Alexandria University Medical Research Institute Biochemistry Department PhD Degree Course title: Molecular Biology IV Course code: 1701806 Final exam ______________________________________________________________________________

All questions are to be answered

I- Multiple Choice Questions (60 Marks)

A. Encircle the correct answer: (1 mark each) Each question below is followed by a few suggested answers, select

the one best response to each question.

1. MicroRNAs are developed from:

a. portions of DNA found in the introns;

b. portions of DNA independent of other genes;

c. both a and b;

d. Neither a or b.

2. MicroRNAs contribute to the regulation of gene expression through:

a. acting as an enhancer in the transcription process by binding to the promoter;

b. inhibiting translation by binding to the 3'end of mRNA;

c. enhancing translation by binding to the TATA box;

d. enhancing translation by binding to the 5'end of mRNA.

3. MicroRNAs are:

P. synthesized as long pri-miRNAs;

Q. transcribed by RNA polymerase II;

R. synthesized from pre-microRNAs by an RNase III enzyme Drosha in the cytoplasm;

Semester: spring Academic year: 2019 – 2020 Time allowed: 120 minutes Date: 16/ 7 / 2020 Total marks: 75

S. synthesized from pri-miRNAs by an enzyme Dicer in the nucleus.

a. P and Q.

b. Q and S.

c. P and S.

d. R and S.

4. MicroRNAs:

a. are specific for a promoter on one specific gene;

b. are specific for many different promoters on many different genes;

c. have a specific site on a single specific mRNA;

d. have a specific site on many different mRNAs.

5. Which of the following describes the function of an enzyme known

as Dicer?

a. It degrades single-stranded DNA.

b. It degrades mRNA with no poly(A) tail.

c. It trims double-stranded RNAs into molecules that can block translation.

d. It degrades single-stranded mRNA.

6. The 5'end of mRNAs made by RNA polymerase II possesses a distinct

cap structure depicted in a short-hand notation:

a. 7-MeGppNPN.

b. 7-MeGpNPN.

c. 7-MeGpppNPN.

d. pppN-7MeGpppNPN.

7. RISC stands for:

a. RNA Interfering Slicing Complex.

b. RNA Interference Sensing Components.

c. RNA Induced Silencing Complex.

d. RNA Interference and Silencing Components.

8. The formation of microRNA is to:

a. serve as part of the structure of ribosome;

b. transfer amino acids from the cellular fluid to the ribosome for protein synthesis;

c. transfer genetic code to the ribosome for protein synthesis;

d. control genetic expression by turning some genes on and others off, thus

controlling gene expression.

9. The type of silencing involved in miRNA is:

a. replicational;

b. transcriptional;

c. posttranscriptional;

d. posttranslational.

10. The first miRNA identified in C.elegans was named ………

a. Lin-2.

b. Let-5.

c. Lin-4.

d. Let-8.

11. Inactive miRNA undergoes how many cleavages before incorporation

into the RISC complex?

a. 0

b. 1

c. 2

d. 3

12. The RNA molecule with its hairpin loop is said to have:

a. primary structure;

b. secondary structure;

c. modified structure;

d. 3D structure.

13. Which is FALSE of the following statements?

a. MicroRNA genes often occur in gene clusters within introns of protein-coding

genes and are usually transcribed by RNA polymerase II.

b. Like a mRNA, a miRNA is initially produced as a larger precursor RNA that like

the great majority of mRNAs, usually has a 5'cap and a poly(A) tail.

c. MicroRNAs are produced by germ-line cells only.

d. A microRNA is initially produced as a duplex RNA but in order to work it needs

to be converted into a single-strand RNA.

14. Which is TRUE of the following statements?

a. A microRNA normally works by binding to perfectly complementary sequences

within an RNA transcript, usually a mRNA.

b. A single type of mRNA can be regulated by multiple different miRNAs.

c. A single miRNA normally binds to transcripts from just one target gene.

d. MicroRNAs normally regulate the expression of just a single gene.

15. Drosha and Pasha:

a. are found in introns of transcribed genes;

b. participate in mRNA degradation;

c. cleave individual stem-loops;

d. convert single-stranded to double-stranded to ssRNA.

16. Where do the spindle fibres connect to the chromosomes?

a. To the centromere.

b. To the kinetochore.

c. To the centriole.

d. To the centrosomes.

