USMLE Biochemistry

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What is the rate-limiting enzyme of glycolysis?
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phosphofructokinase-1 (PFK-1)
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What is the rate-limiting enzyme of gluconeogenesis?
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fructose-1,6-bisphosphatase
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What is the rate-limiting enzyme of the TCA cycle?
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isocitrate dehydrogenase
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What is the rate-limiting enzyme of glycogen synthesis?
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glycogen synthase
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What is the rate-limiting enzyme of glycogenolysis?
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glycogen phosphorylase
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What is the rate-limiting enzyme of the HMP shunt?
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glucose-6-phosphate dehydrogenase (G6PD)
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What is the rate-limiting enzyme of de novo pyrimidine synthesis?
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carbamoyl phosphate synthetase II (CPS II)
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What is the rate-limiting enzyme of de novo purine synthesis?
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glutamine-PRPP amidotransferase
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What is the rate-limiting enzyme of the urea cycle?
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carbamoyl phosphate synthetase I (CPS I)
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What is the rate-limiting enzyme of fatty acid synthesis?
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acetyl-CoA carboxylase
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What is the rate-limiting enzyme of fatty acid oxidation?
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carnitine acyltransferase I
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What is the rate-limiting enzyme of ketogenesis?
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HMG-CoA synthase
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What is the rate-limiting enzyme of cholesterol synthesis?
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HMG-CoA reductase
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How many ATP are formed in the aerobic metabolism of glucose?
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malate-aspartate shuttle (heart/liver): 32 ATP glycerol-3-phosphate shuttle (muscle): 30 ATP
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Compared to glucokinase, what are the Km and Vm of hexokinase?
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low Km (high potency), low Vmax
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What are the cofactors required by the pyruvate dehydrogenase complex?
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pyrophosphate (B1, thiamine, TPP) FAD (B2, riboflavin) NAD (B3, niacin) CoA (B5, pantothenate) Lipoic acid
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What reaction in the TCA cycle requires the same cofactors as the pyruvate dehydrogenase complex?
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alpha-ketoglutarate dehydrogenase, which converts alpha-ketoglutarate to succinyl-CoA
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Poisoning by what substance would result in vomiting, rice water stools, and garlic breath?
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arsenic
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What are the directly ketogenic amino acids?
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lysine and leucine
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What is deficient in a patient with increased pyruvate and alanine, lactic acidosis, and neurologic defects? How can this be treated?
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pyruvate dehydrogenase complex deficiency treat with increased intake of ketogenic nutrients (high fat content, increased lysine and leucine)
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What are the four possible outcomes of pyruvate metabolism? Which of these are made in the cytosol? Which are made in the mitochondria?
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Mitochondria: oxaloacetate, acetyl-CoA Cytosol: lactate, alanine
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Which complex in the electron transport chain is inhibited by amytal (barbiturates), rotenone, and MPP (from opiate synthesis)?
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Complex I
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Which complex in the electron transport chain is inhibited by antimycin A?
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Complex II
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Which complex in the electron transport chain is inhibited by cyanide, sodium azide, carbon monoxide, and hydrogen sulfate?
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Complex IV
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What is the mechanism of action of uncoupling agents? Name some.
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Uncoupling agents increase permeability of the inner mitochondrial membrane to H+ ions, causing a decreased H+ gradient and increased O2 consumption. ATP synthesis stops, but electron transport continues. This produces heat. Examples: 2,4-DNP, aspirin, thermogenin in brown fat (in hibernating animals)
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What are the irreversible enzymes of gluconeogensis? In what part of the cell is each?
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mitochondria: pyruvate carboxylase cytosol: PEP carboxykinase, fructose-1,6-bisphosphatase ER: glucose-6-phosphatase
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What type of fatty acid chains cannot undergo gluconeogenesis? Why?
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Even-chain fatty acids cannot produce new glucose since they yield only acetyl-CoA equivalents. Note: Odd-chain fatty acids yield 1 propionyl-CoA during metabolism, which can enter the TCA cycle as succinyl-CoA.
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What is the purpose of the HMP shunt (pentose phosphate pathway)?
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provides a source of NADPH
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What are the products of the HMP shunt?
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CO2 2 NADPH ribulose-5-phosphate
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What is deficient in a patient who develops a hemolytic anemia after treatment with primaquine or sulfonamides? What would be seen on a blood smear?
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glucose-6-phosphate dehydrogenase On smear: Heinz bodies in RBC, bite cells
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What enzyme is deficient in a patient with fructose in the blood and urine but no other symptoms? What is the name of this disease?
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Essential fructosuria: defect in fructokinase
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What is deficient in a patient with hypoglycemia, jaundice, cirrhosis, and vomiting after drinking a juice box? What is the name of this disease? How can this be treated?
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Fructose intolerance: aldolase B deficiency Patients should avoid intake of fructose and sucrose.
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What enzyme might be deficient in an infant with cataracts, failure to thrive, jaundice, hepatomegaly, and mental retardation? What is the name of this disease? How can it be treated?
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Classic galactosemia: absence of galactose-1-phosphate uridyltransferase Treatment: exclude galactose and lactose from diet
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What symptoms might be seen in an infant with galactokinase deficiency?
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infantile cataracts failure to track objects failure to display a social smile elevated galactose in blood and urine
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Lack of what enzyme in the lens leads to diabetic retinopathy? What substance is accumulating in these tissues? In what other tissues does this enzyme exist?
