Biochemistry: How To Use The Workbook With The Videos

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Biochemistry
How to Use the Workbook with the Videos
Using this table as a guide, read the Facts in First Aid for the USMLE Step 1 2014,
watch the corresponding First Aid Express 2014 videos, and then answer the workbook
questions.

Facts in First Aid for Corresponding First Aid Workbook


the USMLE Step 1 2014 Express 2014 videos questions
66.1–75.4 Molecular (4 videos) 1–24
76.1–81.3 Cellular (3 videos) 25–45
81.4–83.4 Laboratory Techniques (2 videos) 46–52
84.1–91.4 Genetics (5 videos) 53–72
91.5–97.2 Nutrition (2 videos) 73–74
98.1–118.3 Metabolism (16 videos) 75–91

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page 2 First Aid Express 2014 workbook: BIOCHEMISTRY

Questions

MOLECULAR
1. Which histone is not part of the nucleosome core? (p. 66) ________________________________

2. What is DNA called when it is condensed and transcriptionally inactive? (p. 66) _______________

3. What is the name for transcriptionally active DNA? (p. 66)_________________________________

4. What physical property is displayed by nucleic acids that have increasing proportions of guanine-
cytosine bonds? (p. 66) ___________________________________________________________

5. Which enzyme is inhibited by hydroxyurea? (p. 67) ______________________________________

6. 5-Fluorouracil inhibits _______________, whereas both methotrexate and trimethoprim inhibit


_______________. (p. 67)

7. A child has megaloblastic anemia not responsive to vitamin B12 or folate administration. She is
small for her age. Serum studies show increased orotic acid and hyperammonemia. What is the
most likely diagnosis? (pp. 67, 109) __________________________________________________

8. A 12-year-old boy with moderate mental retardation visits his physician because of painful swollen
joints. During the examination, the boy makes several uncontrolled spastic muscle movements. His
medical history includes muscular hypotonia diagnosed when he was 5 months old. When he was
3 years old he was referred to a pediatric dentist for severe repetitive biting of his lip and tongue.
What is the most likely diagnosis? (p. 68) _____________________________________________

9. What enzyme “proofreads” DNA synthesis with its exonuclease activity in prokaryotic DNA replica-
tion? In which direction can it remove nucleotides? (p. 69) ________________________________

10. What enzyme degrades the RNA primer and replaces it with DNA during prokaryotic DNA
replication? (p. 69) _______________________________________________________________

11. Which category of drugs inhibits DNA gyrase? (p. 69) ____________________________________

12. Silent mutations often result from changes in which position of a codon? (p. 70) _______________

13. What kind of mutation denotes a DNA change that results in the misreading of all nucleotides
downstream from it? (p. 70) ________________________________________________________

14. What specific DNA repair mechanism is defective in xeroderma pigmentosum? (p. 71) __________
______________________________________________________________________________

15. In single-stranded DNA repair, how are nucleotide-excision and base-excision repair different? (p.
71) _________________________________________________________________________

16. Hereditary nonpolyposis colorectal cancer results from the loss of which DNA repair mechanism?
(p. 71) _________________________________________________________________________

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17. What commonly results from a mutation within a promoter? (p. 72) _________________________

18. What type of RNA is the largest? The smallest? The most numerous? (p. 73) ________________
______________________________________________________________________________

19. What poisonous protein that inhibits RNA polymerase II is found in death cap mushrooms? (p. 73)
______________________________________________________________________________

20. In eukaryotes, what enzyme makes mRNA? (p. 73) _____________________________________

21. In eukaryotes, what enzyme makes tRNA? (p. 73) ______________________________________

22. Patients with which disease make antibodies to spliceosomal small nuclear ribonucleoproteins?
(p. 73)_________________________________________________________________________

23. β-Thalassemia can be caused by a mutation causing splicing defects in a process that combines
different exons within a single gene. What mechanism allows the same gene to encode for various
different proteins? (p. 74) __________________________________________________________

24. Explain the three steps of protein elongation. (p. 75) _____________________________________
______________________________________________________________________________
______________________________________________________________________________

