Biological Molecules

• carbon containing molecules are known as organic molecules
• monomer examples: monosaccharides, amino acids and nucleotides
• basic monomer sugar unit - saccharide 
• a single monomer is a monosaccharide (di- two, tri- three, tetra- four, poly- many)
• monosaccharide: sweet tasting, soluble, examples (glucose, galactose, fructose)
  
• Alpha glucose - H is above OH. 
• Beta glucose - OH is above H.
• Bond between the condensation of two glucose molecules - glycosidic bond 
• condensation - elimination of water
• hydrolysis - additon of water 
• Reducing sugar test - benedicts test   

- add sample to test tube, if not in liquid form first grind up in water 

- add equal volume of benedicts 

- heat gently in a water bath : colour change: blue - orange red precipitate. 

• disaccharides - when in pairs monosaccharides form disaccharides  example = maltose
• glucose + glucose = maltose 
• glucose + fructose = sucrose 
• glucose + galactose = lactose 
• Forming of glycosidic bond = removal of water 
• Breaking of glycosidic bond = addition of water
• Non reducing sugar test - 

- sample must be in liquid form if not ground up in water first

- add benedicts to a test tube with the food sample and heat gently in a water bath if the solutuon remains blue no reducing sugar is present 

- add another part of the food sample to a new test tube and add hydrochloric acid and heat gently in a water bath (the hydrochloric acid will hydrolyse the disaccharide)    add sodium hydrogencarbonate to the test tube - neutralises the hydrochloric acid  then test the sample using benedicts. (heat, colour change = blue- orange/red)

starch 

• a polysaccharide - found in many parts of plants in forms of granules (eg chloroplast)
• important component of food and major energy source in most diets 
• made of a-glucose - linked by glycosidc bonds formed by condensation reactions 
• branched or unbranched chains (unbranched wound into a tight coill - makes it very compact. ) (branched has many ends = acted upon by enzymes stimutaneously - glucose release rapidly)
• structure suits energy storage due to: 

- insoluble: water potential is not affected (no water drawn up via osmosis)

- large: cannot diffuse out of cells 

- compact: lots in small space

• test for starch :  add sample to test tube, add drops of idodine solution, shake or stir. colour change = yellow- blue/black colouration. 

glycogen :

• found in animals and bacteria (never in plants) sometimes called "animal starch"
• shorter chain and highly branched. (made of a - glucose)
• stored as granules in the liver and muscles

structure suits storage function: 

• insoluble: no water drawn in by osmosis, cannot diffuse out of cells
• compact: lots stored in a small space 
• highly branched (more than starch): more ends that can be acted upon stimultaneously by enzymes, therefore is rapidly broken down to form glucose monomers used in respiration

cellulose:  major component of plants - cell wall, which prevents the cell from bursting as water enters

• made of b-glucose
• straight unbranched chains that run parallel to each other - allows hydrogen bonds to form cross links between adjacent chains 
• the more hydrogen bonds the stronger the overall strength

Structure is suited to function of storage: 

• made of b-glucose so forms straight, unbranched chains 
• cellulose molecular chains run parallel to each other and are linked by hydrogen bonds which collectively add strength. 
• molecules are grouped to form microfibrils which in are grouped to create fibres which provides strength. 

• they contain carbon, hydrogen, oxygen. 
• insoluble in water
• soluble in organic solvents (alcohols)
• two types: triglycerides, phospholipids

roles of lipids:

• cell memebranes (phospholipids) : contribute to the flexibility of memebranes and the transfer of lipid-soluble substances across them. 
• source of energy: when oxidised they provide twice the amount of energy as the same mass of carbohydrates and release valuable water  
• waterproofing: insoluble in water = useful in being water proof 
• insulation: electrical and thermal - good slow conductors of heat 
• protection: fats stored around delicate organs (eg kidneys)

Triglycerides: 

• have three fatty acids (tri)
• each fatty acid forms a ester bond with glycerol in condensation reaction 
• hydrolysis - glycerol and three fatty acids 

• saturated  = no double bonds between carbon
• unsaturated = double bonds between carbon 
• mono- unstaturated = one double bond between carbon 
• polyunsaturated = many double bonds between carbon 

The double bonds cause the molecule to bend - cannot pack close together making them liquid at room temperature. 

structure of triglycerides related to properties: 

• high ratio of energy soring carbon- hydrogen: excellent source of energy 
• low mass to energy ratio: good storage molecule much can be stored in a small space
• large and non polar (insoluble): not affected by osmosis

Phospholipids :

• phosphate molecule and two fatty acids 
• hydrophobic "tail" = repels water (orientates away)
• hydrophilic "head" = attracts water

structure of phospholipids related to their function: 

• polar molecules have a hydrophobic tail and hydrophilic head: in aqueous environment the phospholipid molecule forms a bilayer within cell surface memebranes. 
• hydrophilic head: help hold the surface of the cell surface memebrane. 
• phospholipid structure: allows them to form glycolipids by combining with carbohydrates within the cell surface memebrane: important for cell recognition. 