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Enzyme: sorbitol dehydrogenase Glucose is converted to sorbitol by aldose reductase; hyperglycemia leads to accumulation of sorbitol in tissues without sorbitol dehydrogenase, including Schwann cells, retina, and kidneys.
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What are the essential amino acids?
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proline, valine, tryptophan, threonine, isoleucine, methionine, histidine, leucine, lysine
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What are the acidic amino acids? What is their charge at physiologic pH?
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aspartate (aspartic acid) glutamate (glutamic acid) both are negatively charged at physiologic pH
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What are the basic amino acids? What is their charge at physiologic pH?
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arginine, lysine, histidine arginine and lysine are positively charged at physiologic pH; histidine is electrochemically neutral
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In what part of cell does the rate-limiting step of the urea cycle take place?
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mitochondria
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What amino acids serve as carriers of NH3 as part of the Cori cycle?
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glutamate alanine
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What would be expected in a patient with ornithine transcarbamoylase deficiency?
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hyperammonemia increased orotic acid in blood and urine decreased BUN hepatoencephalopathy: slurring of speech, somnolence, vomiting, asterixis, cerebral edema, blurring of vision
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What amino acid is used to create thyroxine?
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phenylalanine
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What amino acid is used to create melanin?
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phenylalanine
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What amino acid is used to create dopamine?
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phenylalanine
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What amino acid is used to create norepinephrine?
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phenylalanine
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What amino acid is used to create epinephrine?
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phenylalanine
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What amino acid is used to create NAD+/NADP+?
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tryptophan
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What amino acid is used to create seretonin?
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tryptophan
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What amino acid is used to create niacin (B3)?
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tryptophan
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What amino acid is used to create melatonin?
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tryptophan
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What amino acid is used to create histamine?
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histidine
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What amino acid is used to create heme?
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glycine
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What amino acid is used to create creatine?
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arginine
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What amino acid is used to create urea?
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arginine
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What amino acid is used to create nitric oxide?
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arginine
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What amino acid is used to create GABA?
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glutamate
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What amino acid is used to create glutathione?
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glutamate
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What amino acids are in nuclear localization signals?
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lysine, proline, arginine
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What amino acid is important in fighting viral infections, especially HSV?
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lysine
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What is deficient in a patient with mental retardation, growth retardation, seizures, fair skin, eczema, and a musty body odor?
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phenylalanine hydroxylase (or tetrahydrobiopterin cofactor)
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What amino acid is essential in a patient with phenylketonuria?
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tyrosine
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What is deficient in a patient with dark connective tissue, brown pigmented sclera,arthralgias, and a urine sample that turns black on prolonged exposure to air? What is the name of this disorder?
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Alkaptonuria (ochronosis): deficiency of homogentisic acid oxidase
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What are the possible etiologies for albinism?
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tyrosinase or defective tyrosine transporters can also result from a lack of migration of neural crest cells
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What are the possible etiologies for a patient with increased homocysteine in the urine, mental retardation, osteoporosis, tall stature, kyphosis, lens subluxation, and atherosclerosis? What amino acid becomes essential in these patients?
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cystathionine synthase deficiency decreased affinity of cystathionine synthase for pyridoxal phosphate homocysteine methyltransferase deficiency Cysteine becomes essential.
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What might be defective in a patient with recurrent renal staghorn caliculi? What amino acids are affected?
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defect of renal tubular amino acid transporter for cysteine, ornithine, lysine, and arginine
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What is deficient in a patient whose urine smells like maple syrup? What process cannot be completed?
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deficient alpha-ketoacid dehydroenase prevents the degradation of branched amino acids, such as isoleucine, leucine, and valine
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What is deficient in a patient who experiences painful muscle cramps and myglobinuria with strenuous exercise? What is the name of this disease?
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McArdle’s disease (type V): muscle glycogen phosphorylase deficiency
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What is deficient in an infant who dies shortly after birth with cardiomegaly? What is the name of this disease?
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Pompe disease (type II, infantile form): alpha-1,4-glucosidase deficiency
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What is deficient in a patient with normal blood lactate levels with hepatomegaly, hypoglycemia, and hyperlipidemia? What is the name of this disease?
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Cori’s disease (type III): debranching enzyme (alpha-1,6-glucosidase) deficiency
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What is deficient in a patient with diaphragm weakness, respiratory failure, and cardiomegaly? What is the name of this disease?
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Pompe disease (type II, adult form): alpha-1,4-glucosidase deficiency
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What is deficient in a patient with increased normal glycogen in the liver, elevated lactic acid in the blood, hepatomegaly, hyperuricemia, and enlarged kidneys? What is the name of this disease?
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von Gierke’s disease (type I): glucose-6-phosphatase deficiency
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In what part of the cell does the rate-limiting step of fatty acid synthesis synthesis occur?
answer