17. The acetylation / methylation of lysine residues on histone tails controls

the local condensation of chromatin. This is important because:

a. genes in condensed chromatin are inaccessible to the transcriptional

machinery;

b. DNA in condensed chromatin cannot be replicated;

c. DNA in condensed regions is inaccessible to transposable elements;

d. All of the above.

18. Interferons:

a. activate B cells to make virus-specific antibodies;

b. are Th2 cytokines;

c. block virus infection of host cells;

d. inhibit virus replication by infected cells.

19. An inverted repeat is best described as:

a. a DNA sequence followed by its reverse complement on the opposite strand;

b. the cap structure found at the 5'end of some RNAs containing a

5'-5'bond;

c. a run of deoxynucleotides in the nontranscribed strand at the terminus of a gene;

d. a sequence of nucleotides that is the reversed complement of another

sequence further downstream.

20. Suppose a certain gene contains the double-stranded sequence:

5'-ATGTTTAGCGCC-3'

3'-TACAAATCGCGG-5'

If the upper strand is the sense strand and codes for a

mRNA,which of the following would be the corresponding segment of

antisense RNA?

a. 5'-AUGUUUAGCGCC-3';

b. 5'-CCGCGAUUUGUA-3';

c. 5'-UACAAAUCGCGG-3';

d. 5'-GGCGCUAAACAU-3'.

21. Which of the following is mismatched?

a. RNA polymerase III : U6.

b. RNA polymerase II : snoRNAs.

c. RNA polymerase I : most ribosomal RNA.

d. RNA polymerase I : tRNA.

22. The spliceosome is responsible for:

a. transport of the rRNAs from the nucleus to the cytoplasm where they can be

assembled into ribosomes;

b. the removal of introns from the precursor RNA to make the mature

mRNA;

c. the removal of exons from the precursor RNA to make the mature mRNA;

d. the attachment of the amino acid to the tRNA for protein synthesis.

23. The natural role of RNA interference is:

a. controlling development in multicellular organisms;

b. protection against RNA viruses;

c. protection against cancer;

d. disposing of messenger RNA that is no longer needed after cellular

differentiation.

24. The term "chromatin remodeling" refers to:

a. a process that only bacteria perform since they contain no nucleus;

b. a process that is exclusively associated with transcription by RNA

polymerase III in eukaryotes;

c. alteration of chromatin structure in association with transcription;

d. alteration in chromatin structure to facilitate loading and translation by

ribosomes and thus, enhances gene expression.

25. The phenomenon known as RNA interference (RNAi) is used

experimentally to:

a. interfere with replicon;

b. enhance gene expression;

c. reduce transcription rate from a specific gene promoter;

d. reduce expression of a specific target gene.

26. When does exon shuffling occur?

a. During splicing of DNA.

b. During mitotic recombination.

c. As an alternative splicing pattern in posttranscriptional processing.

d. As an alternative cleavage or modification posttranslationally.

27. siRNAs are involved in which of the following?

a. Genome imprinting.

b. Chromatin remodeling.

c. Targeting of specific mRNAs.

d. b and c.

28. Which of the following experimental requirements makes an siRNA

approach unsuitable for determining the consequence of silencing

a gene of interest in an established cell line?

a. Expression of the gene of interest is integral to cell viability.

b. End point RT-PCR and western blots are the only available

validation assays.

c. Lipofectamine is the only available delivery method.

d. The cell line proliferation rate is relatively slow.

29. Which of the statements below is FALSE?

a. Histone variants are often inserted into already formed chromatin.

b. Several different MIR genes encode the same miRNA.

c. Trans-splicing accounts for 1% of nematode mRNAs.

d. Every MIR gene encodes a unique miRNA.

30. Which of the following is an example of epigenetic inheritance?

a. Purine dimmers.

b. Mismatch mutations.

c. Coding regions of genes.

d. Histone methylation patterns.

31. The human genome project was initiated by:

a. NIH and DOE.

b. NIH and DBI.

c. NIH and DDBJ.

d. DOE and DDBJ.

