Proteins
Tertiary structure
- overall 3d shape of protein that forms due to the main chain polypeptide folding and bending back on itself
- Due to the IMF and ionic/covalent bonds being formed between R-groups on alpha chain polypeptides amino acid residues
- Dispersion forces
- Dipole-dipole forces
- Ionic bonds
- Covalent bonds
- Di-sulfide bridges
Protein Data Bank
- The protein data bank is an international online database for macromolecular structural data of proteins
- Its role is to increase collaboration and communication between scientists all over the world
- Serves as an archive that does the following
- Formalise and standardise the presentation and annotation of protein structural data
- Contains information about the primary, secondary, tertiary and quarternary structure of proteins
Enzymes
- Biological catalysts
- A globular protein that acts as a biological catalyst that increase the rate of reaction by providing an alternative chemical reaction pathway with a lower activation energy
- Their specific shape affects the specific reaction they catalyse
Induced Fit model - EXTENSION
- active sites in the un-induced enzymes are shown schematically with rounded contours
- binding of the substrate (orange) induces a physical conformational shift (angular contours) in the protein that facilitates stronger NON COVALENT binding to the substrate
- This decreases the energy of the substrate in a more stable configuration
- Catalysis occurs, after which the enzyme product complex has formed
- The products are released and the enzyme is released
Denaturing
- Process of changing conformation (shape) of a protein by placing the protein in a non optimum environment (temperature or pH)
- Enzymes work best with specific pH and temperature ranges, i.e. optimum pH and optimum temperature
- Non-optimum temperature
- When placed in a non-optimum temperature, the enzyme bonds (IMFS and weaker bonds like disulphide) are broken if the temperature are high and this causes the enzyme to lose its unique 3D shape
- When placed in a very low temperature, the enzymes forms too manu bonds as distant groups are brought closer than usual and this results in a change in the functional group of the pH
- Non-optimum pH
- When pH is increased, the solution is more basic, meaning the amine group will donate a proton (LCP)
- When pH is decreased, the solution is more acidic, meaning the carboxyl group will accept a proton (LCP)
- IMPACTS IONIC BONDS
- Changed pH causes the side groups to accept or donate hydrogen ions if they are COOH or NH2 and so side chain interactions are altered
- This leads to the tertiary structure being affected as the polypeptide does not fold on its own backbone normally
- Thus, the protein loses its function, as this is linked to its structure
Soaps
- Ionic salt containing a long chain carboxylate ion (fatty acid ion) and a Na+ or K+ ion
- That is utilised to clean non-polar “grease” from the surface of many materials
- Hydrophobic tail: non-polar alkyl chain of a soap molecule that does not attract water
- Hydrophilic heads: ionically charged carboxylate end that attracts water
Production - Saponification reaction
- Saponification: formation of soaps in an alkaline hydrolysis reaction between an ester (triglyceride → fat/oil) and sodium hydroxide
- Here a tryglicidide (3 esters joined to a propane backbone) is reacted with NaOH under heated condition
- 3 long chain carboxylic ions form (fatty acid ions) which react with the sodium ions to form a sodium/potassium carboxylate salt. The hydroxide ions react wth the propane backbone to form glycerol
Detergents structure
- An ionic salt comprising of a long carbon chain dodecylbenzene attached to a sulfonate ion
- They have very similar cleaning action to that of soaps. However, detergents are able to work in HARD water
- Hydrophobic tail: non-polar dodecylbenzene chain
- Hydrophilic head: ionically charged sulfonate ion end
Soap/Detergetnt Cleaning Action
- State IMF for tail - the long non-polar hydrophobic tail of soap/detergents dissolves in dirt/grease by forming dispersion forces with the non-polar dirt/grease
- State the IMF for head - the anionic hydrophilic head of soap/detergents form ion-dipole forces with polar H2O molecules
- Draw a diagram
- Discuss orientation - the soap molecules arrange themselves with their non-polar tails immersed in grease and their polar heads dissolving in water
- Discuss dissolving - the ion-dipole forces between the soap hydrophilic heads and water are stronger than the hydrogen bonds between water and so the dissolving process is energetically favourable
- Agitation - agitation of H2O causes it to pull on the detergent/soap which then pulls on the grease. This causes the grease to break up and be suspended in water
- Micelle formation - Micelles now form; spherical structure where the ionic head of soaps remain dissolved in water and the non-polar tails are immersed in the grease that is at the center of the micelle center
- Emulsion formation/washing; these micelles remain suspended in water as an emulsion due to the strong ion-dipole forces and are washed away with it. Thus the surface is cleaned as the grease is removed
- Labelled diagram
- Grease on cloth
- Soap arranges around grease
- Grease is surrounded by detergent; micelle formed
Soap limitation; detergent advantage
- Soap forms insoluble precipitate in hard water, whereas detergents don’t
- sulfonate is more polar than COO- and so detergents better dissolve in water and have a stronger cleaning action
- Due to COO- being a stronger base than SO3- group, it more readily accepts H+ ions in acidic water and this prevents it forming ion-dipole forces with water and thus decrease s its cleaning action
- Hard water is defined as water with a high mineral content, especially magnesium and calcium ions
Biomass and Production of Ethanol
- Biomass: defined as organic matter that is used directly as a fuel source or used to make a fuel source
