The Molecular Calculation Toolkit

Many hard NEET questions on this chapter are short calculations. Keep these ready.

Chargaff (base composition)

  • In double-stranded DNA, A = T and G = C, so A + G = T + C = 50% (purines = pyrimidines).
  • If A = x%, then T = x% and G = C = (100 - 2x)/2. Example: A = 30% -> T = 30%, G = C = 20% each.
  • The ratio (A+T)/(G+C) is characteristic of a species and need not be 1; but (A+G)/(T+C) = 1 always.

Length and base pairs

  • Adjacent base pairs are 0.34 nm (0.34 x 10^-9 m) apart, and one turn = 3.4 nm = 10 bp.
  • Number of base pairs = length / 0.34 nm; number of turns = bp / 10. Example: 1.1 m of DNA -> 1.1 / (0.34 x 10^-9) approximately 3.3 x 10^9 bp (the human haploid genome; the diploid 2.2 m gives 6.6 x 10^9 bp).

Hydrogen bonds

  • A=T has 2 hydrogen bonds; G≡C has 3. Total H-bonds in a duplex = 2 x (number of A-T pairs) + 3 x (number of G-C pairs). GC-rich DNA is more stable and needs more energy to melt.

Polarity of the strands

  • The template strand is read 3' to 5'; the RNA/coding strand runs 5' to 3'. The coding strand has the same sequence as the mRNA (with T for U); the template is complementary and antiparallel to the mRNA.

The genetic code by numbers

  • 64 codons = 4^3; 61 code amino acids, 3 are stop (UAA, UAG, UGA); AUG is start. A frameshift (insertion/deletion not a multiple of 3) changes every downstream codon.

Traps: A=T and G=C, so %A = %T; bp = length / 0.34 nm; G-C pair = 3 H-bonds (more stable); coding strand = mRNA with T; 3 stop codons, no tRNA for them.

Who Did What, lac Logic, and Fine Distinctions

The experiments (a favourite matching set)

  • Griffith - transformation (S/R Streptococcus); Avery, MacLeod & McCarty - the transforming principle is DNA; Hershey & Chase - phage with 32P/35S proves DNA is genetic material; Meselson & Stahl - semiconservative replication (15N/14N); Watson & Crick - the double helix (from Wilkins & Franklin's X-ray); Gamow - proposed the triplet code; Nirenberg & Khorana - deciphered it; Jacob & Monod - the lac operon; Alec Jeffreys - DNA fingerprinting.

lac operon logic

  • No lactose: repressor (from i gene) binds the operator -> operon OFF.
  • Lactose present: lactose (inducer) inactivates the repressor -> operon ON (z, y, a transcribed).
  • i gene mutated so the repressor cannot bind the inducer: the repressor stays on the operator even with lactose -> operon stays OFF (a 'super-repressor').

Fine distinctions worth memorising

  • Leading vs lagging strand: leading is made continuously; lagging is made in Okazaki fragments (joined by ligase) - both by polymerase acting 5' to 3'.
  • Template vs coding strand: only the template (3'->5') is transcribed; the coding strand just carries the mRNA sequence.
  • hnRNA vs mRNA: hnRNA is the unprocessed primary transcript (with introns); mRNA is the mature molecule after splicing, capping and tailing.
  • RNA pol I / II / III: rRNA / hnRNA(mRNA) / tRNA (and 5S rRNA, snRNA) respectively (eukaryotes).
  • Euchromatin vs heterochromatin: loose/light/active vs dense/dark/inactive.
  • Nucleoside vs nucleotide: base + sugar vs base + sugar + phosphate.

Assertion-Reason watch-outs: DNA polymerase works only 5'->3' (so the lagging strand must be discontinuous); the code is degenerate but never ambiguous; rRNA (not a protein) is the peptide-bond catalyst (ribozyme).