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Flashcards in Biochem Deck (422):
1

Purine & Pyrimidine Synthesis

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2

Purine Salvage

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3

PKU

AR Deficiency of Phe Hydroxylase or BH4 cofactor

  • Growth retardation
  • Intellectual disability
  • Seizures
  • Fair skin
  • Eczema
  • Musty odor (aromatic AA metab problem)

Rx: Avoid Phe, Add Tyr +/- BH4

4

Phenylketones

  • phenylacetate
  • phenyllactate
  • phenylpyruvate

5

Maternal PKU

lack of proper dietary therapy during pregnancy → infant:

  • microcephaly
  • intellectual disability
  • growth retardation
  • congenital heart defects

6

Albinism

Tyrosinase deficiency

OR

Defective Tyr transport

7

Homocystinuria

Cystathionine Synthase def

OR

Dec CBS affinity for Vit B6

OR

Homocysteine Methyltransferase def

(all AR)

  • Homocystine in urine
  • Intellectual disability
  • Osteoporosis
  • Kyphosis
  • Marfanoid habitus
  • Atherosclerosis / thrombosis
  • Downward lens subluxation

8

Cystinuria

AR defect of renal PCT and intestinal AA transporter that prevents reabsorption of Cystine, Ornithine, Lysine, Arginine (COLA)

  • cystine renal stones

Dx: Urinary cyanide-nitroprusside test

Rx: urinary alkalinization OR chelators

9

Cystine

made of 2 cysteines connected by a disufide bond

10

MSUD

AR branched-chain α-ketoacid dehydrogenase (B1) def → blocked degradation of branched amino acids (Isoleucine, Leucine, Valine)

  • CNS defects
  • Intellectual disability
  • Poor feeding / vomiting
  • Sweet-smelling urine
  • Death

Rx: Ile / Leu / Val restriction + B1 supp

11

Hartnup disease

AR defect in intestinal transporter for neutral AAs

  • Trp def → niacin + melatonin def
  • Pellagra symp

12

Zn deficiency

  • Dec immune response
  • Dec wound healing
  • Dec growth
  • Dec mental fcn
  • Dec night vision
  • Infertility

13

Mercury poisoning

Accumulates in kidney + brain

  • Acrodynia (fingertip peeling)
  • Abd pain
  • Peripheral neuropathy
  • Tremor
  • Excitability
  • Insomnia

14

Lead poisoning

inhibits ferrochelatase, ALAD → dec heme synthesis + RBC protoporphyrin

AND

inhibits rRNA degradation → RBCs retain rRNA aggregates (basophilic stippling)

  • Lead Lines on gingivae (Burton lines) and long bone metaphyses
  • Encephalopathy
  • Erythrocyte basophilic stippling
  • Abdominal colic
  • Sideroblastic Anemia
  • Wrist and foot drop

Rx: Dimercaprol, EDTA, Succimer

15

Vit A

  • Antioxidant
  • Constituent of visual pigments (retinal)
  • Essential for normal differentiation of epithelial cells into specialized tissue (pancreatic cells, mucus-secreting cells)
  • Prevents squamous metaplasia
  • Used to treat measles and AML subtype M3

16

Vit A def

  • Night blindness (nyctalopia)
  • dry, scaly skin (xerosis cutis)
  • corneal degeneration (keratomalacia)
  • Bitot spots on conjunctiva
  • immunosuppression

17

Vit A toxicity

Acute: nausea, vomiting, vertigo, blurred vision

Chronic:

  • alopecia
  • dry skin (eg, scaliness)
  • hepatic toxicity/enlargement
  • arthralgias
  • pseudotumor cerebri

18

Vit B1

  • Thiamine
  • Cofactor for TCA cycle and PPP:
    • Pyruvate dehydrogenase
    • α-ketoglutarate dehydrogenase
    • Transketolase

 

19

Vit B1 def

Impaired glucose breakdown → ATP depletion worsened by glucose infusion

  • Seen in malnutrition and alcoholism
  • highly aerobic tissues (brain, heart) affected 1st
  • Wernicke-Korsakoff syndrome
  • Wet/Dry Beriberi

Dx: Inc RBC transketolase activity following B1 administration

20

Dry Beriberi

Vit B1 def

  • polyneuritis
  • symmetrical muscle wasting

21

Wet Beriberi

Vit B1 def

  • high-output cardiac failure (dilated cardiomyopathy)
  • edema

22

Vit B2

Riboflavin

  • Component of flavins FAD and FMN
  • Used as cofactors in redox rxns (dehydrogenases)

23

Vit B2 def

  • Cheilosis (inflamm of lips, scaling and fissures at corners of mouth)
  • Corneal vascularization

24

Vit B3

Niacin

  • Derived from tryptophan
  • Constituent of NAD+, NADP+ (used in redox rxns)
  • Synthesis requires vit B2 and B6
  • Rx dyslipidemia: lowers VLDL and raises HDL

25

Vit B3 def

Pellagra

  • Glossitis
  • Dermtitis
  • Diarrhea
  • Dementia

26

3 causes of pellagra

  1. Hartnup disease
  2. Malignant carcinoid syndrome (inc Trp metabolism)
  3. Isoniazid (dec vit B6)

27

Vit B3 toxicity

  • Facial flushing (induced by PGs; can avoid w/aspirin)
  • hypERglycemia
  • hypERuricemia

28

Vit B5

Pantothenic Acid

  • Essential component of:
    • CoA (cofactor for acyl transfers)
    • Fatty acid synthase

29

Vit B5 def

  • Dermatitis
  • enteritis
  • alopecia
  • adrenal insufficiency

30

Vit B6

Pyridoxine

  • Converted to active pyridoxal phosphate (PLP)
  • Cofactor used in:
    • transamination (ALT / AST)
    • decarboxylation rxns
    • glycogen phosphorylase
  • Needed for synth of:
    • cystathionine
    • heme
    • niacin
    • histamine
    • neurotransmitters (5-HT, DA, NE, EPI, GABA)

31

Vit B6 def

  • Convulsions
  • Hyperirritability
  • Peripheral neuropathy (def inducible by isoniazid and oral contraceptives)
  • Sideroblastic anemias (due to impaired Hb synth and iron excess)

32

Vit B7

Biotin

Cofactor for carboxylation enzymes (which add a 1-carbon group):

  • Pyruvate carboxylase: pyruvate (3C) → oxaloacetate (4C)
  • ƒAcetyl-CoA carboxylase: acetyl-CoA (2C) → malonyl-CoA (3C)
  • ƒPropionyl-CoA carboxylase: propionyl-CoA (3C) → methylmalonyl-CoA (4C)

33

Vit B7 def

Caused by antibiotic use or excessive ingestion of raw egg whites. Relatively rare.

  • Dermatitis
  • alopecia
  • enteritis

 

34

Vit B9

Folate

  • Converted to THF, a coenzyme for 1-carbon transfer/methylation reactions.
  • Important for synth of nitrogenous bases in DNA and RNA
  • Found in leafy green vegetables
  • Absorbed in jejunum
  • Small reserve pool stored primarily in liver

35

Vit B9 def

Most common vitamin def in US

  • Seen in alcoholism, pregnancy, drugs (phenytoin, sulfonamides, methotrexate)
  • Macrocytic, megaloblastic anemia
  • Glossitis
  • NO neurologic symp (as opposed to B12 def)
  • Inc homocysteine, normal methylmalonic acid

36

Vit B12

Cobalamin

  • Cofactor for methionine synthase (transfers CH3 groups as methylcobalamin) and methylmalonyl-CoA mutase
  • Found in animal products
  • Synthesized only by microorganisms
  • Absorbed in terminal ileum (bound to IF)
  • Very large reserve pool (several years) stored primarily in liver

37

Vit B12 def

  • Macrocytic, megaloblastic anemia
  • abnormal myelin
    • paresthesias
    • subacute combined degeneration (dorsal columns, lateral corticospinal tracts, spinocerebellar tracts)
  • Inc serum homocysteine and methylmalonic acid
  • Prolonged def → irreversible nerve damage

38

Causes of Vit B12 def

  • Malabsorption (sprue, enteritis, Diphyllobothrium latum)
  • Lack of intrinsic factor (pernicious anemia, gastric bypass surgery)
    • Anti-IF Ab's diagnostic for pernicious anemia
  • Absence of terminal ileum (surgical resection, Crohn's)
  • Long-term insufficient intake (veganism)

 

39

Vitamin C

Ascorbic acid

  • Antioxidant
  • Found in fruits and vegetables
  • Facilitates iron absorption by reducing it to Fe2+ 
  • Necessary for:
    • Hydroxylation of proline and lysine in collagen synth
    • Dopamine β-hydroxylase (DA → NE)

40

Vit C def

Scurvy

  • swollen / bleeding gums
  • poor wound healing
  • bruising / petechiae
  • hemarthrosis
  • perifollicular and subperiosteal hemorrhages
  • anemia
  • “corkscrew” hair
  • Weakened immune response

41

Vit C toxicity

  • Nausea / vomiting
  • diarrhea
  • fatigue
  • calcium oxalate nephrolithiasis
  • Can inc risk of iron toxicity in predisposed individuals (transfusions, hereditary hemochromatosis)

42

Vit D

Forms:

  • D2 = ergocalciferol—ingested from plants
  • D3 = cholecalciferol—consumed in milk, formed in sun-exposed skin (stratum basale)
  • 25-OH D3 = calcidiol—storage form (liver)
  • 1,25-(OH)2 D3 = calcitriol—active form (kidney)

