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USMLE S1 > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

function - single-stranded DNA binding protein

A

stabilisation of unzipped DNA template strands

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2
Q

genetic term ‘transversion’

A

point mutation resulting in purine being replaced with pyramidine or pyramidine replaced with purine c/o transition

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3
Q

vitamin B9 name, deficiency (2)

A

folate/folic acid megaloblastic anaemia neural tube defect (foetus)

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4
Q

carbomyl phosphate synthetase I deficiency

build up

blood findings

inheritance

A
  • build up = NH4+
  • blood findings = hyperammonaemia, low orotic acid, low BUN
  • inheritance = AR
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5
Q

Tay-Sachs disease

enzyme, buildup, features

A
  • enzyme = hexosaminidase A deficiency
  • build up - GM2 gangliosides
  • clinical features = progressive neurodegeneration, developmental delay, ‘cherry-red spot’, lysosomes with onion skin, nil hepatosplenomegaly (c/o Niemann-Pick)
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6
Q

vitamin B6 name, deficiency

A

pyridoxine cheilosis, stomatitis, glossitis

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7
Q

homocystinuria enzyme, build up, features, Rx, inheritance

A
  • enzyme = cysathionine beta-synthase
  • build up = homocystine
  • features = marfanoid body habitus, ectopia lentis, SpLD, thromboembolic occlusion
  • Rx = methionine restriction, vitamin B6 (pyridoxine) supplementation
  • inheritance = AR
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8
Q

acute intermittent porphyria - treatment

A

haemin & glucose - ALA synthetase inhibitor

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9
Q

Niemann-Pick disease enzyme, build up, features, histo

A
  • enzyme = sphingomyelinase
  • build up = sphingomyelin
  • features = progressive neurodegeneration, hepatosplenomegaly, ‘cherry red spot’
  • histo = foam cells (lipid laden macrophages)
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10
Q

tetrahydrobiopterin reductase deficiency lab findings

A

elevated phenylalanine reduced serotonin and catecholamines elevated tryptophan

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11
Q

function of glucose 6-phosphate dehydrogenase

A

convert glucose 6-phosphate to 6-phosphogluconate and NADP+ to NADPH

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12
Q

McArdle disease type, enzyme, build up, features

A

Type IV glycogen storage disease

enzyme = glycogen phosphorylase (specifically, myophosphorylase)

build up = normal glycogen in muscles

features = exercise intolerance relieved by taking oral simple sugars, myoglobinuria

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13
Q

Fructose intolerance enzyme, build up

A
  • enzyme = aldolase B
  • bulid up = fructose-1-phosphate
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14
Q

blotting technique: northern

what does it detect and what is the reagent?

A
  • detects = RNA
  • uses = single stranded DNA or RNA
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15
Q

tRNA struture: D loop

A
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16
Q

Gaucher disease enzyme, build up, features, histo, Rx

A
  • MOST COMMON
  • enzyme = glucocerebrosidase
  • build up = glucocerebroside
  • findings = hepatosplenomegaly, pancytopenia, osteoporosis, aseptic necrosis of femur, bone crises
  • Histo = gucher cells (lipid laden macrophages)
  • Rx = recombinant glucocerebrosidase
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17
Q

acute intermittent porphyria - deficiency in?

A

PBG deaminase deficiency

n.b. not enough to precipitate attack - must have inducer of ALA synthetase

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18
Q

initiation of glycogenolysis; enzyme, its function and its control

A
  • enzyme = glycogen phosphorylase
  • function = removes glucose-1-phosphate from glycogen
  • control = + glycogen phosphorylase kinase, - protein phosphatase
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19
Q

urea cycle - intermediaries from citruline to ornithine, and the enzymes that form them

A

arginosuccinate synthase forms arginosuccinate

arginosuccinate lyase forms arginine

arginase forms ornithine

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20
Q

vitamin B1 name, deficiency (2)

A

thiamine

Beriberi (peripheral neuropathy, heart failure) Wernicke-Korsakoff syndrome

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21
Q

hyperchylomicronaemia (I)

A

increased = chylomicrons

deficiency = lipoprotein lipase or ApoC2

features = pancreatitis, hepatosplenomegaly, xanthoma

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22
Q

Rx Zellweger syndrome

A

avoidance of chlorophyll

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23
Q

vitamin C name, function

A

ascorbic acid

collagen proline and lysine residue hydroxylation

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24
Q

genetic term ‘transition’

A

point mutation resulting in purine being replaced with purine or pyramidine replaced with pyramidine c/o transversion

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25
Q

Function - aconitase

A

catalyzes the isomerisation of citrate to isocitrate in the citric acid cycle

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26
Q

protein sequence change in HbS

A

glutamate (negative) to valine (nonpolar)

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27
Q

which tissue is GLUT-4 found?

