#2.3 Nucleic Acids

• structure of DNA

  • DNA is a polymer as it is made of repeating monomeric units called nucleotides
  • A molecule of DNA consists of two polynucleotide strands
  • the two strands run in opposite directions, so they're described as antiparallel
  • each DNA nucleotide consists of a phosphate group, a five-carbon sugar called deoxyribose and one of four nitrogenous bases : adenine, thymine, cytosine and guanine
  • the covalent bond between the sugar residue and the phosphate group in nucleotide is also called a phosphodiester bond.
  • DNA molecules are long and carry a lot of encoded genetic information
• inside of double helix:

  nitrogenous bases →

  • held together by hydrogen bonds

  outside of double helix:

  DNA backbone →

  • deoxyribose sugar
  • phosphate
• it can consist of either a purine - adenine or guanine (2 rings) or a pyrimidine - thymine or cytosine (1 ring)
• importance of hydrogen bonds

  • adenine always pairs with thymine, by means of 2 hydrogen bonds
  • guanine always pairs with cytosine, by means of 3 hydrogen bonds
  • a purine always pairs with a pyrimidine, giving equal sized “rungs” on ladder

  →these then twist, like twisting a rope ladder around an imaginary axis, into a double helix ; this gives the molecule stability

  • hydrogen bonds allow molecules to unzip for transcription and replication
• the antiparallel sugar - phosphate backbone

  • the upright part of the large DNA molecule that resembles a ladder is formed by the sugar-phosphate backbones of the antiparallel polynucleotide strands
  • the 'opposite directions’ of the two strands refer to the direction that the third and fifth carbon molecules on the five-carbon sugar is facing
  • the 5’ end of the molecule is where the phosphate is attached to fifth carbon atom of deoxyribose sugar
  • the 3’ end is where the phosphate group is attached to third carbon atom of deoxyribose sugar
• antiparallel sugar-phsphate backbone 2

  • the rungs of the ladder consist of the complementary base pairs ,joined by hydrogen bond
  • the carbon atoms of the sugar molecule are numbered as 1’,2’,3’,4’,5’ (1' is read as 'one prime’)

  the phosphate residue attaches to the hydroxl group of the 5’ carbon of one sugar and the hydroxl group of 3’ carbon of the sugar of the next nucleotide

  →the bond is called a 5’-3’ phosphodiester linkage
• eukaryotes have genetic material composed of DNA and proteins (histones) :

  • each large molecule of DNA is tightly wounded around special histone proteins into chromosomes (1 molecule of DNA = 1 Chromosome)
  • there is also a loop of DNA, without histone proteins,inside mitochondria and chloroplasts
• prokaryotes have genetic material composed of DNA (only) in short circular strands:

  • DNA is in a loop and is within the cytoplasm, not enclosed in a nucleus
  • it is not wound around histone proteins, and is described as naked
• INVESTIGATION

  extraction and purification of DNA by precipitation

  strawberries, kiwi and salad-cress cotyledons are a good source

  macerate the tissue, adding a strong detergent (washing up liquid) so that the DNA precipitates out of solution

  → can be further purified for unwanted or removal of salts and then be concentrated
• Semi-conservative replication 1

  to make a copy of itself each DNA molecule:

  unwinds - it un twists, bit by bit, catalysed by a gyrase enzyme

  unzips - hydrogen bonds betweenthe nucleotide bases are broken

  →this is catalysed by DNA helicase, and in result in two single strands of DNA with exposed nucleotide bases

  free phosphorylated nucleotide, present in the nucleoplasm,the nucleus, are bonded to the exposed bases following complementary base-pairing rules
• semi-conservative replication 2

  • the enzyme DNA polymerase catalyses the addition of the new nucleotide bases, in the 5’ to 3’ direction,to the single strands of unzipped DNA as a template
  • the leading strand is synthesised continuously, where the lagging strand is in fragments (discontinuous) that are later joined, catalysed by ligase enzymes
  • hydrolysis of activated nucleotide, to release the extra phosphate groups, supplied the energy to make phosphodiester bond between the sugar residue of one nucleotide and the phosphate group of the next molecule
• characteristics of genetic code

  • universal
  • degenerate
  • non-overlapping
• ATP is called a nucleotide derivative because it is a modified form of a nucleotide (phosphorylated nucleotide)

  components:

  adenine- a nitrogenous base

  ribose- a 5-carbon sugar

  3 phosphate group
• Hydrolysis of ATP

  ATP + H2O →ADP +Pi(+ energy)

  • ATP hydrolase catalyses hydrolysis of ATP to adenosine diphosphate (ADP) an inorganic phosphate group (Pi)
  • energy is used to perform work inside cell
• the hydrolysis of ATP can be coupled to other reactions within cells that need energy

  e.g the transmembrane sodium-potassium pump (Na + /K + pump)

  →energy is need to power the pump that drives Na+ out of the cell and K+ into cell

  the inorganic phosphate can be used to phosphorylate other compounds (which makes them more reactive)
• • Resynthesis of ATP (condensation)
  • ADP + Pi (+ energy)→ATP + H2O

  catalysed by ATP synthase during photosynthesis or respiration