a-glucose is a monosaccharide, that is a simple sugar whose structure is around 6 carbon atoms. The formula for a-glucose is C6H12O6. It is a carbohydrate, which all share the same common components, being Carbon, Hydrogen, and Oxygen. The common formula can be expressed Cx(H2O)y where x and y are variable numbers that can be the same or different. Diagram 1a shows the basic structure of the alpha glucose molecule, where you can see the ring of 6 carbon atoms. (Kent M, 2000, p28)
Asparagine (abbreviation Asn or N) is one of 20 naturally occurring amino acids, all of which are made of Carbon, Hydrogen, Oxygen, and Nitrogen, and all have a general formula consisting of an amino group NH2, a base, and a carboxyl group COOH, which is acidic. The amino group is attached to the central carbon atom (known as the alpha carbon). A hydrogen atom, another carbon atom and a side chain known as the R group are all linked to this central atom. It is the R group of atoms that determines the type of amino acid, and in the case of Asparagine the R is CH2CONH2. In figure 1b, I have highlighted this R group as well as the amino group and the carboxyl group, a double bond between the oxygen and carbon atoms in the carboxyl group can be seen. (Kent M, 2000, p32-33)
Glycerol is the smallest sugar alcohol, a lipid. All Lipids contain carbon oxygen and hydrogen atoms. The molecular formula is C3H5(OH)3 The 3 carbon atoms are each linked to a hydroxyl group (an oxygen atom bound covalently with a hydrogen atom). These hydroxyl groups on the glycerol molecule and the carboxyl groups on a fatty acid molecule, combine in what is known as a condensation reaction (gives off water) to form a triglycerides which are known as 'true' or 'neutral' fats. (Kent M, 2000, p30-31) (Class handout)
Linoleic acid is a polyunsaturated fatty acid. (Wilson K, 1996, p271). In the structure of unsaturated fatty acids, the carbon atoms in the hydrocarbon chain are not bonded to the maximum number of other atoms. Two or more of the carbon atoms have double bonds between them, and these double bonds form a kink in the chain (meaning the chains are not straight and cannot pack tightly together and so form a liquid oil rather than a solid fat). If there is one double bond it is called a monounsaturated fatty acid, and if two or more are present, a polyunsaturated fatty acid. (Kent M, 2000, p30-31)
Proteins (polypeptides) are made up of monomers - small building blocks - called amino acids; of which there are about 20 naturally occurring. Two amino acids can combine to from what is known as a dipeptide in a condensation reaction, where the amino group of one amino acid join together with the carboxyl group of another (see 2a) To this resulting dipeptide, we can add additional amino acids to form a polypeptide chain, and one or more of these polypeptide chains forms a protein (see 2b). (Kent M, 2000, p32-33)
Two a-glucose molecules, monosaccharides, can be combined in a condensation reaction to form a disaccharide, the result being maltose, a simple sugar about half as sweet as glucose. The bond is known as a glycocidic, 1-4 bond, and as you can see from diagram 3a, this is because the join is at the carbon 1 and 4 atoms; water is produced as a result of this reaction, and the resulting dimer with glycocidic bond; shown 3b. (Kent M, 2000, p26)
Proteins are made up of one or more chains of amino acids, known as polypeptide chains. There are up to four aspects of a proteins structure. It is bonding within the structure that gives it its shape, these bonds are as follows;
Table from class notes.
The primary structure of the protein refers to the sequence of the amino acid chains. Using the single letter abbreviation for each amino acid, we can describe this primary structure. Below are the abbreviations for all 20 common amino acids;
Alanine Ala A
Cysteine Cys C
Aspartic Acid Asp D
Glutamic Acid Glu E
Phenylalanine Phe F
Glycine Gly G
Histidine His H
Isoleucine Ile I
Lysine Lys K
Leucine Leu L
Methionine Met M
AsparagiNe Asn N
Proline Pro P
Glutamine Gln Q
Arginine Arg R
Serine Ser S
Threonine Thr T
Valine Val V
Tryptophan Trp W
Tyrosine Tyr Y
Table from Birbeck College (London) Website
Grouping together the letters above, in an exact sequence can describe the primary structure of a protein. These chains can be very long; for example in the myoglobin polypeptide chain there is a sequence of 153 amino acids, below I have listed the first ten amino acids in this chain;
The secondary structure of the protein refers to the folding or coiling that occurs as a result of the forces and bonds within the polypeptide chain. Small charges along the spine of the polypeptide form hydrogen bonds which pull the chain into either the alpha helix or beta pleated sheet. Diagrams 4 a and b show these structures with examples of the bonds.
When we speak of the tertiary structure, we are referring to the overall 3d shape of the polypeptide chain, and this shape is dictated by the interactions between the amino acids at various points in the coiled secondary structure. Proteins are classified into two main groups; Fibrous or globular.
Fibrous proteins are many polypeptide chains that are lined up to form long fibres or sheets. They have mainly structural functions thank to the strength that these fibres possess, and are insoluble in water.
Globular proteins the polypeptides are curled up tightly into a spherical shape, and these are water soluble; enzymes, antibodies and hormones are typical examples of globular proteins.
A quaternary structure refers to the way in which many polypeptide chains are arranged to form a specific protein. IE haemoglobin which is made up of four globular proteins.
Two functions of globular proteins are to transport things, as in the case of haemoglobin which carries oxygen in the blood, or to act as catalysts in the case of enzymes, such as amylase, and it is the structural properties of these proteins that allows them to carry out these functions.
The hydrophobic amino acids are on the inside of the structure and hydrophilic the outside, allowing dipole dipole reactions with a given solvent, hence the molecules solubility.
Haemoglobin consists of four globular proteins, each of which is also tightly associated with a heme unit which contains iron. This iron ion is responsible for binding O and CO2 to the haemoglobin, forming oxyhaemoglobin which is the transported around the body in the blood stream.
In the case of enzymes it is the globular structure that allows the enzyme to take many different shapes, so when a substrate enters the enzyme it allows it to take the correct shape to fit. This is known as induced fit theory.