CH1 - Chemical elements and biological compounds

Macronutrients, which are needed in small concentrations.

Micronutrients, which are needed in minute concentrations.

Magnesium is an important constituent of chlorophyll, it's essential for photosynthesis. Plants that lack magnesium in their soil can't make chlorophyll so their leaves are yellow, chlorosis. Growth is often stunted from lack of glucose. Magnesium is also required in mammals for their bones.

Iron is a constituent of haemoglobin, it transports oxygen in red blood cells. A human diet which lacks iron may lead to anaemia.

Phosphate ions are used for making nucleotides, e.g. ATP. They're also a constituent of phospholipids, found in biological membranes.

Calcium is an important structural component of bones and teeth in mammals. It's also a component of plant cell walls, which provides strength.

The water molecule is a dipole (a polar molecule with a positive and a negative charge separated by a small distance). It has a positively charged end, hydrogen, and also a negatively charged end, oxygen. Water is also polar as the charges are separated. Hydrogen bonds can form between these charges. Individually hydrogen bonds are weak, but collectively they make water molecules difficult to separate, giving water many differnet properties.

• A solvent - as water molecules are dipoles they attract charged particles, these then dissolve in water so chemical reactions can occur. It acts as a transport medium. 
• A metabolite - it's used in many biochemical reactions as a reactant.
• High specific heat capacity - a large amount of heat energy is required to raise the temperature. This is due to the hydrogen bonds between the water molecules, restricting their movement, resisting an increase in kinetic energy, declining the increase in temperature.
• High latent heat of vaporisation - a lot of heat energy is required to change it from a liquid to a vapour.
• Cohesion - water molecules attrach each other, forming hydrogen bonds. Indiviudally they're weak, but collectively they stick together in a lattice, this is called cohestion. 
• High surface tension - at ordinary temperatures it has the highest surface tension of any liquid except mercury. 
• High density - water is denser than air. As a habitat for aquatic organisms it provides support and buoyancy. It has a maximum density of 4 degrees celsius. Ice is less dense than water as hydrogen bonds hold the molecules further apart than they are in the liquid. Ice floats in water. It's a good insulator and prevents large bodies of water losing heat and freezing completely, organisms beneath it survive.
• Transparent - allows light to pass through in order for photosynthesis to occur.

Carbohydrates are organic compounds which contain carbon, hydrogen and oxygen. The basic unit is a monosaccharide - an indiviudal sugar molecule - two monosaccharides combine to form a discaccharide, many combine to form a polysaccharide.

Monosaccharides are small organic molecules, they're the building blocks for the larger carbohydrates. 

They have the general formula (CH2O)n. The names are determined by the number of carbon atoms (n) present. 

• Triose sugar - three carbon atoms
• Pentose sugar - five carbon atoms
• Hexose sugar - six carbon atoms

The OH group is facing downstairs on alpha glucose but upwards on beta glucose. Everything else is in the same position.

• A source of energy in respiration, carbon-hydrogen and carbon-carbon bonds are broken to release energy, transferred into ATP.
• Building blocks for larger molecules.
• Intermediates in reactions.
• Constituents of nucleotides, deoxyribose in DNA, ribose in RNA, ATP in ADP.

Disaccharides are composed of two monosaccharide units bonded together with the formation of a glycosidic bond and the elimination of water (a condensation reaction).

Above is the condensation of glucose and fructose to make sucrose.

Above is the hydrolysis of sucrose to make the component monomers, glucose and fructose.

Maltose is made up of glucose + glucose and it's in germinating seeds.

Sucrose is made up of glucose + fructose and has a role in transport in phloem of flowering plants.

Lactose is made up of glucose + galactose and is in mammalian milk.

Benedicts Test.

• Put a sample in a test tube
• Add an equal volume of Benedict's reagent
• Heat the sample
• Observe the colour chance, if it changes from blue to brick red a reducing sugar is present.