Fcn:

  • inc intestinal absorption of calcium and phosphate
  • bone mineralization at low levels
  • bone resorption at higher levels

43

Vit D synth

Ergocalciferol / D2 (food) or Cholecalciferol / D3 (skin)

liver 25-hydroxylase →

Calcidiol / 25-OH D3

kidney 1-alpha-hydroxylase →

Calcitriol / 1,25-OH D3

44

Vit D def

Breastfed infants should receive oral Vit D supp

Def exacerbated by low sun exposure, pigmented skin, prematurity

  • Rickets in children (bone pain and deformity)
  • Osteomalacia in adults (bone pain and muscle weakness)
  • HypOcalcemic tetany

45

Vit D toxicity

Seen in granulomatous disease (activation of Vit D by epithelioid macrophages)

  • HypeERcalcemia
  • hypERcalciuria
  • loss of appetite
  • stupor

46

Vitamin E

Tocopherol / Tocotrienol

  • Antioxidant (protects RBCs and membranes from free radical damage)
  • Can enhance anticoagulant effects of warfarin

47

Vitamin E toxicity

  • Hemolytic anemia (RBC oxidative damage)
  • Acanthocytosis
  • Muscle weakness
  • Posterior column and spinocerebellar tract demyelination

may appear similar to B12 def, but NO megaloblastic anemia, hypersegmented neutrophils, or inc methylmalonic acid

48

Vitamin K

Phytomenadione, Phylloquinone, Phytonadione

  • Synthesized by intestinal flora
  • Cofactor for γ-carboxylation of glutamic acid residues on proteins required for blood clotting 
  • Necessary for maturation of clotting factors 2, 7, 9, 10, and Proteins C / S

49

Vitamin K def

  • Neonatal hemorrhage with inc PT and aPTT but normal bleeding time
    • neonates given vit K injection at birth to prevent hemorrhagic disease (sterile intestines @ birth)
  • Can also occur after prolonged use of broad-spectrum Abx

50

3 major glycolysis enzymes

  1. Glucokinase/Hexokinase (Glucose → G6P)
  2. PFK-1 (Fructose-6P → Fructose-1,6-BP)
  3. Pyruvate Kinase (PEP → Pyruvate)

51

Pyruvate kinase deficiency

inability to maintain Na+/K+ ATPase → RBC swelling → hemolytic anemia

52

rate-limiting enzyme of glycolysis

PFK-1

53

Regulation of PFK-1

  • Increased activity: AMP, Fructose-2,6-bisphosphate
  • Decreased activity: ATP, Citrate

54

Regulation of pyruvate kinase

  • Increased activity: AMP, Fructose-1,6-bisphosphate
  • Decreased activity: ATP, Alanine

55

Regulation of fructose-2,6-bisphosphate production

  • Insulin → +PFK2 (dephosphorylated) → +F-2,6-BP → +PFK1 → glycolysis
  • Glucagon → +FBPase2 (phosphorylated) → +F-6P → gluconeogenesis

56

3 irreversible steps in glycolysis

  1. Glucose → Glucose-6P (Glucokinase/Hexokinase)
  2. Fructose-6P → Fructose-1,6-BP (PFK-1)
  3. PEP → Pyruvate (Pyruvate Kinase)

57

4 enzymes unique to gluconeogenesis

  1. Pyruvate Carboxylase + biotin (pyruvate → oxaloacetate)
  2. PEP Carboxykinase (oxaloacetate → PEP)
  3. Fructose-1,6-Bisphosphatase (fructose-1,6-bisphosphate → fructose-6-phosphate) *rate-limiting
  4. Glucose-6-Phosphatase (fructose-6-phosphate → glucose-6-phosphate)

58

rate-limiting enzyme of gluconeogenesis

Fructose-1,6-Bisphosphatase

59

rate-limiting enzyme of pyrimidine synth

CPS-2

60

rate-limiting enzyme of purine synth

Glutamine PRPP Amidotransferase

61

rate-limiting enzyme of glycogen synth

Glycogen Synthase

62

rate-limiting enzyme of glycogenolysis

Glycogen Phosphorylase

63

rate-limiting enzyme of TCA Cycle

Isocitrate Dehydrogenase

64

rate-limiting enzyme of Hexose Monophosphate Shunt

Glucose-6-Phosphate Dehydrogenase

65

Gibbs Free Energy Eqn

G = H - TS

66

CPS-1 vs CPS-2

CPS-1

  • Urea cycle
  • Mitochondria
  • N from Ammonia

CPS-2

  • Pyrimidine synth
  • Cytoplasm
  • N from Glutamine

67

McArdle Disease

Glycogen Phosphorylase deficiency

  • Painful mm cramps
  • Rhabdomyolysis w/exercise

68

Von Gierke disease

Glucose-6-Phosphatase deficiency

  • Severe fasting hypOglycemia
  • Hepatomegaly
  • Enlarged kidneys
  • HypERlipidemia
  • Inc Lactate
  • Inc Uric Acid

*remember: symp only in tissues that have g6-phosphatase (liver, kidneys, intestinal epithelium...no muscle!)

69

Cori disease

Alpha-1,6-Glucosidase / Debranching Enzyme deficiency

  • Milder form of Von Gierke
  • No inc lactate or uric acid

70

Pompe disease

Alpha-1,4-Glucosidase deficiency in lysosomes

  • Severe mm weakness
  • Cardiomegaly → HF (infantile)
  • Diaphragm weakness → resp failure (adult)

71

rate-limiting enzyme in carbohydrate digestion

oligosaccharide hydrolases

72

cofactors needed for pyruvate dehydrogenase

  • TPP (Vit B1)
  • Lipoic acid
  • CoA (from Vit B5)
  • FAD (from Vit B2)
  • NAD (from Vit B3)

73

cofactors needed for alpha-ketoglutarate dehydrogenase

  • TPP (Vit B1)
  • Lipoic acid
  • CoA (from Vit B5)
  • FAD (from Vit B2)
  • NAD (from Vit B3)

74

4 possible fates of pyruvate

  1. Oxaolacetate (via Pyruvate Carboxylase + Biotin)
  2. ACoA (via Pyruvate Dehydrogenase + cofactors)
  3. Alanine (via Alanine Transaminase)
  4. Lactate (via Lactate Dehydrogenase)

75

Pyruvate dehydrogenase deficiency

XL or acquired

  • Pyruvate shunted to lactate or alanine (instead of ACoA)
  • Lactic acidosis
  • Neuro defects

Rx: inc intake ketogenic nutrients (Leu + Lys or high fat)

76

Ketogenic AAs

  • Lysine
  • Leucine

77

3 important TCA cycle enzymes

  1. Citrate Synthase (ACoA → Citrate)
  2. Isocitrate Dehydrogenase (Isocitrate → Alpha-ketoglutarate) *rate-limiting
  3. Alpha-Ketoglutarate Dehydrogenase (alpha-ketoglutarate → Succinyl-CoA)

78

ETC Complex I

NADH Reductase

79

ETC Complex II

Succinate Dehydrogenase (+CoQ)

80

ETC Complex III

Cytochrome b + c1

81

ETC Complex IV

Cytochrome a + a3

82

ETC Complex V

ATPase

83

How many ATP per molecule in ETC?

  • 2.5 ATP per NADH
  • 1.5 ATP per FADH2

84

ETC Complex I Inhibitors

  • Amytal
  • Rotenone
  • MPP

85

ETC Complex III Inhibitors

Antimycin A

86

ETC Complex IV Inhibitors

  • Cyanide
  • N3- (Azide)
  • CO
  • H2S

87

ETC Complex V Inhibitors

Oligomycin A

88

ETC Uncouplers

Make IMM more permeable to H+ and ruin gradient

  • Thermogenin
  • High-dose aspirin
  • 2,4-DNP (weight loss supp)

89

Cori Cycle

  • Lactate made from pyruvate in mm/RBC
  • Lactate transported to liver and made back into pyruvate
  • Pyruvate used for gluconeogenesis

90

Alanine Cycle

Transamination + Deamination → N transport

  • Alanine & glutamine produced and transported from mm to liver to excrete N via Urea Cycle

 

91

2 major carriers of N in blood

  • Alanine
  • Glutamine

92

Transamination rxns

  • Transaminases / Aminotransferases transfer amino group from AA to alpha-ketoglutarate → Glutamate
  • Deaminated AA → Ketoacid → used in energy metabolism

93

2 most important transaminases

  1. Alanine Transaminase/ ALT (Alanine + Alpha-kg → Pyruvate + Glutamate)
  2. Aspartate Transaminase / AST (Aspartate + Alpha-kg → Oxaloacetate + Glutamate)

94

Transaminase cofactor

Vit B6

95

Goal of Pentose Phosphate Pathway

make NADPH

96

Uses of NADPH

  • FA synth
  • Cholesterol synth
  • Oxygen free radical generation
  • RBC protection against free radicals
  • Cyt P450 enzymes

97

3 enzymes of oxidative burst

  1. NADPH Oxidase (makes O2-)
  2. Superoxide Dismutase (makes H2O2)
  3. Myeloperoxidase (makes HOCl)

98

Antioxidants

  • Glutathione peroxidase (neutralizes H2O2)
  • Catalase (neutralizes H2O2)
  • SOD (neutralizes O2-)
  • Reduced glutathione (GSH)
  • Vitamins A, C, E
  • Metal Carrier Proteins (Transferrin, Ceruloplasmin)
  • Spontaneous Decay

99

Essential fructosuria

AR Fructokinase def

  • Fructose in blood and urine
  • Benign/asymptomatic

100

Fructose intolerance

AR Aldolase B def

  • Fructose-1P accumulates → decrease in available phosphate → inhibition of glycogenolysis and gluconeogenesis.
  • Symptoms present following consumption of fruit, juice, or honey.
    • hypoglycemia
    • jaundice
    • cirrhosis
    • vomiting
  • Urine dipstick ⊝ (tests for glucose only);
  • Reducing sugar can be detected in urine (nonspecific test for inborn errors of carb metabolism)

101

Galactokinase def

  • AR inheritance
  • Increased galactitol → cataracts

102

Classical galactosemia

AR Galactose-1-Phosphate Uridyltransferase def

  • Accumulation of toxic substances (incl galactitol)
    • failure to thrive
    • jaundice
    • hepatomegaly
    • infantile cataracts
    • intellectual disability
    • Can lead to E coli sepsis in neonates

103

Fructokinase def

Essential fructosuria

104

Aldolase B def

Fructose intolerance

105

Galactose-1-Phosphate Uridyltransferase def

Classical galactosemia

106

Which body tissues use the pentose phosphate pathway?