- Buifules: a fuel derived from biomass, usually in a sustainable manner and in accordance with the 12 principles of green chemistry
| Biofuel Advantage | Biofuel Disadvantage |
|---|---|
| Renewable - this is because biomass is widely available | Produces slightly higher emissions of nitric oxides |
| Non toxic products - the products are non toxic | Technology for their production is still being developed |
| Carbon neutral - the amount of carbon released when the fuel is combusted is equal to the amount of carbon fixed from the atmosphere to make the biomass that is used to make the fuel | Usually produces a lower energy per mole of fuel combusted (less efficient) |
| Clean combustion - does not released SO2 like petroleum based fuels (respiratory irritants) and does not produce soot | |
| Ethanol - ethanol is a biofuel that is used in many modern cars |
- Ethanol can be produce dthrough 2 different methods: catalytic hydration of ethene gas and fermentation
Hydration of Ethene
- A reversible exothermic reaction (forward) is used where ethene gas is reacted with steam using a and catalyst to produce ethanol
- Ethanol is removed as it is produced reducing the concentration of products causing the system to partially counteract this change (decrease in product concentration) by favouring the forward reaction that increases product concentration → increases yield
- Only 5% of the ethene is converted to ethanol, at each pass over the catalyst and so ethene is recycled again and again to ensure a greater yield
- The final yield is around 95%
- In theory, and excess of steam could be used to shift the equilibrium to the right, however, this would wash off the phosphoric acid catalyst supported on the silicon dioxide support and so an excess of ethene is sued so the catalyst is no diluted
Conditions
- High temperatures will increase the average kinetic energy of all particles, which will increase the proportion of particles with sufficient energy to overcome activation energy. Thus, the frequency of successful collisions between all particles increases, and thus the rate of all reactions increases
- As the forward reaction is exothermic, high temperatures will shift equilibrium right and decrease yield.
- Thus, a compromise is formed, and a moderate temperature of 300 ˚C is used
- High pressures will increase the frequency of successful collisions of particles and thus reaction rate
- Furthermore, as the forward reaction combines in a greater molar ration to the reverse (2:1), high pressures will shift equilibrium right and increase yield
- Thus, as high pressures favour yield and reaction rate, a high pressure of 65 atm is used
- Lastly, a phosphoric acid catalyst is used, that increase the rate of reaction by providing an alternative reaction pathway with a lower activation energy.
Fermentation
- Fermentation: an enzyme catalyst reaction that converts simple sugars (monosaccharaides) from plant material into alcohol (ethanol) and carbon dioxide
Process
- Crushing: grains containing starch or biomass waste, which is a polymer made up of repeating unites of monosaccharides is dried and crushed releasing starch
- Hydrolysis: water an enzyme (amylase) is added to starch. The enzyme catalyses the breakdown of start polymer into maltose (2 glucose molecules) and then into glucose. The enzymes act as a biological catalyst which increases the rate of reaction by providing an alternative reaction pathway with a lower activation energy
- Fermentation
- Yeast is then added to the mixture which undergoes anaerobic respiration where it converts glucose to ethanol, eliminating carbon-dioxide with the aid of enzymes
- The yeast mixture is kept warm until fermentation is complete. Air is kept out of the mixture so that oxidation of ethanol does not occur
Yield and Reaction rate
- Ethanol produced from fermentation is in aqueous solution with a max concentration of 15% → this concentration is increased to 95% via distillation
- It is 15% because above 15%, the yeast is poisoned and dies. The reaction rate is also quite slow compared to hydration of ethene as fermentation is a biological process
Compromise conditions
- Temperature and pH must be maintained to 25-37 ˚C and 3-5 pH as enzymes in yeast are denatured at higher temperatures and pH and thus cannot function, causing hydrolysis of starch/maltose and fermentation to cease
| e | Fermentation | Hydration |
|---|---|---|
| Type of process | Batch process: everything is put into a container and left until fermentation is complete then batch is cleared out and a new reaction is set up Inefficient | Continuous flow process: |
Biodiesel
- Short chain ester joined onto a fatty acid group
- Ethyl/methyl group onto free fatty acid via an ester
- Reaction: triglyceride and an alcohol (methanol or ethanol), forming glycerol and 3 biodiesels (with sodium hydroxide catalyst)
- Lipase/base catalyst
- We can also create from free fatty acids by adding an alcohol to it, via esterification
Base catalyse; non-specific reaction
- side reaction (saponification) happening
- Need to treat reactants.
- Faster, cheaper, easier separated, available
- Greater energy, have to treat products, sensitive to fatty acid cooncentration
- filter any foreign mass
- removal of water, so ester does not enter hydrolysis (reverse of condensation)
- This forms emulsion which is hard to separate
- free fatty acid concentration is decreased to below 4% to reduce saponification with NaOH
- The FFA is removed by addition of methanol/alchol and sulfiric acid then placing the vessel with triglyceride in heated conditions; producing alkyl acids, i.e. biodeisel
Lipase (enzyme)
- Only catalyse specific reaction
- free fatty acids and alcohol
- triglyceride and alcohol
- No need to treat reactants
- Lower temperature (mild)
- milder pH and temperature (safer and cheaper)
- cannot have a high alcohol concentration, leads to poisoning
- can catalyse both triglycerides and fatty acids at the same time (they have similar structures)
- Slow for catalyst
- very expensive
- lots of lipase needed
- cannot easily be extracted