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Chemistry basics

An element is a substance that cannot be broken down into a simpler substance by ordinary chemical reactions. There are 92 naturally occurring elements in the known universe, 22 essential to life, but only 6 (C,H,O,N,S, and P) constitute most of what we call living matter. Carbon, oxygen, hydrogen and nitrogen make up 96% of living matter.  The rest are trace elements, which are those required only in extremely small quantities.

The smallest possible amount of an element is an atom. Atoms consist of even smaller particles, the most stable of which are the subatomic protons, neutrons, and electrons. Atoms with different numbers of protons are different elements; that is, an element is a substance composed of atoms having an identical number of protons in each nucleus. For example, an atom with one proton and one electron is elemental hydrogen(H).  A helium (He) atom has two protons, two neutrons, and two electrons.


Atomic weight is the average mass of an atom of an element

 

Sub-atomic particle
Charge Mass(Da)
Neutron0
1
Proton +1
1
Electron-1
0

 Structure of an atom


Only electrons are directly involved in the chemical reactions between elements.  The electrons of an atom have potential energy because of their position in relation to the nucleus.  The negatively charged electrons are attracted to the positively charged nucleus (proton); the more distant the electrons are from the nucleus, the greater their potential energy.  The different states of potential energy for electrons in an atom are called energy levels, orbits, or electron shells.  To move to a shell further from the nucleus, the electron must absorb energy, and to go closer it must lose energy.  Each shell has a maximum number of electrons it can hold.

Chemical properties depend on the number of valence electrons, that is the number in the outermost shell.  An atom with a complete or full valence shell is unreactive; i.e, will not readily interact with other atoms it encounters.  Atoms with incomplete valence shells with unpaired electrons are chemically reactive.


Molecules

Molecules consist of 2 or more bonded atoms.  Atoms combine by chemical bonding to form molecules with each partner completing its valence shell.  Atoms do this by sharing or completely transferring valence electrons, usually resulting in the atoms staying close together, held by attractions called chemical bonds.

Covalent bond

A covalent bond is the sharing of a pair of valence electrons by two atoms and represents the strongest form of bonding.  Each atom sharing electrons must have a certain number of covalent bonds formed for the atom to have its full complement of valence electrons.  The bonding capacity is called valence. Hydrogen forms one bond, oxygen forms two, nitrogen usually forms three, and carbon forms four bonds. The electrons can be equally shared, nonpolar covalent bonds; or unequally shared, polar covalent bond where the electron spends more time around one atom rather than another.  This gives one atom a slight negative charge.  For example, Oxygen is one of the most electronegative of the 92 elements, in a covalent bond between O and H the shared electrons are pulled around the oxygen atom more than the hydrogen.  This unequal sharing in water molecules gives the oxygen a slight negative charge and the hydrogens a small positive charge. This is very important for life.

Ionic bond

An ionic bond is formed when 2 atoms differ so electronegativly that one or more electrons are actually transfered from one atom to another.  The recipient atom becomes negatively charged.  A charged atom or molecule is called an ion.  When the charge is positive, the ion is called a cation.  A negatively charged ion is called an anion.  Because of their opposite charges, cations and anions attract each other in what is called an ionic bond.  Ionic compounds are called salts.  Ionic bonding's strength depends on its environment, in water it is weak.  There is no distinct line between covalent and ionic bonding, they are opposite extremes in a range of situations where atoms share electrons.  Several types of weak bonds enable the molecules of the cell to associate.

Hydrogen bond

Among the various types of weak chemical bonds, hydrogen bonds are so important to life that they need special mention.  Hydrogen bonds are relatively weak bonds between a weakly positive H and a weakly negative polar molecule.  Hydrogen bonds, ionic bonds, and other weak bonds form not only between molecules, but also between regions of a single molecule, such as a large protein.  Although this bonding is weak, their cumulative effect is to reinforce the 3D shape of large molecules.

Molecular shape

A molecules biological function is related to its shape.  Larger molecules that make up living matter have complex shapes which is the basis for how most molecules of life recognise and respond to one another.



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