NAME: DATE: 2002/2003

BIOCHEMISTRY - Example Exam // (US I/4 & N - II/6)

ANSWER THE FOLLOWING QUESTIONS:

Proteins & Enzymes

1. Which of the following statements in respect to collagen synthesis is true?

A. all collagen alpha chains have the same primary structure.

B. the N-terminal and C-terminal peptides of procollagen are cleaved off immediately before the tropocollagen is excreted.

C. assembly of tropocollagen into fibers is catalyzed by lysine oxidase.

D. collagen fibers are crosslinked by oxidized Lys derivatives.

E. after assembly of collagen fibers proline is hydroxylated to form hydroxyproline.

2. The quaternary structure of hemoglobin is:

A. not important for the functioning of this protein

B. rigid and is not affected by oxygen binding

C. maintained by hydrophobic, ionic, and hydrogen bonds

D. stabilized by glycosidic bonds

E. similar to that of myoglobin

3. The sickling of red blood cells in individuals with sickle cell anemia is caused by:

1. denaturation of hemoglobin.

2. oxidation of Fe²⁺ to Fe³⁺.

3. aggregation of oxyhemoglobin.

4. aggregation of deoxyhemoglobin.

5. formation of the hemoglobin R state.

4. A mutation that causes a substitution of glycine onto another amino acid alters the mobility

of a protein in native gel electrophoresis at neutral pH as shown here. Which substitution

would most likely cause this change?

1. 
   glycine to lysine

2. glycine to arginine

3. glycine to tryptophan

4. glycine to glutamate

5. glycine to isoleucine

5. Denaturation of protein is usually caused by the disruption of all the following linkages

EXCEPT:

1. ionic bonds (salt bridges)

2. hydrogen bonds

3. hydrophobic bonds

4. peptide bonds

5. van der Waals bonds

6. The protein has a domain structure if:

1. it is composed of more than one polypeptide chain

2. its tertiary structure contains both α-helical and β-structural fragments

3. it can change its quaternary structure upon ligand binding

4. its polypeptide chain (even if single) is folded into more than one compact globular unit

5. it separates into several polypeptide chains upon denaturing conditions

7. Unlike serum, plasma contains:

1. albumin

2. fibrinogen

3. hemoglobin

4. red blood cells

5. γ-globulins

8. The most abundant protein of human organism is:

1. fibrinogen

2. collagen

3. albumin

4. immunoglobulin G

5. hemoglobin

9. Which of the vitamins is a precursor of diphosphothiamine (DPT) coenzyme:

A. vitamin B1

B. vitamin B2

C. vitamin B6

D. folate

E. vitamin H.

10. Choose the best definition for the Michaelis-Menten constant (K_M):

1. the minimal concentration of an enzyme for initiation of catalysis

2. the substrate concentration required for half-maximal velocity

3. the reciprocal of the substrate concentration required for maximal velocity

4. the minimal substrate concentration required for initiation of product formation

5. the reciprocal of the enzyme concentration required for half-maximal velocity.

11. The activity of enzymes in the living organism is regulated via:

1. proteolytic degradation of the initialy inactive polypeptide(s)

2. covalent modification of the enzyme

3. allosteric modulation

4. changes in the expression of encoding gene(s)

5. all the mechanism that are listed above (answeres A - D)

12. Protein kinases are enzymes that phosphorylate amino acid side chains of proteins in

ATP- dependent reactions. A protein kinase can be classified as a(n):

1. oxidoreductase

2. hydrolase

3. isomerase

4. lyase

5. transferase

13. Values of V_max and K_M determined for an enzyme with and without its inhibitor are:

No inhibitor: K_M = 0.5 (mmol L^-1) V_max = 0.15 (mmol L^-1 min^-1)

With inhibitor: K_M = 0.5 (mmol L^-1) V_max = 0.03 (mmol L^-1 min^-1)

What kind of inhibition is observed?

