Carbon, hydrogen, oxygen and nitrogen are the four most abundant elements in living organisms, and account for more than 99% of atoms found in living things. Carbon is present in all organic molecules and carbon atoms can join together to form chains or ring structures.
Polymers and Macromolecules
Macro refers to something that is large, and so macromolecules simply means large molecules, and there are only three types - polysaccharides, proteins (polypeptides) and nucleic acids (polynucleotides) (poly means 'many'). Macromolecules are such because they are made of many repeating subunits that are connected to each other.
All carbohydrates contain carbon, hydrogen and oxygen, and have hydrogen to oxygen present in the ratio 2:1 respectively.
Monosaccharides are sugars and are soluble - meaning that they dissolve in water, forming sweet solutions. Mono refers to one and saccharide means sugar - so monosaccharide means single sugar. Monosaccharides are classified according to the number of carbon atoms in each molecule - trioses (3 carbons), pentoses(5 carbons) and hexoses(6 carbons).
The structure of the most common monosaccharide, glucose, in both the alpha (on the left) and beta (on the right) isomer (two forms of the same chemical are known as isomers): .
An important note on the structure of both pentoses and hexoses is that the chain of carbon atoms is long enough to close up on itself and form a stable ring structure, as seen in the picture above.
Roles of Monosaccharides
Simple sugars, such as glucose, are often used in biological organisms as a source of energy for respiration - the carbon hydrogen bonds within them are easily broken down to release a great deal of energy which in turn helps make ATP from ADP and phosphate. Secondly, monosaccharides can be used as building blocks for larger molecules (polysaccharides).
If you look at the above image of glucose, you'll see a hydroxl (-OH) group on the top right of the image, highlighted in red. When two glucose molecules come together, the two hydroxyl groups line up along side each other: one combines with a hydrogen atom from the other to form water, in turn forming an oxygen bridge across the two molecules, bonding them and creating a disaccharide- this bond is called a glycosidic bond. The reaction is known as condensation, and the reverse reaction - the addition of water is a hydrolysis reaction, which breaks down di/polysaccharides into their original monosaccharides.
Formation of a glycosidic bond: 
As we saw before, monosaccharides joined by glycosidic bonds in condensation reaction become disaccharides, but if more than two monosaccharides are joined together it is known as a polysaccharide. It is important to note that polysaccharides are not sugars and examples of polysaccharides include starch, glycogen and cellulose, all polysaccharides made from glucose.
The reason glucose is converted into these polysaccharides is storage - left free in cells, glucose will dissolve and affect the osmotic potential of the cell, making it too concentrated. A condensation reaction to convert it to a polysaccharide (compact, inert and insoluble) - and when glucose is required again, the storage molecule (starch in plants, glycogen in animals) can be quickly hydrolysed in an enzyme controlled reaction.
Animal Storage Molecules
Glycogen  is the primary storage molecule in animals. Glycogen, as you can see in the above picture, is made of many 1,4 linked alpha-glucose molecules (1,4 linked means that they are linked by carbon atoms of 1 & 4 of successive glucose units). These chains branch out to the side, and the branches are formed by 1,6 linkages. The chains also coil up into helical structures, making their final structure more compact (useful for storage).
Plant Storage Molecules
Starch is a mixture of two substances, amylose and amylopectin. Amylopectin is very similar to glycogen in that it is made of many 1,4 linked alpha-glucose molecules, and branches via 1,6 linkages - the main difference is that amylopectin branches less than glycogen. Amylose, on the other hand is a very long, unbranching chain of several thousand 1,4 linked glucose molecules, and as in glycogen and amylopectin, these chains curve to coil up into helical structures for compactness. Amylose chains are usually longer than amylopectin.
Cellulose is the other important polysaccharide - and is the most abundant organic molecule on earth. This is partially due to its structural role in cell walls and partially due to its slow rate of breakdown. The main difference between cellulose and the other two storage molecules you've seen is that cellulose is a polymer of beta-glucose, whereas the other two are from alpha-glucose. If you remember, the two isomers of glucose are different only in their location of the -OH and -HO group, on carbon atoms 1 and 4, respectively. See this picture  for more details. This means that to form glycosidic bonds, subsequent glucose molecules must be at 180degrees to each other, or in other words, each must be upside down to the other to allow the -OH and -HO groups to bond. You can see the molecular structure of cellulose here: 
These bonds result in a strong molecules because the hydrogen atoms form hydrogen bonds with oxygen atoms in the same glucose molecule and other neighboring glucose molecules. While these hydrogen bonds are individually weak, due to the large numbers of -OH groups, collectively they develop massive strength. Also, between 60-70 cellulose molecules become tightly cross linked to form bundles called microfibrils, which are in turn held together in bundles called fibres by further hydrogen bonding, making the entire structure even stronger.
