Molecular Bonding
Condensation Reactions – a reaction that joins two molecules and H2O is removed
Hydrogen Bond – A weak interaction between a slightly positively charged atom and a slightly negatively charged atom e.g. between the bases of DNA, between the O(-) of one H2O molecule and the H(+) of another
Hydrolysis – the splitting of a molecule using water
Monomer – a small molecule that binds to many other identical molecules to form a polymer
Polymer – a large molecule made up of many repeating units called monomers
Covalent bonds – the sharing of electrons between atoms
Carbohydrates
Carbohydrates (saccharides) are molecular compounds made from just three elements: carbon, hydrogen and oxygen. Monosaccharides and disaccharides are relatively small molecules.
Carbohydrates are:
- a source of energy for the body e.g. glucose and a store of energy, e.g. starch in plants
- building blocks for polysaccharides (giant carbohydrates), e.g. cellulose in plants and glycogen in the human body
- components of other molecules eg DNA, RNA, glycolipids, glycoproteins, ATP
Monosaccharides
- These are the simplest carbohydrates
- They are a source of energy
- They are soluble in water but insoluble in non-polar solvents
- They have a backbone of single bonded carbon atoms
- hexose have 6 carbon atoms
- pentose have 5 carbon atoms
alpha isomer of glucose
– a hexose sugar and an energy source, a component of starch and glycogen (also energy stores)
beta isomer of glucose
– a hexose sugar and energy source, a component in cellulose in plant cell walls
Deoxyribose– a pentose sugar, a component of deoxyribonucleic acid
Ribose
– a pentose sugar, a component in ribonucleic acid
Disaccharides
Polysaccharides
Amylose is found in plants. It is a long chain of alpha glucose molecules and has glyosidic bonds between carbons 1 – 4. It coils into a spiral shape because of its hydrogen bond. The hydroxyl group on carbon 2 is at the centre of the spiral. This means it is less soluble than it would have been. It is important that Amylose is insoluble because if it dissolved in the cell cytoplasm it would lower the water potential of the cell causing it to take on water and become turgid or burst. It is used for energy storage.
Amylopectin is also found in plants and is a long chain of alpha glucose molecules and has glyosidic bonds between carbons 1 – 4. It also has branches joining carbons 1 – 6. These branches make the molecule more compact. It can also give more energy at once as the end of each branch can be snipped of by hydrolysis, whereas in amylose there are only two ends of the chain available. Both are stored within plant cells as large granules.
Acquerello rice cell containing amylose and amylopectin
Glycogen is present only in plant cells. It is branched like amylopectin but has less tendency to coil. Glyosidic bonds are formed between carbons 1 – 4 in the backbone of the molecule and between carbons 1 – 6 when the polysaccharide branches off.
It is also a good storage of energy and is present in the liver cells and muscle cells. It forms approximately 7% of the mass of the liver. It’s branches also make it a very compact storage molecule and is found in solid grains.
Cellulose
Cellulose is a plant carbohydrate used in cell walls. It is an insoluble fibrous homopolysaccharide made from long chains of beta glucose. They are straighter than other carbohydrates as the hydrogen and hydroxyl groups every other glucose molecule are inverted. The chain is strengthened by hydrogen bonds between the molecules. Hydrogen bonds are also formed between chains.60 – 70 chains bound together make a microfibril which then bundle together into a macrofibril containing around 400 microfibrils. They cross over each other in the cell wall to give high tensile strength to the cell and to the plant. This is important as plants do not have a skeleton or support structure so the plants support is based on each of its cells remaining strong and turgid. There is space between the macrofibrils so that the cell wall is permeable. It can be combined with other molecules such as lignin or cutin for waterproofing.
Bacteria cell walls are made of peptidoglycan – long polysaccharides linked with short peptide chains.
Insects and crustaceans have a hard exoskeleton made of chitin. It differs from cellulose as it has an acetylamino group on each carbon 2 instead of a hydroxyl group. However, it forms cross links which are very similar to cellulose.
Lipids
- Lipids are a group of substances that are soluble in alcohol but not water.
- They contain large amounts of carbon and hydrogen with small amounts of oxygen
- The three most important lipids in living things are: triglycerides, phospholipids and steroids.
- Lipids are macromolecules – not polymers
Triglycerides
Triglycerides are made from glycerol and three fatty acids, joined by three ester bonds between the hydroxyl groups of the glycerol and the carboxyl group of the fatty acids. This is a condensation reaction as water is produced.
Saturated fats have no C=C bonds in the molecule. Unsaturated fats do have C=C bonds. This makes unsaturated fatty acid tails bend.
