Biological Molecules

Covalent Bonds: Atoms share a pair of electrons in their outer shell. Therefore outer shell of atoms is now full & a molecule is formed

Ionic Bonds: Ions with opposite charges are attracted to one another. This electrostatic attraction is an ionic bond is formed

Hydrogen Bond: Electrons within a molecule are not evenly distributed, but tend to spend more time at one position. This region is more negatively charged than the rest of the molecule. Uneven distribution means the molecule is polarised, the molecule is known as a polar molecule. 

Molecules known as monomers can be linked together to form long chains called polymers. This is done via a process called polymerisation. The monomers of a polymer are usually carbon based

Condensation Reactions:

During polymerisation, when each new sub-unit is attached, a water molecule is formed. Reactions that produce water in this way are known as condensation reactions

Hydrolysis Reactions:

Polymers can be broken down through the addition of water. The water molecules are used when breaking the bonds that link the sub-units of a polymer together. This splitting of the molecule into its constituent parts is known as a hydrolysis reaction

Metabolism:

All the chemical processes that take place in a living organism

The basic monomer of a carbohydrate is a sacchaaride (a sugar). A single monomer is therefore called a monosaccharide. A pair of monosaccharides can be combined, making a disaccharide. Monosaccharides can also be combined to form a chain, known as a polysaccharide. 

Monosaccharides are sweet tasting, soluble substances. Examples of monosaccharides include: glucose, galactose and fructose. 

All monosaccharides and some disaccharides are reducing sugars. A reducing sugar is a sugar that can donate electrons to another chemical, in this case Benedict's Reagent. The test is known as the Benedict's Test. The test is carried out as follows:

1) Add food sample to test tube (girnd up in water if it isn't in liquid form)

2) Add an equal volume of benedict's reagent

3) Heat mixture in a boiling water bath for 5 mins

4) If a reducing sugar is present solution turns orange-brown

Pairs of monosaccharides can be combined to form a disaccharide

Examples:

Glucose + Glucose = Maltose

Glucose + Fructose = Sucrose

Glucose + Galactose = Lactose

Two monosaccharides join in a condensation reaction when a molecule of water is removed, creating a glycosidic bond.

When a molecue of water is added, the glycosidic bond breaks in a hydrolysis reaction 

Disaccharides such as sucrose are non-reducing sugars, they don't change the colour of Benedict's reagent when they're heated with it. To detect a non-reducing sugar, it must fisr be hydrolysed into its monosaccharides:

1) If sample isn't in liquid form, grind up in water

2) Add Benedict's reagent 

3) Place test tube in gently boiling water bath for 5 mins, if sample does not chnage colour, then reducing sugar is not present

4) Add food sample to dilute hydrochloric acid and place test tube in boiling water bath for 5 mins. The acid will hydrolyse the disaccharide into its monosacccharides

5) Add sodium hydrogencarbonate solution to test tube in order to nutralise the hydrochloric acid

6) Re-test solution with Benedicts reagent and place in boiling water bath for 5 mins

7) If a non-reducing sugar is present, solution will now turn orange-brown

Polysaccharides are polymers made up of monosaccharides linked via a glycosidic bond as a result of a condensation reaction. 

They're insoluble, making them suitable for storage as they will not change the water potential of whatever it's being stored in. Some polysaccharides, such as cellulose, give structural support to plant cells. 

Test for Starch:

1) Place sample into test tube

2) Add iodine solution & shake/stir solution

3) If starch is present, solution will turn a blue-black colour

• Made up of alpha-glucose joined by glycosidic bonds
• Found in plants as glucose/as an energy store

2Types:

1) Amylose:

• Unbranched and Coiled, making it compact and easy to store glucose
• It is insoluble, so doesnt affect the water potential
• Also means there is no affect on osmosis

2) Amylopectin:

• Branched, which increases the surface area, so more can be hydrolysed simultaneously
• It is insoluble, so doesnt affect the water potential
• Also means there is no affect on osmosis

