2.1 Essential ideas

2.1.1 Molecules to metabolism

  • Molecular biology explains living processes in terms of the chemical substances involved. 

Carbon atoms form four covalent bonds

  • Carbon atoms can form covalent bonds with up to four different atoms, allowing a diversity of stable compounds to exist.

Figure 2.1.1a – Covalent bonds: arrangements of carbonFigure 2.1.1a – Covalent bonds: arrangements of carbon

  • In a covalent bond, each of the two bonding atoms contributes one electron to a shared pair, as shown below.

Figure 2.1.1b – Covalent bonds in methane, CH4Figure 2.1.1b – Covalent bonds in methane, CH4

  • Carbon-based molecules are stable because covalent bonds are strong.

Life is based on carbon compounds

  • Carbon compounds range from very simple molecules (e.g. methane) to complex polymers consisting of billions of subunits (e.g. DNA).

Class

Characteristics

Examples

Carbohydrates

Composed of carbon, hydrogen and oxygen in ratio 1:2:1 (CH2O)

Simple sugars: glucose, fructose, galactose

Polysaccharides: amylose, amylopectin, glycogen, cellulose

Lipids

Hydrophobic molecules:

  • large or small
  • many types, including fatty acids, triglycerides, sterols and waxes, phospholipids, and fat-soluble vitamins

‘Fats’ are solid at room temperature.

‘Oils’ are liquid at room temperature.

Proteins

Composed of amino acid chains of carbon, hydrogen, oxygen and nitrogen (some with sulphur)

Structural proteins: keratin, collagen, elastin

Functional proteins and enzymes: actin, myosin, amylase, lactase, lipase, kinase

Nucleic acids

Composed of sub-units containing C, H, O, N and P (phosphorus)

RNA (ribonucleic acid) and DNA (deoxyribonucleic acid)

 

Metabolism involves enzyme-catalysed reactions

  • Any chemical transformation that occurs in a living system requires the action of specialised proteins called enzymes.
  • Metabolism is the web of all enzyme-catalysed reactions in a cell.
  • Metabolic pathways are very complex – at each step a different enzyme is used to release a small amount of energy (by breaking existing chemical bonds) or to absorb a small amount of energy (by the formation of new chemical bonds).

Figure 2.1.1c – Simplified metabolic pathwayFigure 2.1.1c – Simplified metabolic pathway

  • Anabolism is the synthesis of complex molecules from simpler molecules. This involves the formation of macromolecules from monomers by condensation reactions. 

Figure 2.1.1d – Condensation reactions build molecules and release water. Hydrolysis reactions break molecules and use water.Figure 2.1.1d – Condensation reactions build molecules and release water. Hydrolysis reactions break molecules and use water.

  • Catabolism is the breakdown of complex molecules into simpler molecules. This involves the hydrolysis of macromolecules into monomers.

Application: Urea production in living and non-living systems

  • Urea is the major by-product of protein digestion in mammals. It is a nitrogen-rich compound that is excreted in the urine.

Figure 2.1.1e – Chemical structure of urea, CO(NH2)2, also known as carbamideFigure 2.1.1e – Chemical structure of urea, CO(NH2)2, also known as carbamide

  • In living organisms, urea is produced by the liver. Some of the chemical reactions take place in the mitochondria and some of the reactions take place in the cytoplasm of cells.
  • For all the intermediate steps in the pathway, a different enzyme is required.

Figure 2.1.1f – Urea production in living organisms

  • Urea is produced industrially for use in nitrogen fertiliser. The process requires a high temperature and no enzymes.

Figure 2.1.1g – Metabolic pathwaysFigure 2.1.1g – Metabolic pathways

Essential idea

Living organisms control their composition by a complex web of chemical reactions.

Friedrich WöhlerFigure 2.1.1h – Friedrich Wöhler (1800-1882)

Nature of Science

Falsification of theories: The first artificial synthesis of urea, by Friedrich Wöhler in 1828, helped to falsify the doctrine of vitalism. Vitalism had a long history in French and German natural philosophy and was often associated with a belief in a ‘life force’. Living things were thought to be subject to different principles than non-living things. This contrasts with the mechanistic view of science dominant in the 20th century.

See spontaneous generation in 1.2.5.

TOK

Molecular biology is associated with a reductionist approach – explaining a phenomenon in terms of its component parts (i.e. chemicals). Ecology is associated with a systems approach – explaining a phenomenon in terms of the interactions of whole organisms and environments. To what extent can a systems approach be applied to molecular biology, and vice versa?