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USMLE > Biochem Factoids > Flashcards

Biochem Factoids Flashcards

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USMLE® Step 1 flashcards
1
Q

Type I collagen

A

Strong; skin, bone, dentin

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2
Q

Type II

A

Slippery: cartilage, vitreous, nucleus pulposus

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3
Q

Type III

A

Bloody; blood vessels, skin, uterus, fetal tissue, granulation tissue

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4
Q

Type IV

A

Basement membrane

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5
Q

What type of protein processing occurs in RER

A

N-linked oligosaccharide addition

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6
Q

Nuclear localization signal

A

4-8 Aas of lysine, arginine, and protein (essential for proteins bound for nucleus such as histones)

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7
Q

Golgi protein modification

A

Modifies the N-oligosaccharides on Asparagine

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8
Q

Golgi protein addition

A

O-oligosaccharides are added to Serine and Threonine

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9
Q

Golgi targeting to lysosome

A

Mannose-6-phosphate, defect results in I-cell disease; clouded cornas, coarse facial features, restricted joints, high plasma lysosomal levels.

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10
Q

G1 to S phase

A

Cyclin D binds and activates CDK4 which phosphorylates Rb to release it from E2F –> synthesis of S components. Cell officially enters S phase when CDK2 is activated by Cyclin E

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11
Q

G2 to M phase

A

Mediated by Cyclin A and Cyclin B

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12
Q

Chediak-Higashi syndrome

A

Problem with microtubule assembly; Parital albinism, peripheral neuropathy, recurrent pyogenic infection

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13
Q

Kartageners syndrome

A

immotile cilia due to dynein arm defect. Infertility, bronchiectasis, and recurrent sinusitus; Assoc with situe inversus (10% have transposition of great vessels)

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14
Q

Preprocollagen

A

the newly synthesized alpha chain in the RER

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15
Q

ER Collagen Processing

A

Hydroxylation (vit. C) of proline and lysine; glycosylation of hydroxyllysine residues and formation of procollagen via hydrogen and disulfide bonds (this is the triple helix of 3 alpha chains) procollagen = triple helix

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16
Q

Extracellular processing of procollagen

A

The procollagen is proteolytically cleaved of its terminal regions to an insoluble tropocollagen; the process is completed by cross-linknig it to other molecules by lysyl oxidase (copper dependent) to make collagen fibrils

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17
Q

Elastin

A

Rich in proline and glycine, nonhydroxylated (vs. collagen). Tropoelastin with fibrillin scaffold – Desmosin crosslinking of elastin accounts for its properties

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18
Q

Red infarcts

A

In tissues with multiple blood supplies or in reperfusion after infarction. Commonly, lungs, liver, and Intestins

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19
Q

Pale infarcts

A

In tissues with single blood supply like heart, kidney, spleen

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20
Q

Amino acids modified by golgi apparatus

A

Asparagine, threonine, serine

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21
Q

glycolysis rate limiting step

A

Phosphofructokinase-1 (PFK-1)