• Found in animals and bacteria
• Similar structure to starch, but is more highly branched and has shorter chains
• Is the major carbhydrate storage product of animals
• Stored as small granules, mainly in muscle and liver cells
• It's insoluble, so doesn't tend to draw water in by osmosis and doesn't diffuse out of cells
• Highly branched with a lot of ends, so lots can be acted on simultaneously by enzymes for use in respiration

• Made up of beta-glucose
• Has straight, unbranched chains that run parallel to one another
• Hydrogen bonds form cross-linkages between adjacent chains
• Overall number of hydrogen bonds increases strength of the plant
• Cellulose molecules are grouped to form microfibrils
• Microfibrils are grouped to form fibres
• Plant cell walls contain cellulose as they add rigidity to the cell wall
  • Prevents the cell from bursting from allowing too much water in
  • Exerts and inward force to prevent taking in too much water
  • Helps provide maximum surface area for photosynthesis

Cell Membrane: Phospholipid contribute to the flexibility of membranes and the transfer of lipid-soluble substances acorss them

Energy Source: When oxidised, lipids provide more than twice the energy of carbs, and release water

Waterproofing: Lipids are insoluble in water. Both plants and insects have waxy, lipid cuticles that conserve water. Mammals produce and oily secretion from the sebaceous glands in the skin

Insulation: Fats are conductors of heat and are stored beneath the body's surface to help retain body heat. Also acts as electrical insulators in the myelin sheatha round nerve cells 

Protection: Fat is often stored around delicate organs

• Called this because they have 3 fatty acid tails, combined with a glycerol
• Each fatty acid forms and ester bond with the glycerol in a condensation reaction
• Hydrolysis of a triglyceride produces three fatty acids and a glycerol

• If the chain contains no double carbon-carbon bonds it is said to be saturated 
  • This is because all the carbons are linked to the maximum number of hydrogen atoms
• A single, double bond between carbons in the chain is said to be monosaturated 
• Multiple, double bonds between carbons in the chain is said to be polysaturated

• High ratio of energy-storing carbon-hydrogen bonds to carbon atoms, so are excellent source of energy
• Have a low mass to energy ratio, so are good storage molecules becuase a lot of energy can be stored in a small volume
  • This is especially beneficial to animals as it reduces the mass they have to carry
• Large, non-polar molecules and are insoluble in water, so storage doesn't affect osmosis or water potential in cells 
• Have a high ratio of hydrogen to oxygen atoms, triglycerides release oxygen when oxidised, and therefore provide an important source of water

• Similar to lipids except that one of the fatty acid molecule is replaced by a phosphate molecule

Two Parts to a Phospholipid:

1) Hydrophilic Head: Interacts with water, but not fat

2) Hydrophobic Tail: Orients itself away from water, but mixes readily with fats

• Is a polar molecule, so when placed in water positions itself so that the hydrophilic heads are as close to the water as possible, and the hydrophobic tails are far away from the water as possible

• Are polar molecules, so in an aqueous environment, phospholipid molecules form a bilayer winthin a cell surface membrane. A hydrophilic barrier is formed between the inside and the outside of a cell
• Hydrophilic phosphate heads help to hold at the surface of the cell-surface membrane
• Phospholipid structure allows them to form glycolipids by combining within the cell-surface membrane 

Known as the emulsion test:

1) Make sure test tube is completely dry & greese free

2) Add sample, add ethanol

3) Shake tube thoroughly to dissolve any lipid in the sample

4) Add water and shake gently

5) A cloudy-white colour indicates the presence of a lipid

• Cloudy colour is due to any lipid in the sample being finely dispersed in the water to form an emulsion

Amino acids are the basic monomers that make up polypeptides. Polypeptides are combines to form proteins.  The bonds between two amino acids is a peptide bond. 100 amino acids have been identified, 20 of which occur naturally, each of these 20 appear in all living organisms showing evidence for evolution.