A

adipocytes and skeletal muscle

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28
Q

What biochemical process is Enolase involved in?

A

something in glycolysis

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29
Q

tRNA structure: 3’ end

A

CCA tail added as post-translational modification aka acceptor stem, for accepting the correct amino acid from aminoacyl-tRNA synthetase

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30
Q

medication that incurs oxidative stress on erythrocytes

6 total

A
  • primaquine
  • sulfa-containing drugs - co-trimoxasole - trimethoprim - sulfasalazine - sulfadiazine - sulfamethoxazole
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31
Q

in which cell type can glycolysis yield no ATP and why?

A

erythrocytes the production of 2,3-bisphosphoglycerate shunts glycolysis intermediates before net positive ATP yield is achieved, in order to increase oxygen delivery to end organs in lower blood oxygen levels

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32
Q

Effects of alcohol on the liver (HALF)

A
  • H - hypoglycaemia
  • A - Acidosis (lactic)
  • (L - in the liver)
  • F - fatty change (steatosis)
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33
Q

porphyria with neuropsychiatric symptoms likely due to which enzyme deficiency? disease name?

A

will be early step enzyme –> PBG deaminase acute intermittent porphyria

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34
Q

lab findings - methylmalonic acidaemia

A

(AR mutation in methylmalonyl CoA mutase) acidaemia ketosis increased urine propionic acid hypoglycaemia hyperammonaemia

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35
Q

vitamin B9 name, function

A

folate/folic acid methyl group carrier - purine and thymine synthesis

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36
Q

metabolism 1 g of alcohol = ? cal

A

7

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37
Q

process of base excision repair

A

base-specific glycosylase - endonuclease - lyase - DNA polymerase - DNA ligase

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38
Q

Lesch-Nyhan syndrome enzyme, build up, features, Rx

A
  • enzyme = HGPRT (hypoxanthine-guanine phosphoribosyltransferase)
  • build up = uric acid
  • features = high serum urate, gout, aggression/irritability, SpLD, dystonia
  • Rx = allopurinol, febuxostat (xanthine oxidase inhibitors)
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39
Q

role of vitamin C/ascorbic acid

A

cofactor for hydroxylation of proline and leucine residues on procollagen fibers

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40
Q

familial hypercholesterolaemia (IIa)

A
  • increased = LDL, cholesterol
  • deficiency = LDL receptors
  • features = atherosclerosis, xanthoma, corneal arcus
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41
Q

Essential fructosuria enzyme, build up, features

A
  • enzyme = fructokinase
  • build up = fructose
  • features = none
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42
Q

hypertrigliceridaemia (IV)

A
  • increased = VLDL, TGs
  • patho = POLYGENIC increased VLDL production in liver
  • features = acute pancreatitis
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43
Q

Kartagner’s syndrome define, clinical features

A
  • B/g = genetic defect in dynein protein, ciliary dysfunction
  • clin features = sinusitis, otitis media, pneumonia, bronchitis, male infertility
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44
Q

vitamin B6 name, function

A

pyridoxine

transaminase cofactor

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45
Q

VLCFA and branched chain fatty acids broken down where?