A. competitive

B. noncompetitive

C. uncompetitive

D. allosteric

E. none of the above

14. Methotrexate (amethopterin) and aspirin are used in medical treatment of some diseases.

Methotrexate competes with a substrate for the dihydrofolate reductase active site while

aspirin covalently and irreversibly modifies side chain of the amino acid in the active site

of cyclooxygenase. Choose the statements that correctly describes their effect on the

kinetic parameters of the enzyme-catalyzed reactions:

1. methotrexate decreases Km while aspirin increases Km

2. they both increase Km

3. they both decrease Vmax

4. methotrexate increases Km while aspirin decreases Vmax

5. methotrexate and aspirin both decrease Km as well as Vmax

15. Which of the following enzymes would show the greatest increase of the activity in serum

due to viral hepatitis?
A. creatine kinase (CK)
B. alkaline phosphatase
C. alanine transaminase (ALT or SGPT)
D. amylase
E. acid phosphatase

Nucleic Acids, Protein synthesis, Control of gene expression & Biotechnology

16. Which of the following statement concerning DNA structure IS NOT true:

1. two strands of the Z-DNA helix are antiparallell.

2. AT rich regions have lower melting temperature than GC rich regions

3. interactions between adjacent base pairs lead to the decrease of absorbance at 260nm.

4. palindrome nucleotide sequences are present only in Prokaryotes.

5. in B-DNA, keto- and amino- tautomeric forms of bases predominate.

17. The proofreading activity of nucleic acid polymerases:

1. is necessary to remove primers

2. concerns both DNA and RNA polymerases

3. requires the 5' 3' exonuclease activity

4. removes errors caused by rare tautomeric forms of bases

5. requires 3' 5' endonuclease activity

18. Uracil in DNA:

1. is found commonly and forms a base pair with adenine.

2. can never appear.

3. can appear as a product of deamination of cytosine.

4. can appear as a product of spontaneous demethylation of thymine.

5. is commonly observed in viral DNA.

19. Which of the following enzymes IS NOT involved in base excision repair of DNA in E.Coli:

1. AP-endonuclease

2. N-glycosylase

3. ligase

4. DNA polymerase I

5. primase

20. The most common mutation, that rate is increased by nitrates (NO₂^- ) is:

1. depurination

2. alkylation

3. formation of thymine dimers

4. deamination

5. breaking of N-glycosidic bonds.

21. In the process of an amino acid “activation” to protein biosynthesis:

A. amino group of the amino acid reacts with 2' or 3' -OH of ribose of the first adenylate in the sequence of tRNA

B. amino group of the amino acid reacts with 2' or 3' -OH of ribose of the last adenylate in the sequence of tRNA

C. carboxyl group of the amino acid reacts with 2' or 3' -OH of ribose of the first adenylate in the sequence of tRNA

D. carboxyl group of the amino acid reacts with 2' or 3' -OH of ribose of the last adenylate in the sequence of DNA.

22. Tetracycline, streptomycin, and erythromycin are effective inhibitors of:

1. prokaryotic RNA synthesis

2. eukaryotic mRNA synthesis

3. prokaryotic protein biosynthesis

4. eukaryotic protein biosynthesis

5. prokaryotic and eukaryotic assembly of ribosomes

23. Indicate the FALSE sentence concerning regulation of protein biosynthesis in eukaryotes:

1. protein biosynthesis may be controlled only at the level of initiation of transcription

2. synthesis of globin in reticulocytes is tightly dependent on the heme concentration

3. steroid hormones basically affect gene expression at the level of initiation of transcription

4. hypermethylated genes are transcribed less efficiently than hypomethylated ones

5. the same transcription unit may be used to produce different although related proteins

24. All the following enzymes require a DNA or RNA template EXCEPT:

1. DNA polymerase

2. Reverse transcriptase

3. Primase

4. RNA polymerase II

5. all enzymes listed above

25. The genetic code is highly degenerate. It means that:

A. each amino acid is specified by single codon;

B. most amino acids are specified by more than one codon;

C. some codons specify more than one amino acid;

D. there are at least 10 different STOP codons;

E. codons are overlapping.

26. Which of the nucleic acids listed below does not function in the cytoplasm?

1. mRNA

2. rRNA

3. tRNA

4. scRNA

5. snRNA

27. The nucleic acid chosen as a answer in the above question (23) participates in:

1. transcription

2. postranscriptional polyadenylation of hnRNA

3. nucleotide excision DNA repair

4. cap formation

5. splicing of hnRNA

28. DNA replication originates at the indicated origin of replication. Which segment(s) serve

as template(s) for leading strand synthesis?

