Proteins

• Transcription


  DNA is transcribed and an mRNA (messenger RNA) molecule is produced
• Translation


  mRNA is translated and an amino acid sequence is produced
• mRNA


  • It is a single-stranded molecule made up of many RNA nucleotides joined together
  • Its role is to carry the information encoded in the DNA from the nucleus to the site of translation on ribosomes
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  • It contains a ribose sugar while DNA contains deoxyribose
  • It is usually single-stranded while DNA is double-stranded
  • It contains the base uracil instead of the DNA base thymine
• Transcription


  1. Part of a DNA molecule unwinds and the hydrogen bonds between the complementary base pairs break

  2. A complimentary copy of the code from the gene is made by building a single-stranded nucleic acid molecule known as mRNA

  3. This reaction is catalysed by RNA polymerase

  4. Free activated RNA nucleotides pair up, via hydrogen bonds, with their complementary bases on the exposed strand of the 'unzipped' DNA molecule

  5. The sugar-phosphate groups of these RNA nucleotides are then bonded together in a reaction catalysed by the enzyme RNA polymerase to form the sugar-phosphate backbone of the mRNA molecule

  6. When the gene has been transcribed and the mRNA molecule is complete, the hydrogen bonds between the mRNA and DNA strands break and the double-stranded DNA molecule reforms

  7. The mRNA molecule then leaves the nucleus via a pore in the nuclear envelope
• Antisense strand


  The strand of the DNA molecule that is used to produce the mRNA molecule
• Sense strand


  The other strand of the DNA molecule that is not transcribed
• RNA polymerase moves along the template strand in the 3' to 5' direction
• The mRNA molecule grows in the 5' to 3' direction
• The mRNA molecule contains the exact same sequence of nucleotides as the DNA coding strand, except the mRNA will contain uracil instead of thymine
• Translation


  1. The mRNA molecule attaches to a ribosome

  2. tRNA molecules bind with their specific amino acids and bring them to the mRNA molecule on the ribosome

  3. The triplet of bases (anticodon) on each tRNA molecule pairs with a complementary triplet on the mRNA molecule called the codon

  4. Near the beginning of the mRNA is a triplet of bases called the start codon (AUG) which codes for the amino acid methionine

  5. Two tRNA molecules fit onto the ribosome at any one time, bringing the amino acid they are each carrying side by side

  6. A peptide bond is then formed, via a condensation reaction, between the two amino acids

  7. This process continues until a 'stop' codon on the mRNA molecule is reached – this acts as a signal for translation to stop and at this point the amino acid chain coded for by the mRNA molecule is complete

  8. The amino acid chain then forms the final polypeptide
• Triplet code


  The sequence of DNA nucleotide bases found within a gene is determined by a triplet (three-letter) code
• Genetic code


  • It is non-overlapping - each base is only read once, the adjacent codons do not overlap
  • It is degenerate - multiple codons can code for the same amino acids
  • It is universal - the same triplet codes code for the same amino acids in all living things
• Amino acid


  The monomers of polypeptides, there are 20 amino acids found in proteins common to all living organisms
• Peptide bond


  Covalent bonds that form between amino acids, releasing a molecule of water
• Levels of protein structure


  • Primary
  • Secondary
  • Tertiary
  • Quaternary
• Primary structure


  The sequence of amino acids bonded by covalent peptide bonds
• Levels of protein structure


  • Primary
  • Secondary
  • Tertiary
  • Quaternary
• Polypeptide or protein molecules


  Can have anywhere from 3 amino acids (Glutathione) to more than 34,000 amino acids (Titan) bonded together in chains
• The DNA of a cell determines the primary structure of a protein by instructing the cell to add certain amino acids in specific quantities in a certain sequence</b>
• The primary structure is specific for each protein (one alteration in the sequence of amino acids can affect the function of the protein)
• Secondary structure


  The weak negatively charged nitrogen and oxygen atoms interact with the weak positively charged hydrogen atoms to form hydrogen bonds
• Shapes that can form within proteins due to hydrogen bonds


  • α-helix
  • β-pleated sheet
• Most fibrous proteins have secondary structures (e.g. collagen and keratin)
• The secondary structure only relates to hydrogen bonds forming between the amino group and the carboxyl group (the 'protein backbone')
• The hydrogen bonds can be broken by high temperatures and pH changes
• Tertiary structure


  Further conformational change of the secondary structure leads to additional bonds forming between the R groups (side chains)
• Additional bonds in tertiary structure


  • Hydrogen (between R groups)
  • Disulphide (only occurs between cysteine amino acids)
  • Ionic (occurs between charged R groups)
  • Weak hydrophobic interactions (between non-polar R groups)
• The tertiary structure is common in 3D globular proteins
• Quaternary structure


  Occurs in proteins that have more than one polypeptide chain working together as a functional macromolecule
• The same bonds responsible for maintaining the tertiary structure of a protein will also be involved in forming the quaternary structure
• Subunit


  Each polypeptide chain in the quaternary structure is referred to as a subunit of the protein
• Bonds in proteins


  • Hydrogen (in secondary structure)
  • Hydrogen (in tertiary structure between R groups)
  • Disulphide
  • Ionic
  • Hydrophobic interactions
• Globular proteins are compact and roughly spherical (circular) in shape
• Globular proteins


  • Their non-polar hydrophobic R groups are orientated towards the centre of the protein away from the aqueous surroundings
  • Their polar hydrophilic R groups orientate themselves on the outside of the protein
• Some globular proteins are conjugated protein that contain a prosthetic group
• Solubility of globular proteins


  The orientation of their R groups enables globular proteins to be (generally) soluble in water as the water molecules can surround the polar hydrophilic R groups
• The solubility of globular proteins in water means they play important physiological roles as they can be easily transported around organisms and be involved in metabolic reactions
• Functions of globular proteins


  • Enzymes can catalyse specific reactions
  • Immunoglobulins can respond to specific antigens
• Haemoglobin


  • It has a quaternary structure as there are four polypeptide chains
  • These chains or subunits are globin proteins (two α–globins and two β–globins) and each subunit has a prosthetic haem group
  • The four globin subunits are held together by disulphide bonds
  • Their hydrophobic R groups are facing inwards (helping preserve the three-dimensional spherical shape)
  • Their hydrophilic R groups are facing outwards (helping maintain its solubility)