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Biochemistry Flashcards

1
Q

Fabry dz

A

XLR; alpha-galactosidase; ceramide trihexoside; pw painful neuropathy, angiokeratomas, hypohydrosis; will develop progressive renal failure

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2
Q

Gauncher dz

A

AR; beta-glucocerebrosidase; glucocerebroside; gaucher cells (“crumpled tissue paper” macrophages), HSM, pancytopenia, severe bone and joint pain

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3
Q

Hurlur syndrome

A

AR; alpha-L-iduronidase; dermatan and heparan sulfate; gargoylism, developmental delay, corneal clouding, HSM

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4
Q

Hunter syndrome

A

XLR; iduronate sulfatase; dermatan and heparan sulfate; similar to, but milder than, Hurlur syndrome (no corneal clouding however)

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5
Q

Niemann-Pick dz

A

AR; sphingomyelinase; sphingomyelin; HSM, cherry-red spot in macula, foam cells, progressive neurodegeneration

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6
Q

TaySachs

A

AR; beta-hexosaminidase; Gm2 ganglioside; cherry-red spot in macula, progressive neurodegeneration, no HSM

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7
Q

Krabbe dz

A

AR; galactocerebrosidase; galactosylspingosine & galactocerebroside; progressive neurodegeneration, optic atrophy

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8
Q

Metachromatic leukodystrophy

A

AR; arylsulfatase A; cerebroside sulfate; muscle wasting, dementia, ataxia

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9
Q

Histones: AA?

A

lysine, arginine

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10
Q

In DNA methylation, which nucleotides are methylated?

A

cytosine and adenine

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11
Q

DNA methylation of what sequence represses transcription?

A

CpG islands

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12
Q

Histone methylation makes DNA what?

A

Mute

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13
Q

Histone acetylation makes DNA what?

A

Active

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14
Q

Uracil: made from what nucleotide, replaces what in RNA

A

Cytosine, thymine

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15
Q

Why does increased G-C content increase the melting temperature of DNA?

A

3 H bonds over 2

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16
Q

AA needed for purine synthesis (GAG)

A

Glycine, aspartate, glutamine

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17
Q

Adenosine deaminase deficiency MOA

A

Excess ATP and dATP imbalances nucleotide pool, prevent DNA synthesis and reduces lymphocyte count (cause autosomal recessive SCID)

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18
Q

Lesch-Nyhan syndrome MOA, pw

A

absent HGPRT leads to defective purine salvage (normally converts hypoxanthine to IMP and guanine to GMP). results in excess uric acid production and de novo purine synthesis; Hyperuricemia, Gout, Pissed off, Retardation, dysTonia

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19
Q

AUG

A

Methionine in eukoaryotes; fMet in prokaryotes (stimulates PMN chemotaxis)

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20
Q

non-degenerate AA

A

methionin (AUG), tryptophan (UGG)

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21
Q

DNA polymerase III

A

prokaryotic only; proofreads with 3’-5’ exonuclease

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22
Q

DNA polymerase I

A

degrades RNA primer and replaces it with DNA (5’-3’ exonuclease)

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23
Q

DNA ligase

A

catalyze the formation of phosphodiester bond within a strand of dsDNA (okazaki fragments)

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24
Q

telomerase

A

RNA-dependent DNA polymerase that adds DNA to 3’ ends of chromosomes to avoid loss of genetic material with every duplications, eukaryotes only

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25
Q

silent mutations often occur

A

3rd position of codon (tRNA wobble)

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26
Q

missense mutations example

A

sickle cell dz (substitution of glutamic acid with valine)

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27
Q

nonsense mutation

A

stop the nonsense!

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28
Q

frameshit mutation example

A

duchenne muscular dystrophy

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29
Q

nucleotide excision repair occurs when, moa, and defect

A

G1; endonucleases release damaged bases (esp during UV exposure), DNA polymerase/ligase reseal gap; xerderma pigmentosum

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30
Q

base excision repair occurs when, moa

A

occurs throughout cell cycle; base-specific glycosylase removes altered base and creates AP site, with AP-endonuclease cleaving 5’ end and lyase cleaving 3’ end; DNA polymerase-beta fill s gap and DNA ligase seals it

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31
Q

mismatch repair occurs when, moa, and defect

A

G2; mismatched nucleotides on newly synthesized strand are removed and fixed; defective in HNPCC

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32
Q

nonhomologous end joining moa, defect

A

repairs double-stranded breaks, no homology requirements; mutated in ataxia telangiectasia, fanconi anemia

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33
Q

protein synthesis direction

A

N to C terminus

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34
Q

DNA replication inhibiting drugs have what modification that prevents addition?

