Levels of protein structure Flashcards Preview

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Flashcards in Levels of protein structure Deck (17)
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1
Q
  • What is the primary structure?
A
  • sequence of amino acids along a protein chain is called its primary structure
2
Q

How is primary structure represented?

A

sequence of three later names of the relevant amino acids

3
Q

How is the primary structure held together

A
  • covalent bond
  • peptide linkage
  • relatively stable
  • requires harsh condition - e.g. boiling with 6 mol dm-3 hydrochloric acid - to break the amino acids apart
4
Q

What is the secondary structure?

A
  • hled in place by hydrogen bonds
  • between - for example - C=O and -N-H groups
5
Q

WHat are teh structures formed from the secondary structure?

A
  • protein chain may form a helix (alpha helix)
  • or a folded sheet (beta pleated sheet
6
Q

What are the characteristics of the secondary structure?

A
  • hydrogen bonds are much weaker than covalent bonds
  • can be relatively easily be disrupted
  • e.g. by gentle heating or changes in pH
7
Q

What is the tertiary structure?

A
  • the alpha-helix or beta-pleated sheet can itself be folded into a three dimensional structure
  • this is called the tertiary structure
8
Q

How is the teritiary structure held in place?

A

mixture of:

  • hydrogen bonding
  • ionic interiactions
  • disulfide briges
  • (van der Waals exist between all molecules
9
Q

How are proteins determind?

A
  • for secondary and tertiary - X-ray diffraction
  • for primary
    • find out the number of each type of amino acid present
    • reflux with HCl (yina the craic ) hydrolysis and that
    • breaks the amide bonds
    • results in a mixture containing all the individual acids in the original protein
10
Q

What is thin-layer chromotography?

A
  • similar to p[aper chromotography but the paper is replaced by a chromotography plate
    • consists of a thin, flexible plastic sheet coated with a thin layer of silica (silicon dioxide)
  • this white poweder is called the stationary phase
11
Q

How is TLC began?

A
  • small spot containing the mixture of amino acids to be seperated is placed on a line about 1cm
  • plate is placed in a tank with suitable solvent of depth 0.5cm
  • the starting line must be above the initial level of the solvent
  • the solvent (or mixture) is called the mobile phase or the eluent
12
Q

What is done with the tank in TLC?

A
  • a lid is placed on the tank so that the inside of it is saturated with solvent vapour
  • and the solvent is allowed to rise up the place
  • as it does so, it carries the amino acids with it
  • each amino acids lages behind the solvent from to an extent that depends on its affinity for the solvent compared with its affinity of the affinity with the stationary phase
  • this depends on the intermolecular forces that act between the amino acid and the solvent
    • the stronger they are, the closer the amino acid is to the solvent from
13
Q

What happens when the solvent has almost reached the top of the plate?

A
  • the plate is removed from the tank
  • the position to which the solvent front has moved is marked
  • amino acids are colourless. so the positions they have reached need to be made visible
14
Q

How are the amino acids made visible?

A
  • plate is sprayed with a develop[ing agent, such as ninhydring
  • this reacts with amino acids to from a purple compound
  • or by shing uv light on the plate
    • if the solvent is suitable, the amino acids will be completly sparated
15
Q

How are Rf values calculated

A

distanced moved by the spot / distance moved by solvent

16
Q

How are amino acids identified?

A

comparing Rf values of each spot with the values obtained by known pure amino acids run in the same solvent mixture

17
Q

What is 2 dimensional TLC?

A
  • plate turned 90
  • chromatogram run again with different solvent
  • makes it easier to see the separation between spots and gives two Rf values
  • if these 2 values match those for a known amino acid you can be more confident in your identification