Biochemical tests using Benedict’s reagent for reducing sugars and non-reducing sugars. Iodine/potassium iodide solution for starch.

Add Benedicts solution to the sample and heat:

• If it turns orange it is a reducing sugar
• If its blue then do the following:

Add hydrochloric acid and heat for a further 5 minutes, after this add hydrogen carbonate to neutralise it. Now repeat the process from the begining of the test and add benedicts solution and then heat:

• If it turns orange then it is a non-reducing sugar
• If it stays blue then it is not a sugar at all.

Acid is added to hydrolyse the non-reducing sugars breaking them down into monomers- reducing sugars.
The solution is neutralised as acid would prevent the Benedicts test from working.

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To test for starch pipette a couple of drops of iodine on to the sample you are testing.

• If it stays red then there is no starch
• If it goes blue/black then there is starch.

Biological molecules such as carbohydrates and proteins are often polymers and are based on a small number of chemical elements. Monosaccharides are the basic molecular units (monomers) of which carbohydrates are composed. The structure of a-glucose as... and the linking of a-glucose by glycosidic bonds formed by condensation to form maltose and starch.

Carbohydrates are biological molecules (this means they are produced by living things) they contain Carbon, Hydrogen and Oxygen. They have the empirical formula CH20.

Carbohydrates are often polymers made up of monomers; polysaccharides made up of monosaccharides.

Glucose is a monosaccharide, it is a hexose- which means it contains 6 carbons- so its molecular formula is C6H12O6. There are other hexose which will be made up of the same components, but they are different molecules due to their structure, the structure of alpha-glucose is:

Structure of alpha-glucose

Two monosaccharides join together by a condensation reaction, to make a disaccharide; when more are joined it becomes a polysaccharide. In the condensation reaction between two glucose molecules, a glycosidic bond is formed (bond between the two sugars) creating a disaccharide and water:

Products of a condensation reaction between two glucoses

Two glucoses are joined they form the disaccharide maltose. Many glucoses joined together form the polysaccharide starch,

Starch, the role of salivary and pancreatic amylases and of maltase located in the intestinal epithelium; disaccharides, sucrase and lactase; Sucrose is a disaccharide formed by condensation of glucose and fructose. Lactose is a disaccharide formed by condensation of glucose and galactose. Lactose intolerance.

Starch is a polysaccharide, it is broken down by the body into monosaccharides, in two stages:

• Amylase (released from the salivary and pancreatic glands) breaks starch down into maltose,
• Maltase (found in the intestines) breaks maltose down into glucose.

Sucrose is a disaccharide, it is digested in to two monosaccharides:

• Sucrase breaks sucrose down into glucose and fructose.

Lactose is a disaccharide, it is digested in to two monosaccharides:

• Lactase breaks lactose down into glucose and galactose.

Some peoples bodies do not produce enough lactase, this means there will be undigested lactase in their digestive system (after eating a product containing this sugar, like milk.) This lactase is fermented by bacteria which produces methane. The symptom of this is painful wind and the name of this condition is lactose intolerance.

Having lactose in the intestine decreases the water potential, this causes water to move in by osmosis, diluting the faeces and giving diarrhoea to the sufferer.

Candidates should be able to use the lock and key model to explain the properties of enzymes. They should also recognise its limitations and be able to explain why the induced fit model provides a better explanation of specific enzyme properties

The lock and key theory helps us to understand that an enzyme has an active site that bonds with one kind of substrate.

However it suggests that the structure is rigid and that bonds can only be made to the active site.

Induced fit theory shows us that the structure is flexible and can be changed by the substrate or by bonds at an allosteric site (not the active site.) This helps us see how reactions are sped up- because the substrate does not have to fit into the enzyme in exactly the right way as the enzyme moulds around it.

Description and explanation of the effects of temperature, competitive and non-competitive inhibitors, pH and substrate concentration.

