Levels of protein structure Flashcards
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