A

Modified 3’OH that prevents addition of the next nucleotide

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35
Q

mRNA stop codons

A

UGA, UAG, UAA

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36
Q

RNA polymerase I, II (opens up DNA at promoter site), III

A

rRNA (rampant), mRNA (massive), and tRNA (tiny)

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37
Q

alpha-amanitin (amanita phalloides) effects which

A

RNA polymerase II

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38
Q

hnRNA to mRNA transition

A

5’ capping (7-methyl guanosine cap), 3’ polyadenylation, and intron splicing

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39
Q

mRNA quality control occurs where?

A

cytoplasmic P-bodies (exonucleases, decapping enzymes, microRNAs)

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40
Q

SLE pts have antibodies to what structure?

A

anti-smith (spliceosomal snRNP)

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41
Q

MCTD pts have antibodies to what structure?

A

Anti-U1 RNP

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42
Q

Labile cells

A

BM, gut epithelium, skim, hair follicles, germ cells

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43
Q

What cells are rich in RER?

A

goblet cells, plasma cells

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44
Q

What cells are rich in SER?

A

Liver hepatocytes (detoxification of drugs and poisons), and adrenal cortex (steroid synthesis)

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45
Q

Golgi adds which molecule to proteins to signal movement to lysosome?

A

mannose-6-phosphate

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46
Q

inclusion cell disease

A

defect in N-acetylglucosaminyl-1-phosphotransferase, golgi fails to phosphorylate mannose residues to proteins, sending proteins extracellular as opposed to lysosomes. pw coarse facial features, clouded corneas, restrictd joint movement, and high plasma levels of lysosomal enzymes

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47
Q

signal recognition particle

A

cytosolic ribonucleoprotein that traffics protein from the ribosome to the RER

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48
Q

COPII

A

anterograde transport: ER - Golgi

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49
Q

COPI

A

retrograde transport: golgi - ER

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50
Q

clathrin

A

trans-golgi to lysosomes; plasma membrane to endosome (receptor -mediated endocytosis)

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51
Q

Peroxisome

A

catabolism of very-LC FA, branched-chain FA, AA

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52
Q

Defects in ubiquitin-proteasome system implicated in what disease

A

Parkinson

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53
Q

Type I collagen

A

Bone, skin, tendon, teeth (decreased production in osteogenesis imperfecta)

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54
Q

Type II collagen

A

Cartilage

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55
Q

Type III collagen

A

reticulin (blood vessels, skin, uterus)

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56
Q

Type IV collagen

A

basement membrane (defective in alport, targeted by antibodies in goodpasture syndrome)

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57
Q

Menkes dz MOA

A

XLR CT dz caused by impaired copper absorption and transport due to defective Menkes protin; decreased activity of lysyl oxidase (as Cu is an essential cofactor); leads to brittle, kinky hair, growth retardation, and hypotonia

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58
Q

elastin is rich in what?

A

nonhydroxylated glycine, proline, and lysine

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59
Q

marfan syndrome

A

defect in fibrillin, a glycoprotein that forms a sheath around elastin

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60
Q

Cre-lox system

A

inducibly manipulate genes at specific development points (e.g. to study a gene whose deletion causes embryonic death)

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61
Q

RNA interference

A

dsRNA complementary to mRNA sequence of interest is transfected into human cells, where it separates and promots degradation of target mRNA, knocking down gene expression

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62
Q

Hardy weinberg assumptions

A

no mutations, no natural selection, random mating, and no net migration

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63
Q

Prader-willi moa

A

deletion on c15 (paternal); results in hyperphagia, obesity, hypogonadism, hypotonia, and intellectual disability

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64
Q

angelman moa

A

deletion on c15 (maternal); results in inappropriate laughter, seizures, ataxia, severe intellectual disability

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65
Q

X-linkd dominant example

A

Hypophosophatemic rickets: increased phosphate wasting at proximal tubule, results in rickets-like presentation