  • RBCs
  • Liver
  • Adrenal cortex
  • Mammary glands during lactation

107

Classical galactosemia presentation

  • Cataracts
  • Jaundice
  • Hepatomegaly
  • Intellectual disability
  • Failure to thrive

108

Kwashiorkor

Protein malnutrition: FLAMES

  • Fatty Liver (dec apolipoprotein synth)
  • Anemia
  • Malnutrition (protein)
  • Edema
  • Skin lesions

109

Marasmus

Total calorie malnutrition

  • emaciation
  • tissue and muscle wasting
  • loss of subcutaneous fat
  • +/– edema

110

Refeeding syndrome

Fasting for >5 days → intracellular ion + ATP depletion

  • Food → dec Mg2+, K+, PO43-
  • Inc insulin → hypOphosphatemia → cardiac complications

111

When does gluconeogenesis begin?

4-6h after last meal

112

When does gluconeogenesis become fully active?

10-18h after last meal

113

what fuels used 24h after last meal?

  • Brain: glucose
  • Muscle/other: mostly FAs, some glucose

114

what fuels used 48h after last meal?

  • Brain: glucose, some ketones
  • Muscle/other: mostly FAs, some ketones

115

what fuels used 5 days after last meal?

  • Brain: ketones
  • Muscle/other: FAs, some ketones / glucose

116

Ketone bodies

  • Acetoacetate (measured in urine)
  • Beta-hydroxybutyrate

117

Rate-limiting enzyme in ketone synthesis

HMG-CoA Synthase

118

Why does EtOH cause hypoglycemia?

Produces NADH, so tries to regenerate NAD+ via:

  • Pyruvate → Lactate
  • Oxaloacetate → Malate

Once these substrates are gone, gluconeogenesis can't occur → severe fasting hypOglycemia

119

ACoA used for?

Comes from acetate, pyruvate

  1. TCA Cycle
  2. FA Synth
  3. Cholesterol Synth
  4. Ketone Synth

120

Apo-B48

Chylomicrons from enterocytes → lymphatics

121

Apo-B100

VLDL from liver → circulation

122

ApoE

Mediates extra remnant uptake

123

Apo-AI

Activates LCAT on HDL

124

Apo-CII

Cofactor for LPL (TG → FFA)

125

Abetalipoproteinemia

AR mut in MTP gene → Apo-B48 and Apo-B100 def

  • Steatorrhea
  • Fat-soluble vitamin def
  • Enterocytes swollen w/TGs
  • Ataxia
  • Night blindness
  • Acanthocytes

Rx: Vit E

126

Lipoprotein Lipase (LPL)

Breaks down TGs into FFAs

127

Lecithin-Cholesterol Acyltransferase (LCAT)

Mediates HDL uptake of cholesterol from periphery

128

Cholesterol-Ester Transfer Protein (CETP)

  • Transfers cholesterol from HDL → VLDL / LDL
  • Transfers TGs from VLDL / LDL → HDL

129

Rate-limiting enzyme of FA Synth

ACoA Carboxylase

130

Rate-limiting enzyme of FA beta-oxidation

Carnitine Palmitoyltransferase / Acetyltransferase-1 (CAT-1)

131

Rate-limiting enzyme of cholesterol synth

HMG-CoA Reductase

132

Type I Hyperchylomicronemia

AR def of LPL OR defect in Apo-CII

  • Inc chylomicrons, TGs, cholesterol
  • Pancreatitis
  • HSmegaly
  • Xanthomas

NO inc risk atherosclerosis

133

Type IIa Familial Hypercholesterolemia

AD defect in LDLR

  • Tendinous xanthomas
  • Accelerated atherosclerosis
  • Early MI

134

Type IV Hypertriglyceridemia

AD overproduction of VLDL

  • Inc TGs
  • Pancreatitis

135

4 major ECG changes in MI

  • ST elevation
  • T wave inversion
  • New Q waves
  • New LBBB

136

Rate-limiting enzyme of urea cycle

CPS-1

137

2 important urea cycle enzymes

  1. CPS-1
  2. Ornithine transcarbamylase

138

Ornithine transcarbamylase deficiency

Most common urea cycle disorder

  • XLR
  • Inc carbamoyl phosphate → orotic acid
  • Inc ammonia
  • Dec BUN

NO megaloblastic anemia

139

CPS-1 cofactor

N-acetylglutamate (allosteric activator)

140

N-acetylglutamate deficiency

CPS-1 can't function

  • presents in neonates
  • hyperammonemia
  • poorly regulated respiration, body temp
  • poor feeding
  • developmental delay
  • intellectual disability

141

CPS-1 deficiency

  • presents in neonates
  • hyperammonemia
  • poorly regulated respiration, body temp
  • poor feeding
  • developmental delay
  • intellectual disability

142

Hyperammonemia

Excess NH3 → alpha-ketoglutarate depletion → TCA cycle arrest

  • Tremor / asterixis
  • Slurred speech
  • Somnolence
  • Vomiting
  • Cerebral edema
  • Blurred vision

143

Rx Hyperammonemia

  1. Lactulose: acidifies GI tract, traps NH4+ for excretion
  2. Rifaximin: decreases colonic ammoniagenic bacteria
  3. Benzoate / Phenylacetate / Phenylbutyrate: bind NH4+ for excretion

144

Aldose reductase

Glucose → Sorbitol

145

Sorbitol Dehydrogenase

Sorbitol → Fructose

146

Which tissues have aldose reductase and sorbitol dehydrogenase?

  • Liver
  • ovaries
  • seminal vesicles

147

4 tissues that have aldose reductase only

  1. Schwann cells
  2. retina
  3. lens
  4. kidneys

148

sorbitol dehydrogenase deficiency

intracellular sorbitol accumulation → osmotic damage

  • cataracts
  • retinopathy
  • peripheral neuropathy

149

lactase deficiency presentation

Usually age-dependent decline after childhood; congenital genetic deficiency rare

  • Inc stool pH
  • Inc breath H+ content
  • Bloating
  • Cramps
  • Flatulence
  • Osmotic diarrhea

150

AA type found in proteins

L-AAs

151

3 Glucogenic AAs

  1. methionine (Met)
  2. valine (Val)
  3. histidine (His)

152

4 Glucogenic/ketogenic AAs

  1. isoleucine (Ile)
  2. phenylalanine (Phe)
  3. threonine (Thr)
  4. tryptophan (Trp)

153

Essential AAs

PVT TIM HaLL

  • Phe
  • Val
  • Thr
  • Tyr
  • Ile
  • Met
  • His
  • Leu
  • Lys

154

Acidic AAs

Negatively charged at body pH

  • Aspartate
  • Glutamate

155

Basic AAs

Usually positively-charged at body pH

  • Histidine → Neutral @ body pH
  • Arginine → Most basic
  • Lysine

Note:

  • Arg and His are required during periods of growth
  • Arg and Lys are in histones, which bind negatively charged DNA

156

Phe derivatives

  • Tyrosine
  • DOPA
  • Melanin
  • DA
  • Catecholamines

157

Tyr derivatives

  • Thyroxine
  • Melanin
  • Homogentisic acid
  • DOPA
  • Catecholamines

158

Trp derivatives

  • Niacin → NAD+ / NADH
  • Serotonin → Melatonin

159

His derivatives

Histamine

160

Glycine derivatives

Porphyrin → Heme

161

Glutamate derviatives

  • GABA
  • Glutathione

162

Arginine derivatives

  • Creatine
  • Urea
  • Nitric Oxide

163

Alkaptonuria

AR Homogentisic oxidase deficiency

  • Dark urine when exposed to air
  • Dark pigment in connective tissue
  • Arthralgias

Rx: Supp Vit C, avoid Phe / Tyr

164

2 important Pentose Phosphate Pathway enzymes

  1. G6PD: oxidative / irreversible (G6P → Ribulose-5P + 2NADPH)
  2. Transketolase + Vit B1: non-oxidative / reversible (Ribulose-5P → Ribose-5P, Glyceraldehyde-3P,  Fructose-6P)

165

Arsenic MOA

inhibits Lipoic Acid → pyruvate dehydrogenase + alpha-ketoglutarate dehydrogenase can't function

