Week 4 (amino acids) Flashcards
What is a salt bridge?
An ionic interaction within a protein
Which amino acids have acidic side groups?
Tyrosine
Aspartic acid
Glutamic acid
Which amino acids are basic?
- Histidine
- Lysine
- Arginine
Often found in active site of enzymes AND On surface because their side chains interact well with water
Which amino acids are amides?
Asparagine
Glutamine
(Tryptophan- amine)
which amino acids are Hydrophobic?
Alanine
Valine
Leucine
Isoleucine
Methionine
Proline
Phenylalanine
What amino acids are Nucleophilic?
Serine
Threonine
Cysteine
Which amino acids are hydrophilic?
Aspartic acid
Glutamic acid
Asparagine
Glutamine
Serine
Threone
Tyrosine
cysteine
Lysine
Arginine
Histidine
What is the isotonic point? What is this equal to for amino acids?
- The pH at which predominates in aqueous solution
- This means it is the pH at which the amino acid is neutral, i.e. the zwitterion form is dominant.
- For AAs this is equal, to the isoelectric point
What happens To an AA at low pH?
Everything that can be protonated will be:
NH3+ and COOH
What happens at high pH?
Everything that can be deprotonated will be:
NH2 and COO-
Why is proline special?
- Only amino acid where the side chain is connected to the protein backbone twice, forming a five-membered nitrogen-containing ring.
- The only imino acid
- Can change the direction of a polypeptide chain
What is special about tryptophan?
- Aromatic indole (heterocyclic) ring-: The lone pair of electrons is part of the delocalised Pi system not available for bonding
- It has a nitrogen containing side chain (amine)
Why is pH measured using a glass electrode?
- A glass electrode is selectively permeable to hydrogen ions and is used for measuring the pH of solution
- A combination electrode (double electrode system) consisting of a glass electrode and a calomel electrode combined in one probe
How does a glass electrode work?
- The glass electrode consists of a Ag-Cl electrode in a reference solution of hydrochloric acid contained in a glass membrane
- The membrane is made of a special glass, selectively permeable to hydrogen ions
- The potential that develops across the membrane depends upon the hydrogen ion concentration of the test solution compared with the reference acid solution inside the electrode
- This potential is measured against a reference calomel electrode
- For ease of operation the glass electrode is often combined with a reference calomel electrode in a single probe.
6 There is an almost linear relationship between potential and pH range of 2-10
What pH promotes the formation of the zwitterion?
pH 7
How do you calculate the pH of the isoelectric point?
pKa1+pKa2
pI= –————––
2
- The average pKa for the ionisable groups
- Where pKa1 and pKa2 is the ionisable groups (NH2 and COOH)
Ionisation of the terminal carboxyl
COOH—> COO- + H+
Ionisation of the amino terminal
NH3+—> NH2 + H+
which ammonium group is deprotonated first in an AA with multiple NH groups
The NH2 attached to the alpha carbon
Which COOH group inonises first in an AA with multiple COOH?
The COOH attached to the alpha carbon
What is the Henderson Hasselbach equation for a weak acid?
pH= pKa + log (([conjugate base] (ionised form)/acid)
where the square brackets indicate the molar concentration of the named substance
What is the Henderson Hassalbach equation for a weak base?
pH= pKa + log (( [base] (unionised form)/ [conjugate acid] (ionised form))
where the square brackets indicate the molar concentration of the named substance
Explain the titration curve for alanine
- At a pH equivalent to pKa1 there are equal amounts of forms 1 and 2
- at a pH equivalent to pKa2, forms 2 and 3 are in equal concentrations
- the pI value for alanine is 6 and is the mean of pKa 1(2.4) and pKa 2 (9.6)
- at a pH below it’s pI value an amino acid will carry a net positive charge it it will carry a net negative charge at pH greater than pI
(Typical curve of an amino acid with only two ionizable groups (one carboxyl and one amino)
What are the labels on this diagram?
What do the the two shaded areas of a titration curve show?
The two shaded areas show the pH range over which the addition of alkali results in only a very small change in pH and where the amino acid exhibits its most significant buffering action
What is K, Ka and pKa?
The dissociated and undissociated forms of each group exist in equilibrium having the equilibrium constant K often termed Ka because it refers to the dissociation of groups that liberate protons.
The actual values for Ka are often very small and are conventionally expressed as the negative logarithm of the value, a term known as the pKa value: pKa = -log Ka
What does the Henderson-Hasselbalch equation show?
How the concentration of hydrogen ions liberated by the dissociation of an acid is related to the dissociation constant for that acid.
What are the 4 key points of amino acids and titration?
- The nature of the amino acid species present in solution will depend upon the pH.
- For amino acids, at the isoelectric point (pI), the molecule carries no net charge and is electrophoretically immobile.
- 7 of the 20 common amino acids have readily ionisable side chains
- Amino acids with ionizable side chains give complex titration curves.