Every amino acid has a central carbon atom, which is attached to 4 groups:

• Amino group (-NH2)
• Carboxyl group (-COOH), an acidic group
• A Hydrogen Atom (-H)
• An R group - A variety of different chemical groups, each amino acid has a sifferent R group

Through many condensation reactions, many amino acids monomers join together during polymerisation. This results in a chain of many hundreds of amino acids, a polypeptide. The sequece of amino acids in a polypeptide chain forms the primary structure of a protein. 

Amino acids can be joined together in any order, so there is an almost limitless number of possible combinations, and therefore types of primary protein structure. The primary structure of a protein determines its shape and therefore its function. A protein's shape is very specific to its function. so any change to just one amino acid in the primary structure could cause the protein to stop functioning all together.

• The H of the amino group (-NH2) has an overall positive charge, whereas the O of the carboxyl group (-COOH) has an overall negative charge.
• These two groups readily form a weak hydrogen bond.
• This causes the long polypeptide chain to be twisted into a 3-D coil, known as an alpha-helix

The alpha-helix of the seconndary protein can be twisted and folded even more to give a more complex, specific 3-D shape, the tertiary structure. This shape is maintained by a number of different bonds, including:

• Disulphide bridges: fairly strong, therefore not easily broken
• Ionic bonds: Formed between any carboxyl and amino group that are not involved in peptide bonds. They're weaker than disulfide bridges and are easily broken is pH is changed
• Hydrogen bonds: Numerous, but easily broken

Large proteins containing a number of individual polypeptide chains that are linked in various ways. Also may have non-protein groups associated with the molecule, e.g. the iron-containing haem group in haemoglobin.

The biuret Test detects peptide bonds:

1) Add sodium hydroxide solution at room temperature

2) Add a few drops of dilute copper(II) sulfate solution and mix

3) Purple colouration indecated that protein is present. If there is no protein present, the solution will remain blue

Activation energy is the munimum amount of energy needed for a reaction to take place. Enzymes work by lowering the activation energy level, this is done by allowing chemical reactions to take place at a lower temperature than normal. This enables metabolic processes to occur rapidly at the human body temp, 37'C. Without enzymes, these reactions would take place too slowly to sustain life as we know it.

Activation energy is the munimum amount of energy needed for a reaction to take place. Enzymes work by lowering the activation energy level, this is done by allowing chemical reactions to take place at a lower temperature than normal. This enables metabolic processes to occur rapidly at the human body temp, 37'C. Without enzymes, these reactions would take place too slowly to sustain life as we know it.

Enzymes are globular protiens that have a specific 3-D shape, that comes as a result of their amino acid sequence.

The active site is the functional part of the enzyme. It is made up of a relatively small number of amino acids. It forms a small depression within the much larger enzyme molcule. 

A substrate is what the enzyme acts on as it neatly fits into the depression, forming an enzyme-substrate complex. The substarte molecule is temporarily held in place by bonds that form between certain amino acids of the acitve site, and groups on the substarte moleucle.

The induced fit model proposes that the active site forms as the enzyme and substrate interacts. The proximity of the substrate causes a change in the enzyme that forms a functional active site. The enzyme is flexible and can mould itself around the substrate. 

The enzyme has a certain geenral shape, but this alters in the presence. As it changes its shape, the enzyme puts strain on the substrate molecule. The strain distorts particular bonds in the substrate, therefore lowering the actvation energy needed to break the bond.

Any change in an enzyme's environment is likely to change its shape. The collision between the enzyme and the substrate is a change in the envronment, causing the change in shape. 

The model proposed that enzyme action works the same way as a lock and key. Each substrate will only fit the active site of one particular enzyme.

This was supported by the observation that enzymes are specific in the reactions they catalyse. The shape of the substrate exactly fits the active site of the enzyme. 

One limitation of this model is the enzyme is considered to be rigid, however it was discovered that other molecules could bind to the enzyme at sites of than the active site, suggesting that the enzyme's shape was being altered by the binding molecule. Therefore the shape of an enzyme was not rigid, but flexible. 

