Usmle Biochem

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RLE of Glycolysis

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Phosphofructokinase-1 (PFK1)

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RLE of gluconeogenesis

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Fructose 1,6 Bisphosphatase

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RLE of TCA cycle

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Isocitrate dehydrogenase

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RLE of glycogen synthesis

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Glycogen synthase

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RLE of HMP shunt

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Glucose-6-phosphate dehydrogenase (G6PD)

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RLE of Glycogenolysis

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Glycogen phosphorylase

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RLE of de novo pyrimidine synthesis

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Carbamoyl Phosphate synthetase II

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RLE of de novo purine synthesis

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Glutamine PRPP amidotransferase

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RLE of Urea cycle

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Carbamoyl Phosphate synthetase I

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RLE for Fatty acid synthesis

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Acetyl CoA carboxylase

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RLE for Fatty acid oxidation

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Carnitine acyltransferase I

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RLE for ketogenesis

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HMG CoA synthase

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RLE for Cholesterol synthesis

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HMG CoA reductase

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Defective enzymes in Orotic aciduria

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orotic acid phosphoribosyltransferase or orotidine 5' phosphate decarboxylase

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amino acids necessary for purine synthesis

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Glycine, Apartate and glutamine (and non aa- THF and CO2)

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source of carbon for purine synthesis

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CO2, glycine, and THF

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Carbamoyl Phosphate + aspartate=

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Orotic acid

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4 Substances needed for pyrimidine synthesis

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CO2, Glutamine, aspartate, THF

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Glutamine + CO2 + ATP + CPS II =

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carbamoyl phosphate

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UMP-->UDP (in pyrimidine synthesis) is catalyzed by

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Ribonucleotide reductase

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dUMP-->dTMP is catalyzed by

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Thymidylate synthase (requires THF)

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DHF-->THF is catalyzed by

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Dihydrofolate reductase

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Drug that inhibits Ribonucleotide reductase

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Hydroxyurea (used in sickle cell and cancer)

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Drug that blocks de novo purine synthesis by inhbiting 5 PRPP synthetase

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6- mercaptopurine (6MP)

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Drug that inhibits thymidylate synthase (decrease dTMP)

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5- Fluorouracic (5FU)

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Drug that inhibits eukaryotic dihydrofolate reductase (decrease dTMP)

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Methotrexate (MTX)

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Drug that inhibits prokaryotic dihydrofolate reductase (decrease dTMP)

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Trimethoprim

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Dx where you cant convert ortotic acid to UMP

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Orotic aciduria (Tx- oral uridine)

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Enzyme deficiency in SCID

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Adenosine deaminase (-->excess ATP and dATP--imbalance in nuecleotide pool--> feed back inhibition or ribonucleotide reductase -->prevents DNA synthesis -->decrease lymphocyte count --> SCID)

SCID= recurrent infections, chronic diarrhea, FTT, abscence of thymic shadow on chest x-ray

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Enzyme deficiency in Lesch - Nyhan syndrome

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HGPRT (-->defect of purine salvage), HGPRT normally converts hypoxanthine --> IMP and guanine -->GMP --> excess uric acid production and de novo purine synthesis
-findings= retardation, agression, self mutilation (classically lip biting), hyperuricemia-->gout, Choreoathetosis
Tx- allopurinol (no tx for neurologic problems)

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Drug that inhibits DNA gyrase (prokaryotic topoII)

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Fluoroquinolones

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DNA repair mechanism mutated in ataxia telangiectasia

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Non homologous end joining repair of double strands

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where is rRNA synthesized?

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Nucleolus (rRNA is most Rampant)

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where mRNA and tRNA are synthesized

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Nucleoplasm (mRNA= massive, tRNA= tiny)

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alpha-amantin-

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found in death cap mushrooms, inhibits RNA pol II (cant make mRNA) --> liver failure

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Disease that makes antibodies to splicesomal snRNPs

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Lupus (Splicosomes splice out introns)

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Enzyme that converts lactose--> glucose and galactose

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Beta galactosidase (lac operon)

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Enzyme that charges the tRNA

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aminoacyl- tRNA synthestase
-works by scrutinizing the aa after it binds to tRNA, if incorrect it hydrolyzes the bond - responsible for the accuracy of amino acid selections

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Drug that binds the 30S subunit and prevents the attachment of aminoacyl-tRNA

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Tetracyclines

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activates the initiation protein synthesis on a ribosome

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GTP hydrolysis

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Drug that binds the 30S and inhibits the formation of the initiation complex -> misreading of mRNA

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Aminoglycosides

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Drug that inhibits 50S peptidyltransferase

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Chloramphenicol

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Movement of vesicular trafficking protein COPI

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retrograde movement, from gogli--ER

