OCR AS Biology - Unit 2: Biological Molecules

- Vital to all living organisms
* Reactant in many important chemical reactions within cells
* Solvent
* Transport medium
* Aids with temperature control

- Makes up 80% of cell content

- Simple structure
* Two hydrogens covalently bonded to an oxygen (H2O)
* Dipole forms - each hydrogen atom is left with slight positive charge
* Unshared electrons on oxygen atom give it a slight negative charge

- This structure is important as many important substances are ionic.
* Positive H's of water are attracted to negative ion in the substance.
* Negative O of water is attracted to positive ion in substance.
* As such, the ionic substance gets completely surounded by water molecules - it has dissolved.

- Made of long chains of amino acids
* Dipeptides form when two amino acids join together
* Polypeptide is more than two in a chain
* Proteins consist of one or more polypeptide chains

- Amino acids have the same general structure
* a carboxyl group (-COOH)
* an amine group (-NH2)
* a carbon atom (C)

- What makes amino acids different from each other is the variable group, represented as R on a diagram. R can be a number of different molecules or atoms

- Amino acids join together via peptide bonds
* The OH in the carboxyl (COOH) group bonds to the H of the amine group (NH2) to form H2O
* Water is formed, as such this is a condensation reaction. The reverse of the reaction adds a water molecule to break the bond and is a hydrolosis reaction

- Proteins have 4 structural levels

* Primary structure is the order of the sequence of amino acids in the polypeptide chain

* Secondary structure is the hydrogen bonding between amino acids in the chain - this makes it coil automatically into an alpha helix or fold into beta pleated sheet (these are the secondary structures the proteins can take)

* Tertiary structure refers to the way the chain coils or folds further. More bonds form between different parts of the chain. In proteins made up of a single polypeptide chain the tertiary structure is the final 3D structure

* Quaternary structure is determined by the way polypeptide chains within a protein bond together - Haemoglobin, for example, is made of four polypeptide chains bonded together. For proteins with more than one polypeptide chains the quaternary structure is the final 3D structure

- 2 examples needed for OCR AS Biology

- Collagen
* Fibrous protein which acts as supportive tissue in animals - needs to be strong
* Made up of 3 polypeptide chains tightly coiled into a strong triple helix (Sec. Struc.) 
* Chains interlinked by strong covalent bonds (Tert. Struc.)
* Minerals can bind to triple helix to increase its rigidity

- Haemoglobin
* Globular protein containing haem groups that bind to oxygen in order to transport it.
* Structure is curled so that the hydrophliic side chains are on the outside and the hydrophobic side chains face inwards - this makes haemoglobin soluble in water and as such good for transport in the blood.

Q) Name the 2 forms of secondary structure.
A) Alpha helix and beta pleated sheet 

- Made up of monosaccharides
* Monosaccharides are still called carbohydrates

- Glucose is a monosaccharide with 6 carbon atoms in each molecule
* Two forms - apha and beta
* In alpha glucose the end hydrogen atom is bonded above the plain and the OH
* In beta glucose the end hydrogen atom is bonded below the plain and the OH

- Monosaccharides join to form dissacharides and polysaccharides
* They join via glycosidic bonds; a hydrogen atom on one bonds to the hydroxyl (OH) group on the other, releasing water and so this is a condensation reaction

- Two alpha glucose molecles join via a glycosidic bond to form maltose

- Multiple alpha glucose molecules join via glycosidic bonds to form amylose

Q) How do amino acids join together?
A) Peptide bonds 

- Starch is the main energy storage molecule in plants

- Excess glucose in plants is stored as starch

- Starch is a mixture of two polysaccharides of alpha glucose - amylose and amylopectin
*Amylose is a long unbranched chain of alpha glucose. The angles of the glycosidic bonds give it a coiled structure, making it compact and as such good for storage
*Amylopectin is a long branched chain of alpha glucose which, given the number of side branches, has a higher surface area and is as such easier for enzymes to break down. This means the glucose can be released quickly

- Starch is insoluble and so cant enter cells by osmosis, which would cause them to swell. As such it is good for storage

Q) 3 structural features of collagen?
A) 3 polypeptide chains form triple helix/chains interlinked by covalent bonds (strong)/minerals can bind to triple helix (increases rigidity) 

- Glycogen is the main energy storage material in animals

- Animals also use glucose for energy, but they store their excess as glycogen - another polysaccharide of alpha glucose
* Its stucture is very similar to amyloectin, except that it has even more branches.
* This increased surface area makes it even easier for enzymes to break it down and so the glucose can be released even more quickly, which is important for energy release in animals

- Glycogen is very compact, and as such good for storage

Q) Describe the difference between alpha and beta glucose.
A) Hydrogen above the plane (and OH group) in alpha glucose/hydrogen is below plain (and OH group) in beta glucose.

