Proteins and Enzymes

The monomer of proteins are amino acids. When two amino acids join together during a condensation reaction, a dipeptide is formed. A polypeptide is formed when more than two amino acids join together and a protein is made of one or more polypeptides.

Structure of amino acids

All amino acids have the same general structure- a carboxyl group (COOH) and and amino group (NH2) attached to a carbon atom. The difference between the different amino acids is the variable group (R group). 

Amino acids are linked together by condensation reactions to form peptides. During this process a molecule of water is released. A peptide bond is formed between the carbon and nitrogen atoms.

Primary Structure

The primary structure of a protein refers to the sequence of amino acids in a polypeptide chain. Each amino acid is joined to another by a peptide bond.

Secondary Structure

There are two main types of secondary structure, the alpha helix and the beta pleated sheet. These structures form because of hydrogen bonds between amino acids in the chain.

Tertiary structure

More hydrogen bonds and disulfide bonds form between the amino acids which causes the alpha-helixes and beta pleated-sheets to be folded into a compact globula structure. This forms the final 3D structure. 

Quaternary Structure

Some proteins are made of more than one polypeptide chain, which are held together by hydrogen bonds.

There are many different proteins found in living organisms and each one has a different structure and shape. This makes them specialised for their specific role. 

Enzymes

A very common example of proteins are enzymes, they're usually roughly a spherical due to the tighy folding of the polypeptide chains. They are soluble and often have roles in metabolism. E.g. some enzymes break down large food molecules into small monecules and others synthesise large molecules.

Antibodies 

Antibodies are involved in the immune response. Ther're made up of two light (short) and two heavy (long) polypeptide chains. Antibodies have variable reigons and the amino acid  sequense in these reigons vary greatly.

Transport Proteins

Transport protiens are present in the cell membranes to transport molecules and ions across it. They fold up to form a channel due to the hydrophobic and hydrophillic amino acids. 

If you want to find out is there are proteins in a substance then you would use the biuret test. 

There are two stages to this process;

1.  The solution needs to be alkaline, so first you add a few drops of sodiums hydroxide solution.

2. Add some copper (II) sulfate solution. If a purple layer forms then a protein is present, and if the solution stays blue then there is no protein in the solution.

Role of enzymes

Enzymes are biological molecules that act as catalysts by lowering the activation energy or a reaction so it can occur at a lower temperature. Any one enzyme will only catalyse one reaction, this is because;

• Enzymes have a highly specific shape due to the their tertiary structure.
• Their active site is complementary to only one substrate.

How do they work

• When the substate binds to the enzyme it forms an enzyme-substrate complex.
• The enzyme puts pressure one the bonds in the substrate, this breaks the the substrate down into smaller products.
• For example Lactase binds to lactose and breaks it down into glucose and galactose 

Lock and Key

Enzymes only work when they bind to a subastate that **** their active site. Early scientists studying the action of enzymes came up with the 'lock and key' model. This iswhere the substrate fits into the enzyme the same way a key fits into a lock.

Induced Fit

Scientists realised that the lock and key model didnt goive the fell story. The enzyme and the substrate till have to fit togwther but evidence shows that the enzyme-subatrate complex changes shape slightly to complete the fit. This locks the substrate in more tightly to the enzyme. Scientists modified the lock and key model and came up with the induced fit model. One the products have been released from the enzyme the active site returns to its original shape, ready to bind to another substrate. 

Competative Inhibitors

• A competative inhibitior is a molecule with a similar shape to the substratre. 
• They compete with the substrate to bind to the active site but no reaction occurs.
• They block the active site so the substrate cant bind to it and form enzyme-substrate complexes.
• This lowers the rate of reaction as less enzyme-substrate complexes are formed per second.

Non-Competative Inhibitors

• Non-competative inhibitors are molecules that bind to the enzyme away from the active site, an allosteric site.
• This alters the shape of the tertiary structure and therefore the active site, this means the substrate is no longer able to bing to the active site becaure they aren't complementary of each other. 
• Increasing the concentration of substrate won't make a difference because the enzymes will still be denatured. 

There are two types of inhibitors and they both affect the rate of a reaction.

Competative Inhibitors

• A competative inhibitior is a molecule with a similar shape to the substratre. 
• They compete with the substrate to bind to the active site but no reaction occurs.
• They block the active site so the substrate cant bind to it and form enzyme-substrate complexes.
• This lowers the rate of reaction as less enzyme-substrate complexes are formed per second.

Non-Competative Inhibitors

• Non-competative inhibitors are molecules that bind to the enzyme away from the active site, an allosteric site.
• This alters the shape of the tertiary structure and therefore the active site, this means the substrate is no longer able to bing to the active site becaure they aren't complementary of each other. 
• Increasing the concentration of substrate won't make a difference because the enzymes will still be denatured. 

Temperature

Increasing the temperature will increase the rate of reaction, this is because the molecules vibrate more and have more kinetic energy and will move faster. The faster the molecule moves, the more collisions there will be per second. of the temperature is raised too high the bonds in the enzyme will break and the enzyme will denatured.

pH

Above and below the optimum pH, the hydroxide and hydrogen ions foun in acds and alkalis mess up the ionic and covalent bonds that hold the enzyme together. This makes the shape of the active site change and the enzyme becomes denatured.

Substrate Concentration

The higher the substrate concentration, the higher the rate of reaction. This is because the substrate molecules are more likely to collide woth the enzyme. This is ture up until a saturation point. After this all the enzymes are full so adding more subatrate wont make a difference.