DNA

DNA

  1. Deoxyribonucleic acid
    1. Genetic material that encodes all of the traits that make up a specifies. It is transmitted from one generation to the next (inheritance)
  2. Consists of sugar (deoxyribose) a nitrogenous base and a phosphate group. One unit is a nucleotide
  3. Adenine and Guanine are purines, Thymine and Cytosine are pyrimidines
  4. A=T (30% each) G=C (20% each)

DNA goes from 5' end to 3' end (top to bottom)

Organized in a double helix

Discovery of how it was organizes

Feb 1953

Discovery of the Alpha Helix Structure

  • Rosalind Franklin

James and Francis Crick

  • Received the novel price for the discovery of DNA replication

DNA Replication: Semiconservative Model

  • DNA separates into 2 strands
  • The daughter DNA molecules matches and pairs with the parent molecule to create 2 new DNA
  • Semi-conservative because

DNA Replication Process (Rewrite Process)

  1. 2 strands unwind
    1. Helicase enzyme unwinds
  2. 2 strands separate
    1. Single-strand binding protein make sure that the DNA stays apart long enough to replication
    2. Topoisomerase straightens the strands. It breaks, turns and rejoins the strand to relieve pressure
    3. Primase enzyme starts replication
  3. New nucleotides are added
    1. Attaches a short RNA molecules (primer) which is 5-10 nucleotides that corresponds to the DNA section at each origin of replication site. Allows for polymerase to bind and start
    2. DNA polymerase 3 enzymes begins to add nucleotides to the position where the primer is located, 50 nucleotides per second
  4. The nucleotides correspond to A-T and G-C
  5. The hydrogen bonds reform between the bases
  6. The initial strands are in "antiparallel" orientation (5' to 3' next to 3' to 5')
  7. Each nucleotide is added as a nucleotide triphosphate (energy-requiring process)
    1. Must add ATP to form a bind to add the nucleotide
    2. DNA polymerase adds on the nucleotides

Replisome

  • A complex of DNA replication enzymes
  • List all the enzymes and the single-strand biding protein and RNA primer

Replication start at origins of replication

  • Creates bubbles in the DNA
  • Goes from 5' to the 3' direction

DNA Replication enzymes

  1. Helicase
    1. Unwind DNA molecule
  2. Topoisomerase
    1. Relieves strain in DNA molecule
  3. Primase
    1. Adds RNA primer to make a 3' end
  4. DNA polymerase 3
    1. Adds nucleotides to both strands
  5. DNA polymerase 1
    1. Converts primers to DNA on both strands
  6. Ligase
    1. Joins up all Okazaki fragments

Replication starts at origin of replication

  • Strands in the middle of the strand
  • DNA replicates in both direction from the origin

DNA replication only takes place in the 5' to the 3' direction

The original DNA strand is separated. The top template strand give the "leading strand" and the Bottom the "Lagging strand"

DNA replication process

  1. The nucleotides are added to the new leading strand at the 3' end. Therefore the new strand forms in a 5' to 3' direction
  2. The DNA polymerase can only add nucleotides to an existing strand. Therefore the primer molecule had to start the replication process by providing a starting site for the polymerase
  3. RNA is used to start the strand as DNA cannot be synthesize
  4. The initiate replication of the lagging strand a primer molecule is also needed
  5. But the lagging strand is oriented in the 3' to 5' direction
  6. To accomplish the new strand development in the 5' to 3' direction, the DNA polymerase begins "downstream" from th point of origin
  7. It adds nucleotides in 100-200 segments that are called Okazaki fragments

Okazaki Fragments

  • Added to meet the requirement for a 3' to 5' direction of synthesis
  • All fragments need to be joined together by the enzyme DNA ligase
  • The RNA primers in both strands need to replaced by DNA nucleotides. Done by DNA polymerase 1. There are multiple primers to replace in the lagging strand, just one primer in the leading strand

The End replication Problem

  • The last primer site on the lagging strands cannot be replaced by DNA polymerase 1 as there Is no 3' site available for the enzyme to attach
  • As a result, the DNA molecule gets shorter in each cycle fo replication
  • A telomere region is present which is added by the telomerase enzyme that extend each end of the DNA molecule. It is first added as an RNA strand, then changed to DNA. It is a region of non-coding DNA (TTAGGG) repeated up to 1000 times

Telomere

  • It is a region of repetitive DNA sequence at the ends of a chromosome. Each time a cell divides, the telomere become slightly shorter.
  • Maintain chromosomal stability and prevent chromosomal degradation

The Telomerase Enzyme

  • Some researchers consider this to be a "cell immortalizing enzyme"
  • Highest levels of the enzyme are found in gametes and in newborn babies
  • Enzyme levels decline rapidly with age, Except in cancer cells, they have higher levels
  • Telomere regions are longer in children compare to adults and longer in cancer cells compared to healthy cells
  • Those who exercise daily have longer telomeres

Correction of errors and DNA Damage

  • Very high rate of nucleotide addition during replication can cause errors in nucleotides that are added. About 1 in 10,000 are incorrect (A-G instead of A-T). These errors can give rise to mutations and in some case result in cancer
  • Cell must check for these errors done by DNA polymerase enzyme, which proof-reads the DNA. Called "mis-match repair". Reduces the error rate to 1 in 10 billion nucleotides

The mismatch nucleotides and it's neighbors are removed and is replaced with the correct nucleotides by DNA polymerase. Then DNA ligase seals the gap in the DNA backbone

Repair of DNA damage

  1. DNA can be damaged by exposure of cell to UV light, X-rays, cigarette smoke, mutagenic agents
  2. If this is not repair it can lead to many types of cancers
  3. Cells continuously check the DNA and repair it using a set of enzymes
  4. The damaged area is cut out using a nuclease enzyme, the new nucleotides are added by DNA polymerase 3 and the ends are joined by DNA ligase

Basic DNA Repair Mechanisms (thymine)

  • Thymies dimer distorts DNA
  • Nuclease enzyme cuts the damaged DNA strand at 2 points Excision
  • Repair synthesis of DNA polymerase fills the gap Re-synthesis
  • Ligase seals the remaining nick Ligation