CELLULAR
25. Fill in the boxes on the following diagram, noting the phases of the mitotic cell cycle. (p. 76)

26. Which transition in the cell cycle is prevented by Rb and p53 tumor suppressors? (p. 76) ________
______________________________________________________________________________

27. Match the cell type with its description. (p. 76)
_____ A. Cells remain in G0 and regenerate from stem cells 1. Labile cells
_____ B. Enter G1 from G0 when stimulated 2. Permanent cells
_____ C. Never go to G0 and divide rapidly with a short G1 3. Stable (quiescent) cells

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page 4 First Aid Express 2014 workbook: BIOCHEMISTRY

28. Name two cells that are rich in rough endoplasmic reticulum. (p. 76) ________________________

29. Name two cells that are rich in smooth endoplasmic reticulum. (p. 76) _______________________

30. A child presents with coarse facial features, clouded corneas, restricted joint movement, and high
plasma levels of lysosomal enzymes. What is the most likely diagnosis? (p. 77) _______________

31. Which molecular motor protein is used for anterograde transport along microtubules? (p. 78) _____

32. Which antifungal agent targets microtubules? (p. 78) ____________________________________

33. Which antihelminthic drugs target microtubules? (p. 78) __________________________________

34. A 22-year-old woman presents with a history of recurrent pneumonia. X-ray of the chest shows
dextrocardia. What is the most likely diagnosis? (p. 78) __________________________________

35. Cilia, flagella, mitotic spindles, neurons, and centrioles are composed of which cytoskeletal
element? (p. 78) _________________________________________________________________

36. Vimentin, desmin, cytokeratin, glial fibrillary acid proteins, and neurofilaments are examples of
which type of cytoskeletal element? (p. 78) ____________________________________________
+ +
37. What effect does digoxin’s inhibition of Na -K ATPase have on cardiac contractility? (p. 79) _____
______________________________________________________________________________

38. What type of collagen is found in each structure? (p. 79)


_____ A. Basement membrane or basal lamina 1. Type I collagen
_____ B. Bone, skin, tendon, dentin, fascia, cornea, 2. Type II collagen
late wound repair 3. Type III collagen
_____ C. Cartilage, vitreous body, nucleus pulposus 4. Type IV collagen
_____ D. Skin, blood vessels, uterus, fetal tissue, granulation
tissue
39. British sailors in the 17th century were often unable to hydroxylate proline and lysine residues for
collagen synthesis. What disease did they have, and why did the treatment work? (p. 80)
______________________________________________________________________________
40. What disease leads to an inability to form procollagen from pro α chains? (p. 80) _____________

41. A patient presents with hyperextensible skin, easy bruising, and hypermobile joints. What is the
most likely diagnosis? (p. 81) _______________________________________________________

42. A baby is born with multiple fractures and hearing loss. What finding would most likely be seen
during the ophthalmologic examination? (p. 80) ________________________________________

43. Which enzyme involved in collagen synthesis will have decreased activity in a patient who has a
mutation that impairs copper absorption and transport? (p. 81) _____________________________

44. Marfan syndrome is caused by a defect in what protein? (p. 81) ____________________________

45. Which lung disorder can result from excess elastase activity? (p. 81) ________________________

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LABORATORY TECHNIQUES
46. Why can’t human DNA polymerase be used for PCR? (p. 81) ______________________________

47. Which would travel farther on an agarose gel, a fragment of 10 kD or of 100 kD, and why? (p. 81)
______________________________________________________________________________

48. Describe each of the following blot techniques: Southern, Northern, and Western. (p. 82)
Southern blot: ___________________________________________________________________
______________________________________________________________________________
Northern blot: __________________________________________________________________
______________________________________________________________________________
Western blot: ___________________________________________________________________
______________________________________________________________________________

49. Which assay can measure the expression level of many genes simultaneously? (p. 82) _________
_______________________________________________________________________________

50. What information can be obtained from an ELISA using a test antibody? Is this a direct or indirect
ELISA? (p. 82) __________________________________________________________________

_______________________________________________________________________________

51. What is the advantage of fluorescence in situ hybridization over karyotyping? (p. 83) ___________
______________________________________________________________________________

