DNA

• Topoisomerases remove supercoiling upstream of the replication fork.
• Okazaki fragments are short pieces of newly synthesized DNA that form on the lagging strand as it is being copied.
• Helicases unwind the DNA double helix and separate the two strands.
• Primases synthesise short RNA primers
• Ligases promote phospho-diester bond formation between adjacent DNA fragments.
• the presence of the -OH group at the carbon-2 position in the ribose sugar of RNA makes it more susceptible to hydrolysis compared to DNA,
• •Nucleic acids are polymers made up of nucleotides.
• Purines are double ringed structures
• pyrimidines are single ringed structures
• DNA nucleotide has a phosphate group, deoxyribose sugar, and a nitrogenous base
• Rna nucleotide is a ribose, a phosphate group and a nitrogenous base
• Nucleoside = a base bonded to a sugar via a β-glycosidic linkage.
• Nucleotide = nucleoside joined to one or more phosphates via an ester linkage.
• •dATP (deoxyadenosine 5’-triphosphate)

  •dGTP (deoxyguanosine 5’-triphosphate)

  •dCTP (deoxycytidine 5’-triphosphate)

  •dTTP (deoxythymidine 5’-triphosphate)
• Deoxyadenosine diphosphate (ADP): A molecule formed from the breakdown of adenosine triphosphate (ATP). It serves as a source of energy for various metabolic reactions in cells.
• Nucleotides are linked together by a phosphodiester bond to form long linear chain.
• •One end of the polymer has a free OH group on the 5’-carbon of the pentose sugar. The other end has a free OH group of the 3’-carbon of the pentose sugar. By convention we write the sequence of bases in DNA from 5’ to 3’.
• •Adjacent bases are ~3.4 angstrom apart.

  •Helical structure repeats every 34 angstrom.

  •Diameter of the helix is constant 20 angstrom.
• Complementary base pairing - must always have a purine and a pyrimidine paired up in the double helix.
• Base pairs are held together by hydrogen bonds.
• •B-DNA – highly hydrated (physiological).

  •A-DNA – less hydrated.

  •Z-DNA – left handed with phosphoryl groups
• Z-DNA is often found in regions of DNA that are under high torsional stress or supercoiling. It can also be induced by certain chemical modifications.
• •DNA double helix is wrapped around histone proteins.

  •Further folded and packaged into chromosomes.
• •Two hydrogen bonds between A-T.

  Three hydrogen bonds between c-G
• Meselson-Stahl experiment :

  1. Isolation of DNA with Heavy Nitrogen (15N)
  2. Transfer to Light Nitrogen (14N) Medium
  3. Removed samples at set time points = 1 generation
  4. Proves semiconservative nature of DNA
• Human genome contains 3.2 x 10^9 bp (base pairs)
• DNA polymerases are enzymes that catalyse the synthesis of new DNA strands from the ends of a DNA molecule, require a primer and a template strand
• •Primer is a short, single-stranded nucleic acid which has a free 3’ OH.

  •Made of RNA (hence RNA synthesis is required for DNA replication).

  •Generated by an enzyme called a primase (an RNA polymerase). 
• DNA priming and replication are fundamental processes in molecular biology that are crucial for the duplication of genetic information.
• DNA replication begins at specific sites on the DNA molecule called origins of replication.
• Enzymes, such as DNA helicase, unwind and separate the DNA strands at the origin.
• Before DNA polymerase can start replicating DNA, it needs a short RNA primer to provide a starting point.
• The enzyme primase synthesizes a short RNA primer complementary to the DNA template at the replication fork.
• DNA polymerase attaches to the RNA primer, providing a starting point for the addition of nucleotides.
• DNA polymerase adds complementary nucleotides to the 3' end of the RNA primer on the leading strand continuously.
• On the lagging strand, DNA polymerase synthesizes short fragments known as Okazaki fragments in the 5' to 3' direction.
• The leading strand is synthesized continuously in the 5' to 3' direction because the DNA polymerase can move toward the replication fork.
• The lagging strand is synthesized discontinuously in the opposite direction of the replication fork.
• As the replication fork opens, short RNA primers are added, and DNA polymerase synthesizes Okazaki fragments away from the fork.
• The RNA primers are temporary and need to be replaced with DNA.