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DNA Structure & Replication

Tier 1 · #3 of 33 · highest yield · topic 2.1 — every high-yield fact from the book chapter, exam-ready.

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  1. Front
    What three components make up a nucleotide ?
    Back
    A nitrogenous base , a five-carbon sugar , and at least one phosphate group
  2. Front
    What is the difference between a nucleoside and a nucleotide ?
    Back
    Nucleoside = base + sugar only ; nucleotide = base + sugar + phosphate(s)
  3. Front
    Which sugar is found in DNA, and how does it differ chemically from RNA's ribose?
    Back
    Deoxyribose — it lacks the 2'-hydroxyl that ribose carries
  4. Front
    The base attaches to the 1' carbon of the sugar via what type of bond?
    Back
    An N-glycosidic bond
  5. Front
    Which two bases are purines (double-ring)?
    Back
    Adenine (A) and guanine (G)
  6. Front
    Cloze: Purines have a ___-ring structure and pyrimidines have a ___-ring structure.
    Back
    double ; single
  7. Front
    Which base replaces thymine in RNA, and how does thymine differ from it chemically?
    Back
    Uracil ; thymine is 5-methyluracil (the only difference is methylation)
  8. Front
    Which form of a deoxyribonucleotide is the active substrate during replication?
    Back
    The triphosphate form (dNTP)
  9. Front
    What bond joins nucleotides into a chain, and between which groups does it form?
    Back
    A phosphodiester bond , between the 3'-OH of one sugar and the 5'-phosphate of the next nucleotide
  10. Front
    What is released when a phosphodiester bond forms, and what makes the reaction irreversible?
    Back
    Pyrophosphate (PPi) is released; its hydrolysis by pyrophosphatase makes the reaction irreversible
  11. Front
    Which end of a DNA strand carries the free phosphate, and which carries the free hydroxyl?
    Back
    5' end has the free phosphate ; 3' end has the free -OH
  12. Front
    In which direction is a DNA sequence conventionally read and written?
    Back
    5' to 3'
  13. Front
    Exonuclease vs endonuclease : which requires a free end to act?
    Back
    Exonucleases require a free end ; endonucleases cut within the interior and do not
  14. Front
    What class of nuclease are restriction enzymes , and what do they recognize?
    Back
    Endonucleases that recognize and cut specific palindromic sequences
  15. Front
    In recombinant DNA cloning, what enzyme joins the vector and insert after cutting?
    Back
    DNA ligase
  16. Front
    State Chargaff's rules .
    Back
    A equals T and G equals C (purine:pyrimidine ratio = 1.0)
  17. Front
    How many hydrogen bonds form in an A:T pair versus a G:C pair?
    Back
    A:T forms 2 hydrogen bonds ; G:C forms 3
  18. Front
    Why do GC-rich regions of DNA have a higher melting temperature?
    Back
    G:C pairs have 3 hydrogen bonds (vs 2 for A:T), requiring more energy to separate
  19. Front
    Cloze: The two strands of the double helix run ___ to each other.
    Back
    antiparallel
  20. Front
    Whose data did Watson and Crick use to build the double helix model?
    Back
    Rosalind Franklin's X-ray crystallography (Photo 51) and Chargaff's base-ratio rules
  21. Front
    What two noncovalent interactions stabilize the double helix?
    Back
    Hydrogen bonds between complementary base pairs and base stacking (π-stacking)
  22. Front
    Which interaction is the dominant contributor to helix stability?
    Back
    Base stacking (the hydrophobic core), not hydrogen bonding alone
  23. Front
    What is the handedness and approximate bp-per-turn of B-DNA , the dominant chromosomal form?
    Back
    Right-handed, ~10 bp per turn (2.37 nm wide, 0.34 nm between bases)
  24. Front
    Which DNA conformation is the shape of DNA:RNA hybrid duplexes?
    Back
    A-DNA (right-handed, more compact, ~11 bp per turn)
  25. Front
    Which DNA conformation is left-handed and found in GC-rich regions?
    Back
    Z-DNA
  26. Front
    Through which groove do most transcription factors read DNA sequence, and why?
    Back
    The major groove , where each base pair's chemical fingerprint is most distinctive
  27. Front
    What is the typical genome structure of a prokaryote ?
    Back
    A single circular double-stranded DNA molecule in the nucleoid (no membrane)
  28. Front
    What are plasmids , and what do they often encode?