A

peroxisome

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46
Q

hepatic amino group acceptor for transamination

A

alpha-ketoglutarate (Always)

AA + alpha-ketoglutarate –> TCA intermediary + glutamate

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47
Q

mRNA stop codons

A

UGA (U go away) UAA (U are away) UAG (U are gone)

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48
Q

phenylketonuria (PKU) define, features, Rx

A
  • b/g = phenylalanine hydroxylase deficiency, build up of PhenylAla, deficiency of tyrosine
  • features = mental retardation, albinism, growth restriction, musty odour
  • Rx = aspartame/phenylalanine restricted diet, tyrosine supplement
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49
Q

von Gierke disease type, enzyme, build up, features

A

Type I enzyme = glucose 6-phosphatase

build up = glucose 6-phosphate

features = hepatomegaly and steatosis, fasting hypoglycaemia, lactic acidosis, hyperuricaemia and gout

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50
Q

vitamin B1 name, function

A

thiamine decarboxylation of alpha-keto acids (carbohydrate metabolism)

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51
Q

mRNA start codon

A

AUG

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52
Q

which tissue is GLUT-5 found?

A

fructose transporter in spermatocytes

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53
Q

lab findings - B7 deficiency

A

hyperammonaemia hypoglycaemia metabolic acidosis and ketosis normal urine methylmalonic acid

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54
Q

Marfan’s syndrome define, features,

A
  • b/g = fibrillin gene mutation, fibrillin component of extracellular matrix
  • features = arachnodactyle, hypermobility, high arching palate, AAA, valvular disease, retinal detachment, lens dislocation, aortic dissection, pectus excavatum
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55
Q

I-cell disease define, features, lab findings

A
  • B/g = golgi cannot phosphorylate mannose residues on lysosomal enzymes so are trafficked out to cell membrane
  • features = coarse facial features, clouded cornea, restricted joint movement
  • findings = lysosomal enzymes in serum
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56
Q

key enzyme in de novo purine synthesis

A

PRPP phosphoribosyl pyrophosphate

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57
Q

role of PNMT control highest concentration in body?

A

conversion of norAd to adrenaline under control of cortisol highest concentration in adrenal medulla

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58
Q

sugars detected by copper reduction test

A

Reducing sugars: fructose glucose galactose

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59
Q

which tissue is GLUT-3 found?

A

placenta and neurons

60
Q

Fabry disease enzyme, build up, features

A
  • enzyme = alpha-galactosidase A
  • build up = ceramide trihexoside
  • findings = peripheral neuropathy, angiokeratoma, cardiovasular/renal disease
61
Q

vitamin B12 name, function

A

cobalamin isomerase and methyltransferase cofactor (DNA and methionine synthesis)

62
Q

DNA Pol III

A

5’ to 3’ DNA synthesis 3’ to 5’ exonuclease “proofreading” activity

63
Q

Function - primase (RNA polymerase)

A

synthesis of RNA primer

64
Q

DNA ligase

A

joining of okazaki fragments

65
Q

blotting technique = southwestern

A

detects = DNA-binding proteins

uses = double-stranded DNA

66
Q

tRNA structure: T loop

A

contains TpsiC motif

  • T = ribothymidine
  • psi = pseudouridine
  • C = cystidine

Factilitates binding to ribosome

67
Q

exclusively ketogenic amino acids

A

lysine leucine isoleucine tryotophan tyrosone phenylalanine

68
Q

Function - helicase

A

unwinding of double helix

69
Q

biotin (vitamin B7) deficiency association, enzymes affected, clinical features

A
  • egg white consumption (biotin-binding avadin)
  • enzymes = pyruvate carboxylase, acetyl-CoA carboxylase, propionyl-CoA carboxylase
  • features = macular dermatitis, metabolic acidosis (pyruvate to lactic acid shunt, propionyl CoA to methylmalonyl CoA)
70
Q

process of nucleotide excision repair

A

endonuclease - DNA polymerase - DNA ligase

xeroderma pigmentosum

71
Q

cholesterol 7-alpha reductase function, implication in pathology, pharmacologic inhibition

A
  • function = rate limiting step in bile salt formation from circulating cholesterol.
  • pathology = malfunction results in decreased bile salt:cholesterol ratio predisposing to gall stone formation
  • inhibition = fibrate drugs (fenofibrate, gemifibrozil)
72
Q

Cori disease(s) type, enzyme, build up, features

A

Type III enzymes = debranching enzymes (alpha 1,6-glucosidase)

build up = very short branching chain glycogen

features = hepatomegaly, ketotic hypoglycaemia, weakness - LACTATE normal

73
Q

Substrates needed for NAD+ production

A

Niacin (B3), nicotinamide

Tryptophan can endogenously make niacin

74
Q

porphyria with photosensitivity likely due to which enzyme deficiency? disease name?