32. How many chromosomes do humans have in a somatic cell? a. 46

b. 48

c. 54

d. 56

33.Scientists now think humans have how many protein-encoding genes:

a. 20 - 25,000

b. 40 - 50,000

c. 65 - 75,000

d. more than 100,000

34. The human genome is:

a. All of our genes

b. All of our DNA

c. All of the DNA and RNA in our cells

d. Responsible only for all our physical characteristics

35. The prime objective of Human genome project was:

a. To find out the exact functions of proteins in human.

b. To sequence the entire base pairs that make up the 23 chromosomes.

c. To sequence the entire base pairs that make up the 24 chromosomes.

d. To find out the active genes in human genome.

36. Human genome project was also focused on identifying: a. SNPs

b. VNTRs

c. Minisatellites

d. Junk DNA

37. According to human genome project, genetic similarity between

humans is: a. 90 %

b. 95 %

c. 99.9 %

d. 99.5%

38. The largest gene in human is: a. Titin

b. Dystrophin

c. Insulin

d. Phosphofructokinase

39. The complete draft of human genome was announced in: a.2003

b.1990

c.1998

d.2000

40. HapMap project stands for:

a.study of the functional elements in the human genome

b.study of non-coding DNA

c.study of the common patterns of human genetic variations.

d. study of mitochondrial DNA

41. Junk DNA: a. mitochondrial DNA

b. structural genes

c. sequence of DNA that do not encode protein sequences.

d. None of the above

42. Chromosome 1 has the most genes, their number is: a.1968

b. 2968

c.2100

d.2689

43. The first human chromosome to be sequenced is: a. chromosome 22

b. chromosome 1

c. chromosome Y

d. chromosome 14

44. Satellite DNA: a. Found at centromeres and telomeres

b. Do not play a role in coding of proteins

c. Play a role in cell division

d. All of the above

45. About the goals of the human genome project, which statement is Not

True:

a. Identify all the genes in human DNA

b. Determine the sequence of 3 billion chemical base pairs

c. Identify a combination of alleles at adjacent location on a

chromosome that are transmitted together.

d. Store information in data base.

46. Why is a cloning vector required?

a. Cloning ease

b. Variety

c. Availability

d. Large scale production

47. Saccharomyces cerevisiae is an example of _________

a. Algae

b. Yeast

c. Bacteria

d. Insect

48. What are YAC vectors?

a. Yeast artificial vectors

b. Yeast aggregative vectors

c. Yeast artificial chromosomes

d. Yeast aggregative chromosomes

49. What are the origins of replication?

a. Gene component

b. Initiation sites

c. Initiation codons

d. Stop codons

50. Which of the following strategies can ensure production of a cloned

human gene in a bacterium?

a. use of a fusion plasmid/human viral vector

b. additional insertion of a human origin of replication

c. cloning into a RNA phage

d. Insertion of the cDNA sequence

51. Why it is important to use restriction enzymes with 'sticky ends' for

cloning?

a. For easy identification of plasmids containing inserts

b. For easy identification of plasmids with antibiotic resistance

c. For easy insertion into plasmids of DNA segments from different sources

d. For ease of transformation

52. Why are heat stable DNA polymerases an essential component of the

polymerase chain reaction?

a. All components of a PCR reaction are from thermophilic bacteria

b. These polymerases are needed to melt DNA

c. These polymerases do not denature at the temperatures used to melt DNA

d. These polymerases can be easily synthesised in a laboratory

53. What is a YAC?

a. a microarray

b. a DNA library

c. a probe

d. a vector

54. Why do molecular biologists sometimes compare cytochrome oxidase I

sequences from different sources?

a. to investigate gene function

b. to identify stem cells

c. to investigate evolutionary relationships

d. to map genes

55. Which of the following occurs when a knockout mouse is produced?

a. A mutant gene is replaced by a functional allele

b. A functional gene is replaced by a mutant allele

c. A functional gene is inserted in addition to the mutant allele

d. A mutant gene is inserted in addition to the functional allele

56. For which of the following is PCR not used?

a. site specific mutagenesis

b. to generate double stranded DNA for DNA sequencing

c. to generate copies of microsatellites for DNA fingerprinting

d. to generate cDNA from mRNA

57. Starting from the sequencing primer, what is the sequence of the DNA

sample?

a. G T A C C C G A A A T C A G G A

b. A G G A C T A A A G C C C A T G

c. G T A C C C G A A T T C A G G A

d. A G C A C T A A A G C C C A T G

58. What is the difference between a deoxyribonucleotide and a

dideoxyribonucleotide?

a. A deoxynucleotide is missing a 3'-hydroxyl group on its sugar.

b. A dideoxynucleotide is missing a 3'- hydroxyl group on its sugar.

c. A deoxynucleotide is missing a 5'-phosphate group.

d. A dideoxynucleotide is missing a 5'-phosphate group.

