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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 guaninecytosine bonds? (p. 67) ___________________________________________________________

5.

Which molecule is yielded by deamination of cytosine? (p. 67)_____________________________

6.

Which enzyme is inhibited by hydroxyurea? (p. 68) ______________________________________

7.

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

_______________. (p. 68)

8.

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 a normal ammonia level. What is
the most likely diagnosis? (p. 68) ____________________________________________________

9.

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. 68, 105) __________________________________________________

10.

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. 69) _____________________________________________

11.

Silent mutations often result from changes in which position of a codon? (p. 69) _______________

12.

What kind of mutation denotes a DNA change that results in the misreading of all nucleotides
downstream from it? (p. 69) ________________________________________________________

13.

What enzyme has exonuclease activity in prokaryotic DNA replication? (p. 70) ________________

14.

What enzyme degrades the RNA primer and replaces it with DNA during prokaryotic DNA
replication? (p. 70) _______________________________________________________________

15.

Which category of drugs inhibits DNA gyrase? (p. 70) ____________________________________

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16.

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

17.

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

18.

Hereditary nonpolyposis colon cancer results from the loss of which DNA repair mechanism? (p.
71) ___________________________________________________________________________

19.

What type of RNA is the longest? The smallest? The most abundant? (p. 72) _________________
______________________________________________________________________________

20.

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

21.

What poisonous protein that inhibits RNA polymerase II is found in death cap mushrooms? (p. 72)
______________________________________________________________________________

22.

In eukaryotes, what enzyme makes mRNA? (p. 72) _____________________________________

23.

In eukaryotes, what enzyme makes tRNA? (p. 72) ______________________________________

24.

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

25.

-Thalassemia is due to 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. 73) _________________________________________________________________

26.

How does tetracycline interfere with protein translation? (p. 74) ____________________________

27.

How do aminoglycosides interfere with protein synthesis? (p. 75) ___________________________

28.

Why are antibiotics such as chloramphenicol, clindamycin, and macrolides selective for bacteria
and not toxic to human cells? (p. 75) _________________________________________________

29.

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

______________________________________________________________________________
______________________________________________________________________________

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CELLULAR
30.

Fill in the boxes on the image below, noting the appropriate phases of the cell cycle. (p. 76)

31.

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

32.

Match the cell type with its description. (p. 76)

_____ A. Cells remain in G0 and regenerate from stem cells
_____ B. Enter G1 from G0 when stimulated
_____ C. Never go to G0 and divide rapidly with a short G1

1. Labile cells
2. Permanent cells
3. Stable cells

33.

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

34.

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

35.

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) _______________

36.

What syndrome results from a microtubule polymerization defect that leads to impaired lysosomal
emptying and poor phagocytosis? (p. 78) _____________________________________________

37.

Which anticancer drug used to treat breast cancer can stabilize microtubules? (p. 78) __________

38.

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

39.

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

40.

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) __________________________________

41.

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

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42.

Vimentin, desmin, cytokeratin, glial fibrillary acid proteins, and neurofilaments are examples of
which type of cytoskeletal element? (p. 78) ____________________________________________

43.

What effect does digoxins inhibition of Na -K ATPase have on cardiac contractility? (p. 79) _____

______________________________________________________________________________
44.

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

_____ A.
_____ B.

Basement membrane or basal lamina

1.
Bone, skin, tendon, dentin, fascia, cornea,
2.
late wound repair
3.
_____ C. Cartilage, vitreous body, nucleus pulposus
4.
_____ D. Skin, blood vessels, uterus, fetal tissue, granulation tissue

Type I collagen
Type II collagen
Type III collagen
Type IV collagen

45.

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. 79)
______________________________________________________________________________

46.

What disease leads to an inability to form procollagen from pro chains? (pp. 79, 80) __________

47.

A patient presents with hyperextensible skin, easy bruising, and hypermobile joints. What is the
most likely diagnosis? (pp. 79, 80) ___________________________________________________

48.

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

49.

What is the relationship between Alport's syndrome and Goodpasture's syndrome? (pp. 80, 467)
______________________________________________________________________________

50.

Marfan's syndrome is caused by a defect in what protein? (p. 80) __________________________

51.

Which lung disorder can result from excess elastase activity? (p. 80) ________________________

LABORATORY TECHNIQUES
52.

A team of researchers is studying the mechanisms of genetic shift and genetic drift in HIV. To
further the investigation, the scientists need to amplify the sequence of DNA shown. Which primer
would be appropriate for use with PCR? (p. 81)

53.