A

will be late step enzyme –> UroD (uroporphyrinogen decarboxylase) porphyria cutanea tarda (PCT)

75
Q

vitaminB2 name, function

A

riboflavin mitochondrial electron carrier

76
Q

metabolism 1 g of fat = ? cal

77
Q

familial dysbetalipoproteinaemia (III)

A

increased = chylomicrons and VLDL (decreased HDLs)

deficiency = ApoE

features = xanthoma, xanthoma striatum palmare, atherosclerosis

78
Q

role of COMT

A

breakdown of catecholamines adrenaline –> metanephrine norAd –> normetanephrine

79
Q

alkaptonuria enzyme, bulid up, features

A

enzyme = homogentisic acid dehydrogenase

build up = homogentisate - intermediate break down product of tyrosine when it doesn’t go on to make DOPA (melanin and catecholamines)

features = arthritis, ankylosis, blue-black sclera and ears

80
Q

metabolism 1 g of protein = ? cal

81
Q

role of vitamin B12 (cobalamin)

A

cofactor for methylmalonyl CoA mutase converts methylmalonyl CoA to succinyl CoA which enters the TCA cycle for gluconeogenesis

82
Q

clinical findings: hyperammonaemia

A

cerebral oedema, vomiting, hyperventilation, lethargy, blurred vision

83
Q

Methanol poisoning toxins, biochemical pathway, features, Rx

A
  • toxins = antifreeze, paint thinner, moonshine
  • b/g = formaldehyde is toxic clearance product
  • features = snow storm vision, death
  • treatment = fomepezole and alcohol (competitive inhibition)
84
Q

initiation of glycogenesis

A

enzyme = glycogen synthase

function = bind UDP-glucose together into glycogen

control = + insulin receptor and protein phosphatase, - PKA

85
Q

vitamin B1; name, 4 enzymes dependent on it

A

thiamine

  1. pyruvate dehyrogenase
  2. alpha-ketoglutarate dehydrogenase
  3. branched chain a-keto acid dehydrogenase
  4. transketolase (ribulose 5-P to glyceraldehyde 3-P)
86
Q

Essential amino acids

A

PVT TIM HALL P - phenylalanine, V - valine, T - threonine, T - tryptophan, I - isoleucine, M - methionine, H - histidine, A - Arginine - L - Leucine, L - lysine

87
Q

primary carnitine deficiency enzyme, build up, clinical features (3)

A
  • plasma membrane carnitine transporter
  • fatty acids in cytoplasm - cannot enter mitochondria for beta-oxidation or ketone body production
  • myopathy, cardiomyopathy, hypoketotic hypoglycaemia (eventually encephalopathy)
88
Q

metabolism 1 g of carbohydrate = ? cal

89
Q

Pompe disease type, enzyme, build up, features

A
  • Type II
  • enzyme = acid alpha 1,4-glucosidase/acid maltase
  • build up = lysosomes containing glycogen
  • features = normal glucose levels in the blood, severe CARDIOMEGALY, exercise intolerance, hepatomegaly, infant death
90
Q

blotting technique = southern

A

detects = DNA

uses = single stranded DNA or RNA

91
Q

which is the insulin dependent GLUT?

92
Q

vitamin B12 name, deficiency

A

cobalamin

megaloblastic anaemia, peripheral neuropathy (subacute combinded degeneration of the spine)

93
Q

urea cycle - rate limiting step, enzyme, regulator and subcellular location

A
  • step = CO2 + NH4+ + ATP –> carbomyl phosphate
  • enzyme = carbomyl phosphate synthetase I
  • regulator = n-acteylcystine (positive, only available in excess aa)
  • location = mitochondrial matrix
94
Q

blood results in urea cycle dysfunction

A

hyperammonaemia increased glutamine in blood decreased blood urea nitrogen

95
Q

poison mushrooms contain? what does this inhibit? clinical features?

A
  • amatoxin
  • RNA Pol II
  • abdo pain, NandV, watery diarrhoea with blood and mucus. acute hepatic and renal failure, death.
96
Q

amino acids required for purine synthesis

A

GAG G - glycine A - aspartate G - glutamine

97
Q

which tissue is GLUT-1 found?

