Exam Questions - Lesson 4 - Structure, Function, & Replication of Informational Macromolecules - Harper’s Illustrated Biochemistry, 29th Edition (2012)

Harper’s Illustrated Biochemistry, 29th Edition (2012)

SECTION IV. Structure, Function, & Replication of Informational Macromolecules

Exam Questions

Section IV

1. Which of the following statements about β,γ-methylene and β,γ-imino derivatives of purine and pyrimidine triphosphates is CORRECT?

A. They are potential anticancer drugs.

B. They are precursors of B-vitamins.

C. They readily undergo hydrolytic removal of the terminal phosphate.

D. They can be used to implicate involvement of nucleotide triphosphates by effects other than phosphoryl transfer.

E. They serve as polynucleotide precursors.

2. Which of the following statements about nucleotide structures is NOT CORRECT?

A. Nucleotides are polyfunctional acids.

B. Caffeine and theobromine differ structurally solely with respect to the number of methyl groups attached to their ring nitrogens.

C. The atoms of the purine ring portion of pyrimidines are numbered in the same direction as those of a pyrimidine.

D. NAD+, FMN, “active methionine” and coenzyme A all are derivatives of ribonucleotides.

E. 3’,5’-Cyclic AMP and GMP (cAMP and cGMP) serve as second messengers in human biochemistry.

3. Which of the following statements about purine nucleotide metabolism is NOT CORRECT?

A. An early step in purine biosynthesis is the formation of PRPP (phosphoribosyl 1-pyrophosphate).

B. Inosine monophosphate (IMP) is a precursor of both AMP and GMP.

C. Orotic acid is an intermediate in pyrimidine nucleotide biosynthesis.

D. Humans catabolize uridine and pseudouridine by analogous reactions.

E. Ribonucleotide reductase converts nucleoside diphosphates to the corresponding deoxyribonucleoside diphosphates.

4. Which of the following statements is NOT CORRECT?

A. Metabolic disorders are only infrequently associated with defects in the catabolism of purines.

B. Immune dysfunctions are associated both with a defective adenosine deaminase and with a defective purine nucleoside phosphorylase.

C. The Lesch-Nyhan syndrome reflects a defect in hypoxanthine-guanine phosphoribosyl transferase.

D. Xanthine lithiasis can be due to a severe defect in xanthine oxidase.

E. Hyperuricemia can result from conditions such as cancer characterized by enhanced tissue turnover.

5. Which of the following components are found in DNA?

A. A phosphate group, adenine, and ribose.

B. A phosphate group, guanine, and deoxyribose.

C. Cytosine and ribose.

D. Thymine and deoxyribose.

E. A phosphate group and adenine.

6. The backbone of a DNA molecule is composed of which of the following?

A. Alternating sugars and nitrogenous bases.

B. Nitrogenous bases alone.

C. Phosphate groups alone.

D. Alternating phosphate and sugar groups.

E. Five carbon sugars alone.

7. The interconnecting bonds that connecting the nucleotides of RNA and DNA are termed:

A. N-glycosidic bonds.

B. 3′-5’-phosphodiester linkages.

C. Phosphomonoesters.

D. 3′-2’-phosphodiester linkages.

E. Peptide nucleic acid bonds.

8. Which component of the DNA duplex causes the molecule to have a net negative charge at physiological pH?

A. Deoxyribose

B. Ribose

C. Phosphate groups

D. Chlorine ion

E. Adenine

9. Which molecular feature listed causes duplex DNA to exhibit a near constant width along its long axis?

A. A purine nitrogenous base always pairs with another purine nitrogenous base.

B. A pyrimidine nitrogenous base always pairs with another pyrimidine nitrogenous base.

C. A pyrimidine nitrogenous base always pairs with a purine nitrogenous base.

D. Repulsion between phosphate groups keeps the strands a uniform distance apart.

E. Attraction between phosphate groups keeps the strands a uniform distance apart.

10. The model for DNA replication first proposed by Watson and Crick’s posited that every newly replicated double stranded daughter duplex DNA molecule

A. Was composed of the two strands from the parent DNA molecule.

B. Contained solely the two newly synthesized strands of DNA.

C. Contained two strands that are random mixtures of new and old DNA within each strand.

D. Was composed of one strand derived from the original parental DNA duplex and one strand that was newly synthesized.

E. Was composed of nucleotide sequences completely distinct from either parental DNA strand.

11. Name the mechanism through which RNAs are synthesized from DNA?

A. Replicational duplication

B. Translation

C. Translesion repair

D. Transesterification

E. Transcription

12. Which of the forces or interactions listed below play the predominant role in driving RNA secondary and tertiary structure formation?

