Chapter at a glance
- Living tissues and earth’s crust contain the same elements, but living matter shows higher relative abundance of carbon and hydrogen.
- Chemical analysis of living tissue yields an acid-soluble pool (micromolecules, <1000 Da) and an acid-insoluble fraction (macromolecules).
- Primary metabolites (amino acids, sugars, nucleotides, etc.) perform identifiable roles in normal physiology; secondary metabolites (alkaloids, flavonoids, rubber, etc.) have ecological or human-use value but undefined host roles.
- Biomacromolecules (proteins, nucleic acids, polysaccharides) are polymers; lipids (<800 Da) appear in the macromolecular fraction because they form membrane vesicles.
- Proteins are heteropolymers of 20 α-amino acids linked by peptide bonds; they exhibit four levels of structural organisation.
- Polysaccharides are homopolymers (cellulose, starch, glycogen) or complex polymers (chitin) serving structural or storage roles.
- Nucleic acids are polynucleotides; DNA contains deoxyribose and thymine, RNA contains ribose and uracil.
- Enzymes (mostly proteins) lower activation energy via active-site catalysis; activity is affected by temperature, pH and substrate concentration.
Definitions and laws
- α-amino acids: “organic compounds containing an amino group and an acidic group as substituents on the same carbon i.e., the α-carbon.”
- Zwitterionic form: the ionizable structure adopted by amino acids in solution at certain pH.
- Lipids: “generally water insoluble.”
- Nucleosides: nitrogen bases attached to a sugar.
- Nucleotides: nucleosides with an esterified phosphate group.
- Primary metabolites: compounds with identifiable functions in normal physiological processes.
- Secondary metabolites: compounds other than primary metabolites found in plant, fungal and microbial cells (e.g., alkaloids, rubber).
- Biomacromolecules: “chemical compounds found in living organisms … with molecular weights in the range of ten thousand daltons and above.”
- Micromolecules / biomolecules: compounds with molecular weights less than one thousand dalton.
- Proteins: “polypeptides … linear chains of amino acids linked by peptide bonds.”
- Polysaccharides: “long chains of sugars … threads containing different monosaccharides as building blocks.”
- Reducing end / non-reducing end: right and left ends, respectively, of a polysaccharide chain such as glycogen.
- Primary structure of protein: “the sequence of amino acids i.e., the positional information in a protein.”
- Secondary structure: portions of the polypeptide chain folded into helices or β-pleated sheets.
- Tertiary structure: the three-dimensional folding of the entire polypeptide chain.
- Quaternary structure: “the manner in which … individual folded polypeptides or subunits are arranged with respect to each other.”
- Active site: “a crevice or pocket into which the substrate fits.”
- Activation energy: “the difference in average energy content of ‘S’ from that of this transition state.”
- Rate of reaction: “rate = δP/δt” (amount of product formed per unit time).
- Competitive inhibitor: an inhibitor that “closely resembles the substrate in its molecular structure” and competes for the active site.
Important diagrams and activities
- Figure 9.1 – Diagrammatic representation of small molecular weight organic compounds (amino acids, sugars, fatty acids, nucleotides) in living tissues.
- Figure 9.2 – Portion of glycogen showing reducing and non-reducing ends and branching.
- Figure 9.3 – Four levels of protein structure (primary, secondary, tertiary, quaternary) with α-helix, β-pleated sheet, disulphide and hydrogen bonds.
- Figure 9.4 – Energy profile showing activation energy with and without enzyme, transition state, substrate and product.
- Figure 9.5 – Graphs of enzyme activity versus pH, temperature and substrate concentration (Vmax, Km).
Common misconceptions and exam pitfalls
- Lipids are macromolecules yet they are not polymers; they separate with the acid-insoluble fraction only because membrane fragments form vesicles.
- Only 20 amino acids occur in proteins; the R-group determines their classification (acidic, basic, neutral, aromatic).
- Starch gives blue colour with I₂ because of its helical structure; cellulose does not.
- Enzymes are not consumed; they form transient ES and EP complexes and are regenerated.
- Optimum temperature/pH is not the same as the temperature at which the enzyme is most stable; high temperature denatures the protein.
- Competitive inhibition is reversible and overcome by increasing substrate concentration; it is not the same as allosteric regulation (not mentioned in chapter).
- RuBisCO is the most abundant protein in the biosphere; collagen is the most abundant in the animal world.
Formula sheet
No mathematical formulae are given in the chapter. The only quantitative expression supplied is:
rate = δP/δt