Change and shape in biological reactions Flashcards
How are cations formed?
Loss of electrons
How are anions formed?
Gain of electrons
What is a hydrogen bond?
An attraction between N, O or F and a H on another molecule
What type of bonding is present in liquid water?
Covalent bonds: sharing electrons between oxygen and hydrogen
Hydrogen bonds: between adjacent molecules
What kind of environment is water?
Polar
What will water easily solubilise?
Other polar molecules, regions of molecules or ions
What makes something hydrophilic?
Charge
Hydrogen bonding potential
Low proportion of carbon atoms
What makes something hydrophobic
No charge
High proportion of carbon atoms
What is an acid?
A compound that can lose an H+ ion and become negatively charged in the process
What is a base?
A compound that can (reversibly) form covalent bonds with a H+ ion to become positively charged
What will happen to amino acids with low pKa at physiological pH?
They will be negatively charged and anionic
Predominantly ionised
What will happen to amino acids with high pKa at physiological pH?
They will be positively charged and cationic
Predominantly ionised
What happens to amides at physiological pH?
Amides are neutral at physiological pH
What determines secondary structure?
Shape and conformation preference of the residues
Maintained by regular hydrogen bonding pattern
Can be predicted from primary structure
What is tertiary structure?
The overall shape of a protein chain
What determines tertiary structure?
Bonding interactions:
Ionic & hydrogen
Conformation of residues e.g. proline-induced turns
How does hydrophobicity influence structure?
Hydrophobicity residues prefer to be at the centre of the protein away from the water
What is quaternary structure?
Chains forming complexes
What determines quaternary structure?
Bonding between chains
Hydrophobicity
Name three things hydrophobicity determines
Structure
Function
Cellular distribution
What is pH?
Measure of concentration of H+
How do we calculate pH?
pH = -log10[H+]
Why is water polar
the electrons shared in the covalent bond are attracted to it pulling the electrons away from the H, polarising the bond
- O has a partial negative charge
- each H has a partial positive charge
What types of molecules tend to be hydrophilic?
molecules with charge, good H-bonding pot and a low proportion of C atoms
What types of acid are predominately ionised (negative charge) at physiological PH?
Acids with a low pKA (<7.4)
What determines the hydrophobicity/hydrophilicity in an amino acid?
The R group
-amides are neutral across physiological PH
Why are weak acids usually in equilibrium?
Because the energy between reactants and products is very small so it is easy to go forwards and backwards
What is Chatelier’s principle?
If an equilibrium is disturbed by a change of environment the system will tend to shift its equilibrium position to counteract the effect of the disturbance
What is Ka?
equilibrium constant
What is the equation for KA?
[HA]
What is pKA?
A logarithmic constant which is proportional to the free energy of the acid-base reaction which tells us how acidic/basic the compound is so can tell us the quantative behaviour of the equilibrium
What is the equation for pKA?
pKa = -log10(Ka)
When does pH =pKa?
When [A-] = [HA]
when the compound is 50% ionised
What is the Henderson-Hasselbach equation?
pH= pKa + log ([A-]/[HA])
How do you work out the percentage ionisation of a compound?
1 + 10^(charge(pH-pKa)
When the charge for acids = -1
charge for bases = +1
What happens when PH =pKa -1 for an acid.
Acid will be around 10% disassociated
What happenes when PH =pKa + 1 for an acid
Acid will be around 90% dissociated
What happens when PH >pKa +2
acid will be more than 99% disassociated
What is a deprotonated termed as and why?
Conjugate base because it acts as a base, receiving a proton in the reverse reaction
What is the Ka for a base?
[HB+]
How can the solvent around a molecule affect pKa?
e.g less exposure to water (shielding) means ionisation is less likely (pKa of acids higher)
What is the isoelectric point?
When there are multiple pKa values then there can be multiple different states with different charges. When the net charge is 0 it is known as the isoelectric point (the PH when theres no charge)
-equal number of + and - charged groups on the protein so its at its minimum aqueous solubility
What moves towards the cathode?
positively charged compounds
What are the ionisable amino acids?
Aspartate
Glutamate
Lysine
Argenine
These amino acids are predmoninantly ionised at phsiological pH meaning there are very hydrophilic
Why does pH and pKa matter?
Can effect the potential conformation of proteins
Can effect the behaviour of certain moleules
What influences pKa?
The solvent around a molecule
Accessibility to water influences the side chain ionisation properties