    Back
    Small circular DNAs that replicate independently; often encode antibiotic resistance
  29. Front
    How much DNA does the nucleosome core wrap, and what is the core octamer composed of?
    Back
    147 bp wrapped around two copies each of histones H2A, H2B, H3, and H4
  30. Front
    Which histone is the linker histone that binds at nucleosome entry/exit points?
    Back
    H1
  31. Front
    Why are histones positively charged, and what does that let them do?
    Back
    They are rich in lysine and arginine ; their positive charge attracts the negative DNA backbone
  32. Front
    How does histone acetylation affect chromatin and transcription?
    Back
    It neutralizes histone positive charge, loosening chromatin to euchromatin (transcriptionally active)
  33. Front
    Euchromatin vs heterochromatin : which is transcriptionally active?
    Back
    Euchromatin is active (loose, acetylated); heterochromatin is silent (tight, deacetylated)
  34. Front
    What term describes changes in gene expression without changing the DNA sequence (e.g., histone acetylation)?
    Back
    Epigenetic regulation
  35. Front
    What does it mean that DNA replication is semiconservative ?
    Back
    Each daughter molecule keeps one parental strand and gains one newly synthesized strand
  36. Front
    Which experiment proved that DNA replication is semiconservative?
    Back
    The Meselson-Stahl experiment
  37. Front
    How do prokaryotes and eukaryotes differ in number of replication origins?
    Back
    Prokaryotes have a single origin ; eukaryotes have multiple origins per linear chromosome
  38. Front
    In which direction is new DNA always synthesized, and in which direction is the template read?
    Back
    New DNA synthesized 5'→3' ; template read 3'→5' ( no 3'→5' polymerization exists )
  39. Front
    What enzyme unwinds the double helix at the fork, and using what energy?
    Back
    DNA helicase , using energy from ATP hydrolysis (it breaks base-pair hydrogen bonds)
  40. Front
    What is the role of single-strand binding proteins (SSB) at the fork?
    Back
    They clamp separated single strands to prevent reannealing/hairpins and keep them as templates
  41. Front
    What problem do topoisomerases solve at the replication fork?
    Back
    They relieve the positive supercoils generated ahead of the fork by helix unwinding
  42. Front
    How does Type II topoisomerase differ mechanistically from Type I ?
    Back
    Type II cuts both strands and passes a duplex segment through (separating catenanes); Type I cuts only one strand
  43. Front
    Why can't DNA polymerase start a new strand de novo?
    Back
    It can only extend an existing strand with a free 3'-OH; it requires a primer
  44. Front
    What enzyme synthesizes the RNA primer, and what kind of enzyme is it?
    Back
    Primase , an RNA polymerase (makes a ~10-nt RNA primer )
  45. Front
    Which eukaryotic polymerase contains a primase subunit and makes the primer plus the initial short DNA segment?
    Back
    DNA polymerase alpha (~10 nt RNA primer + ~20 nt DNA)
  46. Front
    Which is the main bulk-replication polymerase in eukaryotes?
    Back
    DNA polymerase delta
  47. Front
    Which DNA polymerase replicates the mitochondrial genome ?
    Back
    DNA polymerase gamma
  48. Front
    Leading vs lagging : which strand is synthesized continuously toward the fork?
    Back
    The leading strand (continuous) ; the lagging strand is discontinuous
  49. Front
    Why must the lagging strand be made discontinuously?
    Back
    Its template runs 5'→3' toward the fork , so continuous synthesis would require impossible 3'→5' polymerization
  50. Front
    What are the short segments of the lagging strand called, and their size in eukaryotes?
    Back
    Okazaki fragments (150–200 bp in eukaryotes)
  51. Front
    What enzyme removes the RNA primer flaps from Okazaki fragments?
    Back
    FEN1 (flap endonuclease 1)
  52. Front
    What cofactor does DNA ligase use to seal nicks in eukaryotes versus bacteria?
    Back
    ATP in eukaryotes; NAD+ in bacteria
  53. Front
    Cloze: DNA ligase joins pre-existing strands and ___ synthesize DNA de novo.
    Back
    cannot
  54. Front
    What is the function of PCNA in replication?
    Back
    It is a sliding clamp that encircles DNA and tethers the polymerase so it doesn't fall off
  55. Front
    What enzymatic activity carries out proofreading during replication?