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22
Q

Gluneogenesis rate limiting enzyme

A

Fructose-1,6-bisphosphatase

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23
Q

TCA cycle rate limiting enzyme

A

isocitrate dehydrogenase

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24
Q

Glycogen synthesis rate limiting enzyme

A

glyogen synthase

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25
Q

Glycogenolysis rate limiting enzyme

A

glycogen phosphorylase

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26
Q

HMP shunt rate limiting enzyme

A

G6PD

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27
Q

Rate limiting step of de novo pyrimidine synthesis

A

Carbamoyl phosphate synthetase -II

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28
Q

Rate limiting step in purine synthesis

A

Glutamine-PRPP amidotransferase

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29
Q

Urea cycle

A

Carbamoyl phosphate Synthetase I

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30
Q

FA synthesis rate limiting step

A

Acetyl-CoA carboxylase

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31
Q

FA oxidation rate limiting step

A

Carnitine acyltransferase I

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32
Q

Ketogenesis rate limiting step

A

HMG-CoA synthase

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33
Q

Cholesterol synthesis rate limiting step

A

HMG-CoA reductase

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34
Q

malate-astpartate shuttle produces

A

32 ATP per glucose

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35
Q

Glycerol 3 phosphate shuttle

A

30 ATP per glucose

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36
Q

Purine Ring composition

A

Aspartate, CO2, Glutamine (nitrogen), glycine

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37
Q

Pyrimidine ring composition

A

Glycine and carbamoyl phosphate

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38
Q

Enzyme blocked by 6-MP

A

PRPP synthase

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39
Q

Mycophenolate mophetil inhibits what enzyme

A

PRPP synthase

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40
Q

TATA

A

promoter 25 base pairs upstream

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41
Q

CAAT

A

70 to 80 base pairs upstream

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42
Q

Enhancers and repressors location

A

can be anywhere within the gene upstream or downsream

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43
Q

tRNA characteristics

A

75 to 90 nucleotides, cloverleaf, 3’-CCA- aminoacyl end, 5’ guanosine terminal

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44
Q

tRNA charging

A

Aminoacyl-tRNA synthetase; scrutinizes aa before and after binds to tRNA (if accidentally mischarged it will place in wrong aa).

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45
Q

tRNA structure

A

T(psi)C arm- sequence of thymidine and pseudoridine (3’ side); D-arm (5’ end) has dihydrouracil and acetylcytosine; arms are responsible for clover structure

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46
Q

Post-translational modificaiton in the RER

A

N-oligosaccharide addition

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47
Q

Modification in Golgi

A

N-oligosaccharide on Asparagine; O-oligosaccharide on serine and threonine; Mannose-6-phosphate for lysosome targeting

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48
Q

I-cell disease

A

failure of addition of mannose-6-phosphate to lysosome proteins; coarse facial features, clouded corneas. Restricted joints, high lysosomal enzymes in plasma

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49
Q

Peroxisome

A

Degradation of long fatty acids and amino acids

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50
Q

Proteasome

A

degradation of proteins marked by ubiquitin

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51
Q

Aerobic metabolism of glucose produces…

A

32 ATP via malate aspartate shuttle (heart and liver); 30 ATP via glycerol-3-phosphate shuttle (muscle)

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52
Q

Hexokinase

A

ubiquitous, low Km (high affinity) but low Vmax (low capacity)

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53
Q

Glucokinase

A

Liver and beta cells of pancreas. Low affinity (high Km) but really high Vmax (high capacity)

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54
Q

Hunter’s

A

Iduronate sulfatase deficiency; heparan sulfate and dermatan sulfate; XR; Mild hurler’s with aggressive behavior and no corneal clouding

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55
Q

Hurler’s

A

alpha-L-iduronidase deficiency; Heparan sulfate; AR; developmental delay, corneal clouding, gargoylism (flat face, depressed nasal bridge and bulging forehead), hepatosplenomegaly, airway obstruction

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56
Q

Krabbe’s

A

galactocerebroside buildup from lack of beta-galactocerebrosidase; peripheral neuropathy, developmental delay, optic atrophy, globoid cells (macrophages engorged with multiple nuclei in parenchyma and around blood vessels)

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57
Q

Metachromatic leukodystrophy

A

lack of arylsulfatase-A; Cerebroside sulfate buildup; demyelination, dementia, ataxia. AR

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58
Q

Niemann-Pick Disease

A

sphingomyelinase deficiency buildup of sphingomyelin; nerodegeneration, ashkenazi, hepatosplenomegaly, cherry red macula, foam cells

59
Q

Tay Sachs

A

hexoaminidase A deficiency; GM2 buildiup; NO HEPATOSPLENOMEGALY (vs. Neimann pick); Cherry red macula, nervous degeneration, developmental delay, onion skin lysosomes

60
Q

mitochondrial inheritance diseases

A

Leber’s hereditary optic neuropathy (acute loss of central vision); myoclonic epilepsy, mitochondrial encephalopathy. Ragged red fibers on microscopy. Often due to failure in oxidative phosphorylation. All offspring