52. What is the most direct lab technique for detecting autosomal trisomies? (p. 83) _______________
______________________________________________________________________________

GENETICS
53. Explain loss of heterozygosity. (p. 84) ________________________________________________
______________________________________________________________________________

54. A genetic disease that shows _______________________________ may have mutations at one of
several different loci that produce the same phenotype. (p. 84)

55. In terms of p and q, what is the heterozygote prevalence in a population that is in Hardy-Weinberg
equilibrium? (p. 85) _______________________________________________________________

56. How is Prader-Willi syndrome inherited? What are the symptoms? (p. 85) ____________________
______________________________________________________________________________

57. How is Angelman syndrome inherited? What are the symptoms? (p. 85) ____________________
______________________________________________________________________________

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58. Which mode of inheritance is represented by each of the following pedigrees? (p. 86)

_____ A. _____ B. _____ C.

_____ D. _____ E.

1. Autosomal dominant
2. Autosomal recessive
3. Mitochondrial inheritance
4. X-linked dominant
5. X-linked recessive

59. What percentage of sons of a carrier mother is expected to inherit an X-linked recessive disease?
(p. 86) _________________________________________________________________________

60. True or False: A mother with an X-linked dominant disease may pass the disease to her sons but
not to her daughters. (p. 86) ________________________________________________________

61. Adult polycystic kidney disease is inherited in an autosomal- _______________ (dominant/


recessive) pattern, whereas infantile polycystic kidney disease is associated with an autosomal-
_______________ (dominant/recessive) pattern. (p. 87)

62. A patient has multiple telangiectasias and skin discolorations, and notes recurrent epistaxis. What
vascular pathology would you expect to find? (p. 87) ___________________________________

63. What is an effective “cure” for hereditary spherocytosis? (p. 87) ____________________________

64. A tall man comes to the emergency room with the combination of a dissecting ascending aorta and
acute mitral valve prolapsed. What disorder best explains these findings? (p. 87) ______________

65. You notice café-au-lait spots and cutaneous neurofibromas all over a patient’s skin. On which
chromosome is the gene that causes this disorder? (p. 87) _______________________________

66. Cystic fibrosis results from a defect in which gene? Which chromosome? Which ion channel?
(p.88) _________________________________________________________________________

67. Which drug can be used to loosen mucus plugs in patients with cystic fibrosis? (p. 88) __________

68. A patient with cystic fibrosis has an increased risk a deficiency of which vitamins? (p. 88)
______________________________________________________________________________

69. A 4-year-old boy needs to use his upper extremities to push against his legs in order to stand up.
What maneuver is he using? (p. 89) _________________________________________________

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70. A male patient has a long face, a large jaw, large ears, autism, and macroorchidism. What is the
most likely diagnosis? (p. 89) _______________________________________________________

71. Before his anticipated death, a 42-year-old man had received many years of treatment for
depression, severe cognitive decline, and involuntary writhing movements. His father had similar
symptoms shortly before his death. What is the cause of this patient’s most likely disease? (pp. 89,
454) __________________________________________________________________________

72. A newborn is diagnosed with Down syndrome. She is vomiting bilious material. What is the most
likely cause? (p. 90) ______________________________________________________________

NUTRITION
73. Match each set of symptoms/conditions with the vitamin that is deficient. (pp. 92-96)

_____ A. Bruising, anemia, swollen gums, and poor wound healing 1. Biotin
_____ B. Cheilosis and corneal vascularization 2. Folic acid
_____ C. Convulsions, hyperirritability, peripheral neuropathy, 3. Vitamin A
and sideroblastic anemia 4. Vitamin B1
_____ D. Dermatitis, enteritis, and alopecia 5. Vitamin B2
_____ E. Dermatitis, enteritis, alopecia, and adrenal insufficiency 6. Vitamin B3
_____ F. Diarrhea, dermatitis, and dementia 7. Vitamin B5
_____ G. Hemolytic anemia, muscle weakness, and neuropathy 8. Vitamin B6
_____ H. Hemorrhagic disease of the newborn 9. Vitamin B12
_____ I. Hypocalcemic tetany 10. Vitamin C
_____ J. Macrocytic, megaloblastic anemia with no 11. Vitamin D
neurologic problems 12. Vitamin E
_____ K. Macrocytic, megaloblastic anemia, subacute combined 13. Vitamin K
degeneration, paresthesia, and optic neuropathy
_____ L. Night blindness
_____ M. Wernicke-Korsakoff syndrome