A. Hydrophilic repulsion

B. Formation of complementary base pair regions

C. Hydrophobic interaction

D. van der Waals interactions

E. Salt bridge formation

13. Name the enzyme that synthesizes RNA from a double stranded DNA template.

A. RNA-dependent RNA polymerase

B. DNA-dependent RNA convertase

C. RNA-dependent replicase

D. DNA-dependent RNA polymerase

E. Reverse transcriptase

14. Define the most notable characteristic difference with regard to gene expression between eukaryotes and prokaryotes.

A. Ribosomal RNA nucleotide lengths

B. Mitochondria

C. Lysosomes and peroxisomes

D. Sequestration of the genomic material in the nucleus

E. Chlorophyll

15. Which entry below correctly describes the ~ number of bp of DNA_________, which is separated into_________chromosomes in a typical diploid human cell in a nonreplicating state?

A. 64 billion, 23

B. 6.4 trillion, 46

C. 23 billion, 64

D. 64 billion, 46

E. 6.4 billion, 46

16. What is the approximate number of base pairs associated with a single nucleosome?

A. 146

B. 292

C. 73

D. 1460

E. 900

17. All but one of the following histones are found located within the superhelix formed between DNA and the histone octamer; this histone is

A. Histone H2B

B. Histone H3

C. Histone H1

D. Histone H3

E. Hisone H4

18. Chromatin can be broadly defined as active and repressed; a subclass of chromatin that is specifically inactivated at certain times within an organism’s life and/or in particular sets of differentiated cells is termed

A. Constitutive euchromatin

B. Facultative heterochromatin

C. Euchromatin

D. Constitutive heterochromatin

19. Which of the following hypothesizes that the physical and functional status of a certain region of genomic chromatin is dependent upon the patterns of specific histone post-translational modifications (PTMs), and/or DNA methylation status?

A. Morse code

B. PTM hypothesis

C. Nuclear body hypothesis

D. Epigenetic code

E. Genetic code

20. What is the name of the unusual repeated stretch of DNA localized at the tips of all eukaryotic chromosomes?

A. Kinetochore

B. Telomere

C. Centriole

D. Chromomere

E. Micromere

21. Given that DNA polymerases are unable to synthesize DNA without a primer, what molecule serves as the primer for these enzymes during DNA replication?

A. Five carbon sugars

B. Deoxyribose alone

C. A short RNA molecule

D. Proteins with free hydroxyl groups

E. Phosphomonoester

22. The discontinuous DNA replication that occurs during replication is catalyzed via the production of small DNA segments termed

A. Okazaki fragments

B. Toshihiro pieces

C. Onishi oligonucleotides

D. Crick strands

E. Watson fragments

23. What molecule or force supplies the energy that drives the relief of mechanical strain by DNA gyrase?

A. Pyrimidine to purine conversion

B. Hydrolysis of GTP

C. Hydrolysis of ATP

D. Glycolysis

E. A proton gradient molecule or force

24. What is the name of the phase of the cell cycle between the conclusion of cell division and the beginning of DNA synthesis?

A. G1

B. S

C. G2

D. M

E. G0

25. At what stage of the cell cycle are key protein kinases, like cyclin-dependent kinase, activated?

A. Right before mitosis

B. At the beginning of S phase

C. Near the end of G1 phase

D. At the end of the G2 phase

E. All of the above

26. What disease is often associated with a breakdown of a cell’s ability to regulate/control its own division?

A. Kidney disease

B. Cancer

C. Emphysema

D. Diabetes

E. Heart disease

27. What is the molecular mechanism that is responsible for the quick decrease in the Cdk activity that leads to exit from the M phase and the entry into G1?

A. Drop in mitotic cyclin concentration

B. Decreased G1 cyclin concentration

C. Rise in G2 cyclin concentration

D. Rise in mitotic cyclin concentration

E. Rise in G1 cyclin concentration

28. The site to which RNA polymerase binds on the DNA template prior to the initiation of transcription.

A. Intron/exon junction

B. Open reading frame DNA the terminator

C. Terminator

D. Initiator methionine codon

E. Promoter

29. The large eukaryotic rRNA genes, such as 18S and 28S RNA-encoding genes, are transcribed by which of the following RNA polymerases?

