Amino acids and zwitterions
The general formula for and alpha-amino acid is RCH(NH2)COOH. These amino acids have both the amine and carboxyl groups attached to the same carbon.
The acidic carboxyl group and the basic amine in an amino acid can interact with each other to form an internal salt, known as a zwitterion:
- A proton is transferred from the acid carboxyl group (giving COO-) to the basic amine group (giving NH3+)
- A zwitterion has no overall charge because the positive and negative charges cancel each other out.
The isoelectric point is the pH at which the zwitterion exists - the point at which there is no overall charge.
Note: any NH2 or COOH groups in the R group do NOT exist as ions at the isoelectric point.
Amino acids at different pH values
Different R groups in amino acids may result in different isoelectric points:
- More NH2 groups raise the isoelectric point e.g. lysine 9.74
- More COOH groups lower the isoelectric point e.g. glutamine 3.22
Amino acids are amphoteric, which means they can react with both acids and bases.
At a pH that is more acidic that the isoelectric point, the amino acid behaves as a base and accepts a proton from the acids (forming NH3+, COOH).
At a pH that is more alkaline than the isoelectric point, the amino acids behaves as an acid and donates a proton to the base (forming NH2, COO-).
Polymerisation and hydrolysis of polypeptides
Amino acids join together by peptide linkages to form peptides. When two amino acids join together, a dipeptide is formed with the elimination of water - this is a condensation reaction.
A protein or polypeptide is a long chain of amino acids joined together by peptide linkages.
Polypeptides and proteins can by hydrolysed using aqueous acid. A water molecule is needed to break each peptide link to form a mixture of the amino acids that made up the protein. During acid hydrolysis, the amino acids formed are positively charged because of the presence of H+ ions from the acid (NH3+, COOH). Traditionally, the protein or polypeptide is heated under reflux with 6M HCl for 24 hours.
In alkaline hydrolysis, a solution of alkali, in the form of NaOH(aq), is used at just above 100*C. The polypeptide or protein is broken down into amino acids in the form of their sodium salts (carboxylates - NH2, COO-Na+).
Optical isomers and chiral centres
Optical isomers are non-superimposable mirror images about an organic chiral centre: four different groups attached to a carbon atom.
To draw the optical isomer, draw a mirror image.
Optical isomers rotate plane-polarised light differently. One of the optical isomers rotates the light clockwise and the other enantiomer rotates the light anti-clockwise. A mixture containing equal amounts of each isomer is known as a racemic mixture. A racemic mixture has no effect on plane-polarised light because the rotations cancel each other.
When locating chiral centres, remember that if there is a double bond is cannot be a chiral centre because then there will only be 3 groups.
Optical isomerism and E/Z isomerism are different types of stereoisomerism.
Alkenes can have stereoisomers because of the lack of rotation around the C=C double bond. If the two double-bonded carbon atoms each have different atoms or groups attached to them, then you have an 'E-isomer' (trans) and a 'Z-isomer' (cis).
Stereoisomers are species with the same structural formula but with a different arrangement of the atoms in space.
In forming a polyester, monomer units are bonded together by ester linkages and water is eliminated. The monomers have a carboxyl group, -COOH, and a hydroxyl group, -OH.
There are two common types of polyester:
1. Polyesters made by reacting two different monomer units:
- one monomer is a dicarboxylic acid with two -COOH groups
- the other monomer is a diol with two -OH groups.
2. Polyesters made by reacting just one type of monomer unit containing -COOH and -OH groups.
In polyamides, amide linkages join the monomer units together with the elimination of water. The monomers have a carboxyl group, -COOH, and an amine group, -NH2. There are two types of polyamides:
1. Polyamides made by reacting together two different types of monomer units:
- one monomer is a dicarboxylic acid with two -COOH groups
- the other monomer is a diamine with two -NH2 groups.
2. Polyamides made by reacting just one type of monomer unit containing both -COOH and -NH2 groups. Amino acids are this type of monomer, and polypeptides and proteins are this type of polyamide.
