Condensation Polymers (3) Amino acids and Proteins

Relevant Specification Extracts:

OCR

6.2.2 Amino acids

Learning outcomes 

Learners should be able to demonstrate and apply their knowledge and understanding of: 

Reactions of amino acids 

The general formula for an α-amino acid as RCH(NH2)COOH and the following reactions of amino acids: 

(i)  reaction of the carboxylic acid group with alkalis and in the formation of esters
(ii)  reaction of the amine group with acids 

Edexcel 18B

16. understand the properties of 2-amino acids, including: 

i  acidity and basicity in solution, as a result of the formation of zwitterions
ii  effect of aqueous solutions on plane-polarised monochromatic light

17. understand that the peptide bond in proteins: 

i  is formed when amino acids combine, by condensation polymerisation
ii  can be hydrolysed to form the constituent amino acids, which can be separated by chromatography

AQA

3.3.13 Amino acids and proteins 

Amino acids and proteins are the molecules of life.  In this section, the structure and bonding in these molecules and the way they interact is studied.  Drug action is also considered. 

3.3.13.1 Amino acids (A-level only) 

Amino acids have both acidic and basic properties, including the formation of zwitterions. 

Students should be able to draw the structures of amino acids as zwitterions and the ions formed from amino acids: 

in acid solution and in alkaline solution. 

3.3.13.2 Proteins (A-level only) 

Proteins are sequences of amino acids joined by peptide links. 

The importance of hydrogen bonding and sulfur–sulfur bonds in proteins. 

The primary, secondary (α-helix and β–pleated sheets) and tertiary structure of proteins. 

Hydrolysis of the peptide link produces the constituent amino acids. 

Amino acids can be separated and identified by thin-layer chromatography. 

Amino acids can be located on a chromatogram using developing agents such as ninhydrin or ultraviolet light and identified by their Rf values. 

Students should be able to: 

- draw the structure of a peptide formed from up to three amino acids
- draw the structure of the amino acids formed by hydrolysis of a peptide
- identify primary, secondary and tertiary structures in diagrams
- explain how these structures are maintained by hydrogen bonding and S–S bonds
- calculate Rf values from a chromatogram.

Amino acids and Proteins

In this third post on condensation polymers, I’m looking at the properties of amino acids and the formation of proteins from amino acids, defining the repeat units of proteins and explaining the difference between primary, secondary, tertiary and quaternary structures of proteins, and the nature of the intermolecular forces that exist between these polymer molecules.

I’m going to discuss how amino acids combine with each other to form protein chains and how to spot the repeat unit and the peptide linkage between repeat units of protein.

Amino Acids

As their name suggests amino acids are part of both the amine family of molecules and the carboxylic acid family contain the –COOH and the –NH₂ functional groups.

They have the general formula RCH₂(NH₂)COOH

You will also notice that amino acids are called α–aminoacids or 2–aminocarboxylic acids because the –NH₂ group is on the second carbon atom of the chain.

Amino acids as optically active

You will also see that there is the potential for amino acid molecules to contain four different functional groups on the second carbon atom.

Four different functional groups on the second carbon atom means that the amino acid is optically active. It has two enantiomers: they rotate the plan of plane polarised light in opposite directions.

You can see the effect here in these diagrams:

Amino acids as zwitterions

Amino acids then carry the properties of both the carboxylic acid group–they are weak acids and the amino group–they are weak bases.  In fact they exist in an ionic form called a zwitterion (from the German for twin: zwitter).  In this form the proton from the carboxylic acid group has migrated to the amino group.  You can see this in the equation below:

Reaction with alcohols to form esters

Amino acids react with alkalis to form salts and with acids to form salts

Polymerisation of amino acids

Amino acids are the monomers of protein.  Amino acids combine in a condensation reaction i.e. the addition of two amino acids followed by the elimnation of a molecule of water.

The resultant linkage between the two amino acid residues is called a peptide link.

The basic protein structure is called its Primary Structure and this is just a sequence of amino acid residues.  See below and note the peptide linkages:

Note that is writing out the primary structure we begin with the amino nitrogen on the left.

However, amino acid R groups can interact with one another under the appropriate circumstances and this results in two types of secondary structure called α–helix and β–pleated sheet.  These two secondary structures are illustrated below.