A. RNA polymerase III

B. RNA-dependent RNA polymerase δ

C. RNA polymerase I

D. RNA polymerase II

E. Mitochondrial RNA polymerase

30. Eukaryotic RNA polymerases all have a requirement for a large variety of accessory proteins to enable them to bind promoters and form physiologically relevant transcription complexes; these proteins are termed

A. Basal or general transcription factors

B. Activators

C. Accessory factors

D. Elongation factors

E. Facilitator polypeptides

31. The DNA segment from which the primary transcript is copied or transcribed is called

A. Coding region

B. Initiator methionine domain

C. Translation unit

D. Transcriptome

E. Initial codon

32. What class of DNA are the eukaryotic rDNA cistrons?

A. Single copy DNA

B. Highly repetitive DNA

C. Moderately repetitive DNA

D. Mixed sequence DNA

33. Modifications to the nucleotides of the pre-tRNAs, pre-rRNAs and pre-mRNAs occur

A. Postprandially

B. Postmitotically

C. Pretranscriptionally

D. Posttranscriptionally

E. Prematurely

34. RNA polymerase II promoters are located on which side of the transcription unit?

A. Internal

B. 3′

C. Nearest the C-terminus

D. Nearest the N-terminus

E. 5′

35. With regard to eukaryotic mRNAs, one of the following is not a normal property of mRNAs.

A. Eukaryotic mRNAs have special modifications at their 5′ (cap) and 3′ (polyA tail) termini.

B. Are attached to ribosomes when they are translated.

C. They are found in the cytoplasm within peroxisomes.

D. Most have a significant noncoding segment that does not direct assembly of amino acids.

E. Contain continuous nucleotide sequences that encode a particular polypeptide.

36. The bond connecting the initiation nucleotide of the mRNA with the 5me-G Cap structure is a

A. 3′-5’ phosphodiester bridge

B. 5′-5’ triphosphate bridge

C. 3′-3’ triphosphate bridge

D. 3′-5’ triphosphate bridge

E. 5′-3’ triphosphate bridge

37. What sequence feature of mature mRNAs listed below is thought to protect mRNAs from degradation?

A. Special post-translational modifications

B. 3′ Poly(C)n tail

C. 5me-G Cap

D. Introns

E. Lariat structures

38. What could the consequences of inaccurate mRNA splicing be for the RNA?

A. A single base error at a splice junction will cause a large deletion.

B. A single base error at a splice junction will cause a large insertion.

C. A single base error at a splice junction will cause a large inversion.

D. C and E

E. A single base error at a splice junction will change the reading frame and result in mRNA mistranslation.

39. What is the macromolecular complex that associates with introns during mRNA splicing?

A. Splicer

B. Dicer

C. Nuclear body

D. Spliceosome

E. Slicer

40. What reaction does reverse transcriptase catalyze?

A. Translation of RNA to DNA.

B. Transcription of DNA to RNA.

C. Conversion of ribonucleotides into deoxyribonucleotides.

D. Transcription of RNA to DNA.

E. Conversion of a ribonucleotide to deoxynucleotides in the DNA double helix.

41. RNAi or dsRNA-mediated RNA interference mediates

A. RNA ligation

B. RNA silencing

C. RNA inversion

D. RNA restoration

E. RNA quelling

42. While the genetic code has 64 codons, there are only 20 naturally occurring amino acids. Consequently, some amino acids are encoded by more than one codon. This feature of the genetic code is an illustration of the genetic code being

A. Degenerate

B. Duplicitive

C. Nonoverlapping

D. Overlapping

E. Redundant

43. The genetic code contains________termination codons?

A. 3

B. 21

C. 61

D. 64

E. 20

44. If a tRNA has the sequence 5′-CAU-3’, what codon would it recognize (ignore wobble base pairing).

A. 3′-UAC-5’

B. 3′-AUG-5’

C. 5′-ATG-3’

D. 5′-AUC-3’

E. 5′-AUG-3’

45. What is on the 3′ end of all functional, mature tRNAs?

A. The cloverleaf loop

B. The anticodon

C. The sequence CCA

D. The codon

46. Most aminoacyl-tRNA synthetases possess an activity that is shared with DNA polymerases. This activity is a__________function.

A. Proofreading

B. Hydrolysis

C. Proteolytic

D. Helicase

E. Endonucleolytic

47. The three distinct phases of protein synthesis, in the CORRECT order are

A. initiation, termination, elongation

B. termination, initiation, elongation

C. initiation, elongation, termination

D. elongation, initiation, termination

E. elongation, termination, initiation

48. Which amino acid is the initiating amino acid for all proteins?

A. Cysteine

B. Threonine

C. Tryptophan

D. Methionine

E. Glutamic acid

49. The initiator tRNA is placed within the active 80S complex at which of the three canonical ribosomal “sites” during protein synthesis

A. E site

B. I site

C. P site

D. A site

E. Releasing factor binding site

50. Name the enzyme that forms the peptide bond during protein synthesis and define its chemical composition.

A. Pepsynthase, protein

B. Peptidyl transferase, RNA

C. Peptidase, glycolipid

D. Peptidyl transferase, protein

E. GTPase, glycopeptide

51. Mutations in the middle of an open reading frame that create a stop codon are termed:

A. Frameshift mutation

B. Missense mutation

C. No-nonsense mutation

D. Point mutation

E. Nonsense mutation

52. What is the directionality of polypeptide synthesis?

A. C-terminal to N-terminal direction

B. N-terminal to 3′ direction

C. N-terminal to C-terminal direction

D. 3′ to 5′ direction

E. 5′ to 3′ direction

53. Which of the following cis-acting elements typically resides adjacent to or overlaps with many prokaryotic promoters?