Temperature
At low temperatures there is a less energy, the substrates will move around more slowly making them less likely to reach the active site.
At optimum temperature there is a lot of energy and as substrates move around more they more frequently end up in the active site.
Past optimum temperature there is too much energy for an enzyme, and the bonds holding it together will break: this is called denaturing.

PH
Different types of enzymes have very different optimum PHs.
Above and below this PH the bonds holding the enzyme together will break, and the amino acids will have their charges changed, preventing them from forming bonds with the substrate.

Substrate concentration
At low concentration, substrates get into the active site less frequently meaning they react little.
At medium concentrations, substrates will get into the active site a lot meaning they are constantly reacting.
At high concentrations there will be a substrate in the active site all the time: after this, adding more substrate will not speed up the reaction, because the enzymes are always busy anyway (this is why at a certain point increasing the substrate concentration makes no difference to the rate of reaction.)

Competitive inhibitors
These compete with substrates to bond with the active site of an enzyme.
Once they have bonded with the active site they block it so substrates can't bond with it.
The bonds are usually weak hydrogen bonds, however, and will soon break (reversible.)
The effects of competitive inhibitors can be reduced by adding more substrate because that means it has more substrates to compete with, so a lower chance of getting into the active site.

Non-competitive inhibitors
These bind to an allosteric site (away from the active site) which distorts the active site to make it less complimentary to its substrate. This is usually an irreversible strong covalent bond

The properties of enzymes relating to their tertiary structure.

Enzymes have a globular structure- these are suited to metabolic reactions. Globular structures are ball-like and tend to be flexible.

A small area of an enzyme (3-12 amino acids long) will form a depression on the surface of the enzyme due to how the polypeptide chain has been folded- this is the active site. In this area will be R groups which can form bonds with substrates to make the enzyme substrate complex.

The lock and key and induced fit models of enzyme action.

The lock and key theory
An enzyme has a active site which compliments (fits with) a specific substrate exactly (before binding). It states that the enzyme has a fixed shape. A substrate will go into an enzyme like a key goes into a lock and form an enzyme-substrate complex; this then changes the bonds in the substrate to form the products.

http://chsweb.lr.k12.nj.us

The induced fit theory
This states that an enzyme has an active site which is not perfect for a substrate, but that it is flexible.
A substrate will alter the shape of the active site to make it complimentary, the changed shape will alter the bonds in the substrate creating the products.

http://chsweb.lr.k12.nj.us

Enzymes as catalysts lowering activation energy through the formation of enzyme-substrate complexes.

Enzymes form temporary bonds to substrates, this creates an enzyme substrate complex. When the complex is made it alters the bonds in the substrate(s) to create products:

Enzyme + substrate > enzyme-substrate complex > enzyme + products.

Enzymes allow a reaction to happen just by having the necessary substrates in its active site. This needs less energy than if the reaction were to happen with out the enzyme as substrates need to collide with enough force to change their bonds.

boundless.com

A catalyst (like an enzyme) will lower the activation energy of a reaction, but will not change the energy of the reactants or products. The catalyst itself will remain unchanged by a reaction.

http://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter2/animation__how_enzymes_work.html

The biuret test for proteins.

Place your sample in a test tube;
add an equal amount of sodium hydroxide;
add a few drops of dilute copper sulphate;
if it goes purple there are peptide bonds, if it is blue there are no peptide bonds.

http://www.youtube.com/watch?v=ufec89A47uM

The general structure of an amino acid. Condensation and the formation of peptide bonds linking together amino acids to form polypeptides. The relationship between primary, secondary, tertiary and quaternary structure, and protein function.

There are 20 different types of amino acid. In a polypeptide chain there are an average of 400 amino acids, the order of these will dictate which kind of protein it is, and therefore what its function is.

General structure of an amino acid
NH2 on the left is the amine group.

COOH on the right is carboxylic acid.

R represents the R group of the amino acid, the R group is what differs between amino acids. They can contain H, C, N and O but they can also contain Sulphur.

