Chemistry Revision & Glossary

Here are some revision materials about simple chemistry (terminologies, chemical structure and reaction mechanism). If you already have a high school degree in chemistry or beyond, you can ignore this page.

1.) Acid: Chemical substance that turn litmus paper from blue to red. Acid produces free hydrogen ion (or proton, H+) in the presence of water. Acid reacts with an alkali to produce a salt, which is neutral.

 

2.) Alkali (also called base): Chemical substance that turn litmus paper from red to blue. Alkali accepts hydrogen ion from acid to produce salt. Alkali can be ionic like hydroxide, or molecules with non-bonding electron pair like ammonia.

3.) Alkaloid: Naturally occurring substance containing one or more nitrogen atoms which produce strong biological actions on human body. Most but not all alkaloids are alkaline.

 

4.) Aromatic: Chemical substance with planar structure (flat in 3D space), often existing as a ring containing consecutive double bonds. Aromaticity confers chemical stability to a molecule.

 

5.) Atom: The smallest particle of a chemical element which makes up physical substances.

 

6.) Bond: Attraction between atoms, ions or molecules that enables the formation of chemical substances. A bond formed between atoms by sharing of electrons is called covalent bond. A bond that is formed between positive and negative ions is called ionic bond. Both covalent and ionic bonds are very strong. Breaking of chemical bond absorbs energy,  formation of chemical bond releases energy.

 

7.) Catalyst: Chemical substance that increases the speed of a chemical reaction but is not consumed or destroyed during the reaction.

 

8.) Compound: A substance that is made up of two or more chemically bonded atoms.

 

9.) Crystal: A solid containing orderly arranged atoms, ions, or molecules.

 

8.) Electron: Subatomic particle with negative charge. Electrons usually exist in pairs, which form a covalent bond. Lone pair of electrons confer chemical reactivity like basicity and nucleophilicity. Substance with single unpaired electron are called free radicals, they are extremely reactive.

 

9.) Electrophile: Atom or molecule which tends to accept electron pair. Electrophiles usually have positive or partial positive charge.

 

10.) Functional group: A part of a molecule (moiety) that confersspecific chemical reactivity. See Figure 1.

 

11.) Hydrogen bond: Attraction between hydrogen atom of a molecule with fluorine, oxygen, or nitrogen atom of another molecule. Hydrogen bond is generally weaker than covalent and ionic bonds.

 

12.) Hydrolysis: Chemical breakdown of a molecule (bond) by action of water, usually catalysed by acid, alkali or enzymes.

 

13.) Ion: A particle that carries net charge after gaining or losing one or more electrons. Positive ions are called cations; negative ions are called anions.

 

14.) Isomer: Chemical compounds with identical molecular formula (and mass), but different structure or spatial arrangement.

 

15.) Mole: The standard unit of amount of a substance, equal to the quantity containing as many elementary units as there are atoms in 0.012 kg of carbon-12.

16.) Molar concentration (Molarity): number of moles of substance/ Liter of solvent.

17.) Molecule: Atoms that bond together to produce a neutral chemical compound. A molecule is the smallest unit of a chemical substance that can take part in  chemical reaction.

18.) Nucleophile: Atom or molecule which tends donate electron pairs. Nucleophiles usually have  negative or partial negative charge.

 

19.) Oxidation: Chemical reaction in which a reactant loses one or more electrons, or gains oxygen atoms, or loses hydrogen atoms. 

 

20.) Oxidising agent: Chemical substance that causes oxidation of reactant. Oxidising agent is itself reduced in the process.

 

21.) pH: A logarithmic scale of 1 – 14  used to express the acidity or alkalinity of chemical substance. At room temperature, neutral substance like water has a pH of 7; substance with pH < 7 are increasingly acidic; substance with pH > 7 are increasing alkaline.

 

22.) Proton: Subatomic particle with net positive charge. Sometimes used to describe a free hydrogen ion without electron (H⁺).

23.) Protonation: Addition of a hydrogen ion H⁺ or proton into a chemical compound.

 

24.) Solution: A homogeneous mixture of dissolved substance (solute) in a solvent.

 

25.) Stereoisomer: Chemical substance with identical chemical formula but different spatial arrangement. Stereoisomers (in solution) which can rotate polarised light are called optical isomers. Optical isomers which are mirror images of one another are called enantiomers. A 1:1 mixture of enantiomers which does not rotate polarise light is called a racemic mixture. Stereoisomers which are not mirror images are called diastereomers.

 

26.) Valence electron: The outer most electrons of an atom. Only valence electrons take part in chemical reaction.

Figure 1: List of important chemical functional groups.

Many toxins contain chemical functional groups which determine their reactivity, stability and biological effect on human body. Some crucial functional groups of selected plant toxins are listed below.

Plant toxin	Main functional group(s)
Alkaloid	Amine
Amino acid (non-protein), toxalbumins (protein)	Amide (peptide bond)
Carboxyatractyloside	Carboxylic acid
Cyanogenic glycoside	Nitrile + ether (glycosidic bond)
Phorbol	Ester
Saponin	Alcohol + ether + alicyclic alkane
Steroid	Alicyclic alkane (backbone of 4 merged alkane rings)
Urushiol	Alkane + phenol (phenyl + alcohol)
Vanilloid (resiniferatoxin)	Phenol + alicyclic alkane
Sulfur containing (allicin, defensin, glucosinolate)	Thiol

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Figure 2: Basics of chemical structure.

If you are not familiar with organic chemistry, the method we draw complicated organic chemical structure is called the 'chicken wire notation'. Carbon and hydrogen atoms are implicitly hidden within the 'zig zag' formula. Every intersect (including open end) represents a new carbon atom, with implicitly bonded hydrogen atoms. Ions are denoted with their individual charge (+ or -).

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Figure 3: Basics of atoms and bonding.

All atoms of carbon, oxygen and nitrogen must have 8 valence electrons to become stable. This is called the Octet Rule. Hence, carbon with its original 4 valence electrons tend to form 4 bonds to attain stability.  Note: a single bond means two electrons are being shared. An oxygen atom already has 6 valence electrons, thus it requires two more bonds to be formed. In analogy, nitrogen atom needs 3 more bonds to attain 8 valence electrons. A hydrogen atom, being the simplest needs only one bond to attain total of 2 valence electrons. Cchemical bonds can be formed between same elements or with others. Deviation to the Octer Rule will give rise to ions (ammonium, oxide etc), radicals or neutral species with balanced formal charges (like nitronium , N-oxide etc). 

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Figure 4: Basic organic chemical reaction mechanisms.

Understanding organic reaction mechanisms allows you to understand how toxins function at the molecular level. Curly arrows in Figure 4 indicate the movement of electron pair. Follow the coloured arrows (electron pair) and examine the corresponding bonds which are formed or broken. Figure 4 shows some of the most important organic reactions that we will encounter. They include acid base neutralisation, proton transfer, nucleophilic addition/attack, elimination, and hydrolysis.

End of class and I will see you in the next phytochemistry articles!