166

Kinase

Catalyzes transfer of a phosphate group from a high-energy molecule (usually ATP) to a substrate

167

Phosphorylase

Adds inorganic phosphate onto substrate w/o using ATP

168

Phosphatase

Removes phosphate group from substrate

169

Dehydrogenase

Catalyzes oxidation-reduction reactions

170

Hydroxylase

Adds hydroxyl group (−OH) onto substrate

171

Carboxylase

Transfers CO2 groups with the help of biotin

172

Mutase

Relocates a functional group within a molecule

173

5 metabolic processes in Mitochondria

  1. Fatty acid oxidation (β-oxidation)
  2. Acetyl-CoA production
  3. TCA cycle
  4. OXPHOS
  5. Ketogenesis

174

7 metabolic processes in Cytoplasm

  1. Glycolysis
  2. HMP shunt
  3. steroid synth (SER)
  4. protein synth (ribosomes, RER)
  5. fatty acid synth
  6. cholesterol synth
  7. nucleotide synth

175

3 metabolic processes in cytoplasm + mitochondria

  1. Heme synthesis
  2. Urea cycle
  3. Gluconeogenesis

176

PFK-1 regulation

Inc activity:

  • AMP
  • Fructose-2,6-BP

Dec activity:

  • ATP
  • Citrate

177

Fructose-1,6-Bisphosphatase regulation

Inc activity:

  • ATP

Dec activity:

  • AMP
  • Fructose-2,6-BP

178

Isocitrate dehydrogenase regulation

Inc activity:

  • ADP

Dec activity:

  • ATP
  • NADH

179

Glycogen synthase regulation

Inc activity:

  • G6P
  • Insulin
  • Cortisol

Dec activity:

  • EPI
  • Glucagon

180

Glycogen phosphorylase regulation

Inc activity:

  • EPI
  • Glucagon
  • AMP

Dec activity:

  • G6P
  • Insulin
  • ATP

181

G6PD regulation

  • Inc activity: NADP+
  • Dec activity: NADPH

182

CPS-2 regulation

Inc activity:

  • ATP
  • PRPP

Dec activity:

  • UTP

183

Glutamine-PRPP amidotransferase regulation

Dec activity:

  • AMP
  • IMP
  • GMP

184

CPS-1 regulation

Inc activity: N-acetylglutamate

185

Acetyl-CoA carboxylase regulation

Inc activity:

  • Insulin
  • Citrate

Dec activity:

  • Glucagon
  • Palmitoyl-CoA

186

Carnitine acyltransferase I regulation

Dec activity: Malonyl-CoA

187

HMG-CoA reductase regulation

Inc activity:

  • Insulin
  • Thyroxine

Dec activity:

  • Glucagon
  • Cholesterol

188

Carbohydrate absorption

  • Only monosaccharides (glucose, galactose, fructose) are absorbed by enterocytes
  • Glucose and galactose are taken up by SGLT-1 (Na+-dependent)
  • Fructose is taken up by GLUT-5 facilitated diffusion
  • All are transported to blood by GLUT-2

189

D-xylose absorption test

distinguishes GI mucosal damage from other causes of malabsorption

190

rate-limiting enzyme of bile acid synthesis

Cholesterol 7α-hydroxylase

191

Fabry Disease Enzyme/Accum

  • α-galactosidase A
  • Ceramide trihexoside

192

Fabry Disease Presentation

Inheritance: XLR

Early: Triad of

  • episodic peripheral neuropathy
  • angiokeratomas
  • hypohidrosis

Late:

  • progressive renal failure
  • cardiovascular disease

193

Gaucher Disease Enzyme/Accum

  • Glucocerebrosidase (β-glucosidase)
  • Glucocerebroside

194

Gaucher Disease Presentation

Inheritance: AR

  • Hepatosplenomegaly
  • pancytopenia
  • osteoporosis
  • aseptic necrosis of femur
  • bone crises
  • Gaucher cells (lipid-laden macrophages resembling crumpled tissue paper)

195

Niemann-Pick Enzyme/Accum

  • Sphingomyelinase
  • Sphingomyelin

196

Niemann-Pick Presentation

Inheritance: AR

  • Progressive neurodegeneration
  • hepatosplenomegaly
  • foam cells (lipid-laden macrophages)
  • “cherry-red” spot on macula

197

Tay-Sachs Enzyme/Accum

  • Hexosaminidase A
  • GM2 Ganglioside

198

Tay-Sachs Presentation

Inheritance: AR

  • Progressive neurodegeneration
  • developmental delay
  • “cherry-red” spot on macula
  • lysosomes with onion skin
  • NO hepatosplenomegaly (vs Niemann-Pick)

199

Krabbe Disease Enzyme/Accum

  • Galactocerebrosidase
  • Galactocerebroside, psychosine

200

Krabbe Disease Presentation

Inheritance: AR

  • Peripheral neuropathy
  • developmental delay
  • optic atrophy
  • globoid cells

201

Metachromatic Leukodystrophy Enzyme/Accum

  • Arylsulfatase A
  • Cerebroside Sulfate

202

Metachromatic Leukodystrophy Presentation

Inheritance: AR

  • Central and peripheral demyelination w/ataxia, dementia

203

Hurler Enzyme/Accum

  • α-l-iduronidase
  • Heparan sulfate, dermatan sulfate

204

Hurler Presentation

Inheritance: AR

  • Developmental delay
  • gargoylism
  • airway obstruction
  • corneal clouding
  • hepatosplenomegaly

205

Hunter Enyzme/Accum

  • Iduronate sulfatase
  • Heparan sulfate, dermatan sulfate

206

Hunter Presentation

Inheritance: XLR

  • Mild Hurler
  • aggressive behavior
  • NO corneal clouding

207

Von Gierke Disease Enzyme Deficiency

Glucose-6-phosphatase

208

Von Gierke disease Presentation

  • Severe fasting hypoglycemia (Impaired gluconeogenesis and glycogenolysis)
  • Inc glycogen in liver
  • Inc blood lactate
  • Inc triglycerides
  • Inc uric acid (Gout)
  • Hepatomegaly

209

Pompe Disease Enzyme Deficiency

Lysosomal α-1,4-glucosidase with α-1,6-glucosidase activity (acid maltase)

210

Pompe Disease Presentation

  • Cardiomegaly
  • hypertrophic cardiomyopathy
  • exercise intolerance
  • systemic findings

→ early death

211

Cori Disease Enzyme Deficiency

Debranching enzyme ( α - 1 , 6 - g l u c o s i d a s e)

212

Cori Disease Presentation

  • Milder form of von Gierke (type I) w/normal blood lactate levels
  • Accumulation of limit dextrin–like structures in cytosol
  • Gluconeogenesis is intact

213

McArdle Disease Enzyme Deficiency

Skeletal muscle glycogen phosphorylase (Myophosphorylase)

214

McArdle Disease Presentation

Inc glycogen in muscle, but muscle cannot break it down →

  • painful Muscle cramps + Myoglobinuria (red urine) w/strenuous exercise
  • Arrhythmia from electrolyte abnormalities
  • Second-wind phenomenon noted during exercise due to inc muscular blood flow

215

Chromatin

  • Condensed form of DNA that allows fit into nucleus
  • Negatively charged DNA loops twice around positively charged histone octamer to form nucleosome “beads on a string.”

216

Histones

  • Rich in lysine and arginine
  • Positively-charged
  • DNA wraps around to form chromatin
  • H1 binds to nucleosome and to “linker DNA,” thereby stabilizing the chromatin fiber.

217

DNA synthesis occurs during this phase of replication

S phase

218

Histone synthesis occurs during this phase of replication

S Phase

219

Nucleosomes

  • "Beads on a string"
  • DNA wound around histone

220

Chromatin Structure

A image thumb
222

Histone Acetylation

Relaxes DNA coiling, allowing for transcription

223

Histone methylation

  • Usually reversibly represses DNA transcription
  • can activate it in some cases depending on location.

224

NucleoSide

base + (deoxy)ribose

225

Purines

  • Adenosine, Guanine (PURe As Gold)
  • 2 rings

A image thumb
226

Pyrimidines

  • Cytosine, Thymine
    • Cytosine deamination → Uracil
  • 1 ring

A image thumb
227

NucleoTide

  • base + (deoxy)ribose + phosphaTe
  • linked by 3′-5′ phosphodiester bond

230

Strength of bonds btwn DNA bases

  • G-C bond (3 H bonds) stronger than A-T (2 H bonds)
  • Increased G-C content → increased DNA melting temp

231

3 Amino acids necessary for purine synthesis

  1. Glycine
  2. Aspartate
  3. Glutamine

232

Leflunomide

  • Disrupts pyrimidine synth
  • inhibits dihydroorotate dehydrogenase (carbamoyl phosphate → orotic acid)

233

Methotrexate

  • Disrupts pyrimidine synth
  • inhibit dihydrofolate reductase (dUMP → dTMP) in humans
  • Same MOA: TMP in bacteria, pyrimethamine in protozoa

234

5-FU

  • Disrupts pyrimidine synth
  • Forms 5-F-dUMP, which inhibits thymidylate synthase (dUMP → dTMP)

235

Azathioprine / 6-MP

  • Disrupt purine synth
  • Inhibit Glutamine PRPP Amidotransferase (rate-limiting; PRPP → IMP)
  • Activated by HGPRT
  • Metabolized by Xanthine Oxidase

236

Mycophenolate

  • Disrupts purine synth
  • inhibits inosine monophosphate dehydrogenase

237

Ribavirin

  • Disrupts purine synth
  • Inhibits inosine monophosphate dehydrogenase

238

Hydroxyurea

  • Disrupts purine and pyrimidine synthesis
  • Inhibits ribonucleotide reductase (UDP → dUDP)

239

Adenosine deaminase deficiency

  • One of the major causes of AR SCID
  • ADA is required for degradation of adenosine and deoxyadenosine
  • Increased dATP → toxicity in lymphocytes

240

Lesch-Nyhan syndrome

XLR defect in purine salvage due to absent HGPRT → increased de novo purine synth

  • Hyperuricemia (orange crystals in diaper)
  • Gout
  • Pissed off (aggression, self-mutilation)
  • Retardation (intellectual disability)
  • DysTonia

Rx: allopurinol or febuxostat (2nd line)

241

Genetic code: unambiguous

Each codon specifies only 1 amino acid

242

Genetic code: Degenerate/ redundant

  • Most amino acids are coded by multiple codons.
  • Exceptions: methionine and tryptophan encoded by only 1 codon (AUG and UGG, respectively).

