Amino acids, proteins and DNA - AL only (3.3.13)

Amino acids have both an amino and carboxylic acid group.

Amino groups are Brønsted–Lowry bases; they accept protons to form ions.

Carboxylic acids are Brønsted–Lowry acids, and donate protons to form ions.

Amino acids that are used in protein formation are known as alpha () amino acids, or 2-amino acids.

The carbon after the carboxylic acid group carbon, (carbon 2), is the carbon and also holds the amino group, a hydrogen atom and the variable group, .

At values close to seven, the amino acid contains both a group and group.

A molecule that contains both positive and negative ions, whilst remaining neutral overall, is called a zwitterion.

As they contain both positive and negative ions, the zwitterions can form a giant ionic lattice; therefore, pure amino acids form crystalline solids.

In acidic conditions, the basic part of the amino acid is protonated.

The amino group is basic and the lone pair of electrons on the amino nitrogen can be donated to a proton in a dative covalent bond. The product is an ammonium salt made charge neutral by the anion from the acid used.

Note that the carboxylic acid group also remains protonated in acidic conditions.

In alkaline conditions, there is a high concentration of ions, and so the acidic part of the amino acid is deprotonated.

The carboxylic acid group acts as a Brønsted–Lowry acid, and donates a ion to the solution. The products are a carboxylate salt with the cation from the base, and water: a neutralisation reaction.

Note that the amine group remains deprotonated and uncharged in alkaline conditions.

For colourless amino acids to be visible on a TLC plate – and hence their value be calculated – UV light or ninhydrin may be used.

Ninhydrin is a reagent which will bind to the amine group generating a blue or purple coloured complex.

The value is calculated as:

When measuring the distance travelled by the amino acids, you should measure from the centre of the spot on the TLC plate.

Measurements should be made following the direction of travel shown by the solute. This will be from the start point through the spots left by the sample.

Proteins are formed from chains of amino acids which join together through peptide bonds.

When a peptide bond is formed, water is eliminated in a condensation reaction.

The sequence in which amino acids bond together is a protein’s primary structure. The primary structure is held together by peptide bonds, which are strong covalent bonds and not easily broken.

The secondary structure is the local 3D arrangement of the protein: it will either be an -helix or a -pleated sheet.

The secondary structure is held together by hydrogen bonds between nearby amino acids. These are usually represented as dashed lines between nearby amino acids.

The tertiary structure refers to the 3D shape of the entire protein.

The tertiary structure is formed through hydrogen bonds and sulfur–sulfur bridges between the R-groups on amino acids throughout the structure.

The peptide bonds between amino acids in the protein chain are strong covalent bonds, and are not easily broken. This chain of amino acids provides the primary structure of the protein.

The secondary and tertiary structures of the protein are formed by hydrogen bonds. These are much weaker than covalent bonds, and can be broken when heated.

In the tertiary structure, sulfur–sulfur bonds can also form between cysteine amino acids, as they contain sulfur in their group.

Sulfur–sulfur bonds or disulfide bridges are a type of covalent bond, and are therefore stronger than hydrogen bonds. Disulfide bridges make the protein shape more resistant to changes in heat and .

Proteins can be broken down into their constituent amino acids in a hydrolysis reaction (hydro meaning water, and lysis, meaning to split).

In this reaction, water is inserted into the peptide bond, splitting the chain to reform amino acids.

A hydrolysis reaction usually takes place in the presence of an acid catalyst (e.g. concentrated )

The from the water molecule is added back onto the carbonyl carbon to reform the carboxylic acid.

The from the water molecule is added onto the nitrogen to reform the amine.

When amino acids form peptides, a condensation reaction occurs, and water is eliminated.

The is removed from the carboxylic acid group, and the is lost from the amine group on the neighbouring amino acid.

A peptide bond, , is then formed between the fragments of the amino acids left over.

The 3D shape of the active site is a feature of the tertiary structure of the protein, and is held together by hydrogen bonds and disulfide bridges bonds.

If hydrogen bonds or disulfide bridges are broken by high temperatures or extremes of the tertiary structure is disrupted and the shape of the active site will change. This stops the enzyme–substrate complex from forming; the enzyme is denatured and no longer effective.

Stereoisomers have different spatial arrangements. As a result, one stereoisomer will be complementarily shaped to the active site, whereas another may not. This makes the active site stereospecific.

Enantiomers are stereoisomers which are mirror images. The wrong enantiomer will not fit the enzyme’s active site, in the same way that you cannot comfortably put your right shoe on your left foot; their shapes are not complementary.

If the active site is blocked in any way, the substrate can no longer bind to the enzyme, rendering the enzyme inactive.

Scientists can exploit this, by designing inhibitor drugs, which bind to the active site of an enzyme in a bacteria or virus, in place of the substrate, slowing down its action.

Drugs that bind to the enzyme active site are called competitive inhibitors.

DNA is made up of a phosphate–sugar polymer backbone, and the four bases (adenine, cytosine, guanine and thymine).

The structures of the sugar (2-deoxyribose), phosphate group and the bases are given to you in the data booklet in your exams.

DNA is an example of a naturally occurring polymer.

One monomer unit of DNA is a nucleotide.

Each monomer unit comprises:

• a phosphate unit
• 2-deoxyribose (a pentose sugar)
• one of the four DNA bases (adenine,cytosine, guanine, thymine).

DNA nucleotides are formed from two condensation reactions.

1. On one side of the 2-deoxyribose sugar, the OH group from the phosphate combines with the hydrogen from the methanol group on the sugar, releasing water.
2. On the other side of the 2-deoxyribose sugar, the alcohol group of the sugar combines with the acidic hydrogen from the nitrogenous base, also releasing water.

DNA is a polymer of nucleotides.

Two nucleotides link between the phosphate group on one nucleotide and the deoxyribose (sugar) group on the neighbouring nucleotide through covalent bonds.

This produces an alternating sugar–phosphate–sugar–phosphate backbone.

The bases are attached to each of the sugars along the DNA backbone.

Two DNA strands will run antiparallel; parallel but in opposite directions to each other. The two DNA strands form a double helix shape.

Between the two DNA strands, adenine will always pair with thymine and cytosine will always pair with guanine.

These are referred to as complementary base pairs.

Between the two DNA strands, adenine will always pair with thymine (A-T) and cytosine will always pair with guanine, (C-G).

This is because these base pairs have complementary structures which allow hydrogen bonds to form between them.

Two hydrogen bonds form between adenine and thymine.

Three hydrogen bonds form between cytosine and guanine.

The hydrogen bonds between the base pairs on the two strands of DNA are what holds the two DNA strands in the double helix.

Cis-platin is an effective anticancer drug. It is the cis isomer of the platinum complex

Cisplatin is a square planar coordination complex with a central platinum (II) ion bonded to two ammonia ligands and two chloride ligands, arranged in a cis configuration.

Cis-platin prevents DNA replication by binding to the guanine base on the DNA strand.

In a ligand substitution reaction, the chloride, ligands on cisplatin are displaced, and new coordinate bonds form between the ion and a nitrogen atom on the guanine bases.

This distortion prevents the DNA from unzipping and replicating.

As a result, cancerous cells cannot divide, and their growth is impaired. This leads to reduced growth and eventually the shrinking of the tumour due to the inability to replace the cells through mitosis.