Nucleotides and nucleic acids

• Nucleic acids


  -C,H,O,N,P

  • carry the genetic code in all living organisms
  • control of all cellular processes including protein synthesis
• Nucleotides


  -biological molecule

  -phosphate esters of pentose sugars

  -nitrogenous base linked to Carbon-1 of the sugar residue

  -phosphate group linked to Carbon-3/5 by covalent bonds formed by condensation reactions

  -C,H,O,N,P
• Nucleotides


  • form the monomers of nucleic acids, DNA and RNA
  • become phosphorylated nucleotides when they contain more than one phosphate group
  • help regulate many metabolic pathways
  • may be components of coenzymes
• Nucleotide

  
• Nucleotide

  
• DNA


  -macromolecule

  -polymer

  -found in the nuclei of all eukaryotic cells/cytoplasm of prokaryotic cells

  -hereditary material and carries coded instructions used in the development and functioning of all known living organisms

  • stores genetic information
• DNA 


  -deoxyribose sugar with hydrogen at the 2' position

  -two polynucleotide strands in opposite directions(antiparallel) joined together by hydrogen bonds between complementary bases

  -Adenine and thymine-two H bonds

  -Guanine and cytosine-three H bonds

  -deoxyribose, phosphate group, nitrogenous base

  -phosphodiester bond (from condensation reaction) between sugar and the phosphate group

  -double helix
• DNA bases


  Adenine, Guanine-Purine

  Cytosine, Thymine-Pyrimidine

  Purine: two carbon nitrogen rings joined together

  Pyrimidine: one carbon-nitrogen ring

  • A purine always pairs with a pyrimidine giving equal sized 'rungs' on the DNA ladder. These can then twist around an imaginary axis into a double helix giving the molecule stability
• Hydrogen bonds


  -allow the molecules to unzip for transcription
• RNA


  -ribose, phosphate group, nitrogenous base

  -Uracil replaces thymine

  -hydroxyl group at the 2' position

  -single polynucleotide chain

  -presence of the 2' hydroxyl group makes RNA more susceptible to hydrolysis

  • make proteins from the instructions in DNA
• Phosphodiester bonds


  • DNA and RNA are polymers (polynucleotides)
  • Separate nucleotides are joined together via condensation reactions
  • occur between the phosphate group of one nucleotide and the pentose sugar of the next nucleotide
  • A condensation reaction between two nucleotides forms a phosphodiester bond
  • consists of a phosphate group and two ester bonds
  • chain of alternating phosphate groups and pentose sugars produced as a result of many phosphodiester bonds is known as the sugar-phosphate backbone (DNA/RNA)
  • synthesis of polynucleotides requires the formation of phosphodiester bonds
• Antiparallel sugar-phosphate backgrounds


  -upright part of the large DNA molecule that resembles a ladder is formed by the sugar-phosphate backbones of the antiparallel polynucleotide strands

  -opposite directions of two strand-direction that 3rd and 5th carbon molecules on deoxyribose is facing

  -3'/5' end-where the phosphate group is attached to the carbon atom of the deoxyribose sugar

  -rungs of ladder consist of complementary base pairs joined by H bonds

  -molecule is very stable
• DNA(Eukaryotic cells)


  -mainly in nucleus

  -tightly wound around histone proteins into chromosomes. Each chromosome=one molecule of DNA

  -a loop of DNA without histone proteins inside mitochondria and chloroplasts
• DNA(Prokaryotic cells)


  -in a loop within the cytoplasm not enclosed in a nucleus

  -not wound around histone proteins

  -naked
• ATP


  -nucleic acid

  -phosphorylated nucleotide

  -energy-carrying molecule that provides the energy to drive many processes inside living cells

  • Energy is released when ATP is hydrolysed to form ADP and a phosphate molecule. This process is catalysed by ATP hydrolase.

  • The inorganic phosphate can be used to phosphorylate other compounds, as a result making them more reactive.

  • Condensation of ADP and inorganic phosphate catalysed by ATP synthase produces ATP during photosynthesis and respiration.
• ATP


  -provides energy for chemical reactions in the cell

  -synthesises from ADP and inorganic phosphate using the energy from an energy-releasing reaction. ADP is phosphorylated to form ATP and a phosphate is formed

  -Energy is stored in the phosphate bond. When this energy is needed by a cell, ATP is broken back down into ADP and inorganic phosphate. Energy is released from the phosphate bond and used by the cell
• Energy use

  • Anabolic reactions (building larger molecules from smaller molecules)
  • Moving substances across the cell membrane or moving substances within the cell
  • Muscle contraction – to coordinate movement at the whole-organism level
  • The conduction of nerve impulses
• Purification of DNA by precipitation



  1. macerate the tissue
  2. add a strong detergent
  3. add ethanol
  4. remove unwanted salts
  5. concentrate
• Marmur preparation

  1. Breaking (lysing) the cells and disrupting the nuclear membranes to release the DNA
  2. Using enzymes to denature and remove the proteins (histones) associated with the DNA
  3. Precipitating the DNA using an organic solvent (e.g. ethanol)
• Equipment

  • Plastic syringe (1 cm³)
  • Plastic funnel
  • 2 × beakers (250 cm³)
  • 2 × Test tubes
  • Stirrer (e.g. stirring rod or plastic spoon)
  • Chopping board
  • Knife (for chopping onion)
  • Onion
  • Washing-up liquid (10 cm³)
  • Ice-cold ethanol (10 cm³)
  • Protease enzyme (2-3 drops)
  • Coffee filter paper (laboratory filter paper not suitable as the liquid takes too long to pass through)
  • Water bath (60 °C)
  • Ice-water bath
  • Blender or liquidiser
• Method part 1

