- 1. When were alternative non-helical models of DNA briefly considered?
A) Late 1980s
B) Early 1950s
C) Mid 1990s
D) Late 1970s
- 2. Which experimental technique helped set aside non-helical models in favor of the double-helical model?
A) Gas chromatography
B) Nuclear magnetic resonance
C) Electron diffraction
D) Mass spectrometry
E) X-ray crystallography
- 3. What discovery contributed to the acceptance of the double-helical model over non-helical ones?
A) Ribosomes
B) Topoisomerases
C) Golgi apparatus
D) Mitochondria
- 4. How is DNA typically modeled as a polymer?
A) Worm-like chain
B) Completely random coil
C) Rigid crystalline lattice
D) Perfectly straight rod
- 5. Which of these is a significant degree of freedom for DNA?
A) Transmutation
B) Bending
C) Ionization
D) Denaturation
- 6. What is important for the circularization of DNA and orientation of bound proteins?
A) Twisting-torsional stiffness
B) Compression-extension
C) Mass density
D) Electrical conductivity
- 7. Which type of stiffness is important for DNA wrapping and protein interactions?
A) Bending-axial stiffness
B) Thermal stiffness
C) Torsional drag
D) Magnetic stiffness
- 8. Which degree of freedom is considered relatively unimportant in the absence of high tension?
A) Twisting
B) Bending
C) Compression-extension
D) Circularization
- 9. What causes DNA to continually change conformation in solution?
A) Thermal vibration and collisions
B) Magnetic field fluctuations
C) DNA replication enzymes
D) Changes in pH
- 10. How is the bending stiffness of DNA measured?
A) Tensile strength
B) Melting temperature
C) Molecular weight
D) Persistence length
- 11. What tool is used to directly image DNA molecules to measure persistence length?
A) Atomic force microscope
B) Scanning electron microscope
C) Light microscope
D) X-ray diffractometer
- 12. What is the average persistence length of DNA in an aqueous solution?
A) 200 nm
B) 50 nm
C) 10 nm
D) 100 nm
- 13. Approximately how many base pairs correspond to the average persistence length of DNA?
A) 500 base pairs
B) 50 base pairs
C) 150 base pairs
D) 300 base pairs
- 14. What is the diameter of DNA?
A) 10 nm
B) 5 nm
C) 2 nm
D) 1 nm
- 15. What is the approximate range of the persistence length of DNA in base pairs?
A) 200–300 base pairs
B) 50–100 base pairs
C) 132–176 base pairs
D) 400–500 base pairs
- 16. What is a primary factor that causes significant variation in the persistence length of a section of DNA?
A) Light intensity
B) Sequence
C) Air pressure
D) Age of the sample
- 17. What contributes to the variation in persistence length regarding base interactions?
A) Phosphate backbone width
B) Base stacking energies
C) Nucleotide sequence length
D) Hydrogen bond length
- 18. The persistence length is defined as the length below which a polymer behaves like a what?
A) Rigid rod
B) Brittle crystal
C) Circular loop
D) Flexible string
- 19. Which form of DNA is believed to be the most predominant in cells?
A) Z-DNA
B) P-DNA
C) B-DNA
D) A-DNA
- 20. What is the width of B-DNA?
A) 12 Å
B) 34 Å
C) 22 Å
D) 23.7 Å
- 21. How many base pairs constitute one complete turn of B-DNA in solution?
A) 12
B) 23.7
C) 10.4–10.5
D) 10
- 22. Which DNA form is known to have a left-hand twist compared to A and B?
A) P-DNA
B) A-DNA
C) Z-DNA
D) C-DNA
- 23. What is the width of the major groove in DNA?
A) 22 Å
B) 12 Å
C) 23.7 Å
D) 34 Å
- 24. What is the width of the minor groove in DNA?
A) 22 Å
B) 34 Å
C) 12 Å
D) 23.7 Å
- 25. Why do proteins usually bind to the major groove?
A) It is the smaller groove
B) Bases are more accessible
C) It is positively charged
D) It is always on the outside
- 26. Which of the following is a non-helical DNA structure mentioned in the text?
A) Z-DNA
B) A-DNA
C) B-DNA
D) i-motif
- 27. Which letter is NOT among those available to name new DNA structures in the future?
A) B
B) F
C) Y
D) Q
- 28. What was previously thought about the occurrence of A-DNA?
A) Only in protein-DNA complexes
B) Only in RNA hybrids
C) Only in dehydrated laboratory samples
D) Only in methylated DNA
- 29. What happens to the helical pitch of B-DNA every 10 base pairs?
A) It extends 34 Å
B) It extends 23.7 Å
C) It extends 22 Å
D) It extends 12 Å
- 30. Which of the following forms is a quadruplex structure?
A) Z-DNA
B) G-quadruplex
C) A-DNA
D) L-DNA
- 31. Are the major and minor grooves equal in size?
A) No, they are unequal
B) Yes, they are equal
C) Only in A-DNA
D) Only in Z-DNA
- 32. How many coordinates are used to characterize the geometry of a base or base pair step?
A) 12
B) 8
C) 6
D) 4
- 33. Which coordinate represents the rotation of one base with respect to the other in the same base pair?