A

erythrocytes and BBB

98
Q

Haemoglobin C mutation

A

glutamate (negative) to lysine (positive)

99
Q

Function - topoisomerase II

A

removal of supercoils

100
Q

Growth hormone receptor type and main function

A

type = JAK-STAT activator, NOT a RTK.

function = increase transcription of IGF-1

101
Q

ornithine transcarbomylase (OTC) deficiency build up blood findings inheritance

A
  • build up = carbomyl phosphate, shunting to pyrimidine pathway which produced orotic acid blood
  • findings = hyperammonaemia, HIGH orotic acid, low BUN
  • inheritance = XR
102
Q

adenosine deaminase deficiency enzyme, build up, features

A

enzyme = adenosine deaminase

build up = ATP and deoxyATP, inhibition of ribonucleotide reductase, decreased DNA synthesis, decreased lymphocyte count

features = SCID

103
Q

which tissue is GLUT-2 found?

A

liver, renal tubule (basolateral), islet beta cells, small intestine mucosa

104
Q

DNA Pol I (3)

A
  • 5’ to 3’ DNA synthesis
  • 3’ to 5’ exonuclease “proofreading” activity
  • Removal of RNA primer, replaces it with DNA
105
Q

role of MAO

A

breakdown of catecholamines metanephrine and normetanephrine to vanillylmandelic acid

106
Q

Renal ammoniagenesis

A

Glutamine - glutamate - a-ketoglutarate - glucose

products = NH3+ and HCO3- mechanism of increased acid excretion in chronic acidosis

107
Q

vitamin B3 name, function

A

niacin electron transfer reactions (NAD, NADP)

108
Q

vitamin B3 name, deficiency

A

niacin

pellagra - dermatitis, dementia, diarrhoea

109
Q

2 functions of NADPH

A

cholesterol and fatty acid synthesis glutathione antioxidant mechanism

110
Q

vitamin B2 name, deficiency symptoms

A

riboflavin

angular stomatitis, glossitis normocytic anaemia

111
Q

Osteogenesis Imperfecta define, features

A

define = collagen type I deficiency

features = blue sclera, joint pain, recurrent #, hearing loss. parent accused of child abuse

112
Q

blotting technique = western

A

detects = protein

uses = antibodies

113
Q

tetrahydrobiopterin (BH4) is required for synthesis of? (3)

A
  1. tyrosine from phenylalanine
  2. DOPA from tyrosine (catecholamines and melanin)
  3. seretonin from tryptohpan
114
Q

clinically - arthritis and ankylosing spondylitis

what disease? What builds up? enzyme deficiency? special lab finding?

A

Alkaptonuria

Homogentisic acid

homogentisic acid dioxygenase

Urine turns purple/black when left in air as homogentisate is oxidised

115
Q

gross cerebral pathology - periaqueductal grey matter and mammillary bodies haemorrhage and necrosis

disease? epidemiology? deficit? enzyme affected?

A

Wernicke’s encephalopathy

Alcoholics

B1 - thiamine

transketolase (PPP), pyruvate dehydrogenase, alpha-ketoglutarate dehyrogenase, branched chain alpha-keto acid dehydrogenase (catabolism of branched chain amino acids)

116
Q

pellagra-like skin erruptions, cerebellar ataxia, neutral amino acids detected in the urine…

disease? deficiency? treatment?

A

Hartnup disease - neutral amino acid transporter impairment. of note is deficiency in tryptophan that makes up to 50% of NAD+ in the body.

NAD+ deficiency

high protein diet, niacin and nicotinamide replacement.

117
Q

2 causes of elevated orotic acid?

A
  1. uridine monophosphate (UMP) synthase deficiency (megaloblastic anaemia with no ammonaemia)
  2. OTC deficiency (with ammonaemia)
118
Q

in what situation does glycolysis of one glucose molecule yeild 1 molecule of pyruvate, but no net ATP?

A

in erythrocytes when 1,3-bisphosphoglycerate is shunted to produce 2,3-BPG during hypoxia to decrease Hb oxygen affinity, and deliver more oxygen to target tissues

enzyme = bisphosphoglycerate mutase

119
Q

what is the DNA damage caused by UV-B?