- Cellulose is made of beta glucose - long, unbranched chains of it
* The bonds between the sugars are straight, and so the chains of cellulose are straight
* Linked together by hydrogen bonds the chains form microfibrils - these are strong, allowing cellulose to provide structural support in cells 

- An example of this structural support most commonly seen in cells is the cellulose cell wall. 

Q) How do monosaccharides join together?
A) Glycosidic bonds

Q) What is the function of glycogen? 
A) Energy store in animals 

- Triglycerides and phospholipids are similar
* A triglyceride is made up of one molecule of glycerol with 3 fatty acids attached to it
* Phospholipids are almost the same except that one of the fatty acids is replaced with a phosphate group instead
* The tails of the fatty acid molecules make lipids such as glycerol hydrophobic, however, in phospholipids the phosphate group  is ionised and as such phospholipids also have a hydrophilic head 
* Phospholipids therefore have both a hydrophilic head and a hydrophobic tail

- Another lipid is cholesterol
* It has a hydrocarbon ring structure with a hydrocarbon tail attached
* The ring has a polar hydroxyl group which makes cholesterol soluble

Q) Name 2 uses of cholesterol
A) Structural component of cell membranes/to make steroids 

- Triglycerides are used as energy storage molecules in cells
* The long hydrocarbon tails contain a lot of chemical energy, which is released when they are broken down
* These tails help triglycerides contain about twice as much energy per gram as carohydrates
* They're insolube - they don't cause water to enter the cell via osmosis, which would make it swell 

- Phospholipids make up the bilayer of cell membranes
* The hydrophilic heads and hydrophobic tails line up to form a double layer with the heads facing out towards the water on each side of the bilayer
* As the centre (tails) is hydrophobic, water soluble molecules find it harder to pass through it - it acts as a barrier

- Cholesterol binds to the hydrophobic tails within the phospholipid bilayer causing them to pack more closely together. As such cholesterol is important in determining the rigidity and fluidity of the cell membrane

Q) How do two alpha glucose bonds join to form maltose, and how are they split apart again?
A) Join via condensation - H on one binds to OH on the other to form H2O. Split via hydrolysis - addition of water

- Benedict's test for sugars
* Reducing sugars - add Benedict's reagent and heat but don't boil. If sugars are present a coloured precipitate will form
Non-reducing sugars - Boil test solution with dil. HCL then neutralise with NAOCH3 (sodium hydrogen carbonate), then carry out Benedict's test 
Benedict's test will return positive result for red./no. red. sugars, so you need to do both of the procedures above to check which type it is

- Iodine test for starch
* Add iodine dissolved in potassium iodide solution to sample, if starch is present it will change from browny orange to blue/black. If starch is not present it will remain browny orange

- Biuret test for proteins
* Test sol. needs to be alkaline so add a few drops of sodium hydroxide solution. Then add some copper(II) sulfate sol.
* If protein is present a purple layer forms, if not the sol. will stay blue. Note clolour changes are slight and can be hard to spot 

- Emulsion test for lipids
* Shake sample sol. with ethanol, if lipids are present sol. will turn milky

Q) Why do triglycerides contain so much more energy than carbohydrates?
A) The fatty acid tails contain lots of chemical energy 

Q) Describe how you would test for starch and what you would expect if it were present.
A) Add iodine dissolved in potassium iodide to sample. If starch is present colour will change to blue-black

Q) What are triglycerides composed of?
A) Glycerol molecule attached to 3 fatty acids

Q) What bonds are involved in holding together the monosaccharides in polysaccharides?
A) Glycosidic bonds 

Q) Name the 2 groups common in all amino acids.
A) Amine group and carboxyl group

Q) Name 4 functions of water in living organisms.
A) Reactant in biochem. reactions/ transport medium/ solvent/ used in temperature control