Non-reducing sugars, e.g. sucrose, give a negative result when reacted with Benedict's reagent due to where the glycosidic bond forms, not enabling sucrose to break down into its component monomers.

• Put a sample in a test tube
• Heat it with hydrochloric acid to break it into component monomers
• Add Alkali 
• Add Benedict's reagent
• Heat the sample
• Observe the colour chance, if it changes from blue to brick red a reducing sugar is present.

Polysaccharides are large, complex polymers. They're formed from many monosaccharide units linked by glycosidic bonds. The monosaccharide units are combined by a condensation reaction.

Glucose is soluble in water, it would increase the concentration of the cell by drawing water in by osmosis. By converting glucose into starch the problem is avoided as starch is insoluble, having no osmotic effect, can't diffuse out of the cell, is compact, and carries a lot of energy in its C-H and C-C bonds.

The main store of glucose for plants. Starch grains (amlyplasts) are found in seeds and storage organs such as potato tubers. It's made of a-glucose molecules bonded together in two different ways making two polymers, amylose and amylopectin.

• Amylose is a linear, unbrached molecule with a-1,4 glycosidic bonds forming between C1 on one glucose monomer, and C4 on the adjacent one. This is repeated, forming a chain which coils into a helix.
• Amylopectin also has chains of glucose monomers joined with a,1-4 glycosidic bonds. They're cross-linked with a-1,6 glycosidic bonds that fit inside the amylose. When a glycosidic bond forms between C1 on one glucose and C6 on another, a side branch is seen, a-1,4 glycosidic bonds continue on from the start of the branch.

Iodine-potassium iodide test.

• Peel off the skin of the sample (vegetable)
• Place a few drops of iodine solution onto food sample
• Observe, if the colour goes from orange-brown to blue-black then starch is present.

The main storage product in animals. It's very similar to amylopectin but its branchers are shorter and more frequent. It has a-1,4 and a-1,6 bonds. Glycogen molecules have shorter a,1-4 linked chains.

A structural polysaccharide. It makes cell walls strong and it's the most abundant organic molecule on earth. I

t consists of many long, parallel chains of b-glucose units. The glucose monomers are joined by B-1,4 glycosidic bonds and the b-link rotates adjacent molecules by 180 degrees. This allows hydrogen bonds to form between OH groups of adjacent parallel chains, contributing to cellulose structural stability.

Between 60-70 cellulose molecules become tightly cross-linked, forming bundles called microfibrils. Microfibrils are held in bundles called fibres. A cell wall has several layers of fribes, running parallel within a layer but at an angle to adjacent layers. The laminated structure contributes to strength of the cell wall. Cellulose fibres are freely permeable, there's spaces between the fibres. 

A structural polysaccharide, found in the exoskeleton of insects and in fungal cell walls. It resembles cellulose with its long chains of b-1,4 linked monomers. It has amino acids added to it to form a heterpolysaccharide. It's strong, waterproof and lightweight. The monomers are rotated through 1800 degrees in relation to their neighbours, the long parallel chains are cross-linked to each other by hydrogen bonds, forming microfibrils.

They contain carbon, hydrogen and oxygen. They are no-polar copounds and are insolubl in water, but dissolve in organic solvents such as propanone and alcohol.

They're formed by the combination of one glycerol molecule and htree molecules of fatty acids. The glycerol molecule in a lipid is always the same, the fatty acid component varies. The fatty acids join to the glycerol by condensation reactions, three molecules of water are removed and ester bonds are formed between the glycerol and fatty acids.

An oxygen atom joining two atoms, one of which is a carbon atom attached by a double bond to another oxygen atom.

A special type of lipid. One end is soluble in water, one end isn't. They have a polar head which is hydrophillic, it interacts with water. (they have oxygen atoms) They also have non-polar tails which are hydrophobic, they don't interact with what. (don't have any oxygen atoms)

Waxes are lipids, they melt above 45 degrees celcius. They have a waterproofing role in animals, in the insect exoskeleton, and plants, in the leaf's cuticle.

