DNA Structure and Base Pairing

• Complementary base pairing is defined by Chargaff's rule.

  • In a DNA sample, Guanine (G) accounts for 31%, Cytosine (C) also accounts for 31%.
  • Adenine (A) accounts for 19% and Thymine (T) accounts for 19%.
  • The total percentage of all nitrogenous bases equals 100%.

• Rosalind Franklin found the structure of DNA.

  • Watson and Crick are believed to have stolen it.

• James Watson and Francis Crick determined the structure of DNA by taking a picture of it.

• A DNA nucleotide consists of three parts:

  • Deoxyribose sugar
  • Phosphate group
  • Nitrogenous base

• Nitrogenous base pairing:

  • Adenine (A) pairs with Thymine (T).
  • Guanine (G) pairs with Cytosine (C).
  • Purines: Adenine and Guanine.
  • Pyrimidines: Thymine and Cytosine.

• Purines vs. Pyrimidines:

  • Purines have a double-ring structure.
  • Pyrimidines have a single-ring structure.

• 5’ and 3’ Significance:

  • Refer to the 5' end and 3' end of the DNA strand.
  • Critical in nucleic acid structure.

• Complementary DNA Strand Synthesis:

  • Original Strand: A C G A T T G C C
  • Complementary Strand: T G C T A A C G G

• Organization of Genetic Terms (Biggest to Smallest):

  • Chromosome, DNA, Gene, Nucleotide, Sugar, Phosphate, Nitrogen Base

• Semi-Conservative Replication:

  • A replication process, resulting in one original strand (parent) and one newly synthesized strand (daughter).

• Three Major Steps in DNA Replication:

  • Initiation
  • Elongation
  • Termination

Initiation of Replication

• Helicase unwind the DNA by breaking hydrogen bonds.

• Replication bubbles are created.

• Helicase and Single-Stranded Binding Proteins:

  • Helicase unwinds DNA at the origin of replication.

• Replication Fork vs. Replication Bubble:

  • Helicase unwind DNA at the origin of replication, forming a replication fork.
  • Replication bubble is the area where the replication fork is located at

• Primers are necessary for DNA replication.

  • Primase, an enzyme inserts the primers.
  • Primers show polymerase where to start working.

Elongation of Replication

• Leading Strand:

  • Moves in the same direction as the replication fork.

• Lagging Strand:

  • Moves away from the replication fork.

• Roles of DNA Polymerase:

  • Builds nucleotides 5’ to 3’.
  • Removes RNA primers.
  • Replaces RNA primers with DNA nucleotides.

• Determining Leading vs. Lagging Strand:

  • Leading strand is synthesized continuously towards the replication fork.
  • Lagging strand is synthesized in short fragments (Okazaki fragments).

• Okazaki Fragments:

  • Fragments of DNA.
  • Located on the lagging strand.

• Ligase Function:

  • Ligase glues Okazaki fragments together.

Termination

• Termination:

  • Ligase glues Okazaki fragments together.

• Mutation:

  • A permanent change in the DNA sequence of an organism.

• Excision Repair:

  • Impacts the rate of mutation.

• S-Phase:

  • DNA replication happens during the S-Phase of the cell cycle before cell division.
  • Ensures genetic continuity.
  • Each new cell receives a full copy of the genome.
  • Each new cell gets instructions for making protein.

• DNA Replication:

  • It is a semi-conservative process.
  • Each new molecule has one "parent template" strand and one new "daughter" strand

• RNA Primase:

  • Adds a complementary RNA primer to each template strand.
  • This provides a starting point for replication.

• DNA Polymerase:

  • Reads the 3’ end of the template strand (3’ to 5’).
  • It adds new complementary nucleotides (5’ to 3’).
  • DNA is synthesized in the direction of the replication fork, this is called the leading strand.
  • Can only add new nucleotides in the 5’ to 3’ direction.
  • Proofreads its own work and does excision repair.
  • Removes the RNA primer and replaces it with DNA.

• DNA Replication Direction:

  • Due to the antiparallel nature of DNA, replication occurs in two directions.
  • An RNA primer is laid down on the other strand.
  • New nucleotides are added 5’ to 3’, moving away from the replication fork.
  • The lagging strand and the segment of DNA produced are called an Okazaki fragment.

• Leading Strand continuous synthesis:

  • The DNA unwinds some more.
  • The leading strand is extended by DNA polymerase adding more DNA nucleotides.
  • The leading strand is synthesized continuously.

• Lagging Strand discontinuous synthesis:

  • A new RNA primer is synthesized by primase near the replication fork.
  • DNA polymerase adds new DNA which produces the second Okazaki fragment.
  • The lagging strand is synthesized discontinuously.

• Leading vs. Lagging Strand:

  • Leading Strand: 1 primer, 5’ to 3’ continuous.
  • Lagging Strand: multiple primers, 5’ to 3’ discontinuous.

• Rate of Mutation:

  • DNA polymerase adds 50 nucleotides/second.
  • Initially, 1 in 10,000 bases are in error.
  • After proofreading, rate of mutation is 1 in 10,000,000.

• DNA Ligase role:

  • Joins the two Okazaki fragments with phosphodiester bonds.
  • Creates a continuous chain.
  • Each new DNA molecule is rewound by helicase and each molecule is identical.