243

Genetic code: Commaless, nonoverlapping

  • Read from a fixed starting point as a continuous sequence of bases.
  • Exceptions: some viruses.

244

Genetic code: Universal

  • Genetic code is conserved throughout evolution.
  • Exception in humans: mitochondria.

245

Origin of replication

  • Particular consensus sequence of base pairs in genome where DNA replication begins.
    • May be single (prokaryotes) or multiple (eukaryotes).
  • AT-rich sequences are found in promoters and origins of replication.

246

Replication fork

Y-shaped region along DNA template where leading and lagging strands are synthesized.

247

Helicase

Unwinds DNA template at replication fork.

248

Single-stranded binding proteins

Prevent strands from reannealing.

249

DNA topoisomerases

Create a single- or double-stranded break in the helix to add or remove supercoils.

250

Primase

Makes an RNA primer on which DNA polymerase III can initiate replication.

251

DNA polymerase III

  • Prokaryotic only.
  • 5' → 3' synthesis.
  • Elongates leading strand by adding deoxynucleotides to the 3′ end.
  • Elongates lagging strand until it reaches primer of preceding fragment.
  • 3′ → 5′ exonuclease activity “proofreads” each added nucleotide.

252

DNA polymerase I

  • Prokaryotic only.
  • Degrades RNA primer; replaces it with DNA.
  • Has same functions as DNA pol III but also excises RNA primer with 5′ → 3′ exonuclease.

253

DNA ligase

Catalyzes the formation of a phosphodiester bond within a strand of dsDNA (ie, joins Okazaki fragments).

254

Telomerase

  • Eukaryotes only.
  • RNA-dependent DNA polymerase
  • Adds DNA to 3′ ends of chromosomes to avoid loss of genetic material with every duplication.
  • Often dysregulated in cancer cells, allowing unlimited replication.

255

DNA Polymerase Alpha

  • Eukaryotes
  • Makes own primer
  • Builds Okazaki fragments

256

DNA Polymerase Delta

  • Eukaryotes
  • Builds leading strand

257

DNA Polymerase Beta

  • Eukaryotes
  • Base excision repair

258

DNA Polymerase Gamma

  • Eukaryotes
  • Replicates mitochondrial DNA

259

RNA Polymerase I

  • Eukaryotes
  • Makes rRNA (most abundant)

260

RNA Polymerase II

  • Eukaryotes
  • Makes mRNA (largest)
  • Opens DNA at promoter site
  • Inhibited by α-amanitin, found in Amanita phalloides (death cap mushrooms)

261

RNA Polymerase III

  • Eukaryotes
  • Makes tRNA (smallest)

262

Prokaryotic RNA Polymerase

  • Only one!
  • Makes rRNA, mRNA, and tRNA
  • Inhibited by Rifampin

263

Severity of damage of DNA mutations

Frameshift > Nonsense > Missense >> Silent

264

Transition Mutation

purine to purine (A to G) or pyrimidine to pyrimidine (C to T).

265

Transversion Mutation

purine to pyrimidine (A to T) or pyrimidine to purine (C to G)

266

Silent Mutation

  • Nucleotide substitution that codes for same (synonymous) amino acid
  • Often base change in 3rd position of codon (tRNA wobble)

267

Missense Mutation

  • Nucleotide substitution resulting in changed amino acid
  • Called conservative if new AA is similar in chemical structure
  • Ex: SCD (Glu → Val)

268

Nonsense Mutation

  • Nucleotide substitution resulting in early stop codon.
  • Usually results in nonfunctional protein.

269

Frameshift Mutation

  • Deletion or insertion of a number of nucleotides not divisible by 3 → misreading of all nucleotides downstream.
  • Protein may be shorter or longer, and its function may be disrupted or altered.
  • Ex: Duchenne muscular dystrophy, Tay-Sachs

270

Splice Site Mutation

  • Mutation at a splice site → retained intron in mRNA → protein with impaired or altered function.
  • Rare cause of cancers, dementia, epilepsy, some types of β-thalassemia.

271

Lac operon

Glucose is preferred metabolic substrate in E coli, but when glucose is absent and lactose is available, lac operon is activated to switch to lactose metabolism (beta-galactosidase)

  • Low glucose → inc adenylate cyclase activity → generation of cAMP from ATP → activation of catabolite activator protein (CAP) → transcription
  • ƒ High lactose → unbinds repressor protein from repressor/operator site → transcription

272

Nucleotide excision repair

  • Repairs bulky helix-distorting lesions in single strand
  • Specific endonucleases release the oligonucleotides containing damaged bases
  • DNA polymerase fills and ligase reseals the gap
  • Occurs in G1 phase of cell cycle
  • Defective in xeroderma pigmentosum

273

Base excision repair

  • Non-bulky damage in single strand
  • Base-specific glycosylase removes altered base and creates AP site (apurinic/apyrimidinic).
  • One or more nucleotides are removed by AP-endonuclease, which cleaves the 5′ end.
  • Lyase cleaves the 3′ end
  • DNA Pol β fills the gap and DNA ligase seals it
  • Occurs throughout cell cycle
  • Important in repair of spontaneous/toxic deamination

274

Mismatch repair

  • Fixes wrong base in single strand
  • Newly synthesized strand is recognized
  • Mismatched nucleotides are removed
  • Gap is filled and resealed
  • Occurs predominantly in G2 phase of cell cycle
  • Defective in Lynch Synd / HNPCC

275

Nonhomologous end joining

  • Brings together 2 ends of DNA fragments to repair double-stranded breaks.
  • No requirement for homology.
  • Some DNA may be lost.
  • Mutated in ataxia-telangiectasia, Fanconi anemia.

276

DNA/RNA/protein synthesis direction

  • DNA and RNA are both synthesized 5′ → 3′
  • mRNA is read 5′ to 3′
    • 5′ end of incoming nucleotide bears the triphosphate (energy source for bond).
    • The triphosphate bond is the target of 3′ hydroxyl attack.
    • Drugs blocking DNA replication often have modified 3′ OH, preventing addition of the next nucleotide (“chain termination”).
  • Protein synthesis is N-terminus to C-terminus.

277

AUG

mRNA start codon

  • Euk: methionine
  • Prok: N-formylmethionine (stimulates neutrophil chemotaxis)

278

mRNA stop codons

UGA, UAA, UAG

279

Functional organization of a eukaryotic gene

A image thumb
280

Promoter

  • AT-rich upstream sequence w/TATA and CAAT boxes
  • Site where RNA Pol II and multiple other transcription factors bind to DNA upstream from gene locus
  • Mutation commonly results in dramatic decrease in level of gene transcription.

281

Enhancer

  • Stretch of DNA that alters gene expression by binding transcription factors.
  • May be located close to, far from, or even within (in an intron) the gene whose expression it regulates.

282

Silencer

  • Site where negative regulators (repressors) bind.
  • May be located close to, far from, or even within (in an intron) the gene whose expression it regulates.

283

α-amanitin

inhibits RNA polymerase II

284

RNA processing

  • Initial transcript = heterogeneous nuclear RNA (hnRNA)
  • Modifications in nucleus:
    • Capping of 5′ end (addition of 7-methylguanosine cap)
    • Polyadenylation of 3′ end (AAUAAA = polyadenylation signal; Poly-A polymerase does not require a template) ƒ
    • Splicing out of introns
  • Capped, adenylated, & spliced product = mRNA
  • mRNA transported out of the nucleus into the cytosol, where it is translated
  • mRNA quality control occurs at cytoplasmic processing bodies (P-bodies), which contain exonucleases, decapping enzymes, and microRNAs
  • mRNAs may be stored in P-bodies for future translation.

285

Splicing of pre-mRNA

  • Primary transcript combines with small nuclear ribonucleoproteins (snRNPs) and other proteins to form spliceosome.
  • Lariat-shaped (looped) intermediate is generated.
  • Lariat is released to precisely remove intron and join 2 exons.

Ab's to spliceosomal snRNPs (anti-Smith) are highly specific for SLE.

Anti-U1 RNP Ab's are highly associated with mixed connective tissue disease (MCTD).

286

Exons

  • Contain the actual genetic information coding for protein
  • Different exons are frequently combined by alternative splicing to produce a larger number of unique proteins.

287

Introns

intervening noncoding segments of DNA

288

alternative splicing

  • Different exons are frequently combined by alternative splicing to produce a larger number of unique proteins.
  • Abnormal splicing variants are implicated in oncogenesis and many genetic disorders (eg, β-thalassemia).