    Back
    A 3'→5' exonuclease activity intrinsic to the polymerase
  56. Front
    Which eukaryotic replication polymerase lacks proofreading (3'→5' exonuclease) activity?
    Back
    DNA polymerase alpha (all other replicative polymerases have it)
  57. Front
    What is the end-replication problem ?
    Back
    After removing the 5'-end primer of the lagging strand, no upstream 3'-OH exists to fill the gap , so the 5' end shortens each round
  58. Front
    What is the repetitive telomere sequence at the ends of linear chromosomes?
    Back
    TTAGGG (repeated thousands of times)
  59. Front
    What type of enzyme is telomerase , and what does it carry?
    Back
    A reverse transcriptase that carries its own RNA template
  60. Front
    Mechanistically, what does telomerase extend, and with what consequence?
    Back
    It extends the 3' end of the parental strand , providing template so the lagging-strand 5' end doesn't erode coding sequence
  61. Front
    Which cell types reactivate telomerase versus have low/absent activity?
    Back
    Cancer cells and stem cells reactivate it ; most somatic cells have low/absent activity
  62. Front
    Why does telomere shortening in somatic cells act as a tumor-suppression mechanism?
    Back
    Progressive shortening eventually triggers senescence or apoptosis , limiting division
  63. Front
    What are the five ingredients required for PCR ?
    Back
    dsDNA template, two primers (forward + reverse), the four dNTPs, a heat-stable DNA polymerase, and MgCl2
  64. Front
    From what organism is Taq polymerase isolated, and why is it suited to PCR?
    Back
    Thermus aquaticus ; it is heat-stable and survives the 95°C denaturation step
  65. Front
    Cloze: The three PCR thermocycler steps are denaturation at ___°C, annealing at ~___°C, and extension at ___°C.
    Back
    95; 55; 72
  66. Front
    After n PCR cycles, what is the theoretical yield per original dsDNA template?
    Back
    2^n molecules
  67. Front
    In PCR primer design, the forward primer matches which strand, and how is the reverse primer derived?
    Back
    Forward primer matches the sense strand ; the reverse primer is the complement of the antisense strand, written 5'→3'
  68. Front
    How is the PCR product detected after amplification?
    Back
    Ethidium bromide staining on an agarose gel after electrophoresis
  69. Front
    Name three clinical applications of PCR.
    Back
    Detecting infectious organisms ( SARS-CoV-2 , HIV , M. tuberculosis ), identifying mutations ( BRCA1 , CFTR ), and quantifying minimal residual disease in leukemia
  70. Front
    From each replication origin, how many forks form and in what direction do they grow?
    Back
    Two replication forks , growing bidirectionally
  71. Front
    What mechanism packages the prokaryotic genome (e.g., 1.7 mm of E. coli DNA into a 2 μm cell)?
    Back
    Supercoiling
  72. Front
    What is the dual role of DNA polymerase epsilon in eukaryotes?
    Back
    Replication and repair
  73. Front
    Why is the helix width held constant at 2.37 nm?
    Back
    Because a purine always pairs with a pyrimidine (one double-ring + one single-ring per pair)
  74. Front
    The phosphodiester bond has a half-life of ~200 million years — what does this explain?
    Back
    Why DNA (not RNA) is the long-term information-storage molecule
  75. Front
    Which groove of DNA is exploited by some small-molecule DNA-binding drugs?
    Back
    The minor groove
  76. Front
    In the double helix, where do the bases sit versus the sugar-phosphate backbones?
    Back
    Bases point inward and stack to form the hydrophobic core ; the charged backbones face outward toward the aqueous environment
  77. Front
    In which two directions can exonucleases travel along a strand?
    Back
    5'→3' or 3'→5' (either direction, one nucleotide at a time, from a free end)
  78. Front
    What is the approximate size of the haploid human genome, and the nucleus it must fit into?
    Back
    ~3 × 10^9 bp (~1 metre stretched) packed into a ~10 μm nucleus
  79. Front
    To which carbon of the sugar does the phosphate group attach in a nucleotide?
    Back
    The 5' carbon (via an ester bond)
  80. Front
    During which phase of the cell cycle does DNA replication occur?
    Back
    S phase
  81. Front
    What process is the B-DNA to Z-DNA conversion involved in regulating?
    Back
    Transcription
  82. Front
    Why is telomerase considered an attractive oncology drug target?
    Back
    Cancer cells reactivate telomerase to achieve unlimited division ; inhibiting it would limit their replicative immortality

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