1. 
   B and D

2. A and C

3. A and B

4. Only D

5. Only B

29. The most efficient expression of lac-OPERON structural genes in bacteria takes place

when the medium in which they grow is:

1. enriched in glucose and free from lactose

2. enriched in both glucose and lactose

3. free from both glucose and lactose

4. enriched in lactose and free from glucose

5. enriched in lactose and supplemented with inhibitors of cAMP synthesis

30. The HIV virus causing AIDS is a retrovirus and contains an RNA genome. Which enzyme is responsible for converting this genome to DNA in T lymhocytes?

1. ligase

2. restriction endonuclease EcoR1

3. DNA polymerase

4. reverse transcriptase

5. RNA polymerase.

31. Proteins, RNA and DNA were isolated from from brain, liver and muscle of the rabbit.

Which of the methods of analysis should give the same results for each of the tissues:

1. electrophoresis of the isolated proteins

2. quantitative determination of the protein content

3. measurements of the protein biosynthesis rate

4. analysis of the cDNA libraries

5. analysis of the DNA restriction fragments length polymorphism.

32. Restriction Fragments Length Polymorphism (RFLP) used in diagnosis of genetic diseases

includes all the following EXCEPT:

1. comparison of restriction fragments derived from a normal and mutated gene followed their separation and hybridization

2. treatment of patient and reference DNA with the same restriction enzyme(s)

3. recombination of restriction fragments with specific vectors allowing for their amplification prior to hybridization with appropriate labelled probe

4. hybridization of restriction fragments with specific oligonucleotide probe

5. electrophoretic separation of restriction fragments

33. Chain elongation during protein biosynthesis is:

1. carboxyl to the amino terminus

2. amino to the carboxyl terminus

3. dispersed

4. palindromic

5. central to peripheral.

Metabolism

34. How many O₂ moles are consumed or produced directly by the reactions of the citric acid

cycle in course of the conversion of 1 mole of acetyl-CoA to carbon dioxide (CO₂)?

1. 1 produced

2. 2 produced

3. 1 consumed

4. 2 consumed

5. 0 consumed or produced

35. The protein that binds and directly reduces the terminal electron acceptor in mitochondrial

electron transport chain is:

1. cytochrome oxidase.

2. succinate dehydrogenase.

3. coenzyme QH₂

4. NADH:Q reductase

5. cytochrome bc1.

36. After complete metabolism of one molecule of glucose to carbon dioxide via the TCA

cycle, what will be the net change in the amount of oxaloacetate in the mitochondrion?

1. increased by two molecules

2. increased by one molecule

3. unchanged

4. decreased by one molecule

5. decreased by two molecules

37. Which of the following metabolites can NOT be a substrate for gluconeogenesis?

1. alanine

2. acetate

3. glutamate

4. lactate

5. succinate

38. In the breakdown of muscle glycogen, the predominant product is:

1. glucose

2. glucose 1-phosphate

3. UDP-glucose

4. maltose

5. maltotriose

For questions 39 - 45

For each numbered item, select the one heading that is most closely associated with it. Each lettered heading may be selected once, more than once or not at all.

1. HDL

2. Chylomicrons

3. VLDL

4. LDL

5. Free fatty acids

39. Transports mostly exogenous triacylglycerol. ( A / B / C / D / E )

40. Calories in the form of carbohydrate would increase the blood concentration of this

lipoprotein before the others. ( A / B / C / D /E )

41. The amount of this lipoprotein in the blood depends on the presence of the receptors for

B-100 apolipoprotein in extrahepatic tissues. ( A / B / C / D / E )

42. The site of the LCAT reaction. ( A / B / C / D / E )

43. This lipoprotein has the highest ratio of protein to lipid. ( A / B / C / D / E )

44. Lipoprotein lipase is required for its formation. ( A / B / C / D /E )

45. Activation of hormone-sensitive lipase is required to release them. ( A / B / C / D / E )

46. Cholesterol biosynthesis is similar to fatty acids biosynthesis in that:

1. the rate limiting enzymes in both pathways are inactive when they are phosphorylated

2. both pathways utilize mitochondrial acetyl-CoA as the initial compound in the pathway

3. both pathways use NADH as the reducing agent

4. both pathways are inhibited by insulin

5. both pathways have HMG-CoA as an intermediate.

47. Which of the following amino acids contributes both carbon and nitrogen atoms to the

purine ring?

A. aspartate

B. glycine

C. glutamine

D. lysine

E. cysteine

48. What is the major nitrogen containing end-product you would expect to find in human

urine from the metabolism of guanine?

