A chemical bond is the energy or force which holds two or more atoms together in a molecule or compound. It is an incredibly commonly used term, and its very important that the basics behind bonds are understood, if reactions from real life are to be understood. Simply understanding how a collection of substances reacts to form another set of substance requires some knowledge about bonds.
Although there are lots of different types of chemical bond, whenever two substances react together, the bonds must be broken in order to form the products. Lets say that we have chemical A and chemical B. A is a compound which has three atoms in it (e.g. water), and there are two bonds connecting the three atoms. B is a compound with eight atoms in it, and there are seven bonds. The products of the reaction will contain atoms from both chemicals, so all the bonds need to be broken in order to mix these atoms up. To break bonds requires energy - if you imagine a couple of magnets, it requires energy to pull them apart. When the products of the reaction are formed, (e.g. C and D), bonds are formed between the atoms of each chemical. To make bonds releases energy - if you imagine, again, a couple of magnets, when they click together, energy is released in the form of sound.
This is all relatively simple - just appreciating that if you tie two things together, you need to untie them to separate them. However, just like tying things together, where there are different knots that can be used, in chemistry there are a variety of different types of bonds that connect atoms.
A covalent bond is where two atoms share a pair of electrons. Every atom 'wants' to fill its outer shell and it does this by getting an electron from a different atom. However, say you had two fluorine atoms. They have seven electrons in their outer shell, so they each need one more. Well, if fluorine 1 takes an electron from fluorine 2, that will sort fluorine 1 out but it'll leave fluorine 2 with six electrons in its outer shell - which is obviously a bit unfair!!
What happens instead is that the fluorine atoms, being nice to each other as they are, decide to share two electrons - one from each of them (in a co-ordinate or dative bond, one of the atoms contributes both the electrons for the covalent bond. This obviously means that one of the atoms - the one donating - has a complete outer shell with a spare pair of electrons that isn't involved in bonds with anything else; the other atom has a gap for two electrons, e.g. something with six electrons in its outer shell). Despite the fact that each atom has its own electron cloud, each atom also feels like it has a full outer shell because of the shared electrons. All electrons are still spinning round each atom, but because of the sharing, the atoms are bonded together in order to maintain the sense of a full outer shell.
The formation of covalent bonds is often written as dot and cross diagrams. These show where the electrons come from that form the covalent bond, and show only the electrons in the outer shell. In the animation to the right, two fluorine atoms are represented, each with one space for electrons - one vacant orbital. When they come together, they share one electron from each atom, and it is this pair that is the covalent bond.
It is probably significant to note that all elements which are in a gas state at room temperature exist as two atoms joined together. If a chemical has spaces for two electrons (two vacant orbitals), it could form covalent bonds with two other atoms. This is what happens in water, where two hydrogen atoms are joined to one oxygen atom. If two chemicals each require two electrons to fill their outer shell, they could share two electrons, forming a double bond, such as that found in the carboxyl group. A double bond works in the same way as a single covalent bond, except that it is more reactive (because the atoms involved would rather share their electrons with different atoms), it is more electron-dense (there are more electrons concentrated in the same area) and there is no rotation. Usually atoms can rotate around despite being joined, but if there are two bonds, it restricts this movement, and the atoms are kept still in relation to each other.
An ionic bond is the bond which results from the electrostatic interaction between postive and negative ions. That's basically a posh way of saying that if a positive and negative ion get together, they'll attract each other, and form a bond. The fact that they're positive and negative is what causes the attraction (as 'opposites attract').
Basically, like in a covalent bond, the bond results from the use of electrons - this time, to form ions. One atom, the more electronegative one, will need only a small number of electrons to complete its outer shell (e.g. chlorine, which needs just one!) while the other one (usually a metal, e.g. sodium) will have only a small number of electrons in its outer shell, which it will want to loose. Therefore the more electronegative atom will take the electron(s) from the other one; it will have more electrons than protons, giving it an overall ('net') negative charge - it becomes a negative ion, or anion. The atom which lost electrons has more protons than electrons; it has a net positive charge, and becomes a positive ion or cation.
The positive and negative charges attract each other, but because each positive ion will attract all the negative charges around, it will get negative ions around it. And because each negative ion will attract all the positive charges around it, it will get positive ions around it. This leads to an alternate cation-anion-cation-anion structure, and huge, huge structures - you don't just get the two-atom molecules seen with covalent bonds! Instead, enormous (on a minute scale - these atoms are still far too small to see!) three-dimensional structures with positive and negative charges forming bonds with each other are formed; so many attractions between ions makes these very, very strong!
If an atom has a large nucleus (i.e. has lots of protons in it), and the outer electrons are relatively close (e.g. when the shells are reaching their capacity, and are ready to move onto the next shell), it is said to be electronegative. Because of the large charge of the nucleus and relatively small size of the atom as a whole, it will be more likely to attract electrons. These electrons will effectively give it an ever-so-slightly negative charge, also known as 'delta-negative', hence the term 'electronegative'. (See also the section in 'The Atom')
Due to the high electronegativity values of certain elements (e.g. oxygen, nitrogen, fluorine etc.), bonds are formed with between these electronegative elements and hydrogen. If the hydrogen is bonded to an electronegative atom, the positive charge from the electronegative atom's nucleus will be inclined to attract the single electron orbitting the hydrogen atom, leaving it exposed.
This hydrogen is said to be given a 'delta-positive' charge. A different electronegative atom may have a slightly negative charge from attracting the electrons from a different atom. Therefore a highly directional bond will form between this slightly positive hydrogen atom and slightly negative electronegative atom.
Though individually weak, these bonds are collectively strong, and are frequently found in proteins due to the large number of oxygen and nitrogen atoms present in amino acids. The bonds are usually found between the hydrogen atom in an amino group bonded to the oxygen atom in a carboxyl group, but could be found in any combination involving one hydrogen and two of the electronegative atoms.
A peptide bond is the chemical bond formed between two amino acids. It is formed between the carbon of the carboxyl group on one amino acid, and the nitrogen of the amino group on the other amino acid. The oxgyen and hydrogen from the carboxyl group leave to bond with a hydrogen from the amino group, forming water, hence the reaction is known as a condensation reaction. This enables the carbon and nitrogen to bond, with the two amino acids forming a dipeptide. The two amino acids are split by a process called hydrolysis, as water must be introduced to split the molecule and replace the oxygen and hydrogens on their respective groups.
Most bonds in organic molecules can rotate freely; however the amino acids in a peptide bond are usually kept in a certain orientation in relation to each other. Oxygen is ever so slightly more electronegative than nitrogen, and will attract electrons slightly better - it may be considered to have a slightly negative charge. Nitrogen, accordingly, might be considered slightly positive - relatively speaking. There is a partial sharing of a pair of electrons between the oxygen and the nitrogen, so that there is effectively a double bond both between the oxygen and the carbon, and the nitrogen and the carbon. The peptide bond has a partial double bond character, so the carbon and nitrogen atoms cannot rotate relative to each other. It is usual for the oxygen atom bonded to the carbon to be on the opposite side of the molecule to the hydrogen atom bonded to the nitrogen, as shown. Due to the double bond character, these will usually stay on opposite sides.
Phi and Psi are the names given to the bonds which connect the peptide bond with the central (alpha) carbon of each amino acid. This means that the carbon which used to be in the carboxyl group is connected to the central carbon of its amino acid via a psi bond, and the nitrogen is connected to the central cabon atom of its amino acid via a phi bond. These bonds can adopt many different angles, and it is the repeating of the backbone angles phi and psi that gives a protein its secondary structure.