Cellulose in Cell Walls
Cellulose comprises around 20-40% of the average cell wall, with other molecules helping to crosslink the cellulose fibres. This is because cellulose fibres have a tensile strength almost equivalent to that of steel, meaning that it is very difficult to break cellulose, and this very strong cell wall is what allows plant cells to withstand large osmotic pressures - without it, the cell would burst when in a dilute solution. This allowance for high pressures help provide support for the plant by making the tissues rigid and are responsible for cell expansion during growth. Despite all the strength that cellulose has, it is also (very usefully), freely permeable.
The most common type of lipids that you'll be expected to know about are triglycerides, usually known as fats and oils.
All triglycerides are made from a glycerol 'head' and 3 fatty acid 'tails'. Glycerol is a type of alcohol. The fatty acids are organic molecules and all have a -COOH group attached to a hydrocarbon tail. Fatty acids are attached to glycerol by a condensation reaction.
One of their important properties is that they are insoluble in water - but soluble in certain organic solvents, including ether, ethanol and chloroform. This is because of the hydrocarbon tails of the fatty acids - which basically means that the tail is only carbon combined with hydrogen, creating no uneven distribution of electrical charge (unlike water molecules, which are polar). This means that they cannot mix freely with water molecules, and so are hydrophobic and non-polar.
Their roles are usually as fantastic energy reserves - as you'll see in the coming paragraphs they are incredibly rich in carbon-hydrogen bonds ready to be oxidised for energy. The same mass of lipid will have more energy than the same mass of carbohydrate. Fat also provides buoyancy in the form of blubber for sea mammals - whilst providing insulation, as it does for all mammals. They can also, in unusual circumstances be used as a metabolic source of water - oxidising them for energy converts them to carbon dioxide and then water. This is useful for animals living in the desert that do not have much or any water.
Saturated and Unsaturated
Unsaturated fatty acids  are known as such as due to the kink (see picture) caused by the C-C=C-C bond (the C=C part is important), that it does not contain the maximum possible amount of hydrogen, and these form unsaturated lipids. The double bond (C=C) makes the fatty acid melt more easy, for example, most oils are unsaturated (and are usually liquid at room temperature) - it also makes them easier to digest. More than one kink is known as polyunsaturated, one kink is monounsaturated.
Saturated fatty acids on the other hand, , as you can see in the picture, contain the maximum amount of hydrocarbons and have no kinks.
Animal lipids are usually saturated and thus are fats, whereas plant lipids are usually unsaturated, for example olive oil and sunflower oil - usually oils.
These are a special type of lipid, usually found in the plasma membrane of cells (see Chapter 1, among others). Each molecule has one end that is soluble in water, and the other which is not. This is because one of the fatty acids is replaced by a phosphate group which is polar and can dissolve in water - making it hydrophilic. The two remaining tails are still hydrophobic but the head is hydrophilic.
Proteins have many important functions within organisms - and more than 50% of dry mass of most cells is protein. Their functions can include;
- All enzymes are proteins
- Antibodies are proteins
- Essential component of cell membranes (glycoproteins, transport proteins etc.)
- Structural support in the form of collagen
Despite the range of functions listed above (which is by no means exhaustive), all proteins are made from only 20 different amino acids. All amino acids have the same basic structure - a central carbon atom which is bonded to an 'amine' group, -NH2 (on the left in the picture), and a carboxylic acid group, -COOH (on the right in the picture. The third bond to the carbon group is always a hydrogen atom (in purple). The remaining 'R' group, in yellow, is the fourth and variable group of atoms bonded to the central carbon. This is what makes amino acids differ from each other - and it is these R groups that change the shape of protein molecules and thus their functions. See picture: 
The Peptide Bond
A peptide bond is one that is formed after two amino acids join each other in a condensation reaction - one loses a hydroxyl group from the carboxylic acid group (see above picture), which leaves free the carbon atom from the first amino acid to bond with the nitrogen atom of the second - the peptide bond. This molecule is now known as a dipeptide - but can be expanded upoun with additional condensation reactions to form a polypeptide.
