What are proteins?
Fundamental functioning molecules of the cell
Which functions do proteins provide the cell?
- Carriers e.g. trafficking O2
- Metabolic e.g. enzymes
- Cellular machinery e.g. spliceosomes
- Structural scaffolding e.g. microtubules
- Sensory molecules e.g. receptors
How are proteins formed?
Synthesised by the ribosome during translation from amino acids
Which isomer form of amino acid do humans amino acids take?
L- Amino acids (read CORN clockwise)
Where are D form amino acids found?
In peptidoglycan bacterial cell walls
Why are amino acids referred to as ɒ amino acids?
The central C is bonded to the acidic carboxyl group
What is a zwitterion?
The structure amino acids take at an intermediate pH with a net neutral charge
What determines the form an amino acid takes?
pH
Which form does the amino acid take at low pH (acidic)?
positive NH3+ charge
In alkaline conditions what does the amino acid look like?
negative COO- charge
How many amino acids are there in total?
There are 20
How many essential amino acids are there ?
9 essential amino acids obtained from the diet only
What is a residue?
a repeating peptide unit
Describe the structure of a peptide bond
Flat planar structure
Fixed arrangement
Rotational freedom of bonds
- enables movement of rest of the chain
How many levels of protein folding are there?
4 levels of folding
What are the folding structures of a protein?
Primary structure
- amino acids joined by strong covalent bonds
Secondary structure
- H bonding between ɒ helices or Β pleated sheets
Tertiary structure
- Β continuous folding due to intramolecular H bonds stabilised by
covalent disulphide bonds
- globular or fibrous structure formed
Quartenary structure
- dependent on weak ionic bonds
What enables bond rotation within proteins?
The other bonds around the ɒ carbon allow bond rotation as the peptide bond is ridged
In terms of energetic state, how are proteins arranged?
Polypeptides adopt a structure based on energy minimalisation
- each molecular structure has a specific energetic state
Are parallel or anti parallel Β pleated sheets stronger & why?
Anti parallel are stronger
- parallel Β sheets require longer Β turns which are destabilising
Which weak interactions occur within polypeptides to give them their structure
- Ionic Bonds: between -ve and +ve side chains
- Hydrogen Bonds: betwen polar side chains (H+ and ℷ
atoms) - VDW Forces: caused by Hydrophobic residues
- Disulphide bridges: sulfhydryl side chains of Cysteine
What experimental techniques can be used to identify protein structures?
Xray crystallography
NMR
What shape do water soluble proteins take?
Globular shape
Where are hydrophilic proteins located?
Externally on the surface
When many polypeptides assemble together, what are the 2 bigger protein structures they form called?
Filaments (actin)
Tubes (tubulin)
Where are hydrophobic residues located?
Usually buried inside the protein
How do membrane proteins differ from regular protein
molecules?
Their hydrophobic residues externally located
hydrophilic residues internally located
Which non-covalent bonds help stabilise a proteins folded structure?
Several non-covalent bonds which stabilise a protein;
- hydrogen bonds
- van der Waals forces
- ionic interactions
These are weak bonds compared to covalent bonds
but are collectively strong.
Hydrogen bonds form where a H is shared between an N and an O.
VDW forces are dipole-dipole interactions and are weak but as they are often numerous, they are significant in stabilising a folded structure.
The folded form of a polypeptide chain has a lower Gibbs free energy than the unfolded form.
What role does entropy (of the polypeptide and the surrounding water) play in the folding process?
Gibbs free energy is higher in the non-folded form than in the folded form of the polypeptide.
Therefore the folded form is preferred.
Folding is associated with a loss of entropy (gain in structure) of the polypeptide, whereas the surrounding water molecules gain entropy. Thus during
folding (the favourable) entropy gain of the solvent, partially offsets the disfavoured entropy loss
of the polypeptide.
Explain what is meant by the term ‘folding pathway’ and why they are the subject of very intense research activity?
A ‘folding pathway’ is a series of steps an unfolded protein takes to produce the final folded form.
The final shape is not a result of random conformational interconversions but exactly how proteins fold is still a mystery. If this pathway could be determined, the 3D shape a protein could form could be determined by analysis of the amino acid sequence
– i. e. without
having to study the 3D structure which requires a lot of work and money.
A series of steps occur in the folding process but a method has not been found to find out what these are