74. Which vitamin or mineral is a cofactor for many transcription factors, and has dysgeusia as a
symptom of its deficiency? (p. 96) ___________________________________________________

METABOLISM
75. Match each of the following processes with its rate-determining enzyme. (p. 99)

_____ A. Cholesterol synthesis 1. Acetyl-CoA carboxylase


_____ B. De novo purine synthesis 2. Carbamoyl phosphate synthetase I
_____ C. De novo pyrimidine synthesis 3. Carbamoyl phosphate synthetase II
_____ D. Fatty acid oxidation 4. Carnitine acyltransferase I
_____ E. Fatty acid synthesis 5. Fructose-1,6-bisphosphatase
_____ F. Glycogenesis 6. G6PD
_____ G. Glycolysis 7. Glutamine-PRPP amidotransferase
_____ H. Gluconeogenesis 8. Glycogen phosphorylase
_____ I. Glycogenolysis 9. Glycogen synthase
_____ J. HMP shunt 10. HMG-CoA reductase
_____ K. Ketogenesis 11. HMG-CoA synthase
_____ L. TCA cycle 12. Isocitrate dehydrogenase
_____ M. Urea cycle 13. Phosphofructokinase-1

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76. Fill in the rectangles in the following diagram. Which steps of glycolysis are reversible? (Add one-
or two- sided arrows to the squares.) (p. 100)

77. How many ATP molecules can be created by the aerobic and anaerobic metabolism of glucose?
(p. 101) ________________________________________________________________________

78. The α-ketoglutarate dehydrogenase complex and the pyruvate dehydrogenase complex require the
same five cofactors; what are these cofactors? (pp. 102-103) ______________________________
_______________________________________________________________________________

79. List the four irreversible enzymes in gluconeogenesis. (p. 104) _____________________________
_______________________________________________________________________________

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80. What are Heinz bodies? What are bite cells? (pp. 106, 386) _______________________________

_______________________________________________________________________________

81. Fill in the boxes on the image below, noting the substrates of the urea cycle. (p. 108)

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82. Fill in the boxes in the following chart, noting the enzymes that catalyze each step of catecholamine
synthesis. (p. 110)

83. A 16-year-old boy presents for a routine visit. Physical examination shows symptoms consistent
with Fabry disease. What is the inheritance pattern of this disease? (p. 114) _______________

______________________________________________________________________________

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84. For each lysosomal storage disease in the chart below, name the enzyme and accumulated
substrate(s). (p. 114)

Accumulated
Disease Deficient Enzyme
Substrate

Fabry disease

Gaucher disease

Hunter syndrome

Hurler syndrome

Krabbe disease

Metachromatic
leukodystrophy

Niemann-Pick disease

Tay-Sachs disease

85. Most mucopolysaccharidoses are inherited in a(n) _______________-_______________ pattern;


the exception is _______________. (p. 114)

86. Most sphingolipidoses are inherited in a(n) _______________-_______________ pattern; the


exception is _______________. (p. 114)

87. Which cell-type(s) cannot use ketones as an energy source? Why? (p. 116) __________________
_______________________________________________________________________________

88. What is the target enzyme of the lovastatin? (p. 117) ____________________________________

89. Which apolipoprotein binds to the LDL receptor? On which lipoproteins is it found? (p. 118) ______
______________________________________________________________________________

90. Match the lipoprotein with its function. (p. 118)


_____ A. Delivers dietary TGs to peripheral tissues 1. Chylomicron
_____ B. Delivers hepatic cholesterol to peripheral tissues 2. HDL
_____ C. Delivers hepatic TGs to peripheral tissues 3. IDL
_____ D. Delivers TGs and cholesterol to liver 4. LDL
_____ E. Mediates cholesterol transport from periphery to liver 5. VLDL

91. In which organ(s) is HDL produced? (p. 118) __________________________________________

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Answers

MOLECULAR
1. H1.