To measure the progress of an enzyme catalysed reaction, its time-course is measured. This is the time it takes for a particular event to run its course. The two most frequently measure are:

• The formation of the products of the reaction
• The dissapearance of the substrate

You measure the rate of change at any point on the curve of a graph. This is done by measuring the gradient at the chosen point. The gradients it equal to the gradient of the tangent to the curve at that point. This tangent is the point at which a straight line touches the curve, but without cutting across it.

Rise in temperature increases the kinetic energy of molecules, causing them to move around more rapidly and collide with eachother more often. In an enzyme catalysed reaction, this means enzyme and substrate molecules come together more often, this means there are also more successful collisions, meaning more E-S complexes are formed. This increases the rat eof reaction. 

On a graph this is seen as a rising curve. The temperature rise begins to cause the hydrogen and other bonds in the enzyme to break, changing the shape of the enzyme. At first, the substrate fits less easily into the enzyme's changed active site, slowing the rate of reaction. This occurs at around 45'C

At around 60'C the enzyme is so disrupted that it stops working all together, and is therefore denatured. Denaturation is a perminant, irreversible change, so the enzyme will never function again.

The pH of a solution is a measurement of its hydrogen ion concentration. Each enzyme has an optimum pH, the pH at which it works fastest. A change in pH away from the optimum affects the rate of enzyme action. An increase or decrease in pH reduces the rate of enzyme action. If the change in pH is more extreme then the enzyme become denatured.

A change in pH alters the charges of the amino acids that make up the active site of the enzyme. The substrate can no longer become attached to the active site and the E-S complex cannot be formed.

Depending on how significant the chnage in pH is, it may cause the bonds maintaining the enzyme's tertiary structure to break. This causes the active site to change shape.

Once an active site on an enzyme has acted on its substrate, it is free to repeat the procedure on another substrate molecule. This means enzyme molecules are not used up in the reaction, therefore they work efficiently in low concentrations. As long as there is an excess of substrate, an increase in the amount of enzyme lead to a proportionate increase in the rate of reaction.

Low Enzyme Concentration: Too few enezyme molecules to allow allsubstrate molecules to find an active site at one time. The rate of reaction is therefore only half the maximum possible for the number of substrate molecule available.

Intermediate Enzyme Concentration: Twice as many enzyme molecues available, all the substrate molecules can occupy an active site at the same time. The rate of reactionhas doubled to its maximum because all active sites are filled.

High Enzyme Concentration: Addition of further enzymes has no effect on rate of reaction as there are already enough active sites to accomodate all available substrate molecules. There's no increase in the rate of reaction. 

If the concentration of enzyme is fixed and substrate concentration is slowly increased, the rate of reaction increases in proportion to the concentratin of substrate.

At Low substarte concentrations the enzyme molecules have only a limited number of substrate molecules to collide with, therefore the active sites of the enzymes are not working at full capacity. 

As more substrate is added, the active sites gradually become filled, until the point where all of them are working as fast at they can. The rate of reaction is at its maximum (V max). After that, the addition of more substrate will have no effect on the rate of reaction.

• Competitve inhibitors have a molecular shape similar to that of the substrate, allowing them to occupy the active site of an enzyme. They, therefore, compete with the substrate for the available active sites. 
• The difference between the concentration of the inhibitor and substrate determines the effect on enzyme activity. If the substrate concentration is increased, the effect of the inhibitor is decreased. 
• Theinhibitor is not perminantly bound to the active site, and so when it leaves another molecule can take its place. This could be substrate or another inhibitor
• Sooner or later all the substrate molecules will occupy an acitve site, but the greater the concentration of the inhibitor, the longer this will take

• Non-competitive inhibitors attach themselves to the enzyme at the binding site, which is not the active site.
• Upon attaching, the inhibitor alters the shape of the enzyme and thus its active site in such a way that the substrate molecules can no longer bind to it, so the enzyme cannot function
• As the substrate and the inhibitor are not competing for the same site, an increase in substrate concentration does not decrease the effect of the inhibitor.