A image thumb
289

microRNAs

Small, noncoding RNA molecules that posttranscriptionally regulate protein expression.

  • Introns can contain microRNA (miRNA) genes.
  • They can have multiple mRNA targets, typically
  • related to complementary base pairing.
  • miRNA degradation or inactivation of target mRNA → decreased translation into protein.
  • Abnormal expression of miRNAs contributes to certain malignancies (eg, by silencing an mRNA from a tumor suppressor gene).

290

tRNA Structure

  • 75–90 nucleotides
  • 2° structure
  • cloverleaf form
  • anticodon loop is opposite 3′ aminoacyl end
  • 3′ end: CCA sequence; AAs are covalently bound
  • Acceptor stem: the 5′-CCA-3′ is AA acceptor site.
  • T-arm: contains the TΨC (ribothymidine, pseudouridine, cytidine) sequence necessary for tRNA-ribosome binding
  • D-arm: contains dihydrouridine residues necessary for tRNA recognition by correct aminoacyl-tRNA synthetase.

A image thumb
291

Aminoacyl-tRNA synthetase

  • Matches AAs to tRNA
  • Uses ATP
  • Scrutinizes AA before and after it binds to tRNA. If incorrect, bond is hydrolyzed.
  • Amino acid-tRNA bond has energy for formation of peptide bond

292

tRNA Charging

  • aka Aminoacylation
  • Aminoacyl tRNA synthetase matches AA with tRNA and ensures correctness
  • A mischarged tRNA reads usual codon but inserts wrong amino acid.
  • Aminoacyl-tRNA synthetase and binding of charged tRNA to the codon are responsible for accuracy of amino acid selection.

A image thumb
293

tRNA Pairing

A image thumb
294

Wobble

Accurate base pairing is usually required only in the 1st 2 nucleotide positions of an mRNA codon, so codons differing in the 3rd “wobble” position may code for the same tRNA/amino acid (as a result of degeneracy of genetic code).

295

Peptidyl transferase

  • Aminoacyltransferase
  • Used by ribosome to form peptide bonds between adjacent amino acids (using tRNAs) during translation
  • Mediated by rRNA (ribozyme)

296

Protein Synthesis: Initiation

  • Initiated by GTP hydrolysis
  • Initiation factors (eukaryotic IFs) help assemble 40S ribosomal subunit w/initiator tRNA
  • IFs are released when mRNA and the ribosomal 60S subunit assemble w/the complex

Note:

  • ATP—tRNA Activation (charging).
  • GTP—tRNA Gripping and Going places (translocation).

297

Protein Synthesis: Elongation

  1. Aminoacyl-tRNA binds to A site (except for initiator methionine)
  2. rRNA (“ribozyme”) catalyzes peptide bond formation, transfers growing polypeptide to amino acid in A site
  3. Ribosome advances 3 nucleotides toward 3′ end of mRNA, moving peptidyl tRNA to P site (translocation)

298

Protein Synthesis: Termination

Stop codon is recognized by release factor, and completed polypeptide is released from ribosome.

299

A site

incoming Aminoacyl-tRNA

300

P site

accommodates growing Peptide

301

E site

holds Empty tRNA as it Exits

302

Posttranslational modifications

  1. Trimming
  2. Covalent alterations

303

Trimming

Removal of N- or C-terminal propeptides from zymogen to generate mature protein (eg, trypsinogen to trypsin).

304

Covalent alterations

Phosphorylation, glycosylation, hydroxylation, methylation, acetylation, and ubiquitination.

305

Chaperone protein

Intracellular protein involved in facilitating and/or maintaining protein folding.

  • Ex: in yeast, heat shock proteins (Hsp60) are expressed at high temperatures to prevent protein denaturing/misfolding.

306

Primary protein structure

Linear sequence of AAs

307

Secondary protein structure

  • H-bonds
  • Alpha-helix or Beta-sheet

308

Tertiary protein structure

  • 3D structure
  • Hydrophobic interactions
  • Disulfide bonds

309

4 common DNA-binding motifs

  1. Helix-Loop-Helix
  2. Helix-Turn-Helix
  3. Zinc Finger
  4. Leucine Zipper

310

Nuclear Localization Signals

  • 4-8 AA sequences rich in Proline, Arginine, Lysine
  • Recognized by nuclear pores
  • Transported into nucleus via ATPase

311

Centromere

  • the part of a chromosome that links sister chromatids
  • During mitosis, spindle fibers attach to the centromere via the kinetochore

312

Centrosome

  • organelle that serves as the main microtubule organizing center (MTOC) of the animal cell as well as a regulator of cell-cycle progression.
  • composed of two orthogonally arranged centrioles surrounded by an amorphous mass of protein
  • In mitosis the nuclear membrane breaks down and the centrosome nucleated microtubules (parts of the cytoskeleton) can interact with the chromosomes to build the mitotic spindle.

313

Centriole

  • cylindrical cell structure composed mainly of tubulin
  • An associated pair of centrioles, surrounded by a shapeless mass of PCM, makes up a centrosome
  • involved in the organization of the mitotic spindle and in the completion of cytokinesis

314

shortest phase in cell cycle

mitosis

315

Cyclins

  • Regulatory proteins that control cell cycle events
  • phase-specific
  • activate CDKs

316

Cyclin-CDK complexes

  • Phosphorylate other proteins to coordinate cell cycle progression
  • must be activated and inactivated at appropriate times for cell cycle to progress

317

Tumor suppressor regulation of cell cycle

  • p53 induces p21, which inhibits CDKs → hypophosphorylation (activation) of Rb
  • Rb binds to and inactivates transcription factor E2F → inhibition of G1 to S
  • Phsophorylation inactivates Rb → cell cycle progression
  • Mutations in these genes result in unrestrained cell division (eg, Li-Fraumeni syndrome).

318

Permanent Cells

Remain in G0, regenerate from stem cells

Ex: Neurons, skeletal and cardiac muscle, RBCs.

319

Stable / Quiescent Cells

Enter G1 from G0 when stimulated

Ex: Hepatocytes, lymphocytes

320

Labile Cells

Never go to G0, divide rapidly with a short G1

Most affected by chemotherapy

Ex: Bone marrow, gut epithelium, skin, hair follicles, germ cells

321

Rough endoplasmic reticulum

  • Site of synthesis of secretory (exported) proteins and of N-linked oligosaccharide addition to proteins
  • Nissl bodies (neurons)—synthesize peptide NTs for secretion
  • Free ribosomes—site of synthesis of cytosolic and organellar proteins
  • Rich in RER:
    • Small intestine mucus-secreting goblet cells
    • Ab-secreting plasma cells

322

Smooth endoplasmic reticulum

  • Site of steroid synthesis and detox of drugs and poisons.
  • Lacks surface ribosomes
  • Rich in SER:
    • Hepatocytes
    • Adrenal cortex steroid-producing cells

323

Golgi

Distribution center for proteins and lipids from ER to vesicles and plasma membrane.

  • Modifies N-oligosaccharides on asparagine
  • Adds O-oligosaccharides on serine and threonine
  • Adds mannose-6-phosphate to proteins for trafficking to lysosomes

324

Endosomes

  • Sorting centers for material from outside cell or from Golgi
  • Send material to lysosomes for destruction or back to membrane/Golgi for further use

325

I-cell disease

inherited lysosomal storage disorder

  • defect in N-acetylglucosaminyl-1-phosphotransferase → Golgi failure to phosphorylate mannose residues on glycoproteins → proteins secreted extracellularly rather than delivered to lysosomes.
  • Findings:
    • coarse facial features
    • clouded corneas
    • restricted joint movement
    • high plasma levels of lysosomal enzymes
  • Often fatal in childhood

326

N-acetylglucosaminyl-1-phosphotransferase deficiency

I Cell Disease

327

Signal recognition particle

  • Abundant, cytosolic ribonucleoprotein that traffics proteins from ribosome to RER
  • Absent or dysfunctional SRP → proteins accumulate in cytosol

328

COP I

  • Golgi → Golgi (retrograde)
  • cis-Golgi → ER

329

COP II

ER → cis-Golgi (anterograde)

330

Clathrin

  • trans-Golgi → lysosomes
  • plasma membrane → endosomes (receptor-mediated endocytosis [eg, LDLR activity])

331

Trafficking Proteins Summary

A image thumb
332

Peroxisome

Membrane-enclosed organelle involved in catabolism of:

  • very-long-chain fatty acids (β-oxidation)
  • branched-chain fatty acids
  • amino acids
  • ethanol

333

Proteasome

  • Barrel-shaped protein complex that degrades damaged or ubiquitin-tagged proteins.
  • Defects in the ubiquitin-proteasome system have been implicated in some cases of Parkinson disease.

334

Cytoskeletal elements

A network of protein fibers within cytoplasm that supports cell structure, cell and organelle movement, and cell division.