A

pyrimidine dimers, then causes double stranded break when it comes to replication

120
Q

genetic principle

NF1 patients with different disease severity

A

variable expressivity

121
Q

genetic principle

not all BRCA1 ​gene mutations results in breast cancer

A

incomplete penetrance

122
Q

genetic principle

single gene disorder PKU manifests in light hair, musty body odour and intellectual disability

A

pleiotropy

123
Q

genetic principle

trinucleotitde repeat diseases become more severe in progressive generations

A

anticipation

124
Q

genetic principle

heterozygous autosomal recessive inheritance with environmental damage to the wild type allele results in disease

common examples?

A

Two-hit hypothesis, loss of heterozygosity

HNPCC, Li fraumeni (p53), retinoblastoma

125
Q

genetic principle

mutation to one allele of a transcription factor in its allosteric site, allowing binding to promoter sequence but no activation

A

dominant negative mutation

126
Q

explain the importance of germline mosaicism

A

germline (gonadal) mosaicism = gene mutation occurs in the sperm or egg

offspring genotypically distinct from family.

incidence of genetic disorder in previously unaffected family

127
Q

2 mechanisms by which ionizing radiation causes cell death

A
  1. DNA double-strand breakage
  2. free radical formation
128
Q

what are the 5 diseases caused by meiotic nondisjunction?

A

trisomy 13, 18, 21

turner syndrome (45, X)

Klinefelter (47 XXY)

129
Q

VHL is found at which locus?

130
Q

which are the purines?

131
Q

what are the pyrimidines?

132
Q

what part of the cell cycle is a primary oocyte held in?

A

prophase of meiosis I

133
Q

before fertilisation, the seconday oocyte is frozen in what phase of the DNA cycle?

A

metaphase of meiosis II

134
Q

genetic inheritance of PKU?

A

autosomal recessive

135
Q

mutation in transthyretin causes what diseases?

A

transthyretin = prealbumin

mutation leads to misfolding and tissue deposition; familial amyloid polyneuropathy & familial amyloid cardiomyopathy

136
Q

which histone subprotein binds the nucleosome/DNA core from the outside, rather than form part of the middle?

A

H1

others (H2A, H2B, H3, H4) all form the nucleosome core around which the DNA is coiled

137
Q

what is the Kozak consensus sequence and what is its function?

A

(gcc)gccRccAUGg

initiation of translation, so this refers to mRNA sequence

R = purine, A or G; AUG = methionine start codon

138
Q

what enzyme produces mRNA in the eukaryotic nucleus?

A

nuclear RNA Polymerase II

139
Q

explain enhancer sequences

A

enhancer - located upstream, downstream or within a gene. can be very far away.

can promote or enhance transcription

bind activator or silencer proteins, which alter RNA Pol II and TFs binding to promotor region of genes

140
Q

pathoG - blotchy red muscle fibres on Gomori trichrome stain

A

mitochondrial myopathy (MERRF, Leber optic neuropathy, MELAS)

141
Q

what are the numbers relevant to CGG trinucleotide repeats in fragile X syndrome?

A

5 - 55 is normal

> 200 is complete mutation = fragile X syndrome

CGG TNRs results in FMR1 hypermethylation and reduced expression, thereby impairing proper neurological development

142
Q

what do alopecia, epilepsy and glaucoma have in common?

A

polygenic inheritance

143
Q

Homeobox genes are mainly responsible for coordination of which body axis?

A

cranio-caudal

144
Q

what is the most common mutation in cystic fibrosis and what is the effect?

A

deletion of phenylalanine (delF508)

impaired post-translational processing - resulting protein targeted to proteasome and unable to reach cell surface

145
Q

what are the 3 inheritance patterns for down syndrome?

A

mitotic nondisjunction 95%

unstable Robertsonian transloc ation 2-3%

early embryonic nondisjunction (mosaicism) <2%

146
Q

inheritance of neurofibromatosis types 1 and 2

A

NF1 - autosomal dominant Ch 17 with highly variable presentation, NF1 gene

NF2 - autosomal dominant microdeletion syndrome Ch 22q12 “Merlin” gene

USMLE S1 (16 decks)

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