Organic chemistry forms the foundation of understanding the chemical nature of living organisms and their interactions with the environment. In horticulture, knowledge of organic compounds is essential for managing soil fertility, plant nutrition, pest control, and the synthesis of growth regulators. This chapter introduces the fundamental concepts of organic compounds, focusing on their definition and classification relevant to horticultural practices in Kenya. Understanding these concepts enables professionals to make informed decisions on the use of organic inputs and the management of plant health.

3.1 Organic compounds

Organic compounds are chemical substances primarily composed of carbon atoms bonded with hydrogen, oxygen, nitrogen, and other elements. They form the basis of all life forms and are critical in horticulture for processes such as photosynthesis, respiration, and the synthesis of essential biomolecules. Kenyan horticulturists often encounter organic compounds in fertilizers, pesticides, and plant metabolites, making it vital to grasp their nature and classifications.

3.1.1 Definition of a compound

The term "compound" in chemistry refers to a substance formed when two or more elements chemically combine in fixed proportions. Compounds have unique properties distinct from their constituent elements and can be classified broadly into organic and inorganic based on their chemical composition. Example: water (H₂O) is a compound of hydrogen and oxygen, and it behaves very differently from the two gases it is made of. A grower who irrigates a seedbed is applying a compound, while the sugars made inside the leaves are organic compounds.

Chemical composition and bonding

• Fixed Elemental Ratio: Compounds consist of elements combined in specific ratios, such as water (H₂O) with two hydrogen atoms per oxygen atom, ensuring consistent chemical properties.
• Chemical Bonds: Atoms in compounds are held together by chemical bonds such as covalent or ionic bonds; organic compounds predominantly involve covalent bonds between carbon and other atoms.
• Molecular Structure: The arrangement of atoms determines the compound's structure and properties, influencing reactivity and biological function.
• Distinct Properties: Compounds exhibit physical and chemical properties different from their individual elements, for example, methane (CH₄) is a gas, whereas carbon and hydrogen separately have different characteristics.
• Formation and Breakdown: Compounds form through chemical reactions and can be decomposed into simpler substances, a principle crucial in understanding nutrient cycles in horticulture.

Organic and inorganic compounds compared

Importance in horticultural chemistry

• Plant growth: Organic compounds such as carbohydrates and proteins influence plant growth and development.
• Fertilizers: Fertilizers contain compounds that supply essential nutrients in bioavailable forms.
• Crop protection: Pesticides and herbicides are often organic compounds designed to target specific pests or weeds.
• Soil health: Soil organic matter comprises decomposed organic compounds that improve soil structure and fertility.
• Growth regulation: Understanding compounds aids in the synthesis and application of plant growth regulators.

3.1.2 Classes of organic compounds

Organic compounds are diverse and can be grouped into classes based on functional groups and molecular structure. These classes are fundamental to horticulture as they include substances that affect plant physiology, soil health, and pest management. This unit focuses on four classes: carbohydrates, proteins, lipids and hydrocarbons. Further groups of derivatives and related compounds follow after them.

3.1.2.1 Carbohydrates

Carbohydrates are compounds of carbon, hydrogen and oxygen, usually with hydrogen and oxygen in the ratio of water, giving the general formula Cₓ(H₂O)ᵧ. Plants make them during photosynthesis and use them for energy, storage and structure. Example: a tomato plant in a greenhouse converts carbon dioxide and water into glucose in its leaves, then moves sucrose to the developing fruits, where it gives sweetness.