335

Microfilaments

  • Muscle contraction
  • Cytokinesis
  • Ex: Actin, microvilli

336

Intermediate filaments

Maintain cell structure

Ex:

  • Vimentin
  • desmin
  • cytokeratin
  • lamins
  • GFAP
  • neurofilaments

337

Microtubules

Movement, cell division

Ex:

  • Cilia
  • flagella
  • mitotic spindle
  • axonal trafficking
  • centrioles

338

Vimentin

  • Stains for Mesenchymal tissue (fibroblasts, endothelial cells, macrophages)
  • ID: Mesenchymal tumors (sarcoma), but also many other tumors (endometrial carcinoma, renal cell carcinoma, and meningiomas)

339

Desmin

  • Stains for muscle
  • ID: muscle tumors (rhabdomyomas)

340

Cytokeratin

  • Stains for epithelial cells
  • ID: Epithelial tumors (squamous cell carcinoma)

341

GFAP

  • Stains for Neuroglia (astrocytes, Schwann cells, oligodendroglia)
  • ID: Astrocytoma, glioblastoma

342

Neurofilaments

  • Stains for neurons
  • ID: Neuronal tumors (neuroblastoma)

343

Microtubule

  • Cylindrical outer structure composed of helical array of polymerized heterodimers of α- and β-tubulin
  • Each dimer has 2 GTP bound
  • Incorporated into flagella, cilia, mitotic spindles
  • Grows slowly, collapses quickly
  • Also involved in slow axoplasmic transport in neurons

344

Drugs that act on microtubules

Microtubules Get Constructed Very Poorly:

  • ƒMebendazole (antihelminthic)
  • ƒGriseofulvin (antifungal)
  • ƒColchicine (antigout)
  • ƒVincristine/Vinblastine (anticancer) ƒ
  • Paclitaxel (anticancer)

345

Molecular motor proteins

  • transport cellular cargo toward opposite ends of microtubule tracks
  • 2 types: kinesin and dynein

346

Dynein

retrograde to microtubule (+ → −)

347

Kinesin

anterograde to microtubule (− → +)

348

Cilia structure

  • 9 + 2 arrangement of microtubule doublets
  • Base of cilium below cell memb (basal body) consists of 9 microtubule triplets w/no central microtubules
  • Axonemal dynein causes bending

349

Axonemal dynein

ATPase that links peripheral 9 doublets and causes bending of cilium by differential sliding of doublets

350

Kartagener syndrome

  • Immotile cilia due to a dynein arm defect
  • Results in male and female infertility due to immotile sperm / dysfunctional fallopian tube cilia
  • Risk of ectopic pregnancy
  • Can cause bronchiectasis, recurrent sinusitis, and situs inversus (dextrocardia on CXR)

351

Plasma membrane composition

  • Asymmetric lipid bilayer
  • Contains cholesterol, phospholipids, sphingolipids, glycolipids, and proteins
  • Fungal membranes contain ergosterol

352

Na+/K+ ATPase

  • located in plasma memb w/ATP site on cytosolic side
  • For each ATP, 3Na+ go out of cell (pump phosphorylated) and 2K+ come into cell (pump dephosphorylated)
  • Ouabain inhibits by binding to K+ site
  • Cardiac glycosides (digoxin, digitoxin) directly inhibit, which leads to indirect inhibition of Na+/Ca2+ exchange → increased cardiac contractility

353

6 Steps in Collagen Synth

  1. Synthesis (RER): translation; Gly-X-Y
  2. Hydroxylation (RER): req Vit C
  3. Glycosylation (RER): forms procollagen / triple helix
  4. Exocytosis (from Golgi)
  5. Proteolytic Processing (Extracell): terminal region cleavage → tropocollagen
  6. Cross-Linking (Extracell): lysyl oxidase + Cu → fibrils

354

Menkes disease

  • XLR defect in Menkes protein (ATP7A) → impaired copper absorption and transport → decreased activity of lysyl oxidase → connective tissue disease
  • Results in brittle kinky hair, growth retardation, hypotonia

355

Elastin

  • Stretchy protein w/i skin, lungs, large arteries, elastic ligaments, vocal cords, ligamenta flava (connect vertebrae → relaxed and stretched conformations).
  • Rich in nonhydroxylated proline, glycine, lysine residues.
  • Tropoelastin w/fibrillin scaffolding.
  • Cross-linking takes place extracellularly → elastic properties.
  • Broken down by elastase, which is normally inhibited by α1-antitrypsin.
  • Wrinkles of aging due to decreased collagen and elastin production.

356

Flow cytometry

Assesses size, granularity, and protein expression (immunophenotype) of individual cells in a sample.

  • Cells are tagged w/Ab's specific to surface or intracellular proteins.
  • Ab's then tagged w/unique fluorescent dye.
  • Sample analyzed one cell at a time by focusing laser on cell and measuring light scatter and intensity of fluorescence.
  • Data plotted either as histogram or scatter plot

357

Polymerase chain reaction

used to amplify a desired fragment of DNA

  1. DNA is denatured by heating to separate the strands.
  2. During cooling, excess DNA primers anneal to a specific sequence on each strand to be amplified.
  3. Heat-stable DNA polymerase replicates the DNA sequence following each primer.

358

Southern blot

  1. DNA sample is enzymatically cleaved into smaller pieces, which are separated on gel by electrophoresis, and then transferred to filter.
  2. Filter exposed to radiolabeled DNA probe that recognizes and anneals to complementary strand.
  3. Resulting double-stranded, labeled piece of DNA is visualized when filter exposed to film.

359

Northern blot

  • Similar to Southern blot, except w/RNA
  • Useful for studying mRNA levels, which are reflective of gene expression.

360

Western blot

  • Sample protein is separated via gel electrophoresis and transferred to a membrane.
  • Labeled antibody is used to bind to relevant protein.
  • Confirmatory test for HIV after ⊕ ELISA.

361

Southwestern blot

Identifies DNA-binding proteins (eg, transcription factors) using labeled oligonucleotide probes.

362

Enzyme-linked immunosorbent assay

Immunologic test used to detect presence of either a specific antigen (eg, HBsAg) or antibody (eg, anti-HBs) in blood sample.

  • Involves use of Ab linked to enzyme.
  • Added substrate reacts w/enzyme, producing a detectable signal (eg, color change).
  • Major ELISA variations include direct, sandwich, and competitive.
  • Can have high sensitivity and specificity.

363

Fluorescence in situ hybridization

  • Fluorescent DNA or RNA probe binds to specific gene site of interest on chromosomes.
  • Used for specific localization of genes and direct visualization of chromosomal anomalies at molecular level.
    • Microdeletion: no fluorescence on a chromosome compared to fluorescence at the same locus on 2nd copy of that chromosome
    • Translocation: fluorescence outside the original chromosome
    • Duplication: extra site of fluorescence on one chromosome

364

Cloning Steps

production of a recombinant DNA molecule that is self-perpetuating

  1. Isolate eukaryotic mRNA of interest.
  2. Expose mRNA to reverse transcriptase to produce cDNA (lacks introns).
  3. Insert cDNA fragments into bacterial plasmids containing antibiotic resistance genes.
  4. Transform recombinant plasmid into bacteria.
  5. Surviving bacteria on antibiotic medium produce cloned DNA (copies of cDNA).

365

Gene expression modifications

Transgenic strategies in mice involve:

  • ƒ Random insertion of gene into mouse genome
  • ƒ Targeted insertion or deletion of gene thru homologous recombination w/mouse gene

366

Cre-lox system

Can inducibly manipulate genes at specific developmental points (eg, to study a gene whose deletion causes embryonic death).

367

RNA interference

  • dsRNA is synthesized that is complementary to mRNA sequence of interest.
  • When transfected into human cells, dsRNA separates and promotes degradation of target mRNA, “knocking down” gene expression.

368

Codominance

Both alleles contribute to the phenotype of the heterozygote.

  • Blood groups A, B, AB
  • α1-antitrypsin deficiency

369

Variable expressivity

Phenotype varies among individuals with same genotype.

  • NF1

370

Incomplete penetrance

Not all individuals with a mutant genotype show the mutant phenotype.

  • BRCA1 gene mutations do not always result in breast or ovarian cancer.

371

Pleiotropy

One gene contributes to multiple phenotypic effects.

  • Untreated PKU manifests with light skin, intellectual disability, and musty body odor.

372

Anticipation

Increased severity or earlier onset of disease in succeeding generations.

  • Trinucleotide repeat diseases (Huntington disease).

373

Loss of heterozygosity

If a patient inherits or develops a mutation in a tumor suppressor gene, the complementary allele must be deleted/mutated before cancer develops. (This is not true of oncogenes.)

  • Retinoblastoma and the “two-hit hypothesis”
  • Lynch syndrome (HNPCC)
  • Li-Fraumeni syndrome

374

Dominant negative mutation

Exerts a dominant effect. A heterozygote produces a nonfunctional altered protein that also prevents the normal gene product from functioning.

  • Mutation of transcription factor in allosteric site → Nonfunctioning mutant can still bind DNA, preventing wild-type transcription factor from binding.

375

Linkage disequilibrium

  • Tendency for certain alleles at 2 linked loci to occur together more or less often than expected by chance.
  • Measured in a population, not in a family, and often varies in different populations.

376

Mosaicism

Presence of genetically distinct cell lines in the same individual.

  • Somatic: mutation arises from mitotic errors after fertilization and propagates through multiple tissues or organs.
  • Gonadal: mutation only in egg or sperm cells.

377

Locus heterogeneity

Mutations at different loci can produce a similar phenotype.

  • Albinism

378

Allelic heterogeneity

Different mutations in the same locus produce the same phenotype.

  • β-thalassemia

379

Heteroplasmy

Presence of both normal and mutated mtDNA, resulting in variable expression in mitochondrially inherited disease.

380

Uniparental disomy

Offspring receives 2 copies of a chromosome from 1 parent and no copies from the other parent.

