BIOMOLECULES

Living organisms have a remarkably similar chemical composition despite their diversity. Carbon, hydrogen, oxygen and other elements occur in both living and non-living matter, but carbon and hydrogen are relatively more abundant in living tissue. Water is the most abundant chemical in cells.

Grind a living tissue in trichloroacetic acid and strain it to obtain an acid-soluble pool (filtrate) and an acid-insoluble fraction (retentate). The soluble pool contains thousands of small organic compounds as well as inorganic ions and compounds. The insoluble fraction contains proteins, nucleic acids, polysaccharides and lipids.

For elemental analysis, compare wet weight with dry weight after water is removed. On complete burning, carbon compounds leave as gases; the remaining ash reveals inorganic elements such as calcium and magnesium. Inorganic constituents include Na⁺, K⁺, Ca²⁺, Mg²⁺, water, phosphate and sulphate.

Protein amino acids are alpha-amino acids: the alpha-carbon carries hydrogen, an amino group, a carboxyl group and a variable R group. There are 20 amino acids in proteins. Based on amino and carboxyl groups, amino acids can be acidic (glutamic acid), basic (lysine) or neutral (valine); tyrosine, phenylalanine and tryptophan are aromatic. Their ionisable groups produce a zwitterionic form at suitable pH.

Fatty acids have a carboxyl group and a hydrocarbon R group. They are saturated when no C=C bond is present and unsaturated when one or more C=C bonds occur. Glycerol is trihydroxy propane. Fatty acids esterified with glycerol form mono-, di- and triglycerides; fats and oils differ in melting point. Phospholipids, such as lecithin, are important components of cell membranes.

Nitrogen bases include adenine, guanine, cytosine, uracil and thymine. A base plus sugar is a nucleoside; addition of phosphate forms a nucleotide. DNA and RNA are made only of nucleotides and function as genetic material.

Small biomolecules are usually less than 1000 Da. Proteins, nucleic acids and polysaccharides are true biomacromolecules, generally above 10,000 Da and polymeric. Lipids are not strictly macromolecules because their molecular mass usually does not exceed 800 Da; however, membrane fragments form insoluble vesicles during tissue grinding, so lipids occur in the acid-insoluble/macromolecular fraction.

Proteins are linear polypeptide chains in which amino acids are joined by peptide bonds. Since proteins use 20 types of amino acids, they are heteropolymers, not homopolymers. Essential amino acids must be supplied through food; non-essential amino acids can be synthesised by the body.

Polysaccharides are long chains of sugars. Cellulose is a glucose homopolymer and forms plant cell walls; starch is the energy store in plants and glycogen in animals. Inulin is a polymer of fructose. Starch has a helical structure that holds iodine and produces a blue colour; cellulose lacks such complex helices. Chitin is a complex polysaccharide in arthropod exoskeletons.

Nucleic acids are polynucleotides. Each nucleotide has a nitrogenous base, a pentose sugar and phosphate. Adenine and guanine are purines; cytosine, uracil and thymine are pyrimidines. DNA contains 2'-deoxyribose whereas RNA contains ribose.

Adult human haemoglobin has four subunits: two alpha and two beta subunits.

Almost all enzymes are proteins; catalytic nucleic acids are ribozymes. An enzyme has an active site, a crevice or pocket where its substrate fits. Enzymes accelerate reactions without being consumed. They are typically damaged above about 40°C, whereas enzymes from thermophilic organisms can remain active at 80-90°C.

For a chemical reaction, the substrate must reach a high-energy transition state. The energy difference between substrate and transition state is the activation energy. Enzymes lower this energy barrier and make conversion to product easier.

A metabolic pathway is a multistep chemical reaction in which each step is enzyme-catalysed. Carbonic anhydrase can accelerate the formation of carbonic acid by about 10 million times compared with the uncatalysed reaction.

Enzyme activity depends on the tertiary structure of its protein. Each enzyme has an optimum temperature and optimum pH where its activity is highest. Low temperature leaves an enzyme temporarily inactive, while high temperature denatures it. As substrate concentration rises, reaction velocity rises until all available enzyme molecules are saturated; the maximum rate is Vmax.

An inhibitor is a chemical that binds to an enzyme and shuts off its activity. A competitive inhibitor closely resembles the substrate and competes for the substrate-binding site. Malonate competitively inhibits succinate dehydrogenase because it resembles succinate. Competitive inhibitors can help control bacterial pathogens.

Some enzymes require non-protein cofactors. The protein part alone is the apoenzyme. Prosthetic groups are tightly bound organic cofactors, such as haem in peroxidase and catalase. Coenzymes associate transiently during catalysis; NAD and NADP contain niacin. Metal ions can coordinate with active-site side chains and substrate; zinc is a cofactor for carboxypeptidase.

1. How are acid-soluble and acid-insoluble fractions of living tissue obtained?
2. Differentiate primary and secondary metabolites with examples.
3. Why do lipids occur in the acid-insoluble fraction despite low molecular mass?
4. Describe the composition of a triglyceride and phospholipid.
5. Compare cellulose, starch, glycogen and chitin.
6. Differentiate nucleoside, nucleotide, DNA and RNA.
7. Explain all four levels of protein structure.
8. How do enzymes lower activation energy?
9. State the factors affecting enzyme activity and explain competitive inhibition.
10. List the six enzyme classes and the three types of cofactors.