Test for Lipids : Emulsion Test

• take a dry sample, and crush and grind the sample - add to a test tube
• add ethanol to the sample and shake or stir 
• add water to the test tube 
• colour change = clear - a milky/white colour

A control = repeat using water instead of the sample: the final soloution should remain clear. 

• very large molecules
• one group of proteins = enzymes 

structure of an amino acid: 

• amino acids are the basic monomer units which combine to make up a polymer called a polypeptide
• poly peptides can be combined to from proteins 
• every amino acid has : 

- amino group (- NH₂)   

- carboxyl group (-COOH)

- hydrogen atom (-H)

- R side group (this value always changes)

formation of a peptide bond: 

• two amino acids combine via condensation reaction. This causes the elimination of water and the bond linking them together is a peptide bond. (dipeptide formed)
• hydrolysis = additon of water breaks the peptide bond and gives water and two amino acids. 

Structure of Proteins:

primary structure: the sequence of amino acids , this determines its ultimate shape and its function, 

secondary structure: long peptide chain to be twisted and folded  into a 3D shape such as the coil known as the a-helix or the beta- pleated sheet.

tertiary structure: twisted and folded into a more specific detailed 3D structure

• disulfide bridges:   fairly strong and are not easily broken 
• ionic bonds: weaker than disulfide bonds and easily broken by change in pH.

• hydrogen bonds: are weak and easily broken but when together collectively are strong. 

Quaternary structure of a protein:

• a number of polypeptide chains linked together and sometimes associated with non protein groups to form a protein.

Test for Proteins - Biuret test

• place sample into a test tube add sodium hydroxide at room temperature. 
• add a few drops of very dilute copper(II) sulfate and mix gently. 
• colour change = Blue - Purple colouration. 

• enzymes are gobular proteins (3D shape) that acts as catalysts
• Biological Catalyst = a substance that speeds up a reaction without being used up 
• very specific in the reactions they catalyse due to a particular shape of the active site. 

How do enzymes catalyse reactions?

• enzymes speed up chemical reactions by lowering energy barriers. 
• enzymes lower the activation energy of a reaction by providing an alternate pathaway. 
• Activation energy = the minimum amount of energy needed to bring about a reaction. 

Enzyme specificty:

• a specific reactant that the enzyme acts upon is called a substrate. 
• the substrate fits into the "active site" of the enzyme and forms an "enzyme substrate complex" 

Lock and Key :  the enzyme binds with the substrate as they fit "exactly". Binding takes place at the active site, enzyme substrate complex formed. 

Induced fit model: 

• the fit between the enzyme and substrate are not "exact" but once part of the substrate binds to the enzyme the remaining is "induced to fit"
• this change occurs at the active site, which then results in the two molecules then fitting exactly. 

• substrate concentration 
• pH
• temperature 

substrate concentration-

• if the concentration of the enzyme is fixed and the substrate concentration is slowly increased the rate of reaction increases in proportion to the concentration of the substrate. 
• a low substrate concentrations the enzyme molecules only have a small number of substrate molecules to collide with and therefore the active sites are not working at full capacity 
• as more substrate is added, the active sites gradually become filled until the point when they are all working as fast as they can. 
• the rate of reaction is at its maximum and after this the additon of more substrate will NOT increase the rate, you must add more enzyme molecules in order to increase the rate. 

pH -  enzymes have an optimum level. 

• as soon as the pH moves away from this the charges at the active site of the enzyme alter. This may lead to the enzyme no longer being complimentary and will reduce the probability of enzyme substrate complexes forming. 
• At extreme pH levels: the ionic bonds holding the shape of the active site may denature. No enzyme substrate complexes can therefore form. 

temperature -   as temperature increases, the amount of kinetic energy of the substrate and enzyme molecules increases also. 

• this results in more successful collisions between them forming more enzyme susbstrate complexes. 
• At extreme temperature: the chemical bonds that hold the shape of the active site undergo vibrations and these eventually break. this changes the shape of the active site which reuslts in no enzyme substrate complexes forming. the enzyme is now denatured.
• all have an optimum temperature: the rate which they work best. 

enzyme concentration- 

• as long as there is excess substrate then the reaction rate will increase but if the substrate is limiting then the reaction will no longer increase. 
• you would have to increase the substrate in order to increase reaction rate. 

• this is molecules that interact in some way with the enzyme to prevent it from working normally. 
• non - competitve and competitve

Competitve- 

• these "compete" for a place at the active site
• the inhibitor has a simlar shape to the substrate which allows it to compete for a place
• once it binds it prevents the substrate from binding with the enzyme until the inhibitor "unbinds"

Non competitive - 

• these do not bind at the active site it binds elsewhere 
• this causes a change in the structure and shape of the enzyme, and the enzyme can no longer bind with the substrate.