  • Heterodisomy (heterozygous) indicates meiosis I error.
  • Isodisomy (homozygous) indicates meiosis II error OR postzygotic chromosomal duplication of one of a pair of chromosomes, and loss of the other of the original pair.

381

McCune-Albright syndrome

  • Mutation affecting G-protein signaling.
  • Presents with:
    • unilateral café-au-lait spots
    • polyostotic fibrous dysplasia
    • precocious puberty
    • multiple endocrine abnormalities
  • Lethal if mutation occurs before fertilization (affecting all cells), but survivable in patients with mosaicism.

382

Imprinting

  • At some loci, only one allele is active; the other is inactive (imprinted/inactivated by methylation).
  • With one allele inactivated, deletion of active allele → disease.

383

Prader-Willi syndrome

  • Maternal imprinting: gene from mom is normally silent and Paternal gene is deleted/mutated.
  • Results in hyperphagia, obesity, intellectual disability, hypogonadism, and hypotonia.

384

Angelman syndrome

  • Paternal imprinting: gene from dad is normally silent and Maternal gene is deleted/mutated.
  • Results in inappropriate laughter (“happy puppet”), seizures, ataxia, and severe intellectual disability.

385

15 AD Diseases

  1. Achondroplasia
  2. Autosomal dominant polycystic kidney disease
  3. Familial adenomatous polyposis
  4. Familial hypercholesterolemia
  5. Hereditary hemorrhagic telangiectasia
  6. Hereditary spherocytosis
  7. Huntington disease
  8. Li-Fraumeni syndrome
  9. Marfan syndrome
  10. Multiple endocrine neoplasias (MEN)
  11. Neurofibromatosis type 1 (von Recklinghausen disease)
  12. Neurofibromatosis type 2
  13. Tuberous sclerosis
  14. von Hippel-Lindau disease
  15. Myotonic Type 1 Muscular Dystrophy

386

Hereditary hemorrhagic telangiectasia

  • aka Osler-Weber-Rendu syndrome.
  • Inherited disorder of blood vessels.
  • Findings:
    • branching skin lesions (telangiectasias)
    • recurrent epistaxis
    • skin discolorations
    • arteriovenous malformations (AVMs)
    • GI bleeding
    • hematuria

 

387

12 Autosomal recessive diseases

  1. Albinism
  2. autosomal recessive polycystic kidney disease (ARPKD)
  3. cystic fibrosis
  4. glycogen storage diseases
  5. hemochromatosis
  6. Kartagener syndrome
  7. mucopolysaccharidoses (except Hunter syndrome)
  8. phenylketonuria
  9. sickle cell anemia
  10. sphingolipidoses (except Fabry disease)
  11. thalassemias
  12. Wilson disease

388

10 X-linked recessive disorders

Oblivious Female Will Often Give Her Boys Her x-Linked Disorders

  1. Ornithine transcarbamylase deficiency
  2. Fabry disease
  3. Wiskott-Aldrich syndrome
  4. Ocular albinism
  5. G6PD deficiency
  6. Hunter syndrome
  7. Bruton agammaglobulinemia
  8. Hemophilia A and B
  9. Lesch-Nyhan syndrome
  10. Duchenne (and Becker) muscular dystrophy

389

4 Trinucleotide repeat expansion diseases

  1. Fragile X syndrome = (CGG)
  2. Friedreich ataxia = (GAA)
  3. Huntington disease = (CAG)
  4. Myotonic dystrophy = (CTG)

390

Down Synd labs

First-trimester ultrasound:

  • Increased nuchal translucency
  • hypoplastic nasal bone
  • decreased serum PAPP-A
  • Increased free β-hCG

Second-trimester quad screen:

  • decreased α-fetoprotein
  • Increased β-hCG
  • decreased estriol
  • Increased inhibin A

391

Edwards Synd labs

1st trimester: decreased PAPP-A and free β-hCG

Quad screen:

  • decreased α-fetoprotein
  • decreased β-hCG
  • decreased estriol
  • decreased/normal inhibin A

392

Patau Synd labs

1st trimester: decreased free β-hCG and PAPP-A

393

Edwards syndrome

2nd most common trisomy

  • severe intellectual disability
  • rocker- bottom feet
  • micrognathia (small jaw)
  • low-set Ears
  • clenched hands with overlapping fingers
  • prominent occiput
  • congenital heart disease
  • Death usually occurs within 1 year of birth.

394

Patau syndrome

  • severe intellectual disability
  • rocker-bottom feet
  • microphthalmia
  • microcephaly
  • cleft liP/Palate
  • holoProsencephaly
  • Polydactyly
  • congenital heart disease
  • cutis aplasia
  • Death usually occurs within 1 year of birth.

395

Nondisjunction

A image thumb
396

Robertsonian translocation

  • Chromosomal translocation that commonly involves chromosome pairs 13, 14, 15, 21, and 22.
  • One of the most common types of translocation.
  • Long arms of 2 acrocentric chromosomes (chromosomes with centromeres near their ends) fuse at centromere and 2 short arms are lost.
  • Balanced translocations normally do not cause any abnormal phenotype.
  • Unbalanced translocations can result in miscarriage, stillbirth, and chromosomal imbalance (eg, Down syndrome, Patau syndrome).

397

Cri-du-chat syndrome

Congenital microdeletion of short arm of chromosome 5

  • microcephaly
  • moderate-severe intellectual disability
  • high-pitched crying/mewing
  • epicanthal folds
  • cardiac abnormalities (VSD)

398

Williams syndrome

Congenital microdeletion of long arm of chromosome 7 (includes elastin gene)

  • distinctive “elfin” facies
  • intellectual disability
  • hypERcalcemia (increased sensitivity to vitamin D)
  • well-developed verbal skills
  • extreme friendliness with strangers
  • cardiovascular problems

399

ATP as carrier

Phosphoryl groups

400

NADH, NADPH, FADH2 as carriers

electrons

401

CoA, lipoamide as carriers

Acyl groups

402

Biotin as carrier

CO2

403

Tetrahydrofolates as carriers

1-carbon groups

404

S-adenosylmethionine (SAM) as carrier

CH3 groups

405

TPP as carrier

Aldehydes

406

Hexokinase

Phosphorylation of glucose to yield glucose-6-phosphate → 1st committed step of glycolysis / glycogen synthesis

  • Location: Most tissues except liver and pancreatic β cells
  • Lower Km
  • Lower Vmax
  • Feedback-inhibited by glucose-6-phosphate

407

Glucokinase

Phosphorylation of glucose to yield glucose-6-phosphate → 1st committed step of glycolysis / glycogen synthesis

  • Location: Liver, β cells of pancreas
  • Higher Km
  • Higher Vmax
  • Induced by insulin
  • Gene mutation associated with maturity-onset diabetes of the young (MODY)

408

Glycolysis steps that require ATP

  1. Glucose → G6P (glucokinase/hexokinase)
  2. Fructose-6P → Fructose-1,6-BP (PFK-1)

409

Glycolysis steps that produce ATP

  1. 1,3-BPG → 3-PG (phosphoglycerate kinase)
  2. PEP → Pyruvate (pyruvate kinase)

410

Catecholamine Synth / Tyrosine Catabolism

A image thumb
411

Fatty acid synthesis

  • Requires transport of citrate from mitochondria to cytosol.
  • Predominantly occurs in liver, lactating mammary glands, and adipose tissue.

412

Fatty acid degradation

Long-chain fatty acid (LCFA) degradation requires carnitine-dependent transport into the mitochondrial matrix

413

Systemic 1° carnitine deficiency

  • inherited defect in LCFA transport into mitochondria → toxic accumulation
  • Causes weakness, hypotonia, hypoketotic hypoglycemia.

414

Medium-chain acyl-CoA dehydrogenase deficiency

AR disorder of fatty acid oxidation.

  • Decreased ability to break down FAs into Acetyl-CoA → accumulation of 8- to 10-carbon fatty acyl carnitines in blood + hypoketotic hypoglycemia.
  • May present in infancy or early childhood with vomiting, lethargy, seizures, coma, and liver dysfunction

415

Pancreatic lipase

degradation of dietary triglycerides in small intestine

416

Lipoprotein lipase

  • degradation of TGs circulating in chylomicrons and VLDLs
  • Found on vascular endothelial surface

417

Hepatic TG lipase

degradation of TGs remaining in IDL

418

Hormone-sensitive lipase

degradation of TGs stored in adipocytes

419

LCAT

catalyzes esterification of cholesterol

420

Cholesterol ester transfer protein

mediates transfer of cholesterol esters to other lipoprotein particles

421

Chylomicron

  • Delivers dietary TGs to peripheral tissue.
  • Delivers cholesterol to liver in the form of chylomicron remnants, which are mostly depleted of their TGs.
  • Secreted by intestinal epithelial cells.

422

VLDL

  • Delivers hepatic TGs to peripheral tissue.
  • Secreted by liver.

423

IDL

  • Formed in the degradation of VLDL.
  • Delivers TGs and cholesterol to liver.

424

LDL

  • Delivers hepatic cholesterol to peripheral tissues.
  • Formed by hepatic lipase modification of IDL in the liver and peripheral tissue.
  • Taken up by target cells via receptor-mediated endocytosis.

425

HDL

  • Mediates reverse cholesterol transport from periphery to liver.
  • Acts as a repository for Apo C and E (needed for chylomicron and VLDL metabolism).
  • Secreted from liver and intestine.
  • Alcohol increases synthesis.