Comparing condensation/addition polymerisation
Condensation polymerisation is the joining of two monomers with the elimination of a small molecule, such as water or HCl. It requires monomers with two different functional groups.
Alkenes undergo addition polymerisation to produce saturated chains containing no double bonds:
- Addition polymers are made from one type of monomer only
- There is no product other than the polymer.
Uses as fibres in clothing
Polyesters are used in making carpets, sports clothing and shirts. In clothing and bedding, polyesters are often blended with cotton. Almost all polyesters can be machine washed and dried. Polyester is a strong fibre which is resistant to stretching, shrinking and chemical attack. Unfortunately it burns easily and should not be exposed to naked flame.
Polyamides such as nylon-6,6 and Kevlar are used widely in clothing. Kevlar is fire resistant and has a higher strength than steel. It is used to make protective clothing - for example for firefighters, bulletproof vests and crash helmets.
Hydrolysis of polyesters
Polyesters are readily hydrolysed by hot aqueous alkalis, such as NaOH(aq). Each ester linkage is hydrolysed to:
- the sodium salt of a carboxylic acid, COO-Na+
- a hydroxyl group, OH.
Polyesters can also be hydrolysed with hot aqueous acid, such as HCl(aq), although the reaction is much slower than with aqueous alkali:
- the monomer units of the polyester are produced, with COOH and OH.
Hydrolysis of polyamides
Like polyesters, polyamides can be hydrolysed by either hot aqueous acid, such as HCl(aq), or hot aqueous alkali, such as NaOH(aq).
In acidic conditions, the dicarboxylic acid is produced (COOH) together with an ammonium salt of the diamine (NH3+).
In basic conditions, the sodium salt of the dicarboxylic acid (COO-Na+) and the diamine (NH2) are formed.
Condensation polyers may be photodegradable as the C=O bond absorbs radiation. These bonds break, fracturing the polymer chain. Also, light-sensitive additives can be blended with the polymer to catalyse breakdown in the presence of UV radiation.
Condensation polymers may be hydrolysed at the ester or amide group. The ester and amide links are found in nature, so there are fungi and bacteria that can degrade them and convert them into CO2 and H2O. This means that condensation polymers are biodegradable.
Although condensation polymers will break down by hydrolysis, the huge time this takes to happen in nature means that they still create waste problems. Addition polymers are worse because they won't be broken down by hydrolysis. Also, most polymers we use are made from monomers derived from crude oil which is not a renewable resource. Poly(lactic acid) is an example of a biodegradable polymer designed to combat issues:
1. Poly(lactic acid), or PLA, is a polyester made from lactic acid, which is produced by fermenting maize or suger cane, which are renewable crops.
2. PLA will biodegrade easily - it is hydrolysed by water if kept at a high temperature for several days in an industrial composter or more slowly at lower temperatures in landfill or home compost heaps.
3. PLA has many uses, including rubbish bags, food and electrical packaging, disposable eating utensils and internal sutures (stitches) that break down without having to open wounds to remove them.
Optical isomers in pharmaceuticals
Drugs work by binding to active sites on enzymes or other receptor molecules in the body. The drug must be the right shape to fit the active site/receptor - only one optical isomer will. The other optical isomer may have no effect or have harmful side effects. A single isomer must be produced so that half the dose is needed, and the drug company won't get sued for side-effects.
Molecules prepared synthetically in the laboratory often contain a mixture of optical isomers, whereas molecules of the same compound produced naturally by enzymes in living systems will often be present as one optical isomer only.
Problems and solutions to isomerism
Synthesis of a pharmaceutical that is a single optical isomer:
- increases costs due to difficulty in separating the optical isomers
- reduces possible side effects and improves pharmacological activity
Ways that a single isomer can be synthesised:
- using enzymes or bacteria that promote stereoselectivity
- using chemical chiral synthesis or chiral catalysts/transition metal complexes
- using natural chiral molecules, such as L-amino acids or sugars, as starting materials (chiral pool).