The hydrocarbon chain only has single carbon-carbon bonds, all carbon atoms are linked to the maximum possible number of hydrogen atoms. They're saturated with hydrogen atoms. They're solid at room temperature.

Unsaturated fatty acids consist of one or more double carbon-carbon bond in the hydrocarbon chain. They aren't saturated with the maximum number of hydrogen atoms. They are liquid at room temperature.

Phospholipids:

• In biological membranes.
• Electrical insulation (myelin sheath surrounding the axons of nerve cells)

Triglycerides:

• Energy reserves in plants and animals
• Thermal insulation 
• Protection (fat stored around delicate organs)
• Metabolic water

Waxes:

• Waterproofing (waxes reduce water loss, e.g. in the insect exoskeleton and in the cuticle of plants)

The emulsion test.

• The sample is mixed with an equal volume of absolute ethonal
• Distilled water is then added, then shake it
• An emulsion (cloudy-white) will be formed if lipids are present

• Heart disease is caused by fatty deposits in the coronary arteries, and also high blood pressure.
• If the diet is high in saturated fats, low-density lipoproteins (LDL) build up, causing harm as stated above.
• If the diet is high in unsaturated fats, the body makes more high-density lipoprotein (HDL) which carries harmful fats away to the liver for disposal.

Proteins contain carbon, hydrogen, oxygen and also nitrogen. Many contain sulphur and some contain phosphorus.

Polymers, made of monomers, amino acids. Chains of amino acids are called polypeptides. About 20 different amino acids are used to make up proteins, there's thousands of different proteins with their shapes being determined by the specific sequence of amino acids in the chain.

They all have the same basic structure, attached to a central carbon atom.

• An amino group (NH2) - basic 
• A carboxyl group (COOH) - acidic 
• A hydrogen atom
• The R group (differs from amino acid to amino acid)

The amino group of one amino acid reacts with the carboxyl group of another, eliminating water. The bond that's formed from the condensation reaction is a peptide bond, resulting in a dipeptide. 

The chemical bond formed by a condensation reaction between the amino group of one amino acid and the carboxyl group of another.

The order of amino acids in a polypeptide chain. Polypeptides have up to 20 different types of amino acid which can be joined in any number, order of combination making numerous possibilities. The primary structure is determined by the base sequence on one strand of the DNA molecule.

The shape that the polypeptide forms as a result of hydrogen bonding between the =O on -CO groups and the -H on -NH groups in the peptide bonds along the shape. Causes the polypeptide to be twisted into a 3D shape. There's two shapes, the spiral shape is the a-helix and a less common arrangement is the b-pleated sheet. e.g. keratin, a-helix and fibroin, b-pleated sheet.

The a-helix of secondary structure can be folded and twisted, giving a more complex, 3D structure. The shape is maintained by hydrogen bonds, ionic bonds, disulhpide bonds and hydrophobic interactions. 

Two or more polypeptides combine to become functional. For example, the insulin molecule has two chains. However, they may also be associated with non-protein groups, forming large, complex molecules such as haemoglobin.

They have long, thin molecules and their shape makes them insoluble in water, so they have structural functions, e.g. in bone.

The polypeptides are in parallel chains/sheets, with many cross-links forming long fibres, e.g. keratin, the protein in hair. 

Fibrous proteins are strong and tough. Collagen is a fibrous protein, providing the strength and toughness needed in tendons. a single fibre, tropocollagen, consists of three identical polypeptide chains twisted around each other, like a rope. The three chains are linked by hydrogen bonds, making the molecule very stable.

Globular proteins are compact and folded into spherical molecules, making them soluble in water so they have many different functions. They can be enzymes, antibodies, plasma proteins and hormones. 

Haemoglobin is a globular protein, consisting of four polypeptide chains which are folded, at the cnetre of each of which is the iron-containing group, haem.