Option B.2 – Proteins
B.2.1 – Draw the general formula of 2-amino acids
The R group varies between each amino acid.
B.2.2 – Describe the characteristic properties of 2-amino acids
All amino acids have the same general structure. They have an amino (NH2) group, and a carboxylic acid (COOH) group. The R group varies between amino acids, and can be anything from a hydrogen atom, a CH3 group, etc. There are about 20 naturally occurring amino acids.
The R group determines many properties of the amino acid: some are polar whilst others are non-polar. If there is another COOH group in the R group, the amino acid will be acidic. On the other hand, if there is another NH2 group in the R group, then the amino acid will be basic. The name 2-amino acid comes from the fact that the carbon with the amino group attached is the second carbon in the chain. 2-amino acids are also called α-amino acids.
Amino acids form polymers, reacting together to make polypeptide chains. When we write about amino acids, we can use three-letter abbreviated names for them, such as “Ala” for Alanine.
Zwitterions
Since amino acids have both a basic NH2 group and an acidic COOH group, they can form interesting ions, with both a positive charge and a negative charge on the same molecule, or dipolar ions. This is the result of an internal acid-base reaction, with a H+ ion moving from the COOH end to the NH2 end.
In addition, amino acids can react with both acids and bases, being amphoteric. This allows them to act as buffers, being able to resist changes in pH. This is important for maintaining the pH of cells in the human body.
B.2.3 – Describe the condensation reaction of 2-amino acids to form polypeptides
When two amino acids react, a hydrogen atom is removed from one of the NH2 groups, and the OH is removed from the COOH group of the other amino acid. As a result, a water molecule is produced as a by product of the condensation reaction.
The bond between the two monomers is called a peptide bond, or amide bond. The molecule shown below is a dipeptide – more monomers may react together to make much longer chains, forming polypeptides.
B.2.4 – Describe and explain the primary, secondary (a-helix and b-pleated sheets), tertiary and quaternary structure of proteins
Primary Structure
The sequence of the amino acids in the polypeptide chains. With the different amino acids, there are millions of possible combinations of amino acids, forming patterns that have different properties.
Secondary Structure
This is the hydrogen bonding that forms between different parts of the polypeptide chain. The -C=O part of one peptide bond may form a hydrogen bond with the -N-H part of another.
There are two main types of structures that form from this. The first is the α-helix, when the polypeptide chain coils into a spiral. Hydrogen bonds form along the coil, between every fourth amino acid. As a result, there are 3.6 amino acids per turn of the coil, making it very tightly coiled. Helix chains are more flexible and easily stretched.
The other is the ß-sheet, which is when the polypeptide chains form a stair-like structure. This is made up of polypeptide chains bonds alongside each other. They are not as tightly coiled as in the helix. Hydrogen bonds form between each chain. These sheets are very inelastic.
Some proteins have very well-defined secondary structure and are called fibrous proteins. These are tough and insoluble in water.
Tertiary Structure
This is the three-dimensional structure of the protein, also called the conformation, and involves more twisting, coiling and folding. The R groups of the amino acids in the polypeptide chains will determine this. The proteins with more complex tertiary structure tend to be globular proteins, which are soluble in water. There are four types of interactions involved in forming the tertiary structure:
- Hydrogen bonding between the polar R groups
- Hydrophobic interactions between the non-polar R groups, creating Van der Waal’s forces
- Ionic bonds between the charged R groups
- Disulfide bridges between sulfur atoms in the amino acid cysteine, forming covalent bonds
If there are changes in pH or temperature, these bonds will be affected, and the protein will denature, losing its tertiary structure.
Quaternary Structure
This is when different peptide chains come together and interact to form a single protein. They may wind around each other in a large helix, or fit together in other complex arrangements. However, not every protein has a quaternary structure.
B.2.5 – Explain how proteins can be analysed by chromatography and electrophoresis
Chromatography
In chromatography, the amino acids in a protein are separated and identified by dying them with a locating reagent. A sample of the amino acid mixture is placed near the bottom of the chromatography paper, and the point is marked as the origin. The paper is then placed into the chromatographic tank, with the end sitting in the solvent, and the origin above the solvent. The solvent will move up the paper. The amino acids will then move into one of two phases: the mobile phase in the solvent or stationary phase in the water in the paper. This arrangement causes the amino acids to be distributed according to how soluble they are.
The solvent front is the highest place reached by the solvent and is marked before removing the paper from the tank. It is sprayed with ninhydrin (the locating reagent) to show the amino acids as purple. Using the location of an amino acid, its retention factor is calculated:
These values are used to determine the amino acids present.
Electrophoresis
In this process, the amino acids move as a result of an electrical field. The amino acids have varying charges depending on the pH, and can be separated when placed in a buffer solution. The amino acid mixture is inserted into wells in the gel and then exposed to an electric field. The amino acids will be stationary at the point where they carry no charge.
They must reach their isoelectric point – where the pH causes their charges to cancel out. The gel is then stained to identify the positions of the amino acids.
Steps:
- The proteins are broken down into the individual amino acids through hydrolysis o This requires an acid/base and heat
- These are then added to the gel containing a buffer
- A voltage is applied to create the electrical field.
- Amino acids move based on mass and charge
- The amino acids are then dyed with ninhydrin
- The distance travelled by the amino acids is measured and compared with known values to determine which amino acids are present
B.2.6 – List the major functions of proteins in the body
- Biological catalysts, or enzymes, for important reactions in the body that would otherwise proceed too slowly to support life
- Structure and support, such as in nails and hair
- Transport molecules such as haemoglobin
- Connective tissue in skin and tendons
- Source of energy
- Hormones for regulating the functions of the body