Why Cooks Rub Raw Papaya Paste Into Tough Meat

Sugars fuel the cell and build plant walls, fats store energy and form membranes, nucleic acids carry instructions, and enzymes make every reaction happen fast enough to keep life going.

Each has a simple building block that repeats — and small changes in those blocks give very different properties.

This part covers carbohydrates, lipids, nucleic acids, and enzymes.

Monosaccharides are single sugar units, oligosaccharides are short chains of a few, and polysaccharides are long chains; starch and glycogen store glucose, cellulose builds plant cell walls, and chitin, made of amino-sugars, builds insect exoskeletons and fungal walls.

Sugar sizes:

- Monosaccharides — glucose, fructose, ribose
- Oligosaccharides — two to about ten units, such as sucrose (glucose + fructose), lactose and maltose
- Polysaccharides — long chains joined by glycosidic bonds; the right end is reducing and the left end non-reducing

Polysaccharides compared:

- Starch — glucose units; food store in plants; forms helices that trap iodine, giving a blue-black colour
- Glycogen — glucose units, more branched; food store in animals and fungi
- Cellulose — glucose units in straight chains without helices, so it does not hold iodine; forms plant cell walls; cotton and paper are cellulose
- Inulin — a polymer of fructose
- Chitin — built from amino-sugars; forms the exoskeleton of arthropods and fungal cell walls

An everyday example. A drop of iodine on a cut potato turns it blue-black, showing its starch.

The substance. Humans cannot digest cellulose even though it is made of glucose, because its units are linked in a way our enzymes cannot break.

Lipids are generally water-insoluble substances that include fatty acids, glycerides formed from fatty acids and glycerol, and phospholipids that build membranes; they are small molecules, but they collect in the acid-insoluble fraction because they form membranes that break into insoluble vesicles.

Fatty acids. A carboxyl group attached to an R group of carbon chains:

- Palmitic acid — $16$ carbons including the carboxyl carbon
- Arachidonic acid — $20$ carbons
- Saturated — no double bonds; unsaturated — one or more C=C double bonds

Glycerol is trihydroxypropane. Fatty acids esterified with it form monoglycerides, diglycerides and triglycerides — fats and oils, which differ in melting point.

Phospholipids. Lipids containing phosphorus and a phosphorylated group, such as lecithin, are major parts of cell membranes; neural tissue has lipids with more complex structures.

An everyday example. Coconut oil often turns solid on a cold winter morning, while gingelly (til) oil stays liquid, because of their different fatty acids.

The substance. Lipids are not polymers — they are not built from long chains of repeating monomer units.

A nucleotide is made of a nitrogenous base, a pentose sugar and a phosphate group; DNA uses deoxyribose sugar and the bases adenine, guanine, cytosine and thymine and is usually double-stranded, while RNA uses ribose and replaces thymine with uracil and is usually single-stranded.

Building blocks:

- Nucleoside — base + sugar: adenosine, guanosine, thymidine, uridine, cytidine
- Nucleotide — base + sugar + phosphate: adenylic acid, guanylic acid, thymidylic acid, uridylic acid, cytidylic acid

Bases:

- Purines — adenine, guanine
- Pyrimidines — cytosine, thymine, uracil

DNA versus RNA:

- Sugar: deoxyribose versus ribose
- Bases: A, G, C, T versus A, G, C, U
- Strands: usually double versus usually single

Nucleotides link into chains through phosphodiester bonds.

Worked example — identify the nucleic acid. A strand containing uracil and ribose is RNA; a double helix containing thymine is DNA.

An everyday example. In a school activity, mashed banana mixed with salt, detergent and cold alcohol releases white strands — that is DNA made visible.

The substance. Deoxyribose has one oxygen atom fewer than ribose, which is exactly what "deoxy" means.

Enzymes are mostly proteins that bind substrates at an active site to form an enzyme-substrate complex, lowering the activation energy so reactions run far faster; their rate depends on temperature, pH and substrate concentration, and they are grouped into six classes, with many needing cofactors.

How they act:

$$\text{E}+\text{S}\rightleftharpoons \text{ES}\to \text{EP}\to \text{E}+\text{P}$$

The substrate fits into the active site, is converted to product, and the enzyme is released unchanged. Some RNA molecules, ribozymes, also act as enzymes.

Factors affecting activity:

- Temperature and pH — each enzyme works best at an optimum; low temperature slows it reversibly, high temperature denatures it
- Substrate concentration — velocity rises and then levels off at a maximum once all active sites are busy
- Inhibitors — a competitive inhibitor resembles the substrate, as malonate does for succinic dehydrogenase

Six classes: oxidoreductases (dehydrogenases), transferases, hydrolases, lyases, isomerases, ligases.

Cofactors:

- Prosthetic groups — tightly bound, such as haem in peroxidase and catalase
- Coenzymes — loosely bound, often from vitamins, such as NAD containing niacin
- Metal ions — such as zinc for carboxypeptidase

The protein part alone is the apoenzyme.

Worked example — read the curve. If doubling the substrate no longer raises the rate, every enzyme molecule is already busy — the enzyme is saturated.

An everyday example. Raw papaya paste rubbed into meat makes it tender, because an enzyme in papaya breaks down tough proteins.

The substance. Enzymes speed up reactions but do not change the final equilibrium.