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

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54.

page 17

Describe each of the following blot techniques: Southern, Northern and Western. (p. 81)
Southern blot: ___________________________________________________________________
______________________________________________________________________________
Northern blot: __________________________________________________________________
______________________________________________________________________________
Western blot: ___________________________________________________________________
______________________________________________________________________________

55.

Which assay can detect single-nucleotide polymorphisms? (p. 81) __________________________

56.

What information can be obtained from an ELISA using a test antibody coupled to a colorgenerating enzyme? (p. 81) ________________________________________________________

57.

What is the advantage of FISH over karyotyping? (p. 82) _________________________________

______________________________________________________________________________

58.

A DNA fragment is added to four different tubes along with DNA polymerase; a radiolabeled primer;
and the adenine, thymine, cytosine, and guanine deoxynucleotides. Each tube also contains one of
the four bases as dideoxynucleotides. The four tubes are then run on electrophoresis gel and
visualized by autoradiography. Which laboratory technique does this describe? (pp. 81-82) ______
______________________________________________________________________________

59.

Which three chromosome imbalances can be seen on a karyotype? (p. 82) __________________
______________________________________________________________________________

GENETICS
60.

A patient has inherited a mutation in a tumor suppressor gene. Mutation of the remaining
(previously normal) copy of the tumor suppressor gene represents a loss of _______________,
which may lead to the development of cancer. (p. 83)

61.

A genetic disease that shows _______________ _______________ will have mutations at

different loci that produce the same phenotype. (p. 83)

62.

What is the heterozygote prevalence in a population that is in Hardy-Weinberg equilibrium? (p. 84)
______________________________________________________________________________

63.

How is Prader-Willi syndrome inherited? What are the symptoms? (p. 84) ____________________
______________________________________________________________________________

64.

How is Angelmans syndrome inherited? What are the symptoms? (p. 84) ____________________
______________________________________________________________________________

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65.

First Aid for the USMLE Step 1 2011 EXPRESS workbook

Which mode of inheritance is represented by each pedigree? (p. 85)

_____ A.

_____ B.

_____ D.
1.
2.
3.
4.
5.

_____ C.

_____ E.

Autosomal dominant
Autosomal recessive
Mitochondrial inheritance
X-linked dominant
X-linked recessive

66.

What percentage of sons of a carrier mother are expected to inherit an X-linked recessive disease?
(p. 85) _________________________________________________________________________

67.

True or False: A mother with an X-linked dominant disease may pass the disease to her sons but
not to her daughters. (p. 85) ________________________________________________________

68.

Achondroplasia is the result of a defect in which receptor? (p. 86) __________________________

69.

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. 86)

70.

A patient has multiple telangiectasias and skin discolorations, and notes recurrent epistaxis. What
other physical finding is most likely to be seen? (p. 86) _______________________________

71.

Can refractory hereditary spherocytosis be cured? If so, how? (p. 86) _______________________

72.

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. 86) ______________

73.

A patient has hemangioblastomas of the retina and cerebellum, as well as bilateral renal cell
carcinoma. What is the most likely diagnosis? (p. 86) ____________________________________

74.

What renal findings might distinguish a patient with tuberous sclerosis from a patient with adult
polycystic kidney disease? (p. 86) ___________________________________________________

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75.

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 patients most likely disease? (p. 88)
______________________________________________________________________________

76.

Cystic fibrosis results from a defect in which gene? Which chromosome? Which ion channel? (p.
87) ___________________________________________________________________________

77.

Which two pathogens are the most likely to cause recurrent pulmonary infections in a patient with
cystic fibrosis? (p. 87) _____________________________________________________________

78.

A patient with cystic fibrosis has an increased risk a deficiency of which four vitamins? (p. 87)
______________________________________________________________________________

79.

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. 87) _________________________________________________

80.

A male patient has a long face, a large jaw, large ears, autism, and macroorchidism. What is the
most likely diagnosis? (p. 87) _______________________________________________________

81.

A newborn is diagnosed with Down syndrome. She is vomiting bilious material. What is the most
likely cause? (p. 88) ______________________________________________________________

NUTRITION
82.