  • Place the ethanol in a freezer 24 hours before starting the investigation
  • Cut up the onion into small pieces (5 mm × 5 mm)
  • Add the washing-up liquid to 90 cm³ of tap water in a beaker
  • Add some onion pieces to the beaker
  • Place the beaker in a water bath at 60 °C for 15 mins
  • detergent and the heat disrupt the phospholipid bilayer of the onion cell membranes and nuclear membranes, releasing the DNA
  • heat also denatures enzymes released from the cell that would otherwise begin to digest the DNA
  • Cool the mixture in an ice-water bath for 5 minutes, stirring it continually
• Method part 2


  • Lowering the temperature prevents the DNA itself from breaking down, which would occur if the high temperature from the previous step was maintained
  • Continual stirring ensures the whole mixture is cooled
  • Pour the mixture into a blender and blend for 5 seconds
  • Blending breaks down the cell walls and cell membranes of the onion cells even further, releasing more DNA
  • The mixture is only blended for a very short time to ensure the DNA strands themselves are not broken apart
• Method part 3

  • Pour 10 cm³ of the filtrate into a test tube and add 2-3 drops of protease enzyme, mixing well
  • The protease denatures and removes the  protein leaving just the DNA
  • Carefully add the ice-cold ethanol to the test tube and wait 2-3 minutes
  • Nucleic acids are insoluble in ice-cold ethanol and so the DNA forms a precipitate (white layer) at the top of the test tube mixture
• Semi-conservative Replication of DNA

  • Before a (parent) cell divides, it needs to copy the DNA contained within it ensuring that the two new (daughter) cells produced will both receive full copies of the parental DNA
  • one of the polynucleotide DNA strands (half of the new DNA molecule) is from the original DNA molecule being copied
  • The other polynucleotide DNA strand (the other half of the new DNA molecule) has to be newly created by the cell
  • Therefore, the new DNA molecule has conserved half of the original DNA and then used this to create a new strand
• Semi-conservative replication


  • DNA replication occurs in preparation for mitosis, when a parent cell divides to produce two genetically identical daughter cells – as each daughter cell contains the same number of chromosomes as the parent cell, the number of DNA molecules in the parent cell must be doubled before mitosis takes place
  • DNA replication occurs during the S phase of the cell cycle (which occurs during interphase, when a cell is not dividing)
• Semi-conservative replication

  1. The enzyme helicase unwinds the DNA double helix by breaking the hydrogen bonds between the base pairs
  2. Each of these single polynucleotide DNA strands acts as a template for the formation of a new strand made from free nucleotides that are attracted to the exposed DNA bases by base pairing
  3. The new nucleotides are then joined together by the enzyme DNA polymerase which catalyses condensation reactions to form a new strand
  4. The original strand and the new strand join together through hydrogen bonding between base pairs to form the new DNA molecule
• Mutations

  -errors may occur and the wrong nucleotide may be inserted

  -1 in 10^8 base pairs

  -could change the genetic code and is an example of point mutation

  -enzymes present that can proofread and edit out such incorrect nucleotides
• gene


  -a sequence of nucleotides that forms part of a DNA molecule-sequence of nucleotides codes for the production of a specific polypeptide (protein)

  • shape and behaviour of a protein molecule depends on the exact sequence of these amino acids
  • genes in DNA molecules and control protein structure (+protein function) as they determine the exact sequence in which the amino acids join together when proteins are synthesised in a cell
• Nature of genetic code

  -universal, same same triplet of DNA bases codes for the same amino acid

  -non-overlapping meaning that each triplet is only read once and triplets don’t share any bases

  -Genetic code is also degenerate meaning that more than one triplet codes for the same amino acids
• Transcription part 1

  -occurs in the nucleus (involves DNA and mRNA)

  -DNA strand is transcribed into mRNA

  1. RNA polymerase attaches to the DNA double helix at the beginning of a gene
  2. H bonds break separating the strands -> DNA molecule uncoils
  3. One of the strands is then used as a template strand to make a new copy
  4. RNA polymerase lines up free RNA nucleotides alongside the template strand. Complementary base pairing occurs (T is replaced by U in RNA)
  5. RNA polymerase moves along the DNA separating the strands assembling the mRNA strand
• Transcription part 2

  1. H bonds reform between uncoiled strands once RNA polymerase has passed by and the strands coil back into a double-helix
  2. When RNA polymerase reaches a stop codon it stops making mRNA and detaches from DNA
  3. mRNA moves out the nucleus through a nuclear pore in the nuclear envelope and attaches to a ribosome in the cytoplasm where Translation occurs
• Translation part 1

  -occurs at the ribosomes in the cytoplasm

  -amino acids are joined together to make a polypeptide chain following the sequence of codons carried by the mRNA

  1. mRNA attaches itself to a ribosome and tRNA molecules carry amino acids to the ribosome
  2. tRNA molecule with an anticodon that's complementary to the start codon on the mRNA and attaches itself to the mRNA by complementary base pairing
  3. 2nd tRNA attaches itself to next codon on the mRNA
• Translation part 2

  1. rRNA catalyses the formation of a peptide bond between the two amino acids attached to the tRNA -> joining the amino acids together. 1st tRNA molecule moves away leaving its amino acid behind
  2. 3rd tRNA binds to the next codon on the mRNA. Its amino acid binds to the first two and the 2nd tRNA molecule moves away
  3. this process continues producing a polypeptide chain until there's a stop codon on the mRNA molecule
  4. polypeptide chain moves away from the ribosome and translation is complete