The primary structure of a protein simply refers to the type of amino acids in the polypeptide chains and the sequence inwhich they are joined. As you can guess, with 20 different amino acids, and many many different combination, there are many different possible primary structures.
The secondary structure of a protein is the effect that amino acids have on a polypeptide chain even if they are not directly next to each other, for example the α-helix we saw earlier, that is due to the attraction of the oxygen of the -CO group of one amino acid and the hydrogen of the -NH group of the amino acid anywhere else in the chain, forming a hydrogen bond. Another shape is the β-pleated sheet, which is a looser, but straighter shape. Sometimes there is no regular arrangement - it depends on the amino acids present.
The tertiary structure of a protein is the way in which a protein coils up to form a precise 3D shape. This can be because of the hydrogen bonds after the coiling or folding in the secondary structures, but other bonds such as a disulphide bonds can form between cysteine amino acids. Ionic bonds occur between positive and negatively charged 'R' groups. Hydrophobic parts of the polypeptide situate themselves in the centre of the polypeptide chain (away from water) and hydrophilic parts of the polypeptire situate themselves on the outside of the polypeptide chain (next to water). All affecting the tertiary structure of the polypeptide.
The quaternary structure is known as the association of different polypeptide chains within one protein. The same bonds as in the tertiary structure hold together the different polypeptide chains (hydrogen bonds, disulfide bridges and ionic bonds). Two examples of a proteins with a quaternary structure are haemoglobin and collagen.
Globular and Fibrous Proteins
A globular protein is simply one that appears to curl up into a ball - this is usually so that the proteins non-polar, hydrophobic R groups point into the centre of the molecule, making them water soluble, since water clusters around their outward facing hydrophilic groups, but water cannot get into the molecule. Enzymes are always globular proteins and thus globular proteins are involved in metabolic reactions. However, proteins that do not curl up into a ball, but form long strands are known as fibrous proteins, and are mostly insoluble. Keratin and collagen are examples of this.
An example of a globular protein that you must know about is haemoglobin. It is a pigment that carries oxygen and is found in red blood cells. It has four poly peptide chains, two α chains, two β chains, and is almost spherical. Each polypeptide chain contains a haem group, and is important and permanent part of a protein molecule that is not made of amino acids and is known as the prosthetic group. Each of these haem group contains an iron ion, Fe2+, and one oxygen molecule can bind with each iron ion. A complete haemoglobin molecule has four haem groups, and thus can carry four oxygen molecules at a time. The haem group is also responsible for the colour of haemoglobin - if haemoglobin is combined with oxygen (oxyhaemoglobin), it is bright red, else it is purple.
As with all globular proteins, the hydrophilic R groups pointing out maintain it's solubility in water - however this can be affect by a disease known as sickle cell anaemia. In this case, one amino acid of one of the β polypeptide chains, in a hydrophilic section is replaced which a different amino acid, the original being a polar amino acid, the replacement being non-polar. As you will see in the water section, this will cause problems. It makes haemoglobin much less soluble, and is unpleasant and dangerous in anyone whose haemoglobin is all of this faulty type.
As previously mentioned, collagen is a fibrous protein that is found in skin, tendons, bones, teeth, cartilage and importantly in the walls of blood vessels and it is a generally important structural protein in many animals. The reason collagen is so strong is that it consists of three polypeptide chain, each in the shape of a helix, wound together to form a three stranded 'rope'. Nearly every amino acid in the chain is glycine, which is small, and allows the three strands to lie close together and form a tight coil, and hydrogen bonds bond the strands.
The cross-links between the collagen(the complete 3 stranded collagen molecule) form fibres, providing it with tremendous tensile strength (withstanding large pulling forces).
Water is a major component of every cell, usually forming 70-95% of the mass of the cell, and the human body is around 60% water. If it were not for it being a dipole (see 'Dipoles and Hydrogen Bonds' below), water would be a gas at normal earth temperatures.
Water is a good solvent for polar molecules and ions, because water collects around their hydrophilic edges and separates them. This is what happens in the process of dissolving - and so the chemical is free to move about and react with other chemicals within water. Non-polar molecules are insoluble in water and are pushed together by water if surrounded by it, for example, lipids.
It's solvency is also useful when water is used as a transport medium - in the blood, lymphatic, excretory and digestive systems of animals, and in the vascular tissues of plants.