Functions of triglycerides:
Energy source – they can be broken down during respiration to produce carbon dioxide and water. More water is formed in lipid respiration that in carbohydrate respiration.
Energy store – triglycerides are insoluble and therefore can be used as a store of energy. Mammals store fat in adipose cells under their skin and around organs.
Buoyancy – lipids are less dense than water so whales and aquatics can use them to stay afloat.
Insulation – adipose tissue can act as an insulator of heat just as lipids in nerve cells act as electrical insulators
Protection – Fat covers delicate organs to act as a shock absorber for our more delicate organs e.g. kidneys. The peptidoglycan cell wall is covered in a lipid rich capsule for protection.
Waterproofing – insects and leaves are covered in wax for waterproofing. Waxes are lipids formed by fatty acids and larger alcohol molecules.
Phospholipids
Phospholipids have the same structure as triglycerides except that one of the fatty acid tails is replaced with a phosphate group.
The phosphate head is hydrophilic (water loving) and the fatty acid tails are hydrophobic (water fearing).
They form micelles in water as the tails come together in the centre of a sphere in order to avoid the water.
They are amphipathic as they have a polar region at their heads and a nonpolar region between the tails. This means they are well adapted to form the plasma membrane of cells.
The plasma membrane is made up of a phospholipid bilayer, two layers of phospholipids with their tails pointing inwards.
They are fluid as the phospholipids are free to move around within the layer. They will not however, expose their tails to the water, which gives the bilayer some stability.
The bilayer is selectively permeable, meaning that it is only possible for small and non-polar molecules to diffuse into the cell. This helps control what goes in and out of the cell and keeps the cell functioning properly.
Cholesterol is a steroid alcohol. It is small and hydrophobic and fits between the tails of the phospholipids in cell membranes. It functions as a fluidity buffer, preventing the membrane from being too fluid or too stiff.
In animals it is found in the liver. Plants have a derivative called stigmasterol in their cell membranes.
The following steroid hormones are all made from cholesterol: testosterone, oestrogen and vitamin D.
Proteins
- Form structural components – e.g. muscle in animals
- Form specific shapes – e.g. enzymes, antibodies and hormones
- Constituents in cell membranes – e.g. sodium-potassium pump & carrier proteins
Amino Acids
Amino acids are the monomers that make up all proteins. There are 20 that are proteinogenic. They have an amine group, a carboxyl group, and a variable R group which acts as another chain of the molecule, different for each amino acid.
R groups vary in size, polarity, charge and interaction with water.
Almost all amino acid names end in –ine. E.g. cysteine and alanine. Unless they have acidic R groups e.g. glutamic acid.
Amino acids can also be used as buffers as they have both acidic and basic properties. This means they can be used to vary the cell’s pH. The carboxyl group acts as a H+ donor and the amino group acts as a H+ accepter.
Amino acids are joined with peptide bonds to form a polypeptide.
Peptide bonds are formed in a condensation reaction and broken during hydrolysis.
Protein structure
Primary protein structure is the number and sequence of amino acids in the chain. The order of amino acids determine the shape of the molecule.
Secondary structure is split into two alternatives:
Alpha helix – a spiral is formed with 36 amino acids per 10 turns of the helix
Beta pleated sheet – a zigzag structure with many hydrogen bonds
The tertiary structure is a specific shape held in place by several bonds. The composition of each amino acids R group heavily contributes to the overall shape.
Hydrogen bonds – these form between hydrogen atoms with a slightly positive charge and other atoms with a slightly negative charge
Ionic bonds – these form between the R groups and are the attraction of groups that have a strong positive or negative charge.
Disulphide links – a covalent bond formed between two sulphurs.
Hydrophobic/Hydrophilic interactions – R groups that are hydrophobic bend towards the inside of the chain where they can be hidden from contact with water whereas hydrophilic R groups move towards the outside of the molecule.
The quaternary structure of proteins is when there is more than one polypeptide chain to a protein. E.g. haemoglobin.
Fibrous proteins – regular repetitive sequences of amino acids that are insoluble and tend to form structural fibres e.g. collagen, keratin and elastin
- Collagen provides mechanical support such as in artery walls to prevent bursting and in tendons that connect muscle and bone. This is required for movement. Bones are also made of collagen which is then reinforced with calcium phosphate to make them hard. It is also used to make cartilage and connective tissues.
- Keratin is a very strong molecule as it has many disulphide bridges. It is found in nails, hair, claws hooves, horns and scales. It provides mechanical protection and an impermeable barrier to infection and water-borne pollutants.