2. Heterochromatin.

3. Euchromatin. (It is less condensed and accessible to transcription factors.)

4. Increasing melting temperatures due to the tighter binding of the strands.

5. Ribonucleotide reductase.

6. Thymidylate synthase; dihydrofolate reductase.

7. Ornithine transcarbamylase deficiency. (Orotic aciduria does not have hyperammonemia.)

8. This child has Lesch-Nyhan syndrome, which is characterized by mental retardation, self-
mutilation, aggression, hyperuricemia, gout, and choreoathetosis. It is caused by the absence of
HGPRT, which leads to a defective purine salvage pathway.

9. DNA polymerase III has 3' to 5' exonuclease activity for proofreading.

10. DNA polymerase I.

12. The third position (due to tRNA wobble).

13. Frameshift.

11. Fluoroquinolones. (They impair bacterial DNA synthesis.)

14. Nucleotide excision repair.

15. During nucleotide repair, the entire nucleotide structure is removed and replaced. During base
excision repair, the base is clipped off of the sugar and repaired without the entire backbone of the
DNA being taken apart.

16. The mismatch repair system.

17. A significant decrease in gene transcription.

18. mRNA is the largest type, tRNA is the smallest, and rRNA is the most numerous type of RNA.

19. α-Amanitin. (When consumed, it causes liver failure.)

20. RNA polymerase II.

21. RNA polymerase III.

22. Lupus.

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page 13

23. Alternative splicing. (In this case, the alternative splicing yields a pathologic protein.)

24. (1) Aminoacyl-tRNA binds to the A site. (2) Peptidyltransferase adds a peptide to the amino acid
chain at site A. (3) The ribosome advances three nucleotides in the 3′ direction, thereby moving the
peptidyl tRNA to the P site.

CELLULAR
25.

26. Transition from G1 to S phase. (Defective cells are not allowed to undergo DNA synthesis.)

27. A-2, B-3, C-1.

28. Goblet cells (secrete mucus) and plasma cells (secrete antibodies).

29. Liver hepatocytes and steroid-hormone–producing cells of the adrenal cortex.

30. I-cell disease.

31. Kinesin.

32. Griseofulvin.

33. Mebendazole and thiabendazole.

34. Kartagener syndrome.

35. Microtubules.

36. Intermediate filaments.

37. It increases cardiac contractility by increasing intracellular calcium concentration.

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38. A-4, B-1, C-2, D-3.

39. Scurvy; the limes supplied the sailors with the vitamin C they needed during their long voyage (and
earned them the nickname "limeys").

40. Osteogenesis imperfecta.

41. Ehlers-Danlos syndrome.

42. Blue sclerae.

43. Lysyl oxidase.

44. Fibrillin.

45. Emphysema. (α1-Antitrypsin inhibits elastase, which degrades elastin; therefore, lack of α1-
antitrypsin can lead to loss of elastin in the lungs, thereby resulting in emphysema.)

LABORATORY TECHNIQUES
46. The DNA polymerase in PCR needs to be stable at high temperatures, since you need to
repeatedly melt the DNA into a single-stranded form. Therefore, the heat-stable polymerase from
the thermophilic bacteria Thermos aquaticus (Taq polymerase) is used.

47. A fragment of 10 kD; smaller molecules travel farther since they are less hindered by the gel.

48. Southern: DNA is run on an electrophoresis gel and transferred to a filter; the DNA on the filter is
denatured and exposed to a labeled DNA probe; the double-stranded DNA is visualized when the
filter is exposed to film.
Northern: RNA is run on an electrophoresis gel and transferred to a filter; the RNA on the filter is
exposed to a labeled DNA probe; the hybrid DNA-RNA molecule is visualized when the filter is
exposed to film.
Western: Sample protein is separated via gel electrophoresis and transferred to a filter; labeled
antibody is used to bind and detect the protein of interest.

49. Microarrays.

50. An ELISA using a test antibody can determine whether a particular antigen is present in the
patient's blood. This is a direct ELISA.