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66
Q

mitochondrial inheritance example

A

miochondrial myopathies; pw myopathy, lactic acidosis, and CNS dz; 2/2 failure in oxidative phosphorylation, and muscle biopsy shows “ragged red fibers”

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67
Q

ADPKD mutation

A

85 percent: PKD1 on c16; 15 percent: PKD2 on c4

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68
Q

FAP mutation

A

APC gene on c5q (5 letters on polyp)

69
Q

familial hypercholesterolemia

A

absent LDL receptor leads to elevated LDL, leads to athersclerotic dz, corneal arcus, tendon xanthomas

70
Q

hereditary hemorrhagic telangiectasia

A

inherited disorder of blood vessels; pw telangiectasia, epistaxis, AVM, Gi bleeding, hematuria

71
Q

huntington dz

A

caudate atrophy; CAG repeat on gene 4 (hunting 4 food)

72
Q

li-fraumeni mutation

A

TP53 mutation leads to multiple malignancies at early age

73
Q

marfan mutation

A

FBN1 gene mutation on c15 ; cystic medial necrosis of the aorta leads to aortic incompetence and dissections, floppy MV

74
Q

NF1 mutation

A

NF1 gene on c17

75
Q

NF2 mutation

A

NF2 gene on c22

76
Q

VHL dz

A

deletion of VHL gene on c3 (3 words for chromosome 3)

77
Q

duchenne: common cause of death

A

dcm

78
Q

dystrophin function

A

largest protein-coding gene; in skeletal and cardiac muscle, connects intracellular cytoskeleton with transmembrane protein alpha and beta dystroglycan, which are connected to the ECM. loss of dystrophin leads to myonecrosis.

79
Q

myotonic type 1 mutation, presentation

A

CTG repeat on DMPK gene, abnormal expression of myotonin protein kinase; pw myotonia, testicular atrophy, frontal balding, and arrhythmia

80
Q

fragile x syndrome mutation, presentation

A

x-linked defect of the FMR1 gene, trinucleotide repeat disorder CGG; pw eXtra large tests, jaws, ears

81
Q

T21: first-trimester US, serum findings

A

increased nuchal translucency, hypoplastic nasal bone; decreased PAPP-A, increased free beta-hCG

82
Q

T21: other findings

A

duodenal atresia, hirschsprung dz, atrial septal defect, early-onset alzheimer (c21 codes for amyloid)

83
Q

t18: serum lab findings

A

decreased papp-a, decreased estriol, decreased beta-hCG, decreased inhibin A

84
Q

cri-du-chat mutation, pw

A

short arm, c5, severe intellectual disability, high-pitched crying/mewing

85
Q

williams syndrome mutation, pw

A

long arm, c7; pw elfin faces, extreme friendliness with strangers, intellectual disability, hypercalcemia

86
Q

CATCH-22

A

velocardiofacial syndrome (Cleft palate, abnormal facies); diGeorge syndrome (thymic aplasia, cardiac defects, hypocalcemia)

87
Q

vita A function, deficiency, excess

A

essential for normal differentiation of epithelial cells into specialised tissue (pancreatic cells, mucus-producing cells), constituent of visual pigments; used to treat measles, AML, and acne/wrinkles

88
Q

vita A deficiency

A

night blindness, dry skin, immunosuppression;

89
Q

vita A toxicity

A

acute: N/V, blurred vision, vertigo, chronic: pseudotumor cerebri, dry skin/alopecia, hepatic toxicity, arthralgias; teratogenic (cleft palate, heart abnormalities)

90
Q

b1/thiamine fxn, dx

A

cofactor for dehydrogenase enzyme rxn: ATP=alpha-ketoglutarate dehydrogenase, transketolase, pyruvate dehydrogenase); increase in RBC transketolase activity after B1 administration

91
Q

b1/thiamin deficiency

A

impaired glucose breakdown, affects highly aerobic tissues (brain, heart) first; wenicke-korsakoff syndrome, dry beriberi (polyneuritis, symmetrical muscle wasting), wet beriberi (hig-output cardiac failure, edema)

92
Q

b2/riboflavin fxn, deficiency

A

cofactors in redox reactions (FAD, FMN); cheilosis, corneal vascularization

93
Q

b3/niacin fxn, indications

A

synthesized from b2+b6; cofactors in redox reactions (NAD, NADP), derived from tryptophan, used to treat dyslipidemia (lowers VLDL, raises HDL)

