Levels of protein structure

• what is the hierarchy of protein structure?

  primary structure, secondary structure, tertiary structure, quaternary structure
• what levels of protein structure contain covalent bonds?

  primary, secondary, tertiary and quaternary
• what levels of protein structure contain ionic bonds?

  tertiary and quaternary
• what levels of protein structure contain peptide bonds?


  primary
• what levels of protein structure contain dipole bonds?

  tertiary and quaternary
• what levels of protein structure contain hydrogen bonds?

  secondary, tertiary and quaternary
• what levels of protein structure contain disulphide bonds?

  tertiary and quaternary
• what levels of protein structure contain hydrophobic and hydrophilic interactions?

  tertiary and quaternary
• what levels of protein structure contain temporary dipoles?

  tertiary and quaternary
• what is primary structure?

  • the sequence in which the amino acids are joined
  • this is directed by information carried within DNA
  • the particular amino acids in the sequence will influence how the polypeptide folds to give the protein's final shape
  • only involves peptide bonds
• what is secondary structure?

  • the coiling or folding of the chain
  • forming an alpha-helix or a beta-pleated sheet
  • the oxygen, hydrogen, and nitrogen atoms in basic, repeating structure of the amino acid interact
  • hydrogen bonds may form within chain, coiling the chain
• describe the structure of an alpha-helix

  • 36 amino acids per 10 turns of helix
  • hydrogen bonds form between the -NH group of one amino acid and the CO group of the amino acid 4 places ahead, e.g. 1-5, 2-6, 3-7 etc
  • * H bonds don't involve R-groups
• describe the structure of a beta-pleated sheet

  • hydrogen bonds between -NH of one amino acid and the -CO of another further down the strand hold the sheet together
  • forms zig-zag chains
• what is tertiary structure?

  • the overall 3-D shape of the protein
  • the folding of a protein into it's final shape
  • the folding of sections of proteins into their secondary structure brings R-groups of different amino acids closer together so they are close enough to interact and further folding of there sections will occur (tertiary structure)
• describe the bonds that stabilise the tertiary structure?

  • ionic bond between ionised R-groups
  • disulphide bonds between R-groups containing -SH groups
  • hydrogen bonds
  • hydrophobic side chains move to the inside of protein and hydrophilic side chains on the outside
• what is quaternary structure?

  • the arrangement and interaction of more than one polypeptide chain
  • results from the association of two or more individual proteins called subunits, interactions are the same as that in the tertiary structure but are between different protein molecules rather than within one molecule
• how does moving the position of one amino acid affect the structure and function of the protein?

  • could interrupt H bonds - changing shape of secondary structure (alpha-helix/ beta-pleated sheet)
  • could also interrupt disulphide bonds
  • changes shape of active site - is specific for a different substrate
  • could change the hydrophilic/hydrophobic interactions in a membrane
• how does the primary structure affect the tertiary structure?

  • hydrophobic amino acids will need to end up on the inside of the protein, so depending where the hydrophobic amino acids are found on the chain will change how the chain folds up into its final 3-D shape
  • may also cause new bonds to form such as: hydrogen bonds, disulphide bonds etc
• how will the primary structure be affected by temperature?

  will be least affected by temperature as peptide bonds between amino acids are very strong
• how will temperature affect secondary structure?

  the high temps will break hydrogen bonds (will affect the beta-pleated sheet first and then the alpha-helix), this will cause uncoiling and unfolding of the structure
• how will temperature affect tertiary structure?

  • hydrogen bonds which reinforce tertiary structure break due to molecules moving more (have more kinetic energy), this makes the 3-D shape unravel as there are fewer bonds holding it in the correct shape, so protein now has the wrong shape. It is said to be denatured
• what typed of bonds will be found in the enzymes of bacteria that live in hot springs or hydrothermal vents?

  disulphide and covalent bonds - are not disturbed by high temperatures