You should be able to recognise and identify these structures in diagrams.

The structures are held in place when hydrogen bonds form between amino acid side chains or disulphide bridges form between cysteine side chains.  These are illustrated below:

When the secondary structures interact the hydrophobic water–hating side chains tend to move to the centre of the protein molecule and the water–soluble hydrophilic side chains move to the surface of the protein.  This produces a third structure type of structure obviously called the protein tertiary structure.

The α–helix and β–pleated sheet are like the struts and plates that hold the tertiary structure in place.

You can see the tertiary structure of myoglobin below.

Hydrolysis of a protein and analysis of its hydrolysate

To analyse a protein and determine the composition of a protein’s primary structure, the first step is to hydrolyse the molecule.

Hydrolysis is usually accomplished refluxing the protein for several hours in 3M HCl i.e. acid hydrolysis.  The resultant hydrolysate is then neutralised.

Hydrolysis occurs at the peptide linkage.see below

Paper or thin layer chromatography can be used to determine which amino acids are present in the hydrolysate. See the diagram below:

Comparing known amino acid R_f values with those of the components of the hydrolysate will provide the evidence needed to identify the amino acids in the protein’s primary structure. See the illustration below:

 How to determine an Rf value. 

Below are results of using ninhydrin to spot the movement of the amino acids on the chromatogram

Summary of Protein Structure

Amino Acids

Edexcel

Topic 18B/16. 

To be able to understand the properties of 2-amino acids, including: 

i  acidity and basicity in solution, as a result of the formation of zwitterions 


ii  effect of aqueous solutions on plane-polarised monochromatic light 


OCR

6.2.2 Reactions of amino acids

(a) the general formula for an α-amino acid as RCH(NH2)COOH and the following reactions of amino acids: 

(i)  reaction of the carboxylic acid group with alkalis and in the formation of esters


(ii)  reaction of the amine group with acids 


AQA

Amino acids 

Amino acids have both acidic and basic properties, including the formation of zwitterions. 

Students should be able to draw the structures of amino acids as zwitterions and the ions formed from amino acids: 

• in acid solution 

• in alkaline solution.

Amino Acids

Amino acids sometimes referred to as α-amino acids or 2-amino acids depending on the A level specification you are studying from.

Either way their structure looks like this:

The 2– refers to the second carbon atom from the carboxylic acid group to which both the R group and the NH₂groups are attached.

The R– groups varies from amino acid to amino acid and leans each its distinctive properties.

Here are the skeletal formulae of the 21 essential amino acids with their generic names and abbreviations.  

 

They are classified above according to their type of side chain or R– group.

They have certain properties common to them all.

1.  They are acids so react as acids in aqueous solution with the common reagents such as a reactive metal like magnesium or a base such as a carbonate e.g. sodium carbonate Na₂CO₃.

2.  Every amino acid also contains at least one amino group which is basic so amino acids accept protons from strong acids such as Hydrochloric acid (HCl)

3.  Coupling the above two properties together we find that the acid group of the amino acid protonates the amine group and creates what is known as a zwitter ion (on the right in the illustration below)

So in high pH alkaline conditions the amino acid carries an amino group and the carboxyl group is ionised

But in low acidic pH the amino group is protonated and the carboxyl group is free as in the illustration below:

And therefore the amino acid carries two Ka values.

4. If a solution of an amino acid is allowed to evaporate and crystallise then a white crystalline solid forms with a fairly high melting point.

The solid is the crystalline zwitter ion and as that is an ionic structure, the substance has a fairly high melting point.

So amino acids have both acidic and basic properties they both accept protons and donate protons under the appropriate conditions. 

5. Furthermore as we noted in a previous blog (here) amino acids (except glycine are optically active having a chiral centre that is a carbon atom attached to four different functional groups.  

This structural feature a chiral centre means that aqueous solutions of amino acids will rotate the plane of plane-polarised monochromatic light.  

The significance of this behaviour is that all amino acids that occur naturally have the same type of rotation of the plane of plane polarised monochromatic light.  They are all laevo rotatory.  Some have colloquially called this the left-handedness of the natural world!

You can read more about this feature of the natural world hereand also here.