General structure of an amino acid

Primary structure of a protein
Amino acids join together by a condensation reaction: this produces water and a peptide bond (red line.) The oxygen and hydrogen of one amino acid, bond to the hydrogen of another forming H2O (water.) This leaves the carbon of one and nitrogen of the other free to make another bond; a peptide bond to each other.
When this is done to around 400 amino acids consecutively a polypeptide chain is formed (this is the primary structure of a protein.)
O=CNH is a peptide linkage; where as CN is the peptide bond.

Products of a condensation reaction between two amino acids

Secondary structure of a protein
Polypeptide chains bond together to form either alpha helices or beta pleated sheets.
In these structures every four amino acids has a hydrogen bond, this is a weak bond between the positive H (of the NH) and the negative O (of the CO.)

oregonstate.edu

Tertiary structure of a protein
The secondary structure is twisted and folded into an even more complex structure.
This can be held together in a variety of ways:

• Disulphide bridges can form if there are amino acids with sulphur in their R group
• Ionic bonds between carboxylic and amine groups that are not in a peptide bond
• Hydrogen bonds as in the secondary structure (but not regular)

Quaternary structure of a protein
This only happens sometimes, unlike the other stages which all have to be gone through to make a protein.
Several polypeptide chains at the tertiary level may join together to form a new protein.
An example of this is when four polypeptide chains bond around an iron making hemaglobin.

Proteins have a variety of functions within all living organisms.

Proteins can be used for many different functions, for example:

• Enzymes
• Carrier proteins
• Anti-bodies
• Hormones

They are key with in the cell; second in quantity only to water.

The two types of protein carry tend to carry out different functions:

• Fibrous proteins are formed like a rope, they are tightly twisted; this makes them very stable and good for structural functions (like collagen.)
• Globular proteins form a bundle which is more suited to carrying out metabolic functions (like enzymes.) 

Digestion is the process in which large molecules are hydrolysed by enzymes to produce smaller molecules that can be absorbed and assimilated.

Hydrolysis is when a molecule is broken because water has been added to its chemical bonds:
Amylase breaks starch down into maltose;
Lipase breaks lipids down into glycerol and fatty acids;
Protease breaks proteins down into amino acids.

Absorption is when broken down food molecules diffuse into the blood stream.
Assimilation is when the broken down food molecules are taken up by cells (so that they can be used by them.)

The gross structure of the human digestive system limited to oesophagus, stomach, small and large intestines, and rectum. The glands associated with this system limited to the salivary glands and the pancreas.

The salivary glands
Secrete saliva into the mouth.
Saliva contains amylase; this breaks starch down into maltose.
Saliva helps make the food into a slippery sphere called a bolus.

The oesophagus
Connects the mouth and the stomach.
Peristalsis (muscular contractions) moves boluses down.

The stomach
Secretes protease to break down proteins into amino acids.
Acidic PH2 environment (optimum for protease.)
Food in the stomach becomes chime (a runny substance which is what we throw up.)
The stomach produces mucus to prevent its lining being digested.

The pancreas
Produces pancreatic juice containing lipase (lipids into fatty acids and glycerol), amylase and protease.
Secretes this into the duodenum connecting the stomach and the small intestine.

The small intestine
PH7 due to bile which is made in the liver and stored in the gall bladder.
Bile also emulsifies fat; increasing its surface area and making it easier to absorb.
Food molecules are digested here by the enzymes from pancreatic juice.
Absorption happens here through the villi which:
--have a large surface area as they are folded with many protrusions called microvilli
--are only one cell thick (also increasing the rate of diffusion)
Glucose and amino acids are absorbed into the blood, they go through the hepatic portal vein into the liver (which filters blood) and then through the hepatic vein to the rest of the body where they will be assimilated (used by cells.)
Fatty acids and glycerol diffuse into the lymph, to be released into the blood at the neck.

The large intestine
water from the undigested food is absorbed into the blood.
Fibre, undigested food and dead red blood cells form faeces.

The rectum
This is the final section of the intestines.
faeces is stored here before being egested.