59. The dideoxy method is also known as _____________

a. Maxem and Gilbert method

b. Autosequencing

c. Sanger’s sequencing

d. Pyrosequencing 60. Which of the following is NOT required for DNA sequencing? a. Restriction digestion

b. Electrophoresis

c. Cloning

d. Polymerase chain reaction

II- Indicate whether the following statements are TRUE or FALSE :

(9 marks ; 0.5 mark each)

61. Since introns are largely genetic "junk" they do not have to be removed

precisely from the primary transcripts during RNA splicing.

a) True

b) False

62. MicroRNAs are small strands of RNA which contribute to protein synthesis by

its part in transcription regulation.

a) True

b) False

63. There is a close correlation between genome size (in kbp) and complexity of

organisms.

a) True

b) False

64. snoRNAs are involved in modifying the base of rRNA during its maturation.

a) True

b) False

65. DNA is the most important macromolecule for correct cellular function.

a) True

b) False

66. Genetic composition of a species is stable over time.

a) True

b) False

67. The centromere provides the pulling force for the pulling apart of sister

chromatids.

a) True

b) False

68. "Antisense" therapy attempts to silence an unwanted gene expression by use

of oligonucleotide complimentary (antisense) to the non-transcribed region of

pre-mRNA.

a) True

b) False

69. Condensation of DNA occurs in the S phase of the cell cycle.

a) True

b) False

70. The most important difference between miRNA and siRNA is : miRNA is

generated by Dicer but siRNA is generated by Slicer.

a) True

b) False

71. Small cajal body RNAs are likely to be the locations in which snoRNAs and

snRNAs undergo covalent modifications and final assembly with proteins.

a) True

b) False

72. In classical genetics, an investigator can start with a particular gene and

proceed to make mutations in it, creating mutant cells or organisms so as to

analyze the gene's function.

a) True

b) False

73. Lipoplexes are complexes of positively charged lipids and negatively

charged nucleic acids. The lipids surround the siRNA and mask its negative

charge from the positively charged cell-membrane.

a) True

b) False

74. The interchromatin granule clusters have been proposed to be stockpiles

of fully mature snRNPs and RNA processing components that are ready to

be used in the production of mRNA.

a) True

b) False

75. Trans-splicing accounts for only about 10% of trypanosomes mRNAs.

a) True

b) False

76. The process of electrophoresis is the key to sequencing. a) True

b) False

77. About 85% of all differences in human DNA are due to SNPs.

a) True

b) False

78. All genetic information is present in nuclear DNA.

a) True

b) False

Answer the following questions in the exam paper:

III- Match one item from numbered group A with a lettered item from group

B (3 marks ; 0.5 mark each)

Group A

79. The plans of public human genome project a OR d OR f

80. The plans of public human genome project a OR d OR f

81. The plans of public human genome project a OR d OR f

82. The plans of private human genome project b OR c OR e

83. The plans of private human genome project b OR c OR e

84. The plans of private human genome project b OR c OR e

Group B

a. Individual labs are responsible for specific chromosomes.

b. Shotgun the entire genome and make random clones.

c. Use mathematical models and computer programs

to assemble the genome.

d. Each lab constructs An Overlapping BAC clone library for their corresponding

chromosome.

e. use the sequencing technologies developed by Perkin Elmer

f. Divide the genome into chromosomes

IV- Match one item from numbered group A with a lettered item from group

B (3 marks ; 0.5 mark each)

Group A

85. Yeast artificial chromosomes c OR d OR f

86. Yeast artificial chromosomes c OR d OR f

87. Yeast artificial chromosomes c OR d OR f

88. bacterial artificial chromosome a OR b OR e

89. bacterial artificial chromosome a OR b OR e

90. bacterial artificial chromosome a OR b OR e

Group B

a. They are more stable.

b. It is very hard to construct

c. it is not so hard to construct

d. They are unstable.

e. are used to clone the DNA inserts up to 300kb

f. are used for cloning very large (1000-2000kb) DNA segments.

======Good Luck=======