Photosynthesis is summarised as:

6CO₂ + 6H₂O → C₆H₁₂O₆ + 6O₂ (in the presence of light and chlorophyll)

Carbohydrates are grouped by size:

• Monosaccharides: Single sugar units such as glucose and fructose (both C₆H₁₂O₆). Glucose is the main fuel for respiration, and fructose contributes to the sweetness of ripe fruit.
• Disaccharides: Two sugar units joined together, such as sucrose (glucose plus fructose). Sucrose is the main form in which sugars are transported through the phloem to fruits, roots and growing points.
• Polysaccharides: Long chains of sugar units. Starch stores energy in potato tubers, maize grain and bean seeds, while cellulose forms the strong cell walls of stems and leaves.
• Reducing sugars: Sugars such as glucose that give a brick-red precipitate when warmed with Benedict's solution. The test shows that ripening fruit is converting starch to sugars.
• Starch test: Iodine solution turns blue-black in the presence of starch. A grower can use it on a cut unripe fruit or a leaf to show where starch is stored.

Carbohydrates also matter after harvest. Fruits and cut flowers keep respiring and using up their sugar reserves, which is why cooling and handling affect shelf life and quality.

3.1.2.2 Proteins

Proteins are large molecules built from amino acids, which contain carbon, hydrogen, oxygen and nitrogen, and sometimes sulphur. Amino acids are joined by peptide bonds (-CO-NH-) to form long chains that fold into specific shapes. Example: a kale crop that is short of nitrogen cannot make enough amino acids, so the older leaves turn pale yellow and growth slows.

• Amino acids: The building blocks of proteins, each with an amino group (-NH₂) and a carboxyl group (-COOH). Plants make them from nitrate or ammonium taken up from the soil.
• Enzymes: Proteins that speed up reactions such as photosynthesis, respiration and nitrogen assimilation. Heat or extreme pH changes their shape and stops them working, which is why very hot greenhouse conditions damage crops.
• Structural proteins: Proteins that form part of cell membranes and cell structures, supporting normal growth and repair.
• Storage proteins: Proteins held in seeds such as beans and peas, which feed the seedling during germination.
• Transport and defence proteins: Proteins that carry substances across membranes and help plants respond to stress and attack by pests and diseases.
• Nitrogen link: Because proteins contain nitrogen, nitrogen fertilisers and legume crops that fix nitrogen directly influence the protein content of leaves and seeds.

The biuret test, where copper sulphate in alkaline solution turns violet with peptide bonds, is used to show that protein is present.

3.1.2.3 Lipids

Lipids are a group of compounds that do not dissolve in water but dissolve in organic solvents such as ethanol and ether. They include fats, oils, waxes and phospholipids. Example: avocado fruits store large amounts of oil, and the wax layer on the skin of many fruits and leaves reduces water loss during storage and transport.

• Fats and oils: Esters formed from glycerol and three fatty acids. Oils are liquid at room temperature and mostly contain unsaturated fatty acids, while fats are more solid and mostly contain saturated fatty acids.
• Waxes: Esters of fatty acids with long-chain alcohols. They form the cuticle on leaves and fruits, which protects against water loss, and against some infections.
• Phospholipids: Molecules with a water-loving head and water-hating tails. They form the double layer of cell membranes that controls what enters and leaves cells.
• Energy storage: Lipids store more than twice the energy per gram of carbohydrates. Seeds such as sunflower and groundnut store energy as oil for germination.
• Steroids and related lipids: Compounds such as sterols that help maintain membrane structure and act as starting materials for some plant hormones.

Lipids can be recognised by the emulsion test: a sample shaken with ethanol and then poured into water gives a cloudy white emulsion.

3.1.2.4 Hydrocarbons

Hydrocarbons are organic compounds made of carbon and hydrogen only. They form the backbone of more complex organic molecules and are grouped by the type of bonds between carbon atoms. In horticulture they are less common as plant constituents but appear as fuels, solvents and the base of many synthetic pesticides and herbicides.