- Elastin is full of crosslinks and coils which makes it good at stretching. It is used in skin and in lungs during inflation and deflation. It is also a big part of the bladder as this expands to hold urine. Blood vessels also benefit from this stretching as it helps maintain blood pressure.
Globular proteins – a spherical shape that is soluble in water e.g. hormones (insulin), enzymes (pepsin) and haemoglobin.
- Haemoglobin is made up of four polypeptides (two alpha globin chains and two beta globin chains). On each chain there is a prosthetic haem group containing an iron ion. A protein with this kind of group is called a conjugated protein. It functions to bring oxygen from the lungs into the tissues. When the O2 binds to the haem group the molecule turns from purple to red.
- Insulin is made from two poly peptides joined together by disulfide links. Insulin binds to glycoprotein receptors in cell membranes to increase the cells uptake and consumption rate of glucose.
- Pepsin digests protein in the stomach and is made up of a single polypepdide with a symetrical tertiarry structure. Many of its R groups are acidic so as to be stable in such an acidic environement as the stomach.
Computer modelling of protein structure
Ab initio protein modelling – a model is built based on the physical and electrical properties of the atoms in the amino acid sequence. There are multiple solution.
Comparative protein modelling – Protein threading scans the amino acid sequence against a database and produces a set of possible models.
Water
Water consists of two hydrogen molecules and one oxygen. It is dipole as the hydrogens have a slight positive charge while the oxygen has a slight negative charge. Hydrogen bonds form between water molecules.
Properties of water:
- Liquid – It has low viscosity and is liquid at room temperature
- Provides habitats in rivers, lakes and seas
- Forms a major component of tissues
- Provides a reaction medium for chemical reactions
- An effective transport medium e.g. blood or vascular tissue
- Density – Allows floatation in aquatic animals, ice is less dense than water therefore:
- Aquatic animals have a stable environment to live in
- Ponds and water bodies are insulated against extreme cold by the ice layer
- Solvent – good for ionic solutes such as NaCl as it is polar and covalent solutes e.g. glucose.
- Molecules and ions can move and react with each other in solution
- Molecules can be transported around organisms
- Cohesion and Surface Tension – water forms hydrogen bonds to itself and other things
- Columns of water are pulled up together in the xylem
- Bond skaters can use surface tension to stay afloat
- High specific heat capacity – lots of energy needed to raise the temperature
- Living things need a stable temperature for enzyme controlled reactions
- Aquatic organisms need a stable environment to live in
- High latent heat of vaporisation – can be used to help cool things
- Mammals are cooled when sweat evaporates
- Plants are cooled when water evaporates from mesophyll cells
- Reactant
- Used in photosynthesis and hydrolysis
- Very important for digestion and synthesis of large molecules
Qualitative Food Tests
Quantitative Tests
Colorimetry for reducing sugars
- Perform a serial dilution of reducing sugar solution to get around 5 different known concentrations of sucrose and a control of distilled water.
- Do a benedict’s test on each of the samples.
- Centrifuge the precipitate from the samples and collect the supernatants into cuvettes.
- Use a red filter in the colorimeter.
- Take a sample of distilled water in a cuvette to calibrate the colorimeter before each test.
- Test the known concentrations of sucrose in the colorimeter.
- If there was a high concentration of sucrose in the sample, there will be less unreacted copper sulphate, so the sample will be less blue, so more light will pass through and the percentage transmission will be high.
- If there was a low concentration of sucrose in the sample, there will be more unreacted copper sulphate, so the sample will be bluer, so less light will pass through and the percentage transmission will be low.
- Plot the results on a graph and use a curve of best fit.
- Test your sample with a benedict’s test, centrifuge the precipitate, and take a reading on the colorimeter.
- The reading should then be read on the graph to determine from the line of best fit to work out the concentration of reducing sugars in the sample.
Biosensors
Biosensors take a biological or chemical variable and use a transducer to turn the variable into an electrical signal and then display a reading based on the amount of the variable found.
They can be used to detect contaminates in water and pathogens and toxins in food as well as airborne bacteria. This is useful to counter biological terrorism.
Chromatography
- Put a dot of ink about a centimetre up from the bottom of the chromatography paper
- Dip the paper into a beaker with the solvent in, allowing the solvent to climb up the paper
- Wait for it to dry
- Compare results to known pigments and molecules
The aim of chromatography is to separate a mixture into its components.
Stationary phase – the chromatography paper which has free –OH groups facing outwards in contact with the mobile phase
Mobile phase – the solute, water for polar molecules and ethanol for non-polar molecules
The molecules travel up the paper for different
amounts depending on their size, solubility and polarity, allowing us to identify them.