🦠 Biomolecules Study Notes

9.1 Analysing Chemical Composition

What is a living body made of? Grind any tissue, treat it with acid, and the chemicals separate into two pools — this is how we inventory the molecules of life.

The two pools

When tissue is ground in trichloroacetic acid and filtered:

• Acid-soluble pool — the micromolecules (small biomolecules): amino acids, nucleotides, sugars, etc., with molecular weights roughly 18–800 Da.
• Acid-insoluble pool — the macromolecules: proteins, nucleic acids, polysaccharides and lipids (molecular weights in the thousands+).

(Lipids, though their building blocks are small, end up in the insoluble pool because they form large membrane structures.) Burning tissue drives off C, H, O (as gases) and leaves 'ash' — the inorganic elements (Ca, Mg, etc.).

Key point: C, H, O and N are much higher in living organisms than in the Earth's crust. The most abundant molecule overall is water.

Primary vs secondary metabolites

Secondary metabolites (e.g., morphine, codeine, rubber, gums, vinblastin, curcumin) are especially common in plants and microbes.

9.2 Amino Acids & Proteins

Amino acids

The building blocks of proteins. Each has a central carbon bearing an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen, and a variable R group (side chain). There are 20 standard amino acids.

• R = H → glycine; R = CH₃ → alanine; R = CH₂OH → serine.
• By R group they are acidic (e.g., glutamic acid), basic (lysine), neutral, or aromatic (e.g., tyrosine).
• Amino acids are ionisable; the ionic form depends on pH. In solution they exist as a zwitterion (simultaneously +NH₃ and –COO⁻).

Proteins — heteropolymers of amino acids

Amino acids join by a peptide bond (between the –COOH of one and the –NH₂ of the next) to form a polypeptide. A protein is a heteropolymer (many different amino acids), not a homopolymer.

Levels of protein structure

• Primary — the order of amino acids (the first is the N-terminal, the last the C-terminal).
• Secondary — local folding into helices/sheets.
• Tertiary — the overall 3-D shape (like a hollow woollen ball) needed for biological activity.
• Quaternary — assembly of more than one polypeptide. Haemoglobin has 4 subunits: 2α + 2β.

Proteins do nearly everything (Table 9.5): enzymes catalyse, antibodies fight pathogens, receptors sense signals, transporters (like GLUT-4) move glucose, collagen gives structure, and many act as hormones.

9.3 Carbohydrates & Lipids

Carbohydrates (sugars)

• Monosaccharides — simple sugars: glucose, fructose, ribose (single units).
• Disaccharides / oligosaccharides — a few units joined, e.g., sucrose, maltose, lactose.
• Polysaccharides — long chains joined by glycosidic bonds. The right end of a chain is the reducing end, the left the non-reducing end.

Lipids

• Generally water-insoluble; may be simple fatty acids or complex.
• A fatty acid has a carboxyl group attached to an R group (a hydrocarbon chain). Palmitic acid has 16 carbons (incl. the carboxyl C); arachidonic acid has 20 carbons.
• Saturated fatty acids have no C=C double bonds; unsaturated ones have one or more.
• Glycerol is trihydroxy propane. Fatty acids esterified to glycerol give monoglycerides, diglycerides and triglycerides (= fats and oils; oils have lower melting points, e.g., gingelly oil, and stay liquid in winter).
• Phospholipids contain phosphorus and a phosphorylated group; lecithin (in cell membranes) is an example.

9.4 Nucleic Acids

Nucleic acids (DNA and RNA) are the macromolecules of inheritance, built from nucleotides.

Building a nucleotide

• Purines (double ring): Adenine (A) and Guanine (G).
• Pyrimidines (single ring): Cytosine (C), Uracil (U) and Thymine (T).
• Sugar = ribose in RNA, deoxyribose in DNA. RNA uses U; DNA uses T.
• Nucleotides link through a phosphodiester bond (between phosphate and sugars) to form a chain.

The Watson–Crick double helix (B-DNA)

• Two strands run antiparallel (opposite directions), coiled into a right-handed helix.
• Base pairing: A pairs with T via 2 hydrogen bonds; G pairs with C via 3 hydrogen bonds.
• Dimensions: pitch = 34 Å (3.4 nm); rise per base pair = 3.4 Å; therefore about 10 base pairs per turn (each step rotates ~36°).

9.5 Metabolism & the Living State

Every biomolecule is constantly being made and broken. The sum of all these chemical conversions is metabolism, and no biomolecule ever exists in isolation.

Two directions of metabolism

• Anabolic pathways build complex molecules from simpler ones (e.g., amino acids → protein) and consume energy.
• Catabolic pathways break molecules down (e.g., glucose → lactic acid) and release energy.
• Energy released in catabolism is trapped as the 'energy currency' ATP; it powers anabolism, heat, movement and other work.

Glycolysis — a metabolic pathway

Metabolites are converted through such pathways by enzymes; intermediates flow in a steady line from substrate to product.

The living state = a dynamic steady state

The living state is a non-equilibrium steady state able to perform work — metabolite concentrations stay roughly constant not because nothing happens, but because reactions flow continuously. At equilibrium, no work can be done, so reaching equilibrium would mean death. Metabolism and the living state are therefore inseparable.

9.6 Enzymes

Almost all enzymes are proteins (a few RNAs called ribozymes also act as enzymes). Enzymes are biological catalysts that speed up reactions enormously.

How enzymes work

• An enzyme has an active site — a pocket the substrate fits into. The substrate (S) binds to give an enzyme–substrate (ES) complex, passes through a transition state, and is released as product (P): E + S → ES → EP → E + P.
• Enzymes work by lowering the activation energy of a reaction (they do not change the overall energy difference).

Factors affecting enzyme activity

Temperature and pH (each enzyme has an optimum; extremes denature it), and substrate concentration (rate rises then plateaus at the maximum velocity, V_max).

Inhibition

A competitive inhibitor resembles the substrate and competes for the active site. Classic example: malonate inhibits succinic dehydrogenase by mimicking its substrate succinate.

Six classes of enzymes

Cofactors

Many enzymes need a non-protein cofactor; the protein part alone is the apoenzyme. Three kinds of cofactor:

• Prosthetic groups — tightly bound (e.g., haem in peroxidase/catalase).
• Coenzymes — loosely bound organic helpers, often vitamin-derived: NAD and NADP contain niacin.
• Metal ions — e.g., zinc in carboxypeptidase.

Carbonic anhydrase is among the fastest enzymes known, illustrating how dramatically catalysts accelerate reactions.