94
Q

b3/niacin deficiency

A

glossitis; pellagra (diarrhea, dementia, dermatitis - “broad collar” rash) in hartnup dz (decreased tryptophan absorption), malignant carcinoid syndrome, isoniazid (decreased b6)

95
Q

b5/pantothenic acid fxn, deficiency

A

Component of coenzyme A, FA synthase; dermatitis, enteritis, alopecia, adrenal insufficiency

96
Q

b6/pyridoxine fxn

A

converted to PLP, a cofactor in transamination, decarboxylation reactions, and glycogen phosphrylase; synthesis of cystathionine, heme, niacin, histamine, and neurotransmitters

97
Q

b6/pyridoxine deficiency

A

convulsions, hyperirritability, peripheral neuropathy (induced by isoniazid, OCP), sideroblastic anemia 2/2 impaired hemoglobin synthesis and Fe excess

98
Q

b7/biotin fxn, deficiency

A

cofactor for carboxylation enzymes, dermatitis, alopecia, enteritis caused by excess ingestion of raw egg whites

99
Q

b9/folate fxn

A

converted to THF, a coenzyme for methylation reactions,impt for synthesis of nitrogenous bases in DNA/RNA; found in leafy green vegetables, absorbed in jejunum

100
Q

b9/folate deficiency

A

m/c vitamin deficiency (esp in etoh and pregnancy), can be caused by phenytoin, sulfonamides, MTX, megaloblastic anemia, glossitis, increased homocysteine, NT defects

101
Q

b12/cobalamin fxn

A

cofactor for homocysteine methyltransferase, methylmalonyl-coa mutase, found in animal products, very large reserve pool (4 years) stored in liver`

102
Q

b12/cobalamin deficiency

A

insufficient intake (veganism), malabsorption, lack of intrinsic factor (pernicious anemia, gastric bypsas), absence of terminal ileum (CD); megaloblastic anemia, subacute combined degeneration), increased homocysteine and methylmalonic acid; prolonged deficiency leads to irreversible nerve damage

103
Q

vita C fxn

A

facilitates Fe absorption by reducing it to Fe2+ state, necessary for hydroxylation of profline/lysine in collagen synthesis, necessary for dopamine beta-hydrxylase (converts DA to NE)

104
Q

vita C deficiency, excess

A

scurvy (swollen gums, bruising, petechiae, hemarthrosis, anemia, poor wound healing, subperiosteal hemorrhages); N/V, diarrhea, Ca oxalate nephrolithiasis, can increase risk of Fe toxicity in predisposed individuals (transfusions, hereditary hemochromatosis)

105
Q

vita E fxn, deficiency

A

antioxidant (protects RBCs, membranes from free radical dmg); hemolytic anemia, posterior column and spincerebellar tract demyelination

106
Q

vita K fxn, deficiency

A

cofactor for gamma-carboxylation of glutamine acid residues on blood clotting proteins, synthesized by intestinal flora; increase PT, aPTT with normal bleeding time, occurs in infants or after prolonged periods of antibiotic used (esp liver dz, malabsorption syndromes)

107
Q

zinc deficiency

A

acrodermatitis enteropathica, delayed wound healing, anosmia/dysgeusia, hypogonadism, decreased adult hair

108
Q

Kwashiorkor (MEAL)

A

protein malnutrition leads to edema, anemia, liver (fatty)

109
Q

Glucogenic essential AA

A

methionine, valine, histidine

110
Q

Ketogenic essential AA

A

leucine, lysine

111
Q

Acid AA

A

glutamic acid, aspartic acid

112
Q

Basic AA

A

arginine, lysine, histadine (arg/lys in histones; arg/his during growth)

113
Q

Ammonia intoxication

A

asterixis, slurring of speech, somnolence, vomiting, cerebral edema, vision blurring

114
Q

Tryptophan products

A

Niacin then NAD/NADP (requires B6), serotonin then melatonin (b4,b6)

115
Q

Histidine product

A

Histamine (B6)

116
Q

Glycine product

A

Porphyrin (B6) then heme

117
Q

Glutamate products

A

GABA (B6), glutathione

118
Q

Arginine products

A

Creatinine, urea, NO (requires B4)

