Semester Test 1 2018
Discuss the precautions you will take to stabilize the proteins
pH – Different functional acid-base groups react different at various pH levels, use buffers to
maintain correct pH at which protein is stable
Temperature – I will work on ice so as to not denature the proteins (typically starts to happen above
25C )
Protease – Can degrade the protein, and therefore should be inhibited by chemical agents or using a
pH not harmful to the protein but which inactivates the proteases
Microorganism growth – Protein should be stored under conditions that inhibit growth of
microorganisms such as in a fridge, with a toxic substance that does not affect the protein such as
sodium azide
Complete the missing words
Proteins are poyionic macromolecules of which the overall net charge is dependent on pH. In cation
exchange chromatography proteins with an overall net positive charge will bind to the negatively
charged stationary phase. An example of a strong cation resin’s ionisable group is Methyl sulfonate.
Bound proteins can be eluted from cation-exchange resins through increasing salt concentration.
This can later be removed from your protein solution through dialysis.
Discuss the role of TEMED and APS in SDS-PAGE
Polymerization is induced by free radicals resulting from the chemical decomposition of APS. TEMED
is a free radical stabilizer.
Why does the peptide group have a rigid planar structure?
It is the consequence of resonance interactions that give the peptide bond an ~40% double bond
character
Why does the peptide group generally assume a trans conformation?
Because of steric clashes in cis conformation
Which exception to the rule occurs?
Except in peptide bonds followed by a Proline residue, 10% of Proline residues occur after a cis
peptide bond.
Discuss B-bends
Also called reverse turns
They occur at the surface of globular proteins
Most reverse turns involve four consecutive amino acids
Type I and Type II. Type II is a 180 degree flip of Type I’s peptide unit linking residues 2&3. Residue 2
is often a proline and residue 3 is often a glycine in type ii
Which domain fold is obtained when two greek keys combine?
Gamma-beta crystallin
, By changing the connectivity a similar domain can be obtained commonly reffered to as a
Up-and-down beta barrel
Name and discuss the different forces that stabilise tertiary structure
1. Electrostatic- forces
Surface electrostatic interactions that result between aa groups of different ionic charges for
example lys and glu. However they do not play a major role in stability
a) Dipole-Dipole interactions
Significantly stabilise a protein
Carbonyl and amide groups of peptide backbone have permanent dipole moments
b) Dipole induced dipole interactions
A permanent dipole induces a dipole moment on a neighbouring group so as to form an
attractive interaction
c) London Dispersion forces
Forces that occur when neutral molecules have small dipole moment due to rapidly
fluctuation electrons
2. Hydrogen bonding
Predominantly electrostatic interactions between a weakly acidic donor group and an
acceptor that bears a lone pair of electrons. Donor group can be highly electro negative N,
O, or S atom
H Bonding provides a structural basis for the native folding pattern of the protein
3. Hydrophobic forces
When non-polar substances minimize their contact with H2O & amphipathic molecules to
form micelles in aqueous solution. E.g. Val, Leu,Ile
4. Disulfide bonds
Stabilise extracellular proteins. Covalent bonds formed between cysteine residues.
How does protein to protein interfaces differ from protein interiors
Protein interiors have strong hydrophobicity. Protein:protein interactions may be hydrophilic or
hydrophobic depending on how much contact they make. Protein:protein interfaces may contain
salt bridges.
SEMESTER TEST 2 2018
Give an example of a protein that cannot be readily renatured after denaturation
Insulin. Insulin is derived from proinsulin and is proteolytically cleaved after disulphide bonds have
formed
Discuss the precautions you will take to stabilize the proteins
pH – Different functional acid-base groups react different at various pH levels, use buffers to
maintain correct pH at which protein is stable
Temperature – I will work on ice so as to not denature the proteins (typically starts to happen above
25C )
Protease – Can degrade the protein, and therefore should be inhibited by chemical agents or using a
pH not harmful to the protein but which inactivates the proteases
Microorganism growth – Protein should be stored under conditions that inhibit growth of
microorganisms such as in a fridge, with a toxic substance that does not affect the protein such as
sodium azide
Complete the missing words
Proteins are poyionic macromolecules of which the overall net charge is dependent on pH. In cation
exchange chromatography proteins with an overall net positive charge will bind to the negatively
charged stationary phase. An example of a strong cation resin’s ionisable group is Methyl sulfonate.
Bound proteins can be eluted from cation-exchange resins through increasing salt concentration.
This can later be removed from your protein solution through dialysis.
Discuss the role of TEMED and APS in SDS-PAGE
Polymerization is induced by free radicals resulting from the chemical decomposition of APS. TEMED
is a free radical stabilizer.
Why does the peptide group have a rigid planar structure?
It is the consequence of resonance interactions that give the peptide bond an ~40% double bond
character
Why does the peptide group generally assume a trans conformation?
Because of steric clashes in cis conformation
Which exception to the rule occurs?
Except in peptide bonds followed by a Proline residue, 10% of Proline residues occur after a cis
peptide bond.
Discuss B-bends
Also called reverse turns
They occur at the surface of globular proteins
Most reverse turns involve four consecutive amino acids
Type I and Type II. Type II is a 180 degree flip of Type I’s peptide unit linking residues 2&3. Residue 2
is often a proline and residue 3 is often a glycine in type ii
Which domain fold is obtained when two greek keys combine?
Gamma-beta crystallin
, By changing the connectivity a similar domain can be obtained commonly reffered to as a
Up-and-down beta barrel
Name and discuss the different forces that stabilise tertiary structure
1. Electrostatic- forces
Surface electrostatic interactions that result between aa groups of different ionic charges for
example lys and glu. However they do not play a major role in stability
a) Dipole-Dipole interactions
Significantly stabilise a protein
Carbonyl and amide groups of peptide backbone have permanent dipole moments
b) Dipole induced dipole interactions
A permanent dipole induces a dipole moment on a neighbouring group so as to form an
attractive interaction
c) London Dispersion forces
Forces that occur when neutral molecules have small dipole moment due to rapidly
fluctuation electrons
2. Hydrogen bonding
Predominantly electrostatic interactions between a weakly acidic donor group and an
acceptor that bears a lone pair of electrons. Donor group can be highly electro negative N,
O, or S atom
H Bonding provides a structural basis for the native folding pattern of the protein
3. Hydrophobic forces
When non-polar substances minimize their contact with H2O & amphipathic molecules to
form micelles in aqueous solution. E.g. Val, Leu,Ile
4. Disulfide bonds
Stabilise extracellular proteins. Covalent bonds formed between cysteine residues.
How does protein to protein interfaces differ from protein interiors
Protein interiors have strong hydrophobicity. Protein:protein interactions may be hydrophilic or
hydrophobic depending on how much contact they make. Protein:protein interfaces may contain
salt bridges.
SEMESTER TEST 2 2018
Give an example of a protein that cannot be readily renatured after denaturation
Insulin. Insulin is derived from proinsulin and is proteolytically cleaved after disulphide bonds have
formed