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Movement of vesicular trafficking protein COPII

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Anterograde - RER-->cis golgi

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Disease with coarse facial features, clouded corneas, restricted joint movt and high plasma levels of lysosomal enzymes (often fatal in childhood)

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I- cell disease- failure to add mannose 6 phosphate to lysosome ptn--> enzymes are secreted out of the cell (default) rather than to lysosomes

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3 amino acids modified by the golgi

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threonine, serine and asparagine

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Dx affecting microtubules --> recurrent pyogenic infections, partial albinism, peripheral nephropathy

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Chediak Higashi syndrome - microtubule polymerization defect--> decreased fusion of phagosomes and lysosomes

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Dx with immotile cilia due to dynein arm defect

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Kartageners syndrome--> infertility, bronchiectasis, recurrent sinusitis, situs inversus

Dyenein= motor ptn with ATPase that converts energy in ATP--> movement of microtubules relative to one another --> bend cillia back and forth

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4 types of insoluble cytoplasmic inclusions

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glycogen, lipid droplets, pigmented granules, pathologic inclusions

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Histological stain for IF of sarcomas and carcinomas

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Vimentin (Connective tissue)

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Histological stain for IF of myosarcoma

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Desmin (Muscle)

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Histological stain for IF of carcinomas

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Cytokeratin (epithelial cells)

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Histological stain for IF of astrocytoma

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GFAP (NeuroGlia)

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Histological stain for IF of neuroblastoma

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Neurofilaments (Neurons)

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Drug that inhibits binding of K+ site on sodium pump

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Ouabain

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Drug that directly inhibits the Na-K ATPase --> indirect inhibition of Na/Ca exchange--> increase heart contractility

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Cardiac glycosides

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Collagen = GLY-X-Y. x and y can be =

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X= proline, hydroxyproline, Y= hydroxylysine
(with Gly= glycine)

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6 steps of collagen synthesis

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1. synthesis- (RER) translation of alpha chains--> preprocollagen
2. Hydroxylation- (ER) of proline and lysine residues (req vit c)
3. Glycosylation (ER)- of pro alpha chaine hydroxylines --> procollagen via H and disulfide bonds --> triple helix of 3 alpha chains
4. Exocytosis- sent to extracell space
5. proteolytic proessing --> cleavage of terminal regions--> tropocollagen
6. Cross linking- reinforcement by covalent lysine-hydroxylysine cross link--> collagen fibrils

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amino acids in elastin

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proline and glycine (non glycosylated forms)

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Function of S= adenosyl methionine

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ATP+ methionine= SAM
methyl donor
-required for converson of NE--> EPI and regeneration of methionine

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Rash around eyes, mouth, nose anus

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Acrodermatitis enteropathica (zinc deficiency)

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Converts Ethanol--> Acetelaldehyde

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Alcohol dehydrogenase (fomepizole inhibits- used for methanol and ethylene glycol poinsoning)
-in the cytosol

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converts Acetaldehyde-->acetate

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Acetaldehyde dehydrogenase
-inhibited by disulfiram (for alchies to not want to drink)
-in the mitochondria

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The limiting reagent of alcohol metabolism

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NAD+

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Kinase

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uses ATP to add high energy phosphate group to a substrate

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Phosphorylase

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adds inorganic phosphate onto substrate w/o using ATP

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Phosphatase

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removes phosphate group from the substrate

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Dehydrogenase

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oxidizes substrate

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Carboxylase

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Transfers CO2 group w/ help of biotin

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Fructose + Glucose=

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sucrose

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Galactose + glucose=

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lactose

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Glucose + glucose =

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maltose

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Glycolysis shuttle that makes 32 ATP

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Malate aspartate shuttle in the heart and liver

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Glycolysis shuttle that makes 30 ATP

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glycerol 3 phosphate shuttle

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Hexokinase

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everywhere
-high affinity (low Km) low capacity (low VMAx)
uninduced by insulin
-FB by G6P--> ensures its active at normal glucose levels

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Glucokinase

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liver and beta cells of pancreas
-low affinity (high Km), high capacity (high Vmax)
-induced by insulin
-no direct feedback inhibtion
-phosphorylates excess glucose

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5 cofactors needed for the pyruvate dehydrogenase complex

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Thiamine (B1), Lipoic acid, Coa (B5), FAD (B2), and NAD (B3)

TLC For No one
-same cofactors as alpha ketoglutarate dehydrogenase complex

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substance that inhibits lipoic acid --> vomiting, rice water stools and garlic breath

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arsenic

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Pyruvate dehydrogenase deficiency

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--> back up of substrate (pyruvate and alanine)--> lactic acidosis
-congenital or aquired (alchies due to B1 deficiency)