A. urea

B. allantoin

C. hypoxanthine

D. inosinic acid

E. uric acid

49. Insulin inhibits:

1. fat mobilization from adipose tissue

2. cholesterol biosynthesis

3. fatty acid synthesis

4. the transport of glucose into muscle cells

5. the transport of glucose into liver cells.

50. Muscle proteins (amino acids) are the origin of most of glucose in the period(s) represented by:

1. A only

2. B only

3. C only

4. B and D

5. C and D

51. Glucagon:

1. increases glycogen formation by liver

2. inhibits gluconeogenesis in liver

3. inhibits glucose production in hypoglycemia

4. increases glucose transport into skeletal muscle cells

5. increases lipolysis in adipose tissue cells

52. Most of our energy reserves are stores as fat because

1. adipose cells have a high biosynthetic capacity to synthesize fatty acids de novo.

2. the energy spent to store glucose as fat is less than that spent to store glucose as glycogen.

3. the recruitment of fat from adipose can be regulated independently of glycogen breakdown.

4. fat is anhydrous and more reduced than carbohydrate.

5. adipose cells have a high level of glycerol 3-kinase activity.

53. Which of the following statements is TRUE for vitamin A, vitamin D, estrogen and

cortisol?

1. Humans can synthesize all of these molecules de novo.

2. They are all stored in large quantities in the liver.

3. Hormones produced by the hypothalamus and pituitary play an important role in the regulation of the synthesis of all of these molecules.

4. Each of these molecules binds to the same nuclear receptor which mediates their activity.

5. They are all fat soluble molecules that activate separate receptors through which they can increase or decrease the rate of transcription of specific genes in target cells.

54. Indicate a pathway/step of carbohydrate metabolism that is stimulated by insulin in

muscle, but not in liver:

1. glycolysis

2. gluconeogenesis

3. glycogenolysis

4. glycogen synthesis

5. glucose transport.

55. Indicate the expected laboratory findings for a fasting blood sample of a patient suffering

from glucose-6-phosphatase deficiency in hepatocytes:

1. high glucose, low lactate, low FFA

2. low glucose, high lactate, high FFA

3. low glucose, low lactate, low FFA

4. high glucose, high lactate, high FFA

56. Indicate key enzyme in the biosynthesis of cholesterol:

1. 3-hydroxy-3-methylglutaryl-CoA (HMG) synthase

2. HMG reductase

3. HMG lyase

4. mevalonate kinase

5. squalene synthase

57. Choose the amino acid that is used to transport amino group (NH₂-) from most peripheral tissues to the liver:

1. glutamate

2. aspartate

3. asparagine

4. serine

5. glutamine

58. Which of the following types of amino acids are precursors for synthesis of nucleic acids?

1. nonessential amino acids

2. basic amino acids

3. aromatic essential amino acids

4. aliphatic hydrophobic amino acids

5. none amino acids are required

59. Classical galactosemia is caused by the deficiency or lack of activity of:

1. hexokinase

2. glucose-6-phosphatase

3. galactose-1-phosphate / UDP-glucose UDP transferase

4. UDP-galactose epimerase

5. any of the enzymes listed above (A - D)

60. A gallstone that blocked the upper part of the bile duct would cause an increase in:

1. the formation of chylomicrons

2. the formation of chylomicrons

3. the excretion of bile salts

4. the excretion of fat in the feces

5. the deposition of triglycerides in adipose tissue

61. The source of energy in case of erythrocytes is:

1. both ketone bodies and glucose

2. only glucose

3. both short chain fatty acids and glucose

4. only short chain fatty acids

5. both glucose and lactate

62. Liver produces fats mostly from:

1. acetyl CoA derived from degradation of adipose tissue fatty acids

2. acetyl CoA derived from glucose delivered from glycogen

3. exogenously delivered glucose

4. acetyl CoA derived from degradation of fatty acids delivered with VLDLs and HDLs

5. ketone bodies

63. The accumulation of toxic derivatives of phenylalanine, such as phenylpyruvate, is a

symptom of phenylketonuria, which is caused by a defect of:

1. tyrosine transaminase

2. tyrosine hydroxylase

3. tyrosinase

4. phenylalanine transaminase

5. phenylalanine hydroxylase

64. In the normal adult, the fuel store that contains the most calories is (are):

1. adipose triacylglycerols

2. liver glycogen

3. blood glucose

4. muscle protein

5. muscle glycogen

65. Pyruvate carboxylase is a key enzyme of:

1. glycolysis

2. citric acid cycle

3. gluconeogenesis

4. glycogenolysis

5. pentose phosphate pathway

66. The principle function of the TCA cycle is to:

1. transfer electrons from the acetyl portion of acetyl-CoA to NAD⁺ and FAD

2. generate CO₂

3. oxidize the acetyl portion of acetyl-CoA to oxaloacetate

4. dispose of excess pyruvate and fatty acids

5. generate heat from the oxidation of the acetyl portion of acetyl-CoA

67.
X, Y, Z, V and W in the diagram,

represent gluconeogenic substrates.

Match each compound listed below

with the correct letter.

1. lactate

2. malate

3. aspartate

4. glycerol

5. alanine

68. Ketone bodies are formed:

1. in muscle during fasting period

2. in liver, if oxaloacetate is in excess in mitochondria

3. in brain suffering from hypoxia

4. in hepatocytes during starvation

5. in adipose with overactive hormone-dependent lipase.

69. Amino acids are precursors of hormones, neurotransmitters, biogenic amines etc. Which

of the following amino acids is involved in biosynthesis of acetylcholine:

1. tryptophan

2. glycine

3. serine

4. tyrosine

5. threonine

70. Choose the citric acid cycle intermediate which is a substrate for heme biosynthesis is:

1. citrate

2. α-ketoglutarate

3. succinyl-CoA

4. succinate

5. malate

71. When excessive amounts of iron are present in the diet, the excess iron is stored as:

1. hemoglobin

2. transferrin

3. ferritin

4. cytochrome c

5. ceruloplasmin

72. Parkinson disease, a neurological disease, is connected with defects in catecholamines metabolism in brain. Which of the following could be included into this group of metabolites:

1. glycogen

2. a sphingolipid

3. dopamine

4. collagen

5. putrescine

73. Phenylketonuria, alcaptonuria and albinism are caused by deficiencies in enzymes involved in the metabolism of:

1. tryptophan

2. phenylalanine

3. histidine

4. valine

5. lysine

74. The vitamin with antioxidant properties, involved in hydroxylation of dopamine to

epinephrine and influencing absorption of iron from the intestine is:

1. vitamin A

2. vitamin E

3. vitamin C

4. vitamin K

5. vitamin B₅

Free radicals & biochemistry and disease

75. The major enzymes involved in processes of detoxication via increase of solubilization of

hydrophobic xenobiotics are:

1. cytochromes P₄₅₀ and sulfotransferases

2. superoxide dismutase and catalase

3. cytochromes b₅ and glutathione peroxidase

4. cytochromes P₄₅₀ and NADPH oxidase

5. cytochromes b₅ and glucuronyl transferases

76. Which one of the following electron carriers is involved in conversion of xenobiotics:

1. coenzyme Q

2. cytochrome b

3. cytochrome c₁

4. cytochrome P-450

5. iron-sulfur centers

77. The major organ responsible for detoxification processes is:

1. spleen

2. liver

3. lungs

4. kidney

5. intestine

78. Which methods CAN NOT be used in prenatal diagnosis of sickle cell anemia:

1. electrophoresis and chromatography of trypsin treated hemoglobin

2. genetic linkage analysis of RFLP

3. hybridization with allele specific oligonucletide probe (ASO)

4. amplification and sequencing of gene coding β-chain.

79. The reaction - H₂O₂ + H₂O₂ → 2H₂O + O₂ - is catalyzed by:

1. glutathione peroxidase

2. catalase

3. superoxide dismutase

4. cytochrome P-450

80. Protooncogenes discovered so far code for all the listed below EXCEPT:

1. growth factors

2. serine/threonine protein kinases

3. some G proteins

4. membrane bound or cytosolic protein tyrosine kinases

5. reverse transcriptases

81. The most reactive oxygen form (having the greatest oxidizing potential) is:

1. O₂

2. H₂O₂

3. H₃O⁺

4. OH^•

5. OH⁻

82. Choose the enzyme that eliminates excess of H₂O₂ in course of a reaction:

H₂O₂ + 2GSH ⇒ 2H₂O + GS-SG

1. catalase

2. xanthine oxidase

3. glutathione transferase

4. glutathione peroxidase

5. NADPH oxidase

13

---