Biological Molecules (1B)

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DNA

  • Stands for DeoxyriboNucleic Acid
  • Used to store genetic information (the instructions needed to grow and develop)
  • Sugar contained in DNA is deoxyribose
  • Each DNA nucleotide has the same sugar and a phosphate group. The base can vary
  • Four possible bases:
    • Adenine
    • Guanine
    • Thymine
    • Cytosine
  • Complementary base pairs: Cytosine pairs up with Guanine (THREE hydrogen bonds), Adenine pairs up with Thymine (TWO hydrogen bonds)
  • A polymer of nucleotides (or a polynucleotide)
  • Two DNA polynucleotide strands join together by hydrogen bonding between the bases. These are antiparallel, and twist to form the DNA double helix
  • First observed in the 1800s, but scientists at the time doubted it could carry genetic code as it was a relatively simple chemical composition
  • 1953: experiments prove DNA carried genetic code. Double helix structure determined by Watson and Crick
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RNA

  • Similar structure to DNA
  • One of its main functions is to transfer genetic information from the DNA to make ribosomes so that they can read the RNA to make polypeptides (a process called translation)
  • Sugar is called ribose
  • Four complementary bases:
    • Adenine
    • Guanine
    • Uracil
    • Cytosine
  • RNA also has a phosphate group on its nucleotides
  • RNA is much shorter than most DNA polynucleotides
  • Single polynucleotide chain
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Nucleotides

  • Contains a sugar, a phosphate group and a base
  • Connected in a condensation reaction, forming a phosphodiester bond
  • Polymer of nucleotides is a polynucleotide
  • The chain of sugars and phosphates is known as the sugar-phosphate backbone
  • Phosphodiester bond is between the phosphate group of one nucleotide and the sugar of another
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DNA Replication

  • Semi conservative (half of the strands in each new DNA molecule are from the original DNA molecule)
  • Steps:
    • 1) The enzyme DNA helicase breaks the hydrogen bonds between bases on the two polynucleotide DNA strands. The helix unwinds to form two single strands
    • 2) Each original strand acts as a template for a new strand (due to complementary base pairs) and free-floating nucleotides are attracted to their exposed base pairs on each original template strand
    • 3) Condensation reactions join the nucleotides together, catalysed by DNA polymerase (which moves at 5' to 3') . Hydrogen bonds form between the bases on the original and new strands
    • 4) Each new DNA molecule contains one strand from the original DNA and one new strand
  • DNA polymerase moves in opposite directions along the antiparallel strands
    • The active site of DNA polymerase is only complementary to the 3' end of the newly forming DNA, so the enzyme can only add nucleotides at the 3' end
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Proof for Semi-Conservative Replication

Meselson and Stahl's experiment:

  • Two samples of bacteria were grown, one in a nutrient broth of light nitrogen ( 14N) and one with heavy nitrogen ( 15N ) The nitrogen gradually became part of the bacteria's DNA
  • A sample of DNA was taken from each set of bacteria, and spun in a centrifuge. The DNA from the heavy nitrogen bacteria settled lower down in the centrifuge tube than the DNA from the light nitrogen
  • The bacteria grown in the heavy nitrogen were taken out and put in a broth containing only light nitrogen. The bacteria were left for one round of DNA replication and then another DNA sample was taken and spun in the centrifuge
  • If replication was conservative, the orginal heavy DNA would settle at the bottom and the new light DNA would settle at the top
  • If replication was semi-conservative, the new bacterial DNA molecules would contain one strand of old DNA and one strand of new DNA. The DNA would settle out in the middle of the tube (between where the heavy and light DNA settled)
  • The DNA settled in the middle, showing that the DNA molecules contained a mixture of heavy and light nitrogen.
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Water

    • Contains one atom of oxygen and two atoms of hydrogen in a covalent bond
    • Because the shared hydrogen electrons are pulled towards the oxygen atom, the other side of each hydrogen atom has a slight positive charge
    • The unshared electrons on the oxygen give it a slight negative charge
    • This makes it polar: it has a partial negative (δ-) charge on one side and a partial positive (δ) charge on the other
  • Useful properties
    • Water is a metabolite: many metabolic reactions involve condensation or hydrolysis reactions - which involve water
    • High latent heat of vaporisation: takes a lot of enery to break the hydrogen bonds between water molecules. Therefore, organisms can use water loss through evaporation to cool down
  • Can resist changes in temperature
  • The hydrogen bonds can absorb a lot of energy - high specific heat capacity (organisms don't experience rapid temp changes)
  • Good solvent - the positive end of the molecule will attract to any negative ions and the negative end will attract to any positive ions
  • Strong cohesion between water molecules
    • Stick together well due to being polar, which helps water flow.
    • High surface tension when it comes into contact with air (some insects can 'walk' on a pond)
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ATP

  • The immediate source of energy in a cell
  • Plant and animal cells release energy from glucose - but can't get it directly from glucose
  • In respiration, the energy released from glucose is used to make ATP (adenosine triphosphate)
  • Made from the nucleotide base adenine, a ribose sugar and three phosphate groups
  • Once made, it diffuses to the part of the cell whcih needs energy
  • The energy in ATP is stored in very high energy bonds between the phosphate groups. It is released via hydrolysis reactions
  • ATP gets broken down into ADP (Adenosine DiPhosphate) and a Pi ion. A phosphate bond is broken and energy is released. This reaction is catalysed by ATP hydrolase
  • The inorganic phosphate can be put back to use - added to another compound , which makes the compound more reactive
  • ATP can be re-synthesised in a condensation reactiong between ADP and

    a Pi ion. This happens during both respiration and photosynthesis, and is catalysed by ATP synthase

     

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Inorganic Ions - Iron (Fe2+)

  • Have an electric charge:
    • an ion with a positive charge is called a cation
    • an ion with a negative charge is called an anion
  • An inorganic ion ion is one which doesn't contain carbon (though there are exceptions)
  • Found in solution, in cytoplasms of cells and in body fluids of organisms
  • Iron ions:
    • important part of haemoglobin - all 4 polypeptide chains contain iron ( Fe2+ ) in its centre
    • It's the Fe2+ that actually binds to the oxygen in haemoglobin
    • When oxygen is bound, the Fe2+ ion temporarily becomes an Fe3+ ion, until oxygen is released
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Inorganic Ions - Hydrogen (H+)

  • Determines pH
    • The more H+ present, the lower the pH (and the more acidic)
    • The less H+ present, the higher the pH (and the more alkaline)
    • Enzyme controlled reactions are all affected by pH
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Inorganic Ions - Sodium (Na+)

  • Helps transport glucose and amino acids across membranes
    • Co-transport allows glucose or amino acids to be transported into the cell alongside sodium ions
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Inorganic Ions - Phosphate (PO4 3-)

  • When a phosphate ion is attached to another molecule, it is known as a phosphate group
  • DNA, RNA and ATP all contain phosphate groups
  • The bonds between phosphate groups that store energy in ATP
  • The phosphate groups in DNA and RNA allow nucleotides to join up to form the polynucleotides
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