The thread of life

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Rates of reaction

  • Reaction rate is the change in the amount of reactants/products per unit time. If reactants in solution, the rate will be change in conc per second and units moldm^3s^-1.
  • Can follow rate of reaction by:
    • pH measurement - if one of reactants/products is an acid/base can follow reaction by monitoring pH of mixture - use pH meter.
    • gas volume - if gas is product, collect in gas syringe and record how much have at regular intervals.
    • loss of mass - if gas given off, mass will be lost.
    • colour change - use colorimeter, which measures strength of colour by measuring light absorbance.
    • titration - monitor conc in solution by taking small samples at regular intervals and titrate them.  Need to slow reaction down by quenching otherwise conc will be chaning when trying to measure it. Overcome by adding sample to large known volume of distilled water, so chemicals are very dilute. Problem is that titration will be very slow, so only use for reactions taking long time to finish.
  • To find rate using a graph find the gradient at that point.
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Orders and rate equations

  • 0 order - double reactants, rate stays same.
  • 1 order - double reactants, rate doubles.
  • 2 order - double reactants, rate quadruples.
  • Can only find orders of reaction from experiments - not chemical equations.
  • Rate equation links reaction rate to reactant concentrations.
  • RATE = k[A]^m [B]^n
  • m and n are the orders of the reaction.
  • Overall order of reaction = m+n
  • k is rate constant - the bigger, the faster.
  • A higher temperature = higher rate constant
    • Higher temp means particles have more K.E, so more collisions and more will have Ea to react successfully.
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Experimental data and rate equations

  • Initial rates method used to work out rate equations.
  • Initial rate of a reaction is the rate at the start - find by calculating gradient at x=0.
  • To use initial rates method, you have to repeat the experiment changing only one of the concentrations at a time.  From this calculate the initial rate from the graph and figure out the order.  Then carry out the rate equation to find k.
  • Half-life is time taken for a reactant to halve in quantity.
  • Orders can be worked out from half-lives and conc-time graphs.
  • If first order, all half-lives will be constant.
  • If second order, the half-lives increase as the reaction goes on.
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Rates and reaction mechanisms

  • Rate-determining step is SLOWEST STEP in multi-step reaction.
  • If a reactant is in the rate equation - IT AFFECTS RATE, so MUST be in the rate-determining step.
  • Can predict rate equation from rate-determining step.
  • THE ORDER OF A REACTION WITH RESPECT TO A REACTANT SHOWS THE NUMBER OF MOLECULES OF THAT REACTANT WHICH ARE INVOLVED IN THE RATE-DETERMINING STEP.
  • Enzyme catalysted reactions change order as substrate is added - first order at low conc of substrate, but as more substrate is added the reaction becomes zero order as the rate is no longer affected by conc of substrate due to all active sites being full.
  • Order changes because rate-determining step changes - when all active sites become full, the enzyme is saturated, so adding more substrate will not make the reaction any faster.  
  • The rate of reaction now depends on how fast the enzyme can convert the substrate into a product, so making this the rate-determining step.
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Amino acids and proteins

  • Have basic amino group (NH2) and acidic carboxyl group (COOH).
  • This makes them AMPHOTERIC - have acidic and basic properties.
  • A.As can exist as ZWITTERIONS - dipolar ion.  They only exist near an A.As ISOELECTRIC POINT - the pH at which the average overall charge on A.A is 0.  Depends on the A.A's R group.

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  • Proteins are condensation polymers of A.As and there are peptide links between A.As.
  • To hydrolyse the protein: hot aq 6moldm^3 HCl added and mixture heated under reflux for 24 hours.  Final mixture is neutralised.
  • Proteins have primary (sequence of AAs), secondary (alpha helix - coils up) and tertiary (further coiled up - give 3D shape).
  • Secondary - H-bonds between peptide links.  Tertiary - ID-ID, ionic, H-bonds, disulfide bridge (-SH)
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DNA