A) Twist
B) Propeller
C) Tilt
D) Roll
- 34. What is the definition of pitch in a nucleic acid double helix?
A) The height per complete turn of the helix
B) The diameter of the helix
C) The rotation angle of the helix
D) The distance between two bases
- 35. Which displacement is directed from the minor to the major groove?
A) Rise
B) Shift
C) Slide
D) Stagger
- 36. Which coordinate is defined as the rotation around the slide axis?
A) Propeller
B) Twist
C) Tilt
D) Roll
- 37. Which coordinate is defined as the rotation around the shift axis?
A) Roll
B) Twist
C) Tilt
D) Opening
- 38. What does the term 'inclination' refer to in helix-based coordinates?
A) The distance between strands
B) The deviation of the inter-strand base-pair axis from perpendicularity to the helix axis
C) The displacement along the helix axis
D) The rotation around the rise axis
- 39. What is the displacement along the helix axis called?
A) Rise
B) Shift
C) Slide
D) Stagger
- 40. How are roll and tilt typically described in terms of their magnitude?
A) Typically large
B) Typically small
C) Always zero
D) Substantial in all DNA
- 41. What is the rotation around the rise axis called?
A) Tilt
B) Twist
C) Roll
D) Propeller
- 42. Which groove in B-DNA is wider?
A) Minor groove
B) The grooves are equal in width
C) The phosphate groove
D) Major groove
- 43. Who published the book 'The Double Helix: A Personal Account of the Discovery of the Structure of DNA' in 1968?
A) Francis Crick
B) Rosalind Franklin
C) Maurice Wilkins
D) James Watson
- 44. What was the name of the crucial X-ray diffraction image of DNA taken by Rosalind Franklin and Raymond Gosling?
A) Photo 52
B) Structure 1953
C) The Helix Image
D) Photo 51
- 45. In what year was the double-helix model of DNA first published in the journal Nature?
A) 1952
B) 1953
C) 1962
D) 1968
- 46. Whose work on base-pairing chemical and biochemical information contributed to the double-helix discovery?
A) Robert Corey
B) Erwin Chargaff
C) Alexander Stokes
D) Linus Pauling
- 47. What conformation did Linus Pauling incorrectly propose for DNA?
A) Single-stranded
B) Quadruple-stranded
C) Spherical
D) Triple-stranded
- 48. What process involves complementary base pairs binding to form a double helix?
A) Replication
B) Transcription
C) Melting
D) Hybridization
- 49. What is the term for the process of separating the two nucleic acid strands of a double helix?
A) Hybridization
B) Annealing
C) Melting
D) Transcription
- 50. Which sequences are often found at the start of genes to assist RNA polymerase in melting?
A) TATA
B) ATCG
C) TGTG
D) GCGC
- 51. At sub-piconewton forces, what physical law describes DNA bending?
A) Boyle's law
B) Hooke's law
C) Coulomb's law
D) Newton's second law
- 52. Where is tight DNA bending frequently observed?
A) Ribosomal RNA complexes
B) Nucleosome particles
C) Mitochondrial membrane surfaces
D) Single-stranded DNA viruses
- 53. Where was intrinsic bending first observed?
A) Trypanosomatid kinetoplast DNA
B) Human chromosome 21
C) Viral capsid DNA
D) Bacterial plasmid DNA
- 54. If a nick is present in a circularizing DNA molecule, where does bending localize?
A) At the GC-rich segments
B) At the center of the molecule
C) At the AT-rich segments
D) At the nick site
- 55. In whose honor was P-form DNA named?
A) James Watson
B) Rosalind Franklin
C) Francis Crick
D) Linus Pauling
- 56. Which DNA motifs show a sequence preference for the Σ-DNA structure?
A) CCCC motifs
B) GNC motifs
C) TATA motifs
D) ATAT motifs
- 57. What instrument is used to study the entropic stretching of DNA?
A) Electron microscope
B) Centrifuge
C) Optical tweezers
D) X-ray crystallograph
- 58. How many degrees does the B form of the DNA helix twist per 10.4-10.5 base pairs in the absence of torsional strain?
A) 90°
B) 360°
C) 720°
D) 180°
- 59. What is DNA with excess helical twisting called?
A) Positively supercoiled
B) Denatured
C) Relaxed
D) Negatively supercoiled
- 60. What is DNA with insufficient helical twisting called?
A) Positively supercoiled
B) Negatively supercoiled
C) Intercalated
D) Linearized
- 61. Who was one of the first to propose the importance of linking numbers in DNA supercoils?
A) James Watson
B) Francis Collins
C) Francis Crick
D) Rosalind Franklin
- 62. In the equation L = T + W, what does L represent?
A) Length
B) Linking number
C) Loop
D) Left-handedness
- 63. In the equation L = T + W, what does W represent?
A) Writhe
B) Width
C) Weight
D) Wave
- 64. What happens if the twist of a circular DNA molecule is increased or decreased by supercoiling?
A) The writhe is altered
B) The base pairing sequence changes
C) The DNA becomes linear
D) The linking number becomes zero
- 65. What was the topological puzzle regarding residual supercoiling in eukaryotic genomes called?
A) The supercoiling mystery
B) The linking number paradox
C) The chromatin knot
D) The histone puzzle
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