Charge and shape in biological reactions Flashcards
What is the nominal mass of an electron?
0
Do metal lose or gain electrons to become cations?
lose
Why is oxygen electronegative?
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 is the order of strength interactions from strongest to weakest?
- single covalent
- cation-anion
- hydrogen bond
- pi-cation
- pi-pi
- dipole-dipole
- London dispersion
What types of molecules tend to be hydrophilic?
molecules with charge, good H-bonding pot and a low proportion of C 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 types of acid are predominately ionised (negative charge) at physiological PH?
Acids with a low pKA (<7.4)
What happens to bases with a high pKA at physiological PH?
predominantly ionised
What determines the hydrophobicity/hydrophilicity in an amino acid?
The R group
-amides are neutral across physiological PH
What determines the secondary structure of a protein?
the shape (conformational preference) of the residues due to their hydrophobicity/hydrophobicity preference, this is maintained by H bonding
What is the secondary structure?
Arrangement of the primary structure into defined regions (α helix, beta sheet)
What is the tertiary structure of a protein?
Higher folding of the secondary structure maintained by ionic, H bonds and di-sulfide bonds between cysteines
What is the quaternary structure?
How chains can together and arrange to from complexes
What is the equation for PH?
PH= -log10[H^+]
What is PH 0 equal to?
1M HCl
What is the concentration of H^+ in pure water?
PH of pure water = 7
PH = -log10[H^+] = -log10[10^-7]
therefore [H^+] = 10^-7M
Why 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?
Ka= [H+] [A-}
————-
[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?
% compound ionised = 100
————
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 happened 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?
Ka = [H+] [B]
————
[HB+]
Can the solvent around a molecule affect pKa?
Yes
i.e 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
