DNA Structure and Replication

DNA Structure and Replication

• DNA is a polymer of nucleotides, each comprising a nitrogenous base, a sugar, and a phosphate group.
• Nitrogenous bases include adenine (A), thymine (T), guanine (G), and cytosine (C).
• In 1950, Erwin Chargaff observed that DNA composition varies between species.
• His "rules" state the number of A bases equals T bases and the number of C bases equals G bases.

DNA as Genetic Material

• DNA's molecular diversity makes it a strong candidate for the genetic material.
• This is because it possesses varying compositions across different organisms.

Structural Model of DNA

• After DNA's genetic role was established, researchers focused on understanding its structure and its relation to heredity.
• Scientists like Maurice Wilkins and Rosalind Franklin used X-ray crystallography to study DNA's structure.
• Franklin's X-ray images revealed that DNA has a helical shape.
• These images determined the width of the helix and the spacing of nitrogenous bases within.
• The patterns shown strongly suggested a double-helix model.
• Watson and Crick built models that aligned with the X-ray data and chemical properties of DNA.
• Franklin's research highlighted two outer sugar-phosphate backbones, with nitrogenous bases paired in the helix's interior.
• Watson and Crick's model proposed antiparallel backbones (subunits run in opposite directions).
• Base pairings (A with T, G with C) resulted in a uniform helix width consistent with X-ray data, challenging the initial "like with like" pairing hypothesis.

Watson-Crick Model Explains Chargaff's Rules

• The Watson-Crick model demonstrates that in any organism, the amount of adenine equals thymine, and the amount of guanine equals cytosine.

DNA Replication

• DNA replication is the copying process of DNA.
• DNA strands are complementary; each strand serves as a template for a new strand during replication.
• Replication yields two exact replicas of the original molecule (parental DNA).
• Watson and Crick proposed a semiconservative model of DNA replication, in which each daughter double helix contains one original (parental) strand and one newly synthesized strand.
• Other models (conservative and dispersive) were also initially considered before the acceptance of the semiconservative model.
• DNA replication is remarkable in its speed and accuracy, using many enzymes and proteins.
• Notably, the replication mechanisms in bacteria and eukaryotes are essentially similar.

Initiation of DNA Replication

• Replication begins at specific sites called origins of replication.
• DNA at the origin unwinds, forming a replication bubble with replication forks on either side.
• Eukaryotic chromosomes possess multiple origins of replication, enabling faster replication compared to prokaryotes.
• Replication proceeds in both directions from each origin, eventually replicating the entire DNA molecule.
• Enzymes and proteins involved in initiation include helicases which unravel the DNA double helix at the replication forks., single-strand binding proteins (SSBs), stabilizing single-stranded DNA, and topoisomerases which relieve the stresses caused by unwinding.

Synthesizing a New DNA Strand

• DNA polymerases are enzymes that catalyze the synthesis of new DNA strands.
• DNA polymerases require a primer (a short RNA segment) to begin.
• Primase synthesizes the RNA primer.
• The newly synthesized DNA strands grow from the 3' end of the RNA primer.

Antiparallel Elongation

• The difference in the sugars of Deoxyribose in dATP (used in DNA) v/s Ribose in ATP (used in energy metabolism) underlies the different roles.
• DNA polymerase only adds nucleotides to the 3' end of a growing strand, hence DNA synthesis only occurs in the 5' to 3' direction.
• Synthesis of new strands proceeds in two ways, the leading strand is synthesized continuously.
• The lagging strand is synthesized discontinuously in segments called Okazaki fragments that are later bound together by the enzyme DNA ligase.

The DNA Replication Complex

• Proteins involved in DNA replication form a complex structure, known as a "DNA replication machine."
• The replication machine may remain stationary during the DNA replication process in some cases.

Proofreading and Repairing DNA

• DNA polymerases 'proofread' newly synthesized DNA, correcting any mismatched nucleotides.
• Mismatch repair mechanisms involve additional enzymes that further rectify any errors missed by the proofreading process.
• DNA can be damaged by chemicals or physical agents, subsequently undergoing spontaneous changes.
• Nucleotide excision repair involves enzymes that remove and replace damaged stretches of DNA.