A. Regulatory gene

B. Structural gene(s)

C. Repressor

D. Operator

E. Terminator

54. What is the term applied to a segment of a bacterial chromosome where genes for the enzymes of a particular metabolic pathway are clustered and subject to coordinate control?

A. Operon

B. Operator

C. Promoter

D. Terminal controller

E. Origin

55. What is the term applied to the complete collection of proteins present in a particular cell type?

A. Genome

B. Peptide collection

C. Transcriptome

D. Translatome

E. Proteome

56. How does nucleosome formation on genomic DNA affect the initiation and/or elongation phases of transcription?

A. Nucleosomes inhibit access of enzymes involved in all phases of transcription.

B. Nucleosomes recruit histone and DNA modifying enzymes, and the actions of these recruited enzymes affect the access of transcription proteins to DNA.

C. Nucleosomes induce DNA degradation where the DNA contacts the histones.

D. Nucleosomes have no significant effect on transcription.

57. Which types of molecules interact with eukaryotic mRNA gene core promoter sites to facilitate the association of RNA polymerase II?

A. Termination factors

B. Sequence-specific transcription factors (transactivators)

C. Elongation factors.

D. GTPases

E. General, or basal transcription factors (ie, the GTFs)

58. Most eukaryotic transcription factors contain at least two domains, each of which mediate different aspects of transcription factor function; these domains are

A. RNA-binding domain and repression domain.

B. Activation domain and repression domain.

C. DNA-binding domain and activation domain.

D. DNA-binding domain and ligand binding domain.

E. RNA-binding domain and the activation domain.

59. Transcription factors bound at enhancers stimulate the initiation of transcription at the cis-linked core promoter through the action of intermediaries termed

A. Coactivators

B. Cotranscription proteins

C. Corepressors

D. Receptors

E. Coordinators

60. What reactions among transcription proteins greatly expand the diversity of regulatory factors that can be generated from a small number of polypeptides?

A. Recombination

B. Homodimerization

C. Heterozygosity

D. Heterodimerization

E. Trimerization

61. The gene region containing the TATA box and extending to the transcription start site (TSS) is often termed the____________.

A. Polymerase home

B. Initiator

C. Start selector

D. Core promoter

E. Operator

62. Which of the following possible mechanisms for how enhancers can stimulate transcription from great distances are currently thought to be CORRECT?

A. Enhancers can reversibly excise the intervening DNA between enhancers and promoters.

B. RNA polymerase II binds avidly to enhancer sequences.

C. Enhancers unwind DNA.

D. Enhancers can search through DNA and bind directly to the associated core promoter.

E. Enhancers and core promoters are brought into close proximity through DNA loop formation mediated by DNA binding proteins.

63. Which of the following histone amino acids are typically acetylated?

A. Lysine

B. Arginine

C. Asparagine

D. Histidine

E. Leucine

64. Place the following steps in order; what are the steps that occur sequentially during a transcription activation event following the binding of a transcriptional activator to its cognate activator binding site on genomic DNA.

1. The chromatin remodeling complex binds to the core histones at the target region.

2. The combined actions of the various molecular complexes increase promoter accessibility to the transcriptional machinery.

3. The activator recruits a coactivator to a region of chromatin targeted for transcription.

4. Transcriptional machinery assembles at the site where transcription will be initiated.

5. The coactivator acetylates the core histones of nearby nucleosomes.

A. 1 - 2 - 3 - 4 - 5

B. 3 - 1 - 5 - 2 - 4

C. 3 - 5 - 1 - 2 - 4

D. 5 - 3 - 1 - 2 - 4

E. 3 - 5 - 1 - 4 - 2

65. What strategy in transcription factor research allows for the simultaneous identification of all of the genomic sites bound by a given transcription factor under a given set of physiological conditions, monitoring and hence allowing for insights into how gene transcription networks are coordinately regulated?

A. Systematic deletion mapping.

B. DNAase I sensitivity.

C. Chromatin immunoprecipitation (ChIP).

D. FISH.

E. Fluorescence lifetime imaging microscopy.

66. Which sequences extend between the 5′methylguanosine cap present on eukaryotic mRNAs to the AUG initiation codon?

A. Stop codon

B. Last exon

C. Last intron

D. 3′ UTR

E. 5′ UTR

67. Which of the following features of eukaryotic mRNA contribute importantly to message half-life?

A. 5′ UTR sequences

B. The promoter

C. The operator

D. 3′ UTR and poly(A) tail

E. The first intron

*See glossary of terms at the end of this chapter.