119
Q

PKU moa, pw, rx

A

Decreased phenylalanine hydroxylase or BH4, tyrosine because essential; intellectual disability, growth retardation, seizures, fair skin, musty body odor; decrease phenylalanine and increase tyrosine/BH4 intake (must avoid artificial sweetener aspartame)

120
Q

Maternal PKU moa, pw

A

lack of dietary therapy for PKU pts in pregnancy; intellectual disability, growht retardation, microscephaly, heart defects

121
Q

maple syrup urine moa, pw, rx

A

decreased alpha-ketoacid dehydrogenase (B1) impairs degradation of branched AA (isoleucine, leucine, valine); increased alpha-ketoacids in the blood, pw severe CNS defect, intellectual disability, death; restriction of branched AA in diet, thiamine supplementation

122
Q

alkaptonuria moa, pw, rx

A

congenital deficiency of homogentisate oxidase in tyrosine degradation pathway; pw pigment forming homogentisic acid accumulates in tissue (dark connective tissue, brown sclerae, urine turns black, debilitating arthralgies)

123
Q

Homocystinuria pw

A

marfanoid habitus, kyphosis, lens subluxation, intellectual disability, increased homocysteine in urine, thrombosis, athersclerosis (stroke, MI)

124
Q

Cystinuria moa, pw, rx

A

defect of renal PCT and intestinal AA transporter that prevents reabsorption of COLA (cysteine, ornithine, lysine, arginine), leads to recurrent precipitation of hexagonal cysteine stones; urinary aklalinzation (with K citrate, acetazolamide), chelating agents (penicillame), and hydration

125
Q

glycogen storage disease: all types

A

Von gierke; pompe; cori; mcardle dz (very poor carbohydrate metabolism); all AR

126
Q

Von Gierke disease (type 1)

A

Glucose 6 phosphatase deficiency; pw severe fasting hypoglycemia, increased lactate, triglycerides, uric acid, hepatomegaly 2/2 glycogen storage in liver

127
Q

pompe disease (type 2)

A

lysosomal alpha-1,4-glucosidase (acid maltase) deficiency; cardiomegaly, hypertrophic cardiomyopathy, glycogen accumulatoin in lysosomes, normal blood sugar levels

128
Q

cori disease (type 3)

A

alpha-1,6,glucosidase deficiency; pw milder form of type 1 with normal blood lactate levels; gluconeogenesis intact

129
Q

mcardle disease (type 4)

A

SK glycogen phosphorylase; increased glycogen in muscle that it cannot break down, leads to painful muscle cramps, myoglobinuria with exercise, and arrhythmia from electrolyte abnormalities; rx with vitamin B6

130
Q

leptin moa and effect

A

acts on arcuate nucleus of hypothalamus to inhibit production of neuropeptide Y (appetite stimulant) and stimulate production of alpha-MSH (promote satiety)

131
Q

Why do bruises turn green?

A

heme oxygenase converts heme to biliverdin, which is green

132
Q

HbS protein defect

A

At position 6 of the beta subunit, valine replaces glutamic acid. This promotes hydrophobic interaction among hemoglobin molecules and results in polymerization (during hypoxia, increased acidity, low blood volume)

133
Q

HbC protein defect

A

At position 6 of the beta subnit, lysine replaces gluatmic acid. lysine does not induce sickling because it itself is charged (like glutamic acid), and results in chronic hemolytic anemia

134
Q

Pigmented gallstone moa

A

infection of gallbladder release beta-glucuronidase from bacteria (e.coli. ascaris lumbricoides), contributes to the hydrolysis of bilirubin glucouronides and increase amount of unconjugated bilirubin in bile

135
Q

chronic myeloproliferative disorder mutation, moa, presentation

A

mutation (V617F) in cytoplasmic tyrosine kinase (JAK2), which results in constitutive tyrosine kinase activity and cytokine-independent activation of STAT transcription factors

136
Q

pyruvate dehydrogenase deficiency moa, diet supplementation

A

Prevent conversion of pyruvate to acetyl-CoA, thus shunting pyruvate to LA; rx with lysine and leucine (exclusively ketogenic)

137
Q

nitrate deaminates cytosine, adenine, gluanine to form?

A

uracil, xanthine, hypoxanthine

138
Q

how to fix cytosine deamination?

A

base excision repair: glycosylase recognizes, cleaves altered DNA bases, creating AP site; endonuclease cleaves 5’ end and lyase cleaves 3’ sugar phosphate; and DNA polymerase and ligase reform!

139
Q

DNA dmg mechanism and repair mechanisms

A

depurination of DNA (base excision repair); UV induced formation of thymin dimers; ionizing radiatoin induced breaks in DNA chains; chemical agent induced cross-linkage, intercalation, alkylation

140
Q

Elevated argining levels in pt with spastic paresis in LE and choroeoathetoid movements

A

Arginase deficiency (typically produces urea and ornithine)

141
Q

glutamine is the major AA in blood because

A

it transports ammonia from peripheral tissues to the kidney

142
Q

b12 deficiency takes how long to manifest?

A

many years (4)

143
Q

amatoxin (rom poisonous mushrooms) inhibit what structure?

A

RNA polymerase II (halting mRNA synthesis)

144
Q

Acceptor stem and aminoacylation

A

Base pairing of 5’ and 3’ terminal nucleotides; CCA tail hangs off 3’ end where the AA binds to the 3’ terminal hydroxyl group; aminoacylation catalyzed by aminoacyl tRNA synthetsae

145
Q

D arm consists of, fxn

A

dihydrouracil residues; facilitates correct tRNA recogniition by proper aminoacyl tRNA synthestase

146
Q

T arm consists of

A

thymidine (only RNA species that contains thymidine instead of uracil), pseudouridine, cytidine

147
Q

Arginine + aspartate

A

urea

148
Q

glycine + succinyl CoA

A

heme

149
Q

glycine + arginine + SAM

A

creatinine

150
Q

glutamate products

A

GABA, glutathione

151
Q

glutamate + aspartate

A

pyrimidines

152
Q

glutamate + aspartate + glycine

A

purine

153
Q

histidine

A

histamine

154
Q

tyrosine

A

thyroxine, melanin

155
Q

stimuli for vasodilation of vascular endothelium

A

acetylcholine, shear forces, bradykinin, serotonin, substance P

156
Q

enzyme that synthesizes NO

A

eNOS (activated by Ca)

157
Q

NO moa at smooth muscle cell

A

Activates GC, increases cGMP production, activate protein kinase G, reduce cytosolic Ca levels and relax SMC

158
Q

riboflavin deficiency (3 functions)

A

FMN/FAD impt cofactors for flavoproteins (enzymes for redox); form complex I (FMN), complex II (FAD) in electron transport chain; and FAD is a cofactor for succinate dehydrogenase (converts succinate to fumarate in TCA cycle)

159
Q

16S rRNA sequence fxn

A

locatedon 30S unit, complementary to Shine-Dalgarno sequence on mRNA, binding is necessary for initiation of protein translation

160
Q

beta thalassemia moa

A

m/c aberrant splicing of precursor mRNA or premature chain termination during mRNA translation

161
Q

Signs specific to Fe deficiency

A

dysphagia (2/2 esophageal webs) and disfigured fingernails

162
Q

duodenal enteropeptidase fxn

A

activate trypsinogen to trypsin, necessary for protein digestion and absorption via 2 mechanisms (degrades complex peptides to dipeptides/AA, activates othe rproteases such as carboxypeptidase, elastase, chymotrypsin)

163
Q

lipase fxn

A

digestion of triglycerisdes

164
Q

pancreatic amylase fxn

A

hydrolysis of complex carbohydrates to oligo, di, monosaccharides

165
Q

myoglobin

A

monomeric, primary oxygen-storing protien in skeletal and cardiac muscle; much higher affinity for oxygen (P50 is only 1 mmHg, much lower than P50 of hgb, which is 26); only one heme group, thus dissociation curve is hyperbolic

166
Q

precursor of NAD coezyme

A

niacin (before that tryptophan)

167
Q

what happens if a pt with chronic thiamine deficiency is given a gluocse infusion without thamine supplementation?

A

acute cerebral damage

168
Q

UV dmg mechanism, and repair method

A

Pyrimidine dimers in DNA; recognized by specific endonucleases that nick strand at thymine dimer, which signals removal by the 5’ to 3’ exonuclease activity of DNA polymerase; deficiency in UV-specific endonuclease results in xeroderma pigmentosum

step 1 (17 decks)

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