Biomolecules

In this chapter: chemical analysis of tissue; amino acids, lipids and nucleotides; primary and secondary metabolites; proteins and their four levels of structure; polysaccharides; nucleic acids; enzymes: action, factors, inhibition, classification and cofactors.

How living tissue is analysed

Living tissue is ground in trichloroacetic acid (Cl₃CCOOH) and filtered:

• The acid-soluble filtrate contains small molecules (molecular weight below about 1000 Da): micromolecules or biomolecules.
• The acid-insoluble retentate contains macromolecules: proteins, nucleic acids and polysaccharides, and also lipids.
• Lipids have molecular weights not exceeding about 800 Da, yet appear in the acid-insoluble fraction. This is because, when tissue is ground, cell membranes break into vesicles that are insoluble.
• Burning the tissue leaves ash, containing inorganic elements (calcium, magnesium etc.) and compounds (sulphate, phosphate).

The building blocks

Amino acids

Amino acids are organic compounds with an amino group and an acidic (carboxyl) group on the same carbon, the α-carbon: hence α-amino acids. They are substituted methanes: the four substituents are hydrogen, carboxyl, amino and a variable R group. There are 20 types in proteins. When R is hydrogen the amino acid is glycine; a methyl group gives alanine; hydroxymethyl gives serine.

• Acidic (glutamic acid), basic (lysine) or neutral (valine), depending on the number of amino and carboxyl groups.
• Aromatic amino acids: tyrosine, phenylalanine, tryptophan.
• The ionisable NH₂ and COOH groups make the structure change with pH; the form carrying both charges is the zwitterion.

Lipids

Lipids are generally water-insoluble. Simple lipids are fatty acids: a carboxyl group attached to an R group, which may be methyl, ethyl or a longer chain of CH₂ groups (1 to 19 carbons). Palmitic acid has 16 carbons including the carboxyl carbon; arachidonic acid has 20. Fatty acids are saturated (no double bonds) or unsaturated (one or more C=C double bonds). Glycerol is trihydroxy propane. Fatty acids esterified with glycerol give mono-, di- and triglycerides (fats and oils; oils have lower melting points, like gingelly oil, and stay liquid in winter). Lipids with phosphorus and a phosphorylated organic compound are phospholipids (lecithin), found in cell membranes. Neural tissues have lipids with more complex structures.

Nitrogenous bases, nucleosides and nucleotides

• Bases: adenine and guanine (purines); cytosine, uracil and thymine (pyrimidines).
• Base + sugar = nucleoside: adenosine, guanosine, thymidine, uridine, cytidine.
• Nucleoside + phosphate = nucleotide: adenylic acid, thymidylic acid, guanylic acid, uridylic acid, cytidylic acid.

Primary and secondary metabolites

Primary metabolites (amino acids, sugars etc.) have identifiable functions in normal physiology. Secondary metabolites are found in plants, fungi and microbes; their role in the host is not always clear, but many are useful to humans.

Proteins

Proteins are polypeptides, linear chains of amino acids linked by peptide bonds. They are heteropolymers (made of different monomers). Essential amino acids must come from food; non-essential ones are made by the body.

Four levels of protein structure

1. Primary: the sequence of amino acids. The first amino acid is the N-terminal; the last is the C-terminal.
2. Secondary: the chain folds into a helix in some regions. In proteins only right-handed helices are observed.
3. Tertiary: the long chain folds upon itself like a hollow woollen ball, giving a 3-D shape. This is absolutely necessary for biological activity.
4. Quaternary: the arrangement of two or more polypeptide subunits. Adult human haemoglobin has four subunits: two α and two β.

Polysaccharides

• Long chains of monosaccharides joined by glycosidic bonds, formed by dehydration.
• Cellulose: a homopolymer of glucose; the main component of plant cell walls; paper and cotton fibre are cellulose.
• Starch: the plant store of energy. Forms helical secondary structures that can hold iodine, so starch turns blue with iodine. Cellulose has no complex helices and cannot hold iodine.
• Glycogen: the animal storage polysaccharide. Inulin: a polymer of fructose.
• In a polysaccharide chain (e.g. glycogen), the right end is the reducing end and the left the non-reducing end. Branches are present.
• Chitin: a complex polysaccharide with amino-sugars and chemically modified sugars (e.g. glucosamine, N-acetyl galactosamine); in the exoskeletons of arthropods and in fungal cell walls.

Nucleic acids

Nucleic acids are polynucleotides. Each nucleotide has a heterocyclic nitrogenous base, a monosaccharide (ribose in RNA, deoxyribose in DNA) and a phosphate. Nucleotides are linked by a phosphodiester bond (an ester bond between the phosphate and the hydroxyl of the sugar on each side). In the Watson-Crick model, DNA is a double helix; A pairs with T through two hydrogen bonds, and G with C through three. In B-DNA, one full turn has about ten base pairs, with a pitch of 34 Å.

Enzymes

Almost all enzymes are proteins; some nucleic acids that act like enzymes are called ribozymes. An enzyme has a crevice or pocket, the active site, into which the substrate fits.

• Unlike inorganic catalysts, which work best at high temperature and pressure, enzymes work at body conditions. Enzymes from thermophilic organisms (in hot vents and sulphur springs) remain stable at 80 to 90 °C.
• Carbonic anhydrase speeds up CO₂ + H₂O → H₂CO₃ about 10 million times: about 600,000 molecules per second, against about 200 per hour without the enzyme.
• A metabolic pathway is a series of enzyme reactions; glycolysis has ten enzyme-catalysed steps.

How enzymes work

The substrate (S) binds the active site to form an enzyme-substrate complex (ES), which is short-lived. The substrate changes into a transition state, then into product, which is released; the enzyme is free again. Enzymes lower the activation energy needed to reach the transition state; they do not change the energy difference between substrate and product.

Factors affecting enzyme activity

• Temperature and pH: each enzyme has an optimum. Low temperature keeps the enzyme temporarily inactive; high temperature destroys it by denaturing the protein.
• Substrate concentration: velocity rises with substrate concentration and then levels off at the maximum velocity (V_max), when all enzyme molecules are occupied.
• Inhibitors: a competitive inhibitor closely resembles the substrate and competes for the active site. Example: malonate inhibits succinic dehydrogenase because it resembles succinate. Competitive inhibitors are used to control bacterial pathogens.

Six classes of enzymes

Cofactors

The protein part of an enzyme is the apoenzyme. Catalytic activity is lost when the cofactor is removed.

• Prosthetic groups: organic, tightly bound. Example: haem in peroxidase and catalase.
• Co-enzymes: organic, bound only transiently during catalysis. Many contain vitamins: NAD and NADP contain the vitamin niacin.
• Metal ions: form coordination bonds with the active site and substrate. Example: zinc is a cofactor for the proteolytic enzyme carboxypeptidase.

Common traps: (1) Lipids are in the acid-insoluble fraction even though they are small. (2) Collagen = most abundant in animals; RuBisCO = most abundant in the biosphere. (3) Inulin is a fructose polymer, not glucose. (4) Enzymes lower activation energy but do not change the overall energy of the reaction.

NEET focus

• Acid-soluble vs acid-insoluble fractions; cell composition table.
• Secondary metabolite examples, often asked as match the column.
• Protein functions and levels of structure; haemoglobin subunits.
• Starch-iodine test; chitin; reducing end of polysaccharides.
• Enzyme classes, competitive inhibition (malonate), cofactor types and examples.

Practice questions