Match each set of symptoms/conditions with the vitamin that is deficient. (pp. 90-94)
_____ A. Bruising, anemia, swollen gums, and poor wound healing
_____ B. Cheilosis and corneal vascularization
_____ C. Convulsions, hyperirritability, peripheral neuropathy,
and sideroblastic anemia
_____ D. Dermatitis, enteritis, and alopecia
_____ E. Dermatitis, enteritis, alopecia, and adrenal insufficiency
_____ F. Diarrhea, dermatitis, and dementia
_____ G. Hemolytic anemia, muscle weakness, and neuropathy
_____ H. Hemorrhagic disease of the newborn
_____ I. Hypocalecmic tetany
_____ J. Macrocytic, megaloblastic anemia with no
neurologic problems
_____ K. Macrocytic, megaloblastic anemia, subacute combined
degeneration, paresthesia, and optic neuropathy
_____ L. Night blindness
_____ M. Wernicke-Korsakoff syndrome

83.

1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.

Biotin
Folic acid
Vitamin A
Vitamin B1
Vitamin B2
Vitamin B3
Vitamin B5
Vitamin B6
Vitamin B12
Vitamin C
Vitamin D
Vitamin E
Vitamin K

A 64-year-old woman is brought to her primary care physician by her son because of progressive
vision loss. She had emigrated from Southeast Asia 1 week earlier. The son mentions that his
mothers poor vision worsens at night, causing her to frequently run into the bedroom wall. Physical
examination shows dry conjunctivae and a small build-up of keratin debris. The patient is
diagnosed with a vitamin deficiency. What other medical condition results from deficiency of a fatsoluble vitamin? (p. 93) ___________________________________________________________

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METABOLISM
84.

Fill in the rectangles in the image below. Which steps of glycolysis are reversible (add arrows to
squares)? (p. 96)

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85.

Match each of the following processes with its rate-determining enzyme. (pp. 95-96)
_____ A.
_____ B.
_____ C.
_____ D.
_____ E.
_____ F.
_____ G.
_____ H.
_____ I.
_____ J.
_____ K.
_____ L.
_____ M.

86.

page 21

Cholesterol synthesis
De novo purine synthesis
De novo pyrimidine synthesis
Fatty acid oxidation
Fatty acid synthesis
Glycogen synthesis
Glycolysis
Gluconeogenesis
Glycogenolysis
HMP shunt
Ketogenesis
TCA cycle
Urea cycle

1. Acetyl-CoA carboxylase
2. Carbamoyl phosphate synthetase I
3. Carbamoyl phosphate synthetase II
4. Carnitine acyltransferase I
5. Fructose-1,6-bisphosphatase
6. G6PD
7. Glutamine-PRPP amidotransferase
8. Glycogen phosphorylase
9. Glycogen synthase
10. HMG-CoA reductase
11. HMG-CoA synthase
12. Isocitrate dehydrogenase
13. Phosphofructokinase-1

How many ATP molecules can be created by the metabolism of glucose? (p. 97) ______________
______________________________________________________________________________

87.

Fill in the boxes on the image below, noting the substrates of the urea cycle. (p. 105)

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88.

Fill in the boxes on the image below, noting the enzymes that catalyze each step of catecholamine
synthesis. (p. 107)

89.

A 16-year-old boy presents for a routine visit. Physical examination shows symptoms consistent
with Fabry's diseases. Examination of his vascular endothelium would most likely show pathologic
accumulation of which substance? (p. 111) ____________________________________________

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90.

page 23

For each lysosomal storage disease in the chart below, name the enzyme and accumulated
substrate(s). (p. 111)
Disease

Deficient Enzyme

Accumulated
Substance(s)

Fabrys disease
Gauchers disease
Hunters syndrome
Hurlers syndrome
Krabbes disease
Metachromatic
leukodystrophy
Niemann-Pick disease
Tay-Sachs disease

91.

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

the exception is _______________. (p. 111)

92.

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

exception is _______________. (p. 111)

93.

Match the lipoprotein with its function. (p. 115)

_____ A.
_____ B.
_____ C.
_____ D.
_____ E.

Delivers dietary TGs to peripheral tissues

Delivers hepatic cholesterol to peripheral tissues
Delivers hepatic TGs to peripheral tissues
Delivers TGs and cholesterol to liver
Mediates cholesterol transport from periphery to liver

1.
2.
3.
4.
5.

Chylomicron
HDL
IDL
LDL
VLDL

Answers
MOLECULAR
1.

H1.

2.

Heterochromatin.

3.

Euchromatin. (It is less condensed and accessible to replication enzymes.)

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4.

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

5.

Uracil.

6.

Ribonucleotide reductase.

7.

