3.3: Chemistry of Life
To understand life, a basic knowledge of chemistry is needed. This includes atoms (and its components like protons, neutrons and electrons), atomic weight, isotopes, elements, the periodic table, chemical bonds (ionic, covalent, and hydrogen), valence, molecules, and molecular weight:
- Atoms
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The smallest unit of matter undividable by chemical means. An atom is made up of two main parts: a nucleus vibrating in the centre, and a virtual cloud of electrons spinning around in zones at different distances from the nucleus (not to be confused with the cell nuclei). When atoms interact, its less like the bumping of balls and more a matter of attraction and repulsion; at atomic levels, mass is much less an important consideration than charges, which are electrical: positive, negative, or neutral (balanced).
- Protons
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Stable elementary particles having the smallest known positive charge, found in the nuclei of all elements. The proton mass is less than that of a neutron. A proton is the nucleus of the light hydrogen atom, i.e., the hydrogen ion.
- Neutrons
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Like protons but neutral charge and also located in the nucleus.
- Radioactive
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decay occurs in unstable atomic nuclei—that is, ones that do not have enough binding energy to hold the nucleus together due to an excess of either protons or neutrons.
- Electrons
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determine how atoms will interact. Located on the outside of the nucleus known as the outer shell and has a negative charge that determines what type of change it has.
- Atomic weight
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is the average of the masses of naturally-occurring isotopes.
- Isotopes
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each of two or more forms of the same element that contain equal numbers of protons but different numbers of neutrons.
- Periodic table of elements
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The periodic table we use today is based on the one devised and published by Dmitri Mendeleev in 1869. The periodic table of the chemical elements displays the organization of matter.
- Chemical bonds
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are attractive forces between the atoms.
- Valence
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A typical number of chemical bonds in this element. For example, nitrogen (N) has valence 3 and therefore usually makes three bonds.
- Molecules
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Molecules form when two or more atoms form chemical bonds with each other.
- Molecular weight
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calculated as a sum of atomic weights.
- Covalent bonds
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When two atoms bind in one molecule, there are two variants possible. Non-polar bond is when electrons are equally shared between atoms. Polar bond is when one of atoms attract electrons more than another, and therefore becomes partly negative while the second—partly positive.
- Ionic bonds
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Ionic bonding is the complete transfer of some electron(s) between atoms and is a type of chemical bond that generates two oppositely charged ions.
It is essential to know that protons have a charge of \(+1\) , neutrons have no charge, and electrons have a charge of \(-1\) . The atomic weight is equal to the weight of protons and neutrons. Isotopes have the same number of protons but different number of neutrons; some isotopes are unstable (radioactive).
One of the most outstanding molecules is water. Theoretically, water should boil at much lower temperature, but it boils at 100 \(^\circ\) C just because of the hydrogen bonds sealing water molecules. These bonds arise because a water molecule is polar : hydrogens are slightly positively charged, and oxygen is slightly negatively charged.
Another important concept related to water is acidity . If in a solution of water, the molecule takes out proton (H \(^+\) ), it is an acid . One example of this would be hydrochloric acid (HCl) which dissociates into H \(^+\) and Cl \(^-\) . If the molecule takes out OH \(^-\) (hydroxide ion), this is a base . An example of this would be sodium hydroxide (NaOH) which dissociates into Na \(^+\) and hydroxide ion.
To plan chemical reactions properly, we need to know about molar mass and molar concentration . Molar mass is a gram equivalent of molecular mass. This means that (for example) the molecular mass of salt (NaCl) is \(23 + 35\) , which equals 58. Consequently, one mole of salt is 58 grams. One mole of any matter (of molecular structure) always contains \(6.02214078 \times 10^{23}\) molecules ( Avogadro’s number ).
The density of a dissolved substance is the concentration . If in 1 liter of distilled water, 58 grams of salt are diluted, we have 1M (one molar) concentration of salt. Concentration will not change if we take any amount of this liquid (spoon, drop, or half liter).
Depending on the concentration of protons in a substance, a solution can be very acidic. The acidity of a solution can be determined via pH. For example, if the concentration of protons is 0.1 M ( \(1 \times 10^{-1}\) , which 0.1 grams of protons in 1 liter of water), this is an extremely acidic solution. The pH of it is just 1 (the negative logarithm, or negative degree of ten of protons concentration). Another example is distilled water. The concentration of protons there equals \(1 \times 10^{-7}\) M, and therefore pH of distilled water is 7. Distilled water is much less acidic because water molecules dissociate rarely.
When two or more carbon atoms are connected, they form a carbon skeleton . All organic molecules are made of some organic skeleton. Apart from C, elements participate in organic molecules (biogenic elements) are H, O, N, P, and S. These six elements make four types of biomolecules: (1) lipids—hydrophobic organic molecules which do not easily dissolve in water; (2) carbohydrates or sugars, such as glucose (raisins contain lots of glucose) and fructose (honey); by definition, carbohydrates have multiple \(-\) OH group, there are also polymeric carbohydrates (polysaccharides) like cellulose and starch; (3) amino acids (components of proteins) which always contain N, C, O and H; and (4) nucleotides combined from carbon cycle with nitrogen (heterocycle), sugar, and phosphoric acid; polymeric nucleotides are nucleic acids such as DNA and RNA.
On the next page is the most important thing for everyone who need to learn chemistry (and yes, you need to): periodic table. It was invented by Dmitry Mendeleev in 1869 and updated since, mostly by adding newly discovered and/or synthesized elements. Note that Roman numerals were added to standard table to show numbers of main groups .