Nucleic Acids – Study Notes

DNA (deoxyribonucleic acid) identified as the hereditary molecule in all living organisms; only viruses may use RNA instead (e.g., SARS-CoV-2).
Universality of the genetic code supports a single common ancestry: identical codon meanings across taxa.
DNA located in nuclear chromosomes and certain organelles (mitochondria, chloroplasts); RNA largely cytoplasmic.
Viruses carry nucleic acids yet are considered non-living; presence of genetic material ≠ life.

Each nucleotide = three covalently bonded parts:
• Nitrogenous base (four in DNA: adenine A, thymine T, guanine G, cytosine C; uracil U replaces T in RNA).
• Pentose sugar (deoxyribose in DNA, ribose in RNA).
• Phosphate group (phosphate di-ester).
Formed via enzyme-controlled condensation, releasing $H_2O$ .
Two base classes:
• Purines (double ring): adenine, guanine.
• Pyrimidines (single ring): cytosine, thymine, uracil.

Successive nucleotides join by 3′-5′ phosphodiester bonds through condensation.
Generates an unbroken sugar-phosphate ‘backbone’; bases project laterally, carrying information.
Chains of up to $5 \times 10^6$ nucleotides possible in eukaryotic DNA.

Information resides in the order of bases on the coding strand.
Code is a triplet (codon) code: $4^3 = 64$ possible codons encode $20$ amino acids.
One strand (coding or sense) read $3' \rightarrow 5'$ by RNA polymerase; complement is antisense.
Complementary base pairing ensures accurate replication & transcription.

RNA is usually single-stranded, lengths from $10^2$ to $10^4$ nucleotides.
Sugar = ribose; base set = A, C, G, U.
Three main forms:
• mRNA – carries codon sequence from nucleus to ribosome.
• tRNA – adapters that bind specific amino acids; involved in translation.
• rRNA – structural & catalytic component of ribosomes.

Two antiparallel strands form a right-handed double helix, completing one turn every $10$ bases (pitch $3.4\,nm$ ).
Orientation: one strand $5' \rightarrow 3'$ , the other $3' \rightarrow 5'$ .
Specific pairing via hydrogen bonds:
• A–T with $2$ H-bonds.
• C–G with $3$ H-bonds.
Purine–pyrimidine pairing keeps helix diameter constant; contributes to stability.

Carbons numbered $1'$ → $5'$ ; phosphodiester bond links $3'$ -OH of one sugar to $5'$ -phosphate of next.
Processes respect polarity:
• DNA polymerase adds dNTPs to $3'$ -OH (synthesizes $5' \rightarrow 3'$ ).
• RNA polymerase transcribes coding strand $3' \rightarrow 5'$ to make RNA $5' \rightarrow 3'$ .
• Ribosome reads mRNA $5' \rightarrow 3'$ .

Human nuclear DNA length ≈ $2\,m$ packed into nucleus (diameter $\approx 5\,\mu m$ ).
Nucleosome: $\text{DNA}$ (~ $147$ bp) wrapped $1.65$ turns around histone octamer (2×H2A, H2B, H3, H4). Histone H1 clamps DNA.
Chromatin hierarchy: DNA → nucleosome “beads-on-a-string” → $30\,nm$ fiber → looped domains on non-histone scaffold → metaphase chromosome.
Positively charged lysine/arginine in histones interact with negatively charged DNA.
Supercoiling compacts DNA and protects it during mitosis/meiosis; allows controlled gene access.

Virtually limitless sequences: for strand length $n$ , possibilities = $4^n$ .
Gene counts (approx.):
• Human $20\,000–25\,000$ .
• Water flea $31\,000$ (greater than human).
Genome sizes:
• Human $3.2\,Gb$ (~ $3.2 \times 10^9$ bp).
• Rice $430\,Mb$ ; Paris japonica $150\,Gb$ .
DNA in a single human cell stores ≈ $3.2\,Gb$ of digital-like data in ~ $2\,m$ physical length.

$64$ codons map to identical amino acids in nearly all life forms; minor variants rare.
Highly conserved sequences (e.g., rRNA, histone genes) underscore universal ancestry.
Some mutations are synonymous; do not alter amino acid owing to code redundancy.

Miescher ( $1869$ ): discovered “nuclein” (DNA) in nuclei.
Levene (early $1900s$ ): identified ribose & deoxyribose; proposed (incorrect) tetramer model.
Chargaff’s Rules (late $1940s$ ):
• $[A]=[T]$ , $[C]=[G]$ .
• $[\text{purines}]=[\text{pyrimidines}]$ .
Watson & Crick ( $1953$ ): used cardboard models + Franklin & Gosling X-ray data to deduce double helix; showed mechanism for replication.
Hershey-Chase ( $1952$ ):
• Labeled T2 phage with $^{32}P$ (DNA) or $^{35}S$ (protein).
• Only $^{32}P$ entered E.coli and appeared in progeny phages ⇒ DNA carries genetic instructions.

Models simplify complex reality; can be physical (Watson-Crick) or digital.
Inductive vs. Deductive Reasoning; Popperian falsification advances knowledge (e.g., Chargaff disproving Levene’s tetramer hypothesis).
Labels like “junk DNA” illustrate how terminology shapes research focus.
Scientific progress entwines cooperation & competition (Franklin vs. Watson & Crick recognition debate).

Design a DNA extraction protocol using heating, detergents, salt, ethanol precipitation.
Construct classroom DNA models to visualize antiparallel orientation & base pairing.
Use PDB or PyMOL to explore nucleosome 3-D structures; observe histone tails.