consumed cells that escaped splenic macrophage destruction)
what defect causes essential fructosuria
defect in fructokinase
what is the inheritance of essential fructosuria
autosomal recessive
what are the symptoms of essential fructosuria like
essential fructosuria is a benign condition; generally asymptomaticalthough, fructose appears in the blood and urine
are defects in fructose or galactose metabolism more injurious
galactose metabolism(fructose metabolism defects are fairly benign)
what defect causes fructose intolerance
hereditary deficiency of aldolase B
what is the inheritance pattern of fructose intolerance
autosomal recessive
what causes the injurious effects seen in fructose intolerance
F-1-P accumulates leading to a decrease in available phosphate, leading to decreases in glycogenolysis and gluconeogenesis
when do symptoms of fructose intolerance present
after eating fruit, honey, juice (anything with fructose)
what will the urine dipstick show in a patient with fructose intolerance
negative result; it only tests for glucose
what can you detect in the urine of a patient with fructose intolerance
reducing sugars (test for inborn errors of carbohydrate metabolism)
what are the symptoms of fructose intolerance
hypoglycemia, jaundice, cirrhosis, vomitting
what is the treatment for fructose intolerance
decrease intake of fructose and sucrose (glucose + fructose)
