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BI10.1-7 | Molecular Biology — Part 2

Purine Degradation — From Base to Uric Acid

When purine nucleotides are no longer needed, they are broken down step by step:

Figure: Purine Degradation — From Base to Uric Acid

1. AMP → Adenosine → Inosine (by adenosine deaminase, ADA)
2. GMP → Guanosine → Guanine → Xanthine (by guanase)
3. Inosine → Hypoxanthine → Xanthine (by xanthine oxidase)
4. Xanthine → Uric acid (by xanthine oxidase)

Uric acid is the final product of purine degradation in humans. Unlike most mammals, we lack the enzyme uricase that would convert uric acid to the more soluble allantoin. This is why humans are prone to hyperuricaemia and gout.

Drug target: Allopurinol, a xanthine oxidase inhibitor, is the standard treatment for gout. It blocks the final step, reducing uric acid production. Newer drugs like febuxostat work by the same mechanism but are more selective.

The Central Dogma — Replication, Transcription, Translation

The flow of genetic information follows the central dogma of molecular biology (proposed by Francis Crick, 1958):

Figure: The Central Dogma — Replication, Transcription, Translation

DNA → (Replication) → DNA
DNA → (Transcription) → RNA
RNA → (Translation) → Protein

Think of it as a three-step information relay:

1. Replication (copying the master blueprint):
- Occurs during the S phase of the cell cycle
- The enzyme DNA polymerase reads the template strand (3' → 5') and synthesises the new strand (5' → 3')
- Replication is semi-conservative: each daughter DNA molecule has one old strand and one new strand (proved by the Meselson-Stahl experiment)
- Key players: Helicase (unwinds), Primase (makes RNA primer), DNA polymerase III (main synthesiser), Ligase (seals gaps)
- The leading strand is synthesised continuously; the lagging strand is made in short Okazaki fragments

2. Transcription (making an RNA copy):
- RNA polymerase reads the DNA template strand and synthesises a complementary mRNA
- In eukaryotes, the pre-mRNA undergoes processing: 5' capping, 3' polyadenylation (poly-A tail), and splicing (removal of introns, joining of exons)
- Remember: "Exons are Expressed, Introns are In the way"

3. Translation (reading the RNA to build protein):
- Ribosomes read mRNA in sets of three bases called codons
- Each codon specifies an amino acid (the genetic code — 64 codons for 20 amino acids)
- tRNA molecules act as adapters, carrying the correct amino acid to match each codon via their anticodon
- Translation proceeds through three stages: Initiation (AUG start codon, methionine), Elongation (peptide bond formation), Termination (stop codons: UAA, UAG, UGA)

DNA Repair — Protecting the Blueprint

Your DNA is constantly under assault — UV radiation, reactive oxygen species, chemical mutagens, and even simple replication errors. Fortunately, cells have evolved sophisticated repair systems:

Figure: DNA Repair — Protecting the Blueprint

1. Mismatch Repair (MMR):
- Corrects base-pairing errors missed by DNA polymerase proofreading
- Enzymes recognise the mismatch, excise a patch around it, and resynthesise
- Defective MMR causes Lynch syndrome (hereditary non-polyposis colorectal cancer, HNPCC) — one of the most common inherited cancer predispositions

2. Base Excision Repair (BER):
- Removes damaged or abnormal single bases (e.g., deaminated cytosine → uracil)
- DNA glycosylase recognises and clips out the damaged base; the gap is filled by polymerase and sealed by ligase

3. Nucleotide Excision Repair (NER):
- Removes bulky lesions that distort the helix (e.g., thymine dimers caused by UV light)
- A segment of ~30 nucleotides around the damage is excised and replaced
- Defective NER causes Xeroderma Pigmentosum (XP) — extreme UV sensitivity, skin cancers from childhood

4. Double-Strand Break Repair:
- Homologous recombination (accurate, uses sister chromatid) and Non-homologous end joining (NHEJ) (faster but error-prone)
- Defects in BRCA1/BRCA2 genes (homologous recombination) predispose to breast and ovarian cancer