51. FISH allows for identification of anomalies at the molecular level, including deletions that are too
small to see on a karyotype.

52. Karyotyping.

GENETICS
53. When a tumor suppressor gene has only one functional allele due to an inherited mutation or
deletion of the other, and then a cell loses the remaining allele as well. Consequently, having no
functional alleles permits a neoplastic transformation.

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page 15

54. Locus heterogeneity.

55. 2pq.

56. Prader-Willi syndrome is inherited via deactivation of the paternal copies of genes on chromosome
15 or can occur via uniparental disomy. Symptoms include mental retardation, hyperphagia,
obesity, hypogonadism, and hypotonia.

57. Angelman syndrome is inherited via deactivation of the maternal copies of genes on chromosome
15 or can occur via uniparental disomy. Symptoms include mental retardation, seizures, ataxia, and
inappropriate laughter.

58. A-5, B-1, C-2, D-3, E-4.

59. 50%.

60. False. (Her sons and daughters may be affected.)

61. Dominant; recessive.

62. Arteriovenous malformations. (This constellation of symptoms is typical of hereditary hemorrhagic


telangiectasia.)

63. Refractory hereditary spherocytosis can be cured by splenectomy.

64. Marfan syndrome. (It is associated with cystic medial necrosis of the aorta [which may lead to a
dissection] as well as a floppy mitral valve prone to prolapse.)

65. Chromosome 17.

66. CF is due to a defect in the CFTR gene on chromosome 7 that affects the chloride channel.

67. N-acetylcysteine.

68. Vitamins A, D, E, and K (all of which are fat soluble).

69. Gowers maneuver. (This action is necessary due to weakness of the proximal muscles.)

70. Fragile X syndrome. (Remember: Fragile X = eXtra large testes, jaw, and ears.)

71. The patient has classic symptoms of Huntington disease, which is caused by an expansion of CAG
trinucleotide repeats on chromosome 4.

72. Duodenal atresia.

NUTRITION
73. A-10, B-5, C-8, D-1, E-7, F-6, G-12, H-13, I-11, J-2, K-9, L-3, M-4.

74. Zinc.

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METABOLISM
75. A-10, B-7, C-3, D-4, E-1, F-9, G-13, H-5, I-8, J-6, K-11, L-12, M-2.

76.

77. Aerobic glucose metabolism produces 32 ATP molecules per molecule of glucose in heart and liver
and 30 in muscle. Anaerobic glucose metabolism products only 2 net ATP molecules per molecule
of glucose.

78. Vitamins B1, B2, B3, and B5, and lipoic acid.

79. Pyruvate carboxylase, PEP carboxykinase, fructose-1,6-bisphosphatase, and glucose-6-


phosphatase.

80. Heinz bodies are clumps of denatured hemoglobin precipitates that stick to an RBC’s membrane.
When the RBC passes through the spleen, macrophages remove the Heinz bodies, which make
the cell look as if a bite were taken out of it.

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81.

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page 18 First Aid Express 2014 workbook: BIOCHEMISTRY

82.

83. X-linked recessive.

84.

Accumulated
Disease Deficient Enzyme
Substance(s)

Fabry disease α-galactosidase A Ceramide trihexoside

Gaucher disease β-glucocerebrosiderase Glucocereboside

Heparan sulfate,
Hunter syndrome Iduronate sulfatase
dermatan sulfate
Heparan sulfate,
Hurler syndrome α-L-iduronidase
dermatan sulfate

Krabbe disease Galactocerebrosidase Galactocerebroside

Metachromatic
Arylsulfatase A Cerebroside sulfate
leukodystrophy

Niemann-Pick disease Sphingomyelinase Sphingomyelin

Tay-Sachs disease Hexosaminidase A GM2 ganglioside

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page 19

85. Autosomal-recessive; Hunter disease.

86. Autosomal-recessive; Fabry disease.

87. Erythrocytes, because they have no mitochondria.

88. HMG-CoA reductase

89. B-100; VLDL, IDL, LDL.

90. A-1, B-4, C-5, D-3, E-2.

91. Liver and intestine.

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