  • Sugar-phosphate backbone formed by condensation polymerisation.
  • LP on O in deoxyribose sugar makes dative covalent bond with P atom in phosphate group.
  • Phosphate-ester link formed, H2O molecule lost.
  • DNA bases joined to sugar via a condensation reaction.
  • All bases have -NH group.  The N atom bonds to deoxyribose, eliminating H2O.
  • H-bonding causes bases to form specific pairs - complementary base pairing.
  • H-bond forms between +H and an O or N with a LP.
  • To bond, they have to be the right distance apart.
  • A-T form 2 H-bonds.
  • C-G form 3 H-bonds.
  • DNA helix has to twist, so bases are in right alignment and distance apart for base pairs to form.
  • Genetic fingerprinting breaks down DNA and examines the sequences of bases in sections which vary from person to person.  This is used to identify people based on samples of their DNA.
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DNA

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RNA

  • RNA is a polymer of nucleotides with ribose sugar and the base Uracil, instead of Thymine.
  • mRNA is a single polynucleotide strand and is an exact reverse copy of a section of DNA.  A codon has the opposite bases to a base triplet.
  • tRNA is a single polynucleotide strand that's folded into a clover shape.  It has a binding site at one end, where a specific A.A attaches, and at the other end it has a specific sequence of 3 bases - ANTICODON.
  • rRNA is made up of polynucleotide strands that are attached to proteins to make RIBOSOMES.  It is the largest type of DNA.
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Protein synthesis

  • TRANSCRIPTION
    • DNA double helix unwinds - reveals single strand.
    • DNA bases attract free RNA nucleotides with complementary bases.
    • RNA nucleotides joined to each other by enzyme RNA POLYMERASE - forms strand of mRNA.
    • DNA coils up again, unaltered.
    • mRNA strand moves through nucleus pore into the cytoplasm.
  • TRANSLATION
    • Ribosome attaches to mRNA and moves along, looking for start codon.
    • Ribosome moves along mRNA strand and free floating tRNA with correct anticodon bases pairs attaches.  
    • Ribosome moves 3 bases forward and another tRNA binds to complementary codon.
    • These two amino acids are joined together by ribosome with a peptide bond.
    • Ribosome moves forward again and first tRNA leaves ribosome and breaks away from its A.A.  New tRNA brings in 3rd A.A of the chain.
    • Continues until stop codon reached.  Stop codon doesn't code for an A.A, so ribosome releases polypeptide chain.
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Protein synthesis

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Enzymes

  • Active site is 3D - part of tertiary structure.
  • Only work with specific substrates - lock and key model.
  • Temporary bonds - H-bonds, ID-ID - form between substrate and R groups of enzyme's A.A holding the substrate in the active site.
  • Have optimum temperature and pH.  
  • High temp/pH = denature- bonds holding active site break, changing tertiary structure, so no longer correct shape for substrate to fit into.
  • Inhibitors slow down rate of reaction, as they compete with substrate to bond to active site - they BLOCK the active site.  Amount of inhibition depends on conc of inhibitor and substrate and how strongly the inhibitor bonds to active site.
  • Enzymes reduce environmental impact as they:
    • make commercial reactions proceed quickly at low temps.
    • increase yields of reactions, so less unreacted waste chemicals.
    • burn less fuel therefore less pollution.
    • prevent side reactions occurring - reduce unwanted, harmful by-products.
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Molecular shapes and isomerism

  • Single-bonded C have TETRAHEDRAL shape. 109.5
  • Atoms around double-bonded C form TRIGONAL PLANAR shape. 120
  • Structural isomers - same MF, but different SF.
  • Stereoisomers - same MF and SF, but arranged differently in space.  2 types - E/Z and optical.
  • E/Z isomerism happens because:
    • restricted rotation about the double bond.
    • 2 different groups on each C of C double bond.
  • Optical isomers are mirror images of each other.
    • Must be a C with 4 different groups attached - CHIRAL CARBON.
    • Can be arranged so 2 different molecules are made - enantiomers or optical isomers.
    • Definition of an enantiomer - non-superimosable and mirror image.
    • One enantiomer is labelled D, the other L.
    • Usually only find ONE of the enantiomers found naturally.
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