cytoplasm (acetyl CoA carboxylase)
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Where in the cell does beta-oxidation occur?
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mitochondrial matrix
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In alcoholism, oxaloacetate is shuttled to malate due to excess of what?
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NADH
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What is detected in the urine of a patient with ketoacidosis?
answer

acetoacetate
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Between meals, what is the major source of glucose?
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hepatic glycogenolysis
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What are the sources of ATP in the first three days of starvation?
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hepatic glycogenosis adipose release of free fatty acids
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What triacylglycerol components can contribute to gluconeogenesis?
answer

glycerol and propionyl-CoA
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In the first three days of starvation, what amino acids can be used in hepatic gluconeogenesis?
answer

lactate and alanine
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What is the main source of fuel in muscles and the liver in the first three days of starvation?
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free fatty acids
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What is the main source of energy in the brain and red blood cells after 3 days of starvation?
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ketone bodies
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What determines survival time in starvation?
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amount of adipose stores
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What is the suspected diagnosis in an 2-month-old infant who displays failure to thrive, steatorrhea, acanthocytosis, ataxia, and night blindness; intestinal biopsy shows lipid accumulation within enterocytes? What is the inherited mutation?
answer

abetalipoproteinemia: mutation in the microsomal triglyceride transfer protein (MTP) gene, leading to decreased production of B-48 and B-100
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What enzyme is deficient in an infant who presents with lethargy, vomiting, and hypotonia; labs reveal metabolic acidosis with large anion gap and elevated propionic acid, ketosis, and hypoglycemia?
answer

propionyl CoA carboxylase
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What amino acids and other substrates can be used to generate propionyl CoA?
answer

valine, isoleucine, methionine, threonine odd-numbered fatty acids cholesterol side chains
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In what part of the cell does fatty acid degradation take place?
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mitochondria
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In what part of the cell does fatty acid synthesis take place?
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cytosol
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In what part of the cell does glycolysis take place?
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cytosol
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In what part of the cell does the TCA cycle take place?
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mitochondria
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In what part of the cell does the electron transport chain take place?
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mitochondria
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In what part of the cell does gluconeogenesis take place?
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cytoplasm and mitochondria
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In what part of the cell does protein synthesis take place?
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cytoplasm
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In what part of the cell does the urea cycle take place?
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cytoplasm and mitochondria
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In what part of the cell does steroid synthesis take place?
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cytoplasm
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In what part of the cell does heme synthesis take place?
answer

mitochondria and cytoplasm
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What serves as the cofactor for amino acid transamination and in decarboxylation reactions?
answer

B6 (pyridoxal phosphate)
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From where are the nitrogen atoms in the urea molecule produced in the urea cycle derived?
answer

NH3, aspartate

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