Tx- increase intake of ketogenic nutrients (high fat or lysine/leucine)

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2 purely ketogenic amino acids

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lysine and leucine

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3 irreversible enzymes of the TCA cycle

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citrate synthase, isocitrate dehydrogenase, and alpha ketoglutarate dehydrogenase

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Pyruvate --> acetyl- COA via

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pyruvate dehydrogenase

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3 uncoupling agents

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2,4 DNP, aspirin, thermogenin (in brown fat)

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Electron transport inhibitors

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rotenone, CN-, antimycin A, CO

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ATP synthase inhibitor

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Oligomycin

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Pyruvate carboxylase

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in mitochondria, pyruvate--> oxaloacetate
-requires biotin and ATP, activated by acetyl COA
-irreversible enzyme of gluconeo

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PEP carboxylase

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in cytosol, converts oxaloacetate-->phosphoenolpyruvate
-irreversible enzyme of gluconeo

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Fructose 1,6 bisP

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in cytosol
F16BP---> Fructose BP

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Glucose 6 phosphatase

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In ER
Glucose 6P-->glucose

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Why muscle can't participate in gluconeogenesis

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b/c it lacks glucose 6 phosphatase

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Reasons your body needs NADPH

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1. make fatty acids and cholesterol
2. generate free oxygen radicals in phagocytes --> kill bacteria
3. cytochrome P450

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Defect in fructokinase

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essential fructosuria
-benign, w/ fructose in blood
-can break down Fructose --> F-1-P
-AR

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Deficiency of aldolase B

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Fructose intolerance
-accumulation of F1P-->decrease in available phosphate-->inhibit glyocgenolysis and gluconeogenesis --> cant correct hypoglycemia
--> hypoglycemia, jaundice, cirrhosis, vomiting
Tx- decrease intake of fructose and sucrose
-AR

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deficiency of galactokinase

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galactokinase deficiency --> galactitol accumulates if galactose present in diet
-mild, AR
-galactose in blood and urine, infantile cataracts
-may present as failure to track objects or develop a social smile

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Absence of galactose-1-phosphate uridyltransferase

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classic galactosemia
-AR, damage caused by accumulation of toxic substances (galactitol-->lens of the eye)
Sx- FTT, jaundice, hepatomegaly, infantile cataracts, mental retardation
-hyperchloremic, metabolic acidosis and aminoaciduria
tx- exclude galactose, lactose from diet

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Aldose reductase

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converts glucose --> sorbitol
(tissues that lack sorbitol dehydrogenase --> osmotic damage (like in type II diabetes))

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sorbitol --> fructose

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sorbitol dehydrogenase

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Essential amino acids

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Glucogenic- met, val, arg, his
Gluconeogenic/ketogenic- Ile, Phe, Thr, Trp
Ketogenic- leu, lys

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Acidic aa

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Asp and Glu (negatively charged at body pH)

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Basic aa

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Arg, Lys, His
(arg = most basic)- + charge
His has no charge

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amino acids in the nuclear localization signal

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lysine, arginine, and proline

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amino acids required during periods of growth

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arg and his

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amino acid helpful in viral infection

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lysine

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substance that in excess depletes alpha ketoglutarate-->inhibition of the TCA cycle

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Hyperammonemia
Tx- Phenylbutyrate
lactulose- acidifies the GI and traps NH4 for secretion

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symptoms of ammonia intoxication

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tremor, slurring of speech, somnolence, vomiting, cerebral edema, blurring of vision, lethargy, seizures

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Most common urea cycle disorder

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Ornithine Transcarbamylase
-XR
-Interferes with body's ability to eliminate ammonia --> excessive carbamoyl phosphate--> orotic acid --> orotic acid in the blood and urine, low BUN, symp of hyperammonemia

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Phenylalanine-->Tyrosine

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Phenylalanine hydroxlase

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Tryosine-->Dopa

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Tryosine hydroxylase

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DOpa-->Dopamine

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Dopa decarboxylase

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Products of tryptophan

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--> Niacin (via B6)
-->Serotonin (via BH4) -->Melatonin (in pineal gland)

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Glycine + B6-->

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Porphyrin --> Heme

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Rate limiting step for heme synthesis

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aminolevulenate synthase

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Biproducts of arginine

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creatine, urea and NO

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Biproducts of Glutamate

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GABA (via B6) and glutathione

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Dopa -->Dopamine

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via Vit B6 and dopa decarboxylase

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dopamine-->NE

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Dopamine beta hydroxylase (w/ Vit C)

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NE-->Epi

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phenyethanolamine N methyl transferase (PNMT) via SAM

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Deficiency of phenylalanine hydroxylase (or decrease in tetrahydrobiopterin cofactor)

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PKU

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Dx with mental and growth retardation, seizures, fair skin, eczema, musty body odor

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PKU
-tyrosine becomes essential

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3 phenylketones

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phenylacetate, phenylactate and phenylpyruvate

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deficiency in homogenistic acid oxidase

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Alkaptonuria
normally degrades tyrosine --> fumarate
-AR, benign dx
-dark Connective tissue, brown pigmented sclera, urine-->black prolonged to air

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tyrosinase deficiency or defective tyrosinase transporter

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albinism
-cant make melanin from tyrosine or decreased amounts of tyrosine-->less melanin
-may result from lack of migration of neural crest cells

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most common inborn error of methionine metabolism

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Homocystinuria
-due to def in cystathione synthase (MC), decrease affinity of cytathione synthase for pyridoxal phosphate or deficiency of homocysteine methyltransferase
--> excess homocysteine

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elevated homocysteine in urine, mental retardation, osteoporosis, tall stature, kyphosis, lens subluxation (down and inward), atherosclerosis (stroke and MI), hypercoag

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Homocystinuria
tx- inc. b6 in the diet

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Hereditary defect of renal tubular aa transporter for cysteine, ornithine, lysine and arginine in PCT of the kidneys

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cystinuria
-excess cysteine in kidneys can --> kidney stones
-AR
Tx- acetazolamide to alkalinize the urine

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Dx b/c of the blocked degregation of branched chain aa, due to decreased alpha ketoacid dehydrogenase

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maple syrup urine dx --> cns defects, mental retardation, and death b/c of buildup of alpha ketoacids in the blood (esp Leu)

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Ile, Leu, Val

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branched chain aa

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Dermatitis, diarrhea, dementia

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Pellagra (deficiency in vitamin B3)

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AR defect in neutral aa transporter on renal and intestinal epithelial cells --> tryptophan excretion in urine and decrease absorption from gut

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Hartnup dx
(leads to pellagra)
(when you dnt have trypthophan in body, you cant make niacin)

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deficiency in methylmalonate mutase

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methylmalonic aciduria or acidemia

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Makes alpha 1,4 bonds during glycogen production

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Glycogen synthase

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makes alpha 1,6 linkages during glycogen production

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branching enzymes

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breaks down alpha 1,4 lingages in glycogenolysis

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glycogen phosphorylase

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breaks alpha 1,6, bonds in glycogenolysis

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debranching enzyme III aka alpha 1,6 glucosidase

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Deficiency in glucose 6 phosphatase

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Von Gierke's dx (type I)

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Deficiency in Lysosomal alpha 1,4, glucosidase (acid maltase)

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Pompe's disease (type II)

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deficiency in debranching enzyme 1,6 glucosidase

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Cori's disease (type III)

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Deficiency in skeletal muscle glycogen phosphorylase

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McArdle's disease (type V)

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Severe fasting hypoglycemia, large amounts of glycogen stuck in the liver, increased blood lactate-->metabolic acidosis, hepatomegaly

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Von Gierke's dx

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glycogen storage dx + cardiomegaly

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Pompe's dx

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glycogen storage dx, w/ normal blood lactate levels
(milder form of type I)
-in tact glucogenogenesis, impaired glycogenolysis

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Cori's dx

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increased glycogen in muscle --> cramps and myoglobinuria w/ exercise

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McArdles dx

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Ketone not detected in urine

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beta hydroxybutyrate

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esterifies 2/3 of plasma cholesterol

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LCAT- lecithin- cholesterol acyltransferase

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Apo ptn E

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mediates remnant uptake
(all molecules)

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apo A-I

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activates L-cat
- chylomicrons and HDL

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Apo CII

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cofactor for lipoptn lipase -
Chylomicron, LDL, HDL

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APo B48-

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mediate chylomicron secretion
-Chylomicron remnant

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Apo B100

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binds LDL receptor
-VLDL, IDL, LDL

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hyperchylomicronemia

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elevated TG and cholesterol
-lipoptn lipase deficiency of altered apoliptn CII --> pancreatitis, hepatosplenomegaly, and eruptive/ pruritic xanthomas (no increased risk for atherosclerosis)

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familial hypercholesteremia

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elevated LDL --> elevated cholesterol
-AD, due to decreased LDL receptors, causes accelerated atherosclerosis, tendon (achilles), xanthomas, corneal arcus

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hypertrigylceridemia

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increased VLDL, elevated TG
-hepatic overprod--> pancreatitis

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Abetalipoproteinemia

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hereditary inability to synthesize lipoproteins- due to def in apo b100 and apob48
-AR
-accumulation in enterocytes (b/c cant absorb lipid as chylomicron)
-->FTT, steatorrhea, acanthocytosis, ataxia, night blidness
tx- vit E