Thymidylate synthase; dihydrofolate reductase.

8.

Orotic aciduria.

9.

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

10.

This child has Lesch-Nyhan syndrome, which is characterized by mental retardation, selfmutilation, aggression, hyperuricemia, gout, and choreoatheosis. It is caused by the absence of
HGPRT, which leads to defective purine salvage.

11.

The third position (due to tRNA wobble).

12.

Frameshift.

13.

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

14.

DNA polymerase I.

15.

Fluoroquinolones. (They impair bacterial DNA synthesis.)

16.

Nucleotide excision repair.

17.

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.

18.

The mismatch repair system.

19.

mRNA is the longest type, tRNA is the smallest, and rRNA is the most abundant type of RNA.

20.

A significant decrease in gene transcription.

21.

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

22.

RNA polymerase II.

23.

RNA polymerase III.

24.

Lupus.

25.

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

26.

Tetracycline binds to the 30S subunit of the ribosome, blocking attachment of the aminoacyl tRNA.

27.

Aminoglycosides inhibit formation of the initiation complex, causing misreading of mRNA.

28.

They affect the 50S subunit of the ribosome, which is found in prokaryotic cells.

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29.

page 25

(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
30.

31.

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

32.

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

33.

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

34.

Liver hepatocytes and steroid-hormoneproducing cells of the adrenal cortex.

35.

I-cell disease.

36.

Chdiak-Higashi syndrome.

37.

Paclitaxel.

38.

Griseofulvin.

39.

Mebendazole and thiabendazole.

40.

Kartagener's syndrome.

41.

Microtubule.

42.

Intermediate filaments.

43.

It increases cardiac contractility by increasing intracellular calcium concentration.

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44.

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

45.

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

46.

Osteogenesis imperfecta.

47.

Ehlers-Danlos syndrome.

48.

Blue sclerae.

49.

Both are diseases of type IV collagen. (Alport's is genetic; Goodpasture's is autoimmune.)

50.

Fibrillin.

51.

Emphysema. (1-Antitrypsin inhibits elastase, which degrades elastin; therefore, lack of 1antitrypsin can lead to loss of elastin in the lungs, thereby resulting in emphysema.)

LABORATORY TECHNIQUES
52.

ATAGTACCG; GTGCTAGTC.

53.

A fragment of 10 kD; smaller molecules travel further.

54.

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 the protein of interest.

55.

Microarrays.

56.

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

57.

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

58.

Sequencing.

59.

Autosomal trisomies, microdeletions, and sex chromosome disorders.

GENETICS
60.

Heterozygosity. (The patient had been a heterozygote for lost tumor suppressor gene; both genes
must be lost for oncogenesis.)

61.

Locus heterogeneity.
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62.

2pq.

63.

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.

64.

Angelmans 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 (happy puppet).

65.

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

66.

50%.

67.

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

68.

Fibroblast growth factor 3.

69.

Dominant; recessive.

70.

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

telangiectasia.)

71.

Refractory hereditary spherocytosis can be cured by splenectomy.

72.

Marfan's 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.)

73.

von Hippel-Lindau disease.

74.

Although both will have renal cysts, tuberous sclerosis is associated with renal angiomyolipomas.

75.

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

76.

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

77.

Pseudomonas species and Staphylococcus aureus.

78.

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

79.

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

80.

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

81.

Duodenal atresia.

NUTRITION
82.

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.

83.

Osteomalacia.

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METABOLISM
84.

85.

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.

86.

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.

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87.

88.

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89.

First Aid for the USMLE Step 1 2011 EXPRESS workbook

Ceramide trihexoside.

90.
Disease

Deficient Enzyme

Accumulated
Substance(s)

Fabrys disease

-galactosidase A

Ceramide trihexoside

Gauchers disease

-glucocerebrosiderase

Glucocereboside

Hunters syndrome

Iduronate sulfatase

Heparan sulfate,
dermatan sulfate

Hurlers syndrome

-L-iduronidase

Heparan sulfate,
dermatan sulfate

Krabbes disease

Galactocerebrosidase

Galactocerebroside

Metachromatic
leukodystrophy

Arylsulfatase A

Cerebroside sulfate

Niemann-Pick disease

Sphingomyelinase

Sphingomyelin

Tay-Sachs disease

Hexosaminidase A

GM2 ganglioside

91.

Autosomal-recessive; Hunter's disease.

92.

Autosomal-recessive; Fabry's disease.

93.

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

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