The hydrogen bonds formed within water mean that it requires a relatively large amount of energy to change the temperature of water, meaning that large bodies of water are slow to change temperature and as a result are more stable habitats. This is useful in the animal body as there is a high proportion of water, and so a stable body temperature is easier to attain. Also useful in the body is that the process of evaporation transfers a large amount of energy and this is why sweating is effective in cooling the body.
A large amount of energy is required to convert water to ice and thus water is less likely to freeze. Also, ice less dense than water and thus when parts of a river, for example, freeze - the ice floats to the top and acts as an insulator for the rest of the water. This means that aquatic organisms can still survive since the whole river is unlikely to freeze.
Water molecules, partially because of their polarity, have a tendency to stick together, a property known as cohesion. This provides a high surface tension which allows very light animals to use the surface of the water as a habitat. It also means that water can move in long unbroken columns through vascular tissue in plants and is an important property in cells.
Dipoles and Hydrogen Bonds
Atoms in molecules are held together because they share electrons with each other. A shared pair of electrons forms a covalent bond - for example in a water molecule, two hydrogen atoms each share a pair of electrons with an oxygen atom. however, as this  picture shows, there is an uneven distribution of charge, with oxygen getting more than its fair share and receiving a small negative charge, and both of the hydrogen atoms receiving less than their fair share, resulting in a positive charge.
This uneven distribution of charge is called a dipole. In water, the negative charges of the oxygen is attracted to the positive charges of the hydrogen atoms, and the attraction is called a hydrogen bond - weaker than a covalent bond but enough to have a significant effect. Molecules with dipole groups (-OH, -C=0 or >N-H), are known as polar as they are attracted to water molecules (since water is also a dipole molecule). These polar molecules are hydrophilic and tend to be soluble in water. Those molecules that are non-polar are not attracted to water and are hydrophobic.
Information that does not fit into the other sections, or is best grouped.
These are the important food tests - tests that tell you whether certain molecules are present in solutions.
|Testing for||Using what||Method||Results|
|Protein||Biurets reagent||Add biurets reagent to the solution.||A purple colour indicates protein is present|
|Lipids||Ethanol - the emulsion test||Add ethanol to the solution, and shake, then add water.||If a cloudy and white solution occurs between the ethanol and water, lipids are present.|
|Starch||Iodine solution||Add the iodine solution to the substance suspected of containing starch||A blue black colour is quickly produced if it comes into contact with starch|
|Reducing sugar||Benedict's reagent||Add benedict's reagent to the solution you are testing and heat it in a water bath.||If reducing sugars are present, the substance will turn to brick red.|
|Non-reducing sugar||Benedict's reagent||Heat the sugar solution with dilute hydrochloric acid, then add sodium hydroxide to neutralise it, and then perform the test for reducing sugars.||If reducing sugars are present, the substance will turn to brick red.|
An additional note regarding benedict's test - it requires excess benedicts reagent to react with all the present sugar. For the non-reducing sugar test, the reason the sugar solution is heated with dilute hydrocholric acid is to hydrolyse any glycosidic bonds present, to make the sugar a reducing one, so that it may reduce benedicts and cause the colour change. However, benedict's only works in a alkaline environment and thus sodium hydroxide must be added to neutralise it.
Molecules are not the only type of substance that is important for the structure and metabolism of living organisms - they also need a wide variety of ions (see the below table). Ions are formed from individual atoms that have gained or lost one or more electrons and are therefore charged negatively or positively.
|Ion||Functions in organisms|
|Calcium, Ca2+||Important structural component in bones and teeth (when in a compound with phosphate). Calcium ions are used in transmission of electrical impulses across synapses. Also used during the contraction of muscles.|
|Chloride, Cl-||Together with sodium, maintains concentration gradient in loop of Henle (kidney). Also help to balance positive charge of other ions in and around cells.|
|Iron, Fe2+||Haemoglobin's prosthetic haem groups, it is the ion to which oxygen binds.|
|Magnesium, Mg2+||Photosynthesis - chlorophyll molecules contain magnesium.|
|Nitrate, NO3-||Plants use nitrogen from nitrate to make amino acids and nucleotides.|
|Phosphate, PO43-||Used for making nucleotides, including ATP. Compounded with calcium to make calcium phosphate.|
|Potassium, K+||Transmission of nerve impulses in animals. In plants, turgidity of guard cells and thus are also involved in opening and closing of stomata.|
|Sodium, Na+||Nerve impulse transmission, and also maintain concentration gradient in the loop of Henle (kidney).|