• Alkanes: Saturated hydrocarbons with only single bonds and the general formula CₙH₂ₙ₊₂. Methane (CH₄) is released when wet organic waste decays without air, and propane and butane are used as fuel in nursery heaters.
• Alkenes: Unsaturated hydrocarbons with a carbon-carbon double bond and the general formula CₙH₂ₙ. Ethene (C₂H₄) is the gas released by ripening fruit, and it speeds up ripening and leaf fall.
• Alkynes: Hydrocarbons with a carbon-carbon triple bond and the general formula CₙH₂ₙ₋₂. Ethyne (C₂H₂) is the simplest example and is burned in gas cutting and welding.
• Cycloalkanes: Saturated hydrocarbons with carbon atoms joined in a ring, such as cyclohexane (C₆H₁₂).
• Aromatic hydrocarbons: Compounds based on the benzene ring (C₆H₆). Their ring structure is found in many synthetic pesticides and in plant phenolic compounds.
• Mixtures from petroleum: Diesel and petrol powering pumps and tractors are mixtures of hydrocarbons, and refined paraffinic oils are used as horticultural spray oils against soft-bodied pests.

Hydrocarbons burn in air to give carbon dioxide and water. Example: methane burns as follows:

CH₄ + 2O₂ → CO₂ + 2H₂O

Derivatives of hydrocarbons and functional groups

Hydrocarbon derivatives are compounds formed when one or more hydrogen atoms in a hydrocarbon are replaced by other atoms or groups of atoms, such as halogens, oxygen, or nitrogen. These groups, called functional groups, decide how the compound behaves. They are widely used in the formulation of agrochemicals and plant growth regulators.

• Halogenated Hydrocarbons: These compounds contain halogen atoms (chlorine, bromine, etc.) in place of hydrogen. Organochlorine pesticides such as DDT were widely used in the past but are now banned or restricted in many countries because they persist in the environment.
• Alcohols: Contain one or more hydroxyl (-OH) groups. Ethanol is used as a disinfectant for tools and benches in nurseries and as a solvent in agrochemical formulations.
• Carboxylic Acids: Characterised by the carboxyl (-COOH) group. Citric acid in citrus fruits influences flavour and preservation, and acetic acid in vinegar can be used to acidify water.
• Esters: Formed from the reaction of an acid with an alcohol. Esters are responsible for many fruit and flower aromas, for example ethyl butanoate, which smells of pineapple, and they help attract pollinators.
• Amines and Amides: Nitrogen-containing groups found in amino acids, proteins and some synthetic agrochemicals. Certain amide herbicides are used to control weeds in maize without harming the crop.

Nucleic acids and phenolic compounds

Two more groups of plant biomolecules are important in horticulture, although they are not covered as separate classes above.

• Nucleic Acids: DNA and RNA store genetic information and control protein synthesis, influencing plant traits and breeding. Research stations use DNA-based methods when selecting disease-resistant tomato varieties.
• Phenolic Compounds: These include flavonoids and tannins, which protect plants against pests and diseases and contribute to colour. Flavonoids in leafy vegetables act as antioxidants, adding to their nutritional value.

Synthetic organic compounds in horticulture

• Pesticides: Many are synthetic organic compounds designed to control pests, for example, organophosphates.
• Herbicides: Synthetic chemicals that target unwanted plants by interfering with specific biochemical pathways.
• Plant Growth Regulators: Synthetic auxins and gibberellins used to modify plant growth and development, for example to encourage rooting of cuttings.
• Fungicides: Organic compounds that inhibit fungal growth, protecting crops from diseases.
• Soil Amendments: Organic polymers and chelating agents improve nutrient availability and soil structure.

Chapter Summary

This chapter explored the fundamental concepts of organic compounds, beginning with the definition of a compound and progressing to the major classes of organic compounds such as carbohydrates, proteins, lipids, and hydrocarbons. It then examined the physical properties of these compounds, including color, hardness, mass, and solubility, highlighting how these attributes influence their behavior and applications. The chemical properties discussed encompassed pH, chemical stability, radioactivity, flammability, and heat of combustion, providing insight into the reactivity and safety considerations of organic substances. The chapter also addressed the purification of synthesized compounds, emphasizing the importance of obtaining pure substances for accurate results and effective use. Additionally, it outlined the practical uses of purified compounds in various industries. Finally, the chapter covered the necessary materials and procedures for carrying out the purification process, ensuring that learners understand both the theoretical and practical aspects of organic chemistry.