61
Q

codominance

A

2 alleles, equal dominance; ie ABO blood groups

62
Q

variable expression

A

severity of the phenotype varies form one to another; ie NF or Tuberous sclerosis

63
Q

Plieotroy

A

one gene has more than one effect on phenotype; ie PKU

64
Q

Locus heterogeneity

A

Mutations at different loci can produce same phenotype; Ie. Marfan’s, MEN 2B, Homocystinuria (all three of these produce similar Marfan body habitus)

65
Q

Mosaicism

A

cells have different genetic makeup in body;

66
Q

Imprinting

A

uniparental disomy or inactivation or deletion of genes on Chromosome 15; Phenotype differences depend on wether mutaiton comes form mother or fathe

67
Q

Prader-Willi

A

Paternal allel should be active but is deleted; has normally inactivated maternal allel; mental retardation, hyperphagia, obesity, hypogonadism, hypotonia; one of few causes of childhood osteoperosis

68
Q

Angelman’s syndrome

A

Maternal allel is deleted, normally inactivated paternal allele; Mental retardation, seizures, ataxia, inappropriate laughter

69
Q

Rasburicase

A

Analog of Urate Oxidase (not present in humans), can catalyze uric acid into allantoin to help prevent renal toxicity in the case of tumor lysis syndrome. Allopurinol can be given as well.

70
Q

Denosumab

A

Monoclonal antibody against RANKL to prevent osteoclast activation.

71
Q

amino acids involved in the urea cycle

A

Aspartate (donates an NH3 to Citruline), and Argenine (produces urea and ornithine)

72
Q

Electron transport chain complexes

A

I: NADH, II: Succinate dehydrogenase (FADH2) and CoQ, III: CoQ to III to Cytochrome C to IV (reduction of O2) to V (phosphorylation of ADP)

73
Q

Inhibitors of electron transport complexes

A

Oligomycin (Complex V); Rotenone, amytal(barbituate), antimycin A, MPP from MPTP, CO, H2S, and CN-

74
Q

Oxidative phosphorylation uncouplers

A

Thermogenin found in brown fat, aspirin, 2,4-DNP found in wood preservatives

75
Q

Acute Intermittent Porphyria

A

HMB synthase or Uroporphyrinogen I synthase; buildup of porphobilinogen; abdominal pain, red-wine urine upon standing, increased urinary ALA and PBG, neurologic manifestations; can be precipitated by drugs like barbital, griseofulvin, and phenytoin, and alcohol.

76
Q

ALA synthase regulation

A

substrates are glycine and Succinyl-CoA; Inhibited by glucose and heme; promoted by EtOH, Barbituates, and hypoxia

77
Q

Porphyria cutanea tarda

A

Uroporphyrinogen decarboxylase deficiency; buildup of uroporphyrinogen III; Photosensitivity, blisters

78
Q

JAK2 activation mutations relate to these disorders

A

All chronic myeloproliferative disorders except for CML (bcr-abl); Essential thrombocytosis, polycythemia vera, and Primary myelofibrosis (splenomegaly that causes early satiety, hepatomegaly, anemia and bone marrow fibrosis)

79
Q

Ruxolitinib

A

JAK2 inhibitor approed for treatment of primary myelofibrosis

80
Q

substrates for transcarbamoyl phosphate synthetase II

A

Glutamine and CO2 and ATP (for Pyrimidine synthesis)

81
Q

substrates for transcarbamoyl phosphate synthetase I

A

CO2 and ATP and NH4+ (for Urea cycle)

82
Q

Orotic aciduria enzymes

A

Orotate phosphoribosyl transferase (converts Orotic acid to UMP) an Orotidine 5’-phosphate decarboxylase[will NOT have hyperammonemia symptoms]; Ornithine transcarbamoyl transferase (in urea cycle so will cause hyperammonemia)

83
Q

Steps of collagen synthesis and cellular location

A

alpha preprocollagen chains of Gly-X-Y (RER); Hydroxylation or pro and lys (ER); Glycosylation of lysine (ER); Assembly of procollagen (triple helix via disulfide bond formation in C-terminal propeptide); Secretion via golgi of procollagen into ECM; N and C terminal propeptide cleavage by propeptidase into insoluble tropocollagen; collagen fibril is cross-linked by lysyl oxidase to make collagen fibril polymers (copper dependent enzyme)

84
Q

The main allosteric activator of Carbamoyl phosphate synthetase I

A

N-acetylglutamate (the main regulator of the urea cycle)

85
Q

Kozak sequence

A

Methioning AUG codon is positioned near Kozak sequence b/c Kozak sequence (GccRcc, R=adenine or guanine), it serves to initate translation by helping mRNA bind to ribosomes, when there is a mutation in this sequence in beta-heme it can result in beta-thalassemia

86
Q

Translocation step in translation

A

Requires eEF2 and GTP

87
Q

Peptide bond formation on ribosome

A

catalyzed by peptidyl transferase on eurkaryotic ribosomes

88
Q

bisphosphoglycerate mutase

A

enzyme that forms 2,3-BPG from 1,3-BPG from glycolytic pathway to be used by erythrocytes

89
Q

Main allosteric activator of the key first step of gluconeogensis

A

Pyruvate carboxylase is activated by excess acetyl-CoA signaling a well fed state

90
Q

How is oxaloacetate shuttled out of mitochondria for gluconegenesis in cytoplasm

A

oxaloactetate to Malate by malate dehydrogenase then malate is reconverted to oxaloacetate in the cytoplasm where it undergoes conversion to PEP by PEPCK (Uses GTP)

91
Q

Four main metabolites of pyruvate

A

Lactate (regeneration of NAD+), Acetyl-CoA (FA synthesis, cholesterol synthesis, TCA), Oxaloacetate (gluconeogenesis), Alanine (in muscle cells to carry NH3 away to liver)

92
Q

Key regulators of PFK-1

A

F2,6BP; made from F6P by PFK-2, PFK-2 is activated in the fed state (dephosphorylated) and inactivated in the starving state (phosphorylated via glucagon increase of cAMP and PKA). F2,6BP is deactivated by FBPase-2 which is active in starve state (phosphorylation) and inactive in fed state (dephosphorylation).

93
Q

Cofactors for Pyruvate dehydrogenase, alpha-ketoglutarate dehydrogenase and Branched-chain alpha-ketoacid dehydrogenase

A

Lipoic acid, Thiamine, CoA, FAD, NAD

94
Q

Products of B6 conenzyme reactions

A

GABA from glutamate, dopamine from dopa, heme from ALA synthase and glycine, histamine from histidine, Niacin from tryptophan

95
Q

alkaptonuria

A

deficiency in homogentisic acid oxidase (a metabolite of Tyrosine on its way to fumarate); Usually a benign disease; find dark brown pigment in connective tissue and SCLERA because when homogentisate binds to collagen it turns dark; urine turns black on prolonged exposure to air. Can present with debilitating arthralgias

96
Q

Roles of NADPH

A

anabolic reactions such as cholesterol and FA synthesis, reduction of glutathione, and production of oxidative burst

97
Q

Where are Urea’s nitrogens from?

A

Ammonium that is used to form carbamoyl phosphate and transferred to citruline; And Aspartate which donates an amino group to citrulline to form arginosiccinate.

98
Q

How does the nephron rid of ammonium

A

Glutamine carries ammonia from peripheral tissues to the kidney where it is hydrolyzed by glutaminase in the tubule to produce glutamate and free ammonium ion where it is excreted in urine.

99
Q

Two enzymes B12 is essential for

A

homocystein methyltransferase (to make methionine from homocysteine, also invovles folate); Methylmalonyl-CoA Mutase (or isomerase) to make succinyl coA from methylmalonyl-CoA

100
Q

differentiating Cori’s disease from other glycogen storage diseases

A

there is normal lactate levels and biopsy shows accumulation of short outer dextrin-like structures in the cytosol of hepatocytes with absence of histopathological fatty infiltration of the liver. Debranching enzyme affects liver and muscle cells but mainly presents with hepatocyte manifestations

101
Q

Major biochemical defect in beta-thalaseemia

A

mutations affect the transcription, processing and translation of mRNA; this leads to decreased beta chain production

102
Q

tetrahydrobiopterin is involved in what reactions

A

Phenylalanine to Tyrosine, tyrosine to Dopa; Tryptophan to Serotonin

103
Q

Ach is made from

A

choline and acetyl-CoA from cholineacetyltransferase

104
Q

Elastin versus collagen

A

Elastin can be stretched and recoil back; it is composed primarily of non-polar Aas gly, ala, and val. Also contains pro and lys. Fibrillin is the foundation/support. Desmosine corsslinking accounts for properties allowing it to recoil after being stretched. In skin, blood vessels, lungs. Differs from collage: very few proline and lysine are hydroxylated, no triple helix, hydroxylation, glycosylation, and intercahing disulfide bridges at C-terminus do not occur in elastin as in collagen.

105
Q

myc

A

transcription factors

106
Q

Ras

A

G-protein

107
Q

Pyruvate dehydrogenase deficiency

A

congenital or acquired (ie alcohol); neurologic defects; Tx: increase ketogenic Aas (Lysine and Leucine)

108
Q

Essential AA

A

Met, Val, Arg, His; Ile, Phe, The, Trp; Leu, Lys

109
Q

Purely ketogenic Aas

A

Lysine, Leucine

110
Q

Glucogenic and Ketogenic Aas

A

Ile, Phenylalanine, Threonine, Tryptophan

111
Q

Glucogenic Aas

A

Methionine, Valine, Arginine, Histidine

112
Q

Two ways the brain buffers ammonia

A

First alpha-ketoglutarate can be combined with NH4+ to yield glutamate; Glutamate itself can be used as a buffer in the astrocyte for ammonium by combining to make glutamine. Glutamine can be reconverted back to glutamate by glutaminase in the neuron for use by the pre-synaptic neuron

113
Q

Ras-MAP kinase

A

Ras is a G-protein that binds GTP/GDP and is part of tyrosine kinase cascade where the tyrosine kinase receptor autophosphorylates itself, MAP is eventually activated and enters the nucleus where it can interact with the DNA

114
Q

Sorbitol is produced and metabolized by what enzymes

A

Glucose or galactose are converted to sorbitol by aldose reductase. Sorbitol is then converted to Fructose by sorbitol dehydrogenase. Tissues like schwann cells, kidneys, etc. do not contain sorbitol reductase and are at risk for osmotic damage

115
Q

A differentiating feature between Tay-Sachs and Neimann-Pick’s disease is

A

Neimann-Pick’s disease presents with hepatosplenomegaly whereas Sachs has no hepatosplenomegaly

116
Q

NADPH Oxidase

A

Deficient in Chronic Granulomatous Disease; O2 to O2 radical

117
Q

Superoxide dismutase

A

Converts O2radical into H2O2; second step in respiratory burst

118
Q

Myeloperoxidase

A

Combines H2O2 with Chloride to form hypochlorous acid; final step in oxidative burst

119
Q

Asparaginase treatment of Lymphoneoplastic cells

A

asparaginase breaks down normal asparagine to urea and ornithine; this is a useful treatment because lymphoblastic cells can not synthesize own asparagine so you are removing their supply

120
Q

Deamination of glutamate gives

A

alphaketoglutarate

121
Q

Deamination of alanine gives

A

Pyruvate

122
Q

Cori Cycle

A

uses alanine and glutamate from muscle and transfers nitrogen to the liver by converting alpha ketoglutarate to glutamate and pyruvate to alanine; these transamination reactions all require B6

123
Q

Treatment for Hyperammonemia

A

Benzoate, Phenylbutyrate (both bind amino acid); limit protein intake; Lactulose acidifies the GI and traps NH4+ in the colon for excretion

124
Q

Cystinuria

A

AR defect in tubular transporter for cysteine, ornithine, lysine, and arginine in PCT of kidneys; hexagonal crystals of cysteine staghorn calculi; Acetazolamide to alkalinize the urine

125
Q

Enzymes involved and location of Ketogenesis

A

Occurs in the mitochondria from Fatty acids. Fas go through Beta-oxidation and the Acetyl-CoA units are used to synthesize HMG-CoA via HMG-CoA synthase (same as for cholesterol); HMG-CoA is converted to acetoacetate by HMG-CoA Lyase (while cholesterol synthesis would start with HMG-CoA reductase); Acetoacetate can make beta-hydroxybutyrate with reduction by NADH. From there it enters bloodstream

126
Q

Glycogen Phosphorylase Kinase regulation

A

phosphorylated by PKA via glucagon or adrenergic activation a la cAMP. The phosphorylation is activated and goes on to phosphorylate glycogen phosphorylase which does its business. Calcium/calmodulin also will activate Glycogen phosphorylase kinase in muscle; Insulin through its receptor tyrosine kinase will activate protein phosphatase which dephosphorylates glycogen phosphorylase kinase and glycogen phosphorylase

127
Q

Carnitine deficiency

A

Can not transport LCFAs into mitochondira results in toxic accumulation; Weakness, hypotonia, Hypoketotic, Hypoglycemia

128
Q

Acyl-CoA dehydrogenase deficiency

A

hypoglycemic hypoketonemia; increase in dicarboxylic acids and decrease in glucose and ketones

129
Q

Rate limiting step in FA oxidation

A

Carnitine acyetyl transferase (inhibited by malonyl-CoA)

130
Q

FA synthesis regulation

A

Acetyl-CoA carboxylase (uses biotin) is rate limiting step; Forms malonyl-CoA from Acetyl-CoA; Citrate moves from mitochondria via citrate shuttle to cytosol

131
Q

Protein and carbs versus fat as kcal energy source

A

1 g of protein and carbohydrates = 4 kcal; 1 g of fate = 9 kcal

132
Q

Name steps of heme breakdown from RES to Excretion in feces

A

Heme to biliverdin -> bilirubin -> transported to liver bound to albumin -> conjugated by UDP glucuronyl transferase -> conjugated bilirubin -> excretion to feces -> urobilinogen -> reabsorption to liver for reuse, feces and urine for color.

133
Q

Crigler Najar

A

Absence of UDP Glucuronyl transferase

134
Q

Gilbert’s

A

Low levels of UDP-Glucuronyl transferase

135
Q

Rotor’s and Dubin-Johnson syndrome

A

Defective secretion of direct bilirubin into feces

136
Q

Apo E

A

Mediates remnant uptake; seen on chlyomicrons

137
Q

Apo A-1

A

Activates LCAT (Lecithin-cholesterol acyltransferase) which catalyzes esterification of cholesterol; Found on HDL

138
Q

Apo C-II

A

Lipoprotein Lipase cofactor - degrades TG circulating in chlyomicrons and VLDLs

139
Q

Apo B-48

A

Mediates chlyomicron secretion from enterocytes; found on chlyomicrons; deficiency in this leads to abetalipoproteinemia

140
Q

Apo B-100

A

Binds LDL receptor; Found on LDL

141
Q

Type I dyslipidemia: Hyper-Chlyomicronemia

A

Deficiency in Apo C-II or LPL; Increased Chlyomicrons and TG, and cholesterol; Causes pancreatitis, hepatosplenomegaly, eruptive/pruritic xanthomas (no increased atherosclerosis risk)

142
Q

Type Iia - Familia hypercholesterolemia

A

AD, Decreased LDL receptors; cholesterol increase in blood; atherosclerosis, xanthomas and corneal acrus

143
Q

Type IV - Hypertriglyceridemia

A

Hepatic overproduction of VLDL; VLDL is elevated and TGs

144
Q

Abetalipoproteinemia

A

ApoB-48 or Apo-B100; AR; Accumulation of chlyomicrons within enterocytes; failure to thrive, steatorrhea, acanthcytosis of RBCs, ataxia, night blindness (